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<a href="MzMLHandler_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Marc Sturm $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FORMAT_HANDLERS_MZMLHANDLER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_HANDLERS_MZMLHANDLER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="VersionInfo_8h.html">OpenMS/CONCEPT/VersionInfo.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="CVMappings_8h.html">OpenMS/DATASTRUCTURES/CVMappings.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MzMLValidator_8h.html">OpenMS/FORMAT/VALIDATORS/MzMLValidator.h</a>&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeakFileOptions_8h.html">OpenMS/FORMAT/OPTIONS/PeakFileOptions.h</a>&gt;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Base64_8h.html">OpenMS/FORMAT/Base64.h</a>&gt;</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SemanticValidator_8h.html">OpenMS/FORMAT/VALIDATORS/SemanticValidator.h</a>&gt;</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="CVMappingFile_8h.html">OpenMS/FORMAT/CVMappingFile.h</a>&gt;</span></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ControlledVocabulary_8h.html">OpenMS/FORMAT/ControlledVocabulary.h</a>&gt;</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="File_8h.html">OpenMS/SYSTEM/File.h</a>&gt;</span></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;<span class="preprocessor">#include &lt;sstream&gt;</span></div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="preprocessor">#include &lt;iostream&gt;</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;<span class="preprocessor">#include &lt;QRegExp&gt;</span></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;<span class="comment">//MISSING:</span></div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="comment">// - more than one selected ion per precursor (warning if more than one)</span></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;<span class="comment">// - scanWindowList for each acquisition separately (currently for the whole spectrum only)</span></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;<span class="comment">// - instrumentConfigurationRef attribute for scan (why should the instrument change between scans? - warning if used)</span></div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="comment">// - scanSettingsRef attribute for instrumentConfiguration tag (currently no information there because of missing mapping file entry - warning if used)</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="comment">// xs:id/xs:idref prefix list</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="comment">// - sf_ru : sourceFile (run)</span></div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;<span class="comment">// - sf_sp : sourceFile (spectrum)</span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="comment">// - sf_pr : sourceFile (precursor)</span></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;<span class="comment">// - sf_ac : sourceFile (acquisition)</span></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;<span class="comment">// - sa    : sample</span></div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="comment">// - ic    : instrumentConfiguration</span></div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;<span class="comment">// - so_dp : software (data processing)</span></div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;<span class="comment">// - so_in : software (instrument)</span></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;<span class="comment">// - dp_sp : dataProcessing (spectrum)</span></div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="comment">// - dp_bi : dataProcessing (binary data array)</span></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;<span class="comment">// - dp_ch : dataProcessing (chromatogram)</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;{</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;  <span class="keyword">class </span>ControlledVocabulary;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;  {</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html">   94</a></span>&#160;    <span class="keyword">class </span><a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html">MzMLHandler</a> :</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;      <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    {</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a6901ac898ffc10435a46be0b657885b9">MzMLHandler</a>(MapType&amp; exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; version, <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>&amp; logger) :</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2f223274d440404ba700768cd15ef661">XMLHandler</a>(filename, version),</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a21e306967405afb217201901a2d75351">exp_</a>(&amp;exp),</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>(0),</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a>(),</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a56bc42e12243f36ea7d533b03609e30d">spec_</a>(),</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a08b65464af573a073ec2e715efdd0150">chromatogram_</a>(),</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1dc08092ef361e92d6e2cd117c1a63d">data_</a>(),</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a06fab32360dcb446ca8d839b4794f15c">default_array_length_</a>(0),</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a65709a774b1201962e142a6be7c17776">in_spectrum_list_</a>(<span class="keyword">false</span>),</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>(),</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>(logger),</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>(<span class="keyword">false</span>) <span class="comment">/* ,</span></div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;<span class="comment">                validator_(mapping_, cv_) */</span></div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      {</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;MS&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/psi-ms.obo&quot;</span>));</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;PATO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/quality.obo&quot;</span>));</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;UO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/unit.obo&quot;</span>));</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;BTO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/brenda.obo&quot;</span>));</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;GO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/goslim_goa.obo&quot;</span>));</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        <a class="code" href="classOpenMS_1_1CVMappingFile.html">CVMappingFile</a>().<a class="code" href="classOpenMS_1_1CVMappingFile.html#aef23cbef5854e48a0833a7ab174464ba">load</a>(<a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/MAPPING/ms-mapping.xml&quot;</span>), <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a488014fedfa087421abb7f7c9005869a">mapping_</a>);</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;        <span class="comment">//~ validator_ = Internal::MzMLValidator(mapping_, cv_);</span></div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;        <span class="comment">// check the version number of the mzML handler</span></div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a43f7f28c650b47c685b8b059a716f35c">VersionInfo::VersionDetails::create</a>(<a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a>) == <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a8c1650d1d281b01a53b669240c70a4ab">VersionInfo::VersionDetails::EMPTY</a>)</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;        {</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;          <a class="code" href="LogStream_8h.html#aced66975c154ea0e2a8ec3bc818b4e08">LOG_ERROR</a> &lt;&lt; <span class="stringliteral">&quot;MzMLHandler was initialized with an invalid version number: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;        }</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;      }</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0aaf41c383f973bf5a11f3a55022eda5">  133</a></span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0aaf41c383f973bf5a11f3a55022eda5">MzMLHandler</a>(<span class="keyword">const</span> MapType&amp; exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>&amp; logger) :</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a>(filename, version),</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a21e306967405afb217201901a2d75351">exp_</a>(0),</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>(&amp;exp),</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a>(),</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a56bc42e12243f36ea7d533b03609e30d">spec_</a>(),</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a08b65464af573a073ec2e715efdd0150">chromatogram_</a>(),</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1dc08092ef361e92d6e2cd117c1a63d">data_</a>(),</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a06fab32360dcb446ca8d839b4794f15c">default_array_length_</a>(0),</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a65709a774b1201962e142a6be7c17776">in_spectrum_list_</a>(false),</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>(),</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>(logger),</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>(false) <span class="comment">/* ,</span></div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;<span class="comment">                validator_(mapping_, cv_) */</span></div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;      {</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;MS&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/psi-ms.obo&quot;</span>));</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;PATO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/quality.obo&quot;</span>));</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;UO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/unit.obo&quot;</span>));</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;BTO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/brenda.obo&quot;</span>));</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>.<a class="code" href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">loadFromOBO</a>(<span class="stringliteral">&quot;GO&quot;</span>, <a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/CV/goslim_goa.obo&quot;</span>));</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;        <a class="code" href="classOpenMS_1_1CVMappingFile.html">CVMappingFile</a>().<a class="code" href="classOpenMS_1_1CVMappingFile.html#aef23cbef5854e48a0833a7ab174464ba">load</a>(<a class="code" href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">File::find</a>(<span class="stringliteral">&quot;/MAPPING/ms-mapping.xml&quot;</span>), <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a488014fedfa087421abb7f7c9005869a">mapping_</a>);</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        <span class="comment">//~ validator_ = Internal::MzMLValidator(mapping_, cv_);</span></div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        <span class="comment">// check the version number of the mzML handler</span></div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a43f7f28c650b47c685b8b059a716f35c">VersionInfo::VersionDetails::create</a>(<a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a>) == <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a8c1650d1d281b01a53b669240c70a4ab">VersionInfo::VersionDetails::EMPTY</a>)</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;        {</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;          <a class="code" href="LogStream_8h.html#aced66975c154ea0e2a8ec3bc818b4e08">LOG_ERROR</a> &lt;&lt; <span class="stringliteral">&quot;MzMLHandler was initialized with an invalid version number: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a4e87a8f69bbc06cd56776556dc1680ed">version_</a> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;        }</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      }</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa0f96e293e3cf64677e3bd84d26ff6ed">  165</a></span>&#160;      <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa0f96e293e3cf64677e3bd84d26ff6ed">~MzMLHandler</a>()</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;      {</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      }</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9028634d022a74d1fc8db852d99984d6">endElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname);</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a484c33c30ea480bd831a92847f61006e">startElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes&amp; attributes);</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a742bdba7e6348fe6c549aada2a116944">characters</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t length);</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;      <span class="comment">//Docu in base class</span></div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf">writeTo</a>(std::ostream&amp; os);</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;</div>
<div class="line"><a name="l00184"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add88f8d4748f8b7c90f08964ee7938f4">  184</a></span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add88f8d4748f8b7c90f08964ee7938f4">setOptions</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a>&amp; opt)</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;      {</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a> = opt;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      }</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;</div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">  192</a></span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">MapType::PeakType</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a>;</div>
<div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#af50693f3924366b3c157bea5dcbe4355">  194</a></span>&#160;      <span class="keyword">typedef</span> <span class="keyword">typename</span> MapType::ChromatogramPeakType <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#af50693f3924366b3c157bea5dcbe4355">ChromatogramPeakType</a>;</div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a066042ae14211da37d4fa66d466bfa3e">  196</a></span>&#160;      <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum&lt;PeakType&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a066042ae14211da37d4fa66d466bfa3e">SpectrumType</a>;</div>
<div class="line"><a name="l00198"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5bfc152a01835ee1a12f01241b4eda50">  198</a></span>&#160;      <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram&lt;ChromatogramPeakType&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5bfc152a01835ee1a12f01241b4eda50">ChromatogramType</a>;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;</div>
<div class="line"><a name="l00201"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html">  201</a></span>&#160;      <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html">BinaryData</a></div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;      {</div>
<div class="line"><a name="l00203"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a7c587a2ed93cc6d0158daaacb731a840">  203</a></span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a7c587a2ed93cc6d0158daaacb731a840">base64</a>;</div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a4e84dda2309e9dfbb3b2300dd44ec145">  204</a></span>&#160;        <span class="keyword">enum</span> {<a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a4e84dda2309e9dfbb3b2300dd44ec145">PRE_NONE</a>, <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a45f0d43f4806f81088a4c80516b6a8bc">PRE_32</a>, <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a288fa3219db91abed40546c0c9dde29c">PRE_64</a>} <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#af782cf31c1c251c2abb33b48ab6a8366">precision</a>;</div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a693887ab47dee6ab960fb1ef887c56cf">  205</a></span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a693887ab47dee6ab960fb1ef887c56cf">size</a>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a6705637af16394112972298190f7c5b9">  206</a></span>&#160;        <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a6705637af16394112972298190f7c5b9">compression</a>;</div>
<div class="line"><a name="l00207"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da4313207b96335e124ddd0664a0794cad">  207</a></span>&#160;        <span class="keyword">enum</span> {<a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da36f5529746b65d14a498b41e316de090">DT_NONE</a>, <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da4959f950b9d109fcf9b4176c28503843">DT_FLOAT</a>, <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035daf6d3a756d101f02e5aeb13916b1d9eb3">DT_INT</a>, <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da4313207b96335e124ddd0664a0794cad">DT_STRING</a>} <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#ad03e2dba49bef5ed14e9feb41e161ffe">data_type</a>;</div>
<div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#affde898a3bfa71810e8e6d3497e3c49b">  208</a></span>&#160;        std::vector&lt;Real&gt; <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#affde898a3bfa71810e8e6d3497e3c49b">floats_32</a>;</div>
<div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a931a07130d981672ac391f7a27a88dfd">  209</a></span>&#160;        std::vector&lt;DoubleReal&gt; <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a931a07130d981672ac391f7a27a88dfd">floats_64</a>;</div>
<div class="line"><a name="l00210"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a19ae296603b10b298db255e9d873ab32">  210</a></span>&#160;        std::vector&lt;Int32&gt; <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a19ae296603b10b298db255e9d873ab32">ints_32</a>;</div>
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a937618aabd204b43b9974469071419dc">  211</a></span>&#160;        std::vector&lt;Int64&gt; <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a937618aabd204b43b9974469071419dc">ints_64</a>;</div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a714a1e5663fe78f5dc22d232b1319844">  212</a></span>&#160;        std::vector&lt;String&gt; <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a714a1e5663fe78f5dc22d232b1319844">decoded_char</a>;</div>
<div class="line"><a name="l00213"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a8eca4767d3e8964b5d683c2adbfda0b6">  213</a></span>&#160;        <a class="code" href="classOpenMS_1_1MetaInfoDescription.html">MetaInfoDescription</a> <a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a8eca4767d3e8964b5d683c2adbfda0b6">meta</a>;</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      };</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a89efdb9d9ea65cfa7e2065774cd6198c">writeSpectrum_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spec, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s, </div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;              <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator, <span class="keywordtype">bool</span> renew_native_ids, </div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;              std::vector&lt;std::vector&lt;DataProcessing&gt; &gt; &amp; dps);</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9da388304c18a628979434640b7bb9c8">writeChromatogram_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a>&amp; chromatogram, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aeee3146ed1c95bbbc3e69b4d5dca3041">writeHeader_</a>(std::ostream&amp; os, <span class="keyword">const</span> MapType&amp; exp, std::vector&lt;std::vector&lt;DataProcessing&gt; &gt; &amp; dps, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a115d84a31a4be5741fe2eddb197c0d6f">writeFooter_</a>(std::ostream&amp; os);</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;</div>
<div class="line"><a name="l00227"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a21e306967405afb217201901a2d75351">  227</a></span>&#160;      MapType* <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a21e306967405afb217201901a2d75351">exp_</a>;</div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">  229</a></span>&#160;      <span class="keyword">const</span> MapType* <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;</div>
<div class="line"><a name="l00232"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a654a0b5941d937e303c64bc9e732baec">  232</a></span>&#160;      <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a>;</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;      <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a56bc42e12243f36ea7d533b03609e30d">spec_</a>;</div>
<div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a08b65464af573a073ec2e715efdd0150">  239</a></span>&#160;      <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a08b65464af573a073ec2e715efdd0150">chromatogram_</a>;</div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1dc08092ef361e92d6e2cd117c1a63d">  241</a></span>&#160;      std::vector&lt;BinaryData&gt; <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1dc08092ef361e92d6e2cd117c1a63d">data_</a>;</div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a06fab32360dcb446ca8d839b4794f15c">  243</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a06fab32360dcb446ca8d839b4794f15c">default_array_length_</a>;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a65709a774b1201962e142a6be7c17776">  245</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a65709a774b1201962e142a6be7c17776">in_spectrum_list_</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5ca2846674ab26010320d030655cb796">  247</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5ca2846674ab26010320d030655cb796">current_id_</a>;</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5a4f408867d428d90605cbfdf5b4a507">  249</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, std::vector&lt;SemanticValidator::CVTerm&gt;</a> &gt; <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5a4f408867d428d90605cbfdf5b4a507">ref_param_</a>;</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a3dfca77b4f99246a5bf4e9407e27f889">  251</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, SourceFile&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a3dfca77b4f99246a5bf4e9407e27f889">source_files_</a>;</div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a2f4d93dd2e2ea2f50e21f943deeb104f">  253</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, Sample&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a2f4d93dd2e2ea2f50e21f943deeb104f">samples_</a>;</div>
<div class="line"><a name="l00255"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a28d0d143361f7c67c01ef53bd7f3655d">  255</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, Software&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a28d0d143361f7c67c01ef53bd7f3655d">software_</a>;</div>
<div class="line"><a name="l00257"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae921cd780f4f617ca00e45c6c0cd2cf2">  257</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, Instrument&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae921cd780f4f617ca00e45c6c0cd2cf2">instruments_</a>;</div>
<div class="line"><a name="l00259"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#afea2047eedc730597ab0a7bb9c92c551">  259</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, std::vector&lt;DataProcessing&gt;</a> &gt; <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#afea2047eedc730597ab0a7bb9c92c551">processing_</a>;</div>
<div class="line"><a name="l00261"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ad0643828ff3cbe1273be4760164303e4">  261</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ad0643828ff3cbe1273be4760164303e4">default_processing_</a>;</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;</div>
<div class="line"><a name="l00265"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">  265</a></span>&#160;      <a class="code" href="classOpenMS_1_1Base64.html">Base64</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>;</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;</div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">  268</a></span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>&amp; <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>;</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;</div>
<div class="line"><a name="l00271"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">  271</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>;</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;</div>
<div class="line"><a name="l00274"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">  274</a></span>&#160;      <a class="code" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>;</div>
<div class="line"><a name="l00275"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a488014fedfa087421abb7f7c9005869a">  275</a></span>&#160;      <a class="code" href="classOpenMS_1_1CVMappings.html">CVMappings</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a488014fedfa087421abb7f7c9005869a">mapping_</a>;</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;      <span class="comment">//~ Internal::MzMLValidator validator_;</span></div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;</div>
<div class="line"><a name="l00279"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a99395acc13be348e3858856fcc07a933">  279</a></span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a99395acc13be348e3858856fcc07a933">selected_ion_count_</a>;</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add1bc02b038fe1abde05c0352577f1df">fillData_</a>();</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a96e4bd823df13baa5f500b1776d463ea">fillChromatogramData_</a>();</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aaf3831bc627f95286afdf5c6b91c731b">handleCVParam_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_tag, <span class="comment">/*  const String &amp; cvref, */</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; unit_accession = <span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adc972b1eb7fa347dda5ee1d46ca8df79">handleUserParam_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; value);</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adfdc00e52147d9fba0252e78b76ff477">writeUserParam_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a>&amp; meta, <a class="code" href="classunsigned_01int.html">UInt</a> indent, <a class="code" href="classOpenMS_1_1String.html">String</a> path, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1d4f3e01975ac37c2b0f5b0ed1e1d92">getChildWithName_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a78331edae256b2c5de712ed5eda26bc8">writeSoftware_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Software.html">Software</a>&amp; software, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa7d348ccbf286e2aef8b0fa27453a289">writeSourceFile_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a>&amp; software, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;</div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aebeb2035d3f517fa772979211fa2d514">writeDataProcessing_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> std::vector&lt;DataProcessing&gt;&amp; dps, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a77eccf58c9f605c9535709430c66a5be">writePrecursor_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>&amp; precursor, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;</div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7a5d9d8d742f5950d5a3c0fa22805b2a">writeProduct_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Product.html">Product</a>&amp; product, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator);</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5f66b708512374f687a8b6598408e9e8">writeCV_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a>&amp; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>&amp; metaValue) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7240976da5a0394d00fecce6fd8a7baa">validateCV_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a>&amp; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; path, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;    };</div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;    <span class="comment">//--------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00324"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a742bdba7e6348fe6c549aada2a116944">  324</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a742bdba7e6348fe6c549aada2a116944">MzMLHandler&lt;MapType&gt;::characters</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t <span class="comment">/*length*/</span>)</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;    {</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;      <span class="keywordflow">if</span> (skip_spectrum_)</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;        <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;      <span class="keywordtype">char</span>* transcoded_chars = sm_.convert(chars);</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;</div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; current_tag = open_tags_.back();</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;</div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;      <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">&quot;binary&quot;</span> <span class="comment">/* &amp;&amp; in_spectrum_list_*/</span>)</div>
<div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;      {</div>
<div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;        <span class="comment">//chars may be split to several chunks =&gt; concatenate them</span></div>
<div class="line"><a name="l00336"></a><span class="lineno">  336</span>&#160;        data_.back().base64 += transcoded_chars;</div>
<div class="line"><a name="l00337"></a><span class="lineno">  337</span>&#160;      }</div>
<div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">&quot;offset&quot;</span> || current_tag == <span class="stringliteral">&quot;indexListOffset&quot;</span> || current_tag == <span class="stringliteral">&quot;fileChecksum&quot;</span> <span class="comment">/* || current_tag == &quot;binary&quot;*/</span>)</div>
<div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;      {</div>
<div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;        <span class="comment">//do nothing for</span></div>
<div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;        <span class="comment">// - index</span></div>
<div class="line"><a name="l00342"></a><span class="lineno">  342</span>&#160;        <span class="comment">// - checksum</span></div>
<div class="line"><a name="l00343"></a><span class="lineno">  343</span>&#160;        <span class="comment">// - binary chromatogram data</span></div>
<div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;      }</div>
<div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l00346"></a><span class="lineno">  346</span>&#160;      {</div>
<div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> transcoded_chars2 = transcoded_chars;</div>
<div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;        transcoded_chars2.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00349"></a><span class="lineno">  349</span>&#160;        <span class="keywordflow">if</span> (transcoded_chars2 != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled character content in tag &#39;&quot;</span>) + current_tag + <span class="stringliteral">&quot;&#39;: &quot;</span> + transcoded_chars2);</div>
<div class="line"><a name="l00351"></a><span class="lineno">  351</span>&#160;      }</div>
<div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;    }</div>
<div class="line"><a name="l00353"></a><span class="lineno">  353</span>&#160;</div>
<div class="line"><a name="l00354"></a><span class="lineno">  354</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00355"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a484c33c30ea480bd831a92847f61006e">  355</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a484c33c30ea480bd831a92847f61006e">MzMLHandler&lt;MapType&gt;::startElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes&amp; attributes)</div>
<div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;    {</div>
<div class="line"><a name="l00357"></a><span class="lineno">  357</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_count = xercesc::XMLString::transcode(<span class="stringliteral">&quot;count&quot;</span>);</div>
<div class="line"><a name="l00358"></a><span class="lineno">  358</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_default_array_length = xercesc::XMLString::transcode(<span class="stringliteral">&quot;defaultArrayLength&quot;</span>);</div>
<div class="line"><a name="l00359"></a><span class="lineno">  359</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_array_length = xercesc::XMLString::transcode(<span class="stringliteral">&quot;arrayLength&quot;</span>);</div>
<div class="line"><a name="l00360"></a><span class="lineno">  360</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_accession = xercesc::XMLString::transcode(<span class="stringliteral">&quot;accession&quot;</span>);</div>
<div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_name = xercesc::XMLString::transcode(<span class="stringliteral">&quot;name&quot;</span>);</div>
<div class="line"><a name="l00362"></a><span class="lineno">  362</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_type = xercesc::XMLString::transcode(<span class="stringliteral">&quot;type&quot;</span>);</div>
<div class="line"><a name="l00363"></a><span class="lineno">  363</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_value = xercesc::XMLString::transcode(<span class="stringliteral">&quot;value&quot;</span>);</div>
<div class="line"><a name="l00364"></a><span class="lineno">  364</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_unit_accession = xercesc::XMLString::transcode(<span class="stringliteral">&quot;unitAccession&quot;</span>);</div>
<div class="line"><a name="l00365"></a><span class="lineno">  365</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_id = xercesc::XMLString::transcode(<span class="stringliteral">&quot;id&quot;</span>);</div>
<div class="line"><a name="l00366"></a><span class="lineno">  366</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_spot_id = xercesc::XMLString::transcode(<span class="stringliteral">&quot;spotID&quot;</span>);</div>
<div class="line"><a name="l00367"></a><span class="lineno">  367</span>&#160;      <span class="comment">//~ static const XMLCh * s_cvref = xercesc::XMLString::transcode(&quot;cvRef&quot;); TODO</span></div>
<div class="line"><a name="l00368"></a><span class="lineno">  368</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;ref&quot;</span>);</div>
<div class="line"><a name="l00369"></a><span class="lineno">  369</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_version = xercesc::XMLString::transcode(<span class="stringliteral">&quot;version&quot;</span>);</div>
<div class="line"><a name="l00370"></a><span class="lineno">  370</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_order = xercesc::XMLString::transcode(<span class="stringliteral">&quot;order&quot;</span>);</div>
<div class="line"><a name="l00371"></a><span class="lineno">  371</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_location = xercesc::XMLString::transcode(<span class="stringliteral">&quot;location&quot;</span>);</div>
<div class="line"><a name="l00372"></a><span class="lineno">  372</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_sample_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;sampleRef&quot;</span>);</div>
<div class="line"><a name="l00373"></a><span class="lineno">  373</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_software_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;softwareRef&quot;</span>);</div>
<div class="line"><a name="l00374"></a><span class="lineno">  374</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_source_file_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;sourceFileRef&quot;</span>);</div>
<div class="line"><a name="l00375"></a><span class="lineno">  375</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_default_instrument_configuration_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;defaultInstrumentConfigurationRef&quot;</span>);</div>
<div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_instrument_configuration_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;instrumentConfigurationRef&quot;</span>);</div>
<div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_default_data_processing_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;defaultDataProcessingRef&quot;</span>);</div>
<div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_data_processing_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;dataProcessingRef&quot;</span>);</div>
<div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_start_time_stamp = xercesc::XMLString::transcode(<span class="stringliteral">&quot;startTimeStamp&quot;</span>);</div>
<div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_external_spectrum_id = xercesc::XMLString::transcode(<span class="stringliteral">&quot;externalSpectrumID&quot;</span>);</div>
<div class="line"><a name="l00381"></a><span class="lineno">  381</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_default_source_file_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;defaultSourceFileRef&quot;</span>);</div>
<div class="line"><a name="l00382"></a><span class="lineno">  382</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_scan_settings_ref = xercesc::XMLString::transcode(<span class="stringliteral">&quot;scanSettingsRef&quot;</span>);</div>
<div class="line"><a name="l00383"></a><span class="lineno">  383</span>&#160;</div>
<div class="line"><a name="l00384"></a><span class="lineno">  384</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> tag = sm_.convert(qname);</div>
<div class="line"><a name="l00385"></a><span class="lineno">  385</span>&#160;      open_tags_.push_back(tag);</div>
<div class="line"><a name="l00386"></a><span class="lineno">  386</span>&#160;</div>
<div class="line"><a name="l00387"></a><span class="lineno">  387</span>&#160;      <span class="comment">//determine parent tag</span></div>
<div class="line"><a name="l00388"></a><span class="lineno">  388</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> parent_tag;</div>
<div class="line"><a name="l00389"></a><span class="lineno">  389</span>&#160;      <span class="keywordflow">if</span> (open_tags_.size() &gt; 1)</div>
<div class="line"><a name="l00390"></a><span class="lineno">  390</span>&#160;        parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l00391"></a><span class="lineno">  391</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> parent_parent_tag;</div>
<div class="line"><a name="l00392"></a><span class="lineno">  392</span>&#160;      <span class="keywordflow">if</span> (open_tags_.size() &gt; 2)</div>
<div class="line"><a name="l00393"></a><span class="lineno">  393</span>&#160;        parent_parent_tag = *(open_tags_.end() - 3);</div>
<div class="line"><a name="l00394"></a><span class="lineno">  394</span>&#160;</div>
<div class="line"><a name="l00395"></a><span class="lineno">  395</span>&#160;      <span class="comment">//do nothing until a new spectrum is reached</span></div>
<div class="line"><a name="l00396"></a><span class="lineno">  396</span>&#160;      <span class="keywordflow">if</span> (tag != <span class="stringliteral">&quot;spectrum&quot;</span> &amp;&amp; skip_spectrum_)</div>
<div class="line"><a name="l00397"></a><span class="lineno">  397</span>&#160;        <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00398"></a><span class="lineno">  398</span>&#160;</div>
<div class="line"><a name="l00399"></a><span class="lineno">  399</span>&#160;      <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;spectrum&quot;</span>)</div>
<div class="line"><a name="l00400"></a><span class="lineno">  400</span>&#160;      {</div>
<div class="line"><a name="l00401"></a><span class="lineno">  401</span>&#160;        <span class="comment">//number of peaks</span></div>
<div class="line"><a name="l00402"></a><span class="lineno">  402</span>&#160;        spec_ = <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>();</div>
<div class="line"><a name="l00403"></a><span class="lineno">  403</span>&#160;        default_array_length_ = attributeAsInt_(attributes, s_default_array_length);</div>
<div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;        <span class="comment">//spectrum source file</span></div>
<div class="line"><a name="l00405"></a><span class="lineno">  405</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> source_file_ref;</div>
<div class="line"><a name="l00406"></a><span class="lineno">  406</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(source_file_ref, attributes, s_source_file_ref))</div>
<div class="line"><a name="l00407"></a><span class="lineno">  407</span>&#160;        {</div>
<div class="line"><a name="l00408"></a><span class="lineno">  408</span>&#160;          spec_.setSourceFile(source_files_[source_file_ref]);</div>
<div class="line"><a name="l00409"></a><span class="lineno">  409</span>&#160;        }</div>
<div class="line"><a name="l00410"></a><span class="lineno">  410</span>&#160;        <span class="comment">//native id</span></div>
<div class="line"><a name="l00411"></a><span class="lineno">  411</span>&#160;        spec_.setNativeID(attributeAsString_(attributes, s_id));</div>
<div class="line"><a name="l00412"></a><span class="lineno">  412</span>&#160;        <span class="comment">//maldi spot id</span></div>
<div class="line"><a name="l00413"></a><span class="lineno">  413</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> maldi_spot_id;</div>
<div class="line"><a name="l00414"></a><span class="lineno">  414</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(maldi_spot_id, attributes, s_spot_id))</div>
<div class="line"><a name="l00415"></a><span class="lineno">  415</span>&#160;        {</div>
<div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;maldi_spot_id&quot;</span>, maldi_spot_id);</div>
<div class="line"><a name="l00417"></a><span class="lineno">  417</span>&#160;        }</div>
<div class="line"><a name="l00418"></a><span class="lineno">  418</span>&#160;        <span class="comment">//data processing</span></div>
<div class="line"><a name="l00419"></a><span class="lineno">  419</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref;</div>
<div class="line"><a name="l00420"></a><span class="lineno">  420</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(data_processing_ref, attributes, s_data_processing_ref))</div>
<div class="line"><a name="l00421"></a><span class="lineno">  421</span>&#160;        {</div>
<div class="line"><a name="l00422"></a><span class="lineno">  422</span>&#160;          spec_.setDataProcessing(processing_[data_processing_ref]);</div>
<div class="line"><a name="l00423"></a><span class="lineno">  423</span>&#160;        }</div>
<div class="line"><a name="l00424"></a><span class="lineno">  424</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00425"></a><span class="lineno">  425</span>&#160;        {</div>
<div class="line"><a name="l00426"></a><span class="lineno">  426</span>&#160;          spec_.setDataProcessing(processing_[default_processing_]);</div>
<div class="line"><a name="l00427"></a><span class="lineno">  427</span>&#160;        }</div>
<div class="line"><a name="l00428"></a><span class="lineno">  428</span>&#160;      }</div>
<div class="line"><a name="l00429"></a><span class="lineno">  429</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;chromatogram&quot;</span>)</div>
<div class="line"><a name="l00430"></a><span class="lineno">  430</span>&#160;      {</div>
<div class="line"><a name="l00431"></a><span class="lineno">  431</span>&#160;        chromatogram_ = <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a>();</div>
<div class="line"><a name="l00432"></a><span class="lineno">  432</span>&#160;        default_array_length_ = attributeAsInt_(attributes, s_default_array_length);</div>
<div class="line"><a name="l00433"></a><span class="lineno">  433</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> source_file_ref;</div>
<div class="line"><a name="l00434"></a><span class="lineno">  434</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(source_file_ref, attributes, s_source_file_ref))</div>
<div class="line"><a name="l00435"></a><span class="lineno">  435</span>&#160;        {</div>
<div class="line"><a name="l00436"></a><span class="lineno">  436</span>&#160;          chromatogram_.setSourceFile(source_files_[source_file_ref]);</div>
<div class="line"><a name="l00437"></a><span class="lineno">  437</span>&#160;        }</div>
<div class="line"><a name="l00438"></a><span class="lineno">  438</span>&#160;        <span class="comment">// native id</span></div>
<div class="line"><a name="l00439"></a><span class="lineno">  439</span>&#160;        chromatogram_.setNativeID(attributeAsString_(attributes, s_id));</div>
<div class="line"><a name="l00440"></a><span class="lineno">  440</span>&#160;        <span class="comment">// data processing</span></div>
<div class="line"><a name="l00441"></a><span class="lineno">  441</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref;</div>
<div class="line"><a name="l00442"></a><span class="lineno">  442</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(data_processing_ref, attributes, s_data_processing_ref))</div>
<div class="line"><a name="l00443"></a><span class="lineno">  443</span>&#160;        {</div>
<div class="line"><a name="l00444"></a><span class="lineno">  444</span>&#160;          chromatogram_.setDataProcessing(processing_[data_processing_ref]);</div>
<div class="line"><a name="l00445"></a><span class="lineno">  445</span>&#160;        }</div>
<div class="line"><a name="l00446"></a><span class="lineno">  446</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00447"></a><span class="lineno">  447</span>&#160;        {</div>
<div class="line"><a name="l00448"></a><span class="lineno">  448</span>&#160;          chromatogram_.setDataProcessing(processing_[default_processing_]);</div>
<div class="line"><a name="l00449"></a><span class="lineno">  449</span>&#160;        }</div>
<div class="line"><a name="l00450"></a><span class="lineno">  450</span>&#160;      }</div>
<div class="line"><a name="l00451"></a><span class="lineno">  451</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;spectrumList&quot;</span>)</div>
<div class="line"><a name="l00452"></a><span class="lineno">  452</span>&#160;      {</div>
<div class="line"><a name="l00453"></a><span class="lineno">  453</span>&#160;        <span class="comment">//default data processing</span></div>
<div class="line"><a name="l00454"></a><span class="lineno">  454</span>&#160;        default_processing_ = attributeAsString_(attributes, s_default_data_processing_ref);</div>
<div class="line"><a name="l00455"></a><span class="lineno">  455</span>&#160;</div>
<div class="line"><a name="l00456"></a><span class="lineno">  456</span>&#160;        <span class="comment">//Abort if we need meta data only</span></div>
<div class="line"><a name="l00457"></a><span class="lineno">  457</span>&#160;        <span class="keywordflow">if</span> (options_.getMetadataOnly())</div>
<div class="line"><a name="l00458"></a><span class="lineno">  458</span>&#160;          <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly.html">EndParsingSoftly</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__);</div>
<div class="line"><a name="l00459"></a><span class="lineno">  459</span>&#160;</div>
<div class="line"><a name="l00460"></a><span class="lineno">  460</span>&#160;        <a class="code" href="classunsigned_01int.html">UInt</a> count = attributeAsInt_(attributes, s_count);</div>
<div class="line"><a name="l00461"></a><span class="lineno">  461</span>&#160;        exp_-&gt;reserveSpaceSpectra(count);</div>
<div class="line"><a name="l00462"></a><span class="lineno">  462</span>&#160;        logger_.startProgress(0, count, <span class="stringliteral">&quot;loading mzML file&quot;</span>);</div>
<div class="line"><a name="l00463"></a><span class="lineno">  463</span>&#160;        in_spectrum_list_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00464"></a><span class="lineno">  464</span>&#160;      }</div>
<div class="line"><a name="l00465"></a><span class="lineno">  465</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;chromatogramList&quot;</span>)</div>
<div class="line"><a name="l00466"></a><span class="lineno">  466</span>&#160;      {</div>
<div class="line"><a name="l00467"></a><span class="lineno">  467</span>&#160;        <span class="comment">// default data processing</span></div>
<div class="line"><a name="l00468"></a><span class="lineno">  468</span>&#160;        default_processing_ = attributeAsString_(attributes, s_default_data_processing_ref);</div>
<div class="line"><a name="l00469"></a><span class="lineno">  469</span>&#160;</div>
<div class="line"><a name="l00470"></a><span class="lineno">  470</span>&#160;        <span class="comment">//Abort if we need meta data only</span></div>
<div class="line"><a name="l00471"></a><span class="lineno">  471</span>&#160;        <span class="keywordflow">if</span> (options_.getMetadataOnly())</div>
<div class="line"><a name="l00472"></a><span class="lineno">  472</span>&#160;          <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly.html">EndParsingSoftly</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__);</div>
<div class="line"><a name="l00473"></a><span class="lineno">  473</span>&#160;</div>
<div class="line"><a name="l00474"></a><span class="lineno">  474</span>&#160;        <a class="code" href="classunsigned_01int.html">UInt</a> count = attributeAsInt_(attributes, s_count);</div>
<div class="line"><a name="l00475"></a><span class="lineno">  475</span>&#160;        exp_-&gt;reserveSpaceChromatograms(count);</div>
<div class="line"><a name="l00476"></a><span class="lineno">  476</span>&#160;        logger_.startProgress(0, count, <span class="stringliteral">&quot;loading chromatograms&quot;</span>);</div>
<div class="line"><a name="l00477"></a><span class="lineno">  477</span>&#160;        in_spectrum_list_ = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00478"></a><span class="lineno">  478</span>&#160;      }</div>
<div class="line"><a name="l00479"></a><span class="lineno">  479</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;binaryDataArrayList&quot;</span> <span class="comment">/* &amp;&amp; in_spectrum_list_*/</span>)</div>
<div class="line"><a name="l00480"></a><span class="lineno">  480</span>&#160;      {</div>
<div class="line"><a name="l00481"></a><span class="lineno">  481</span>&#160;        data_.reserve(attributeAsInt_(attributes, s_count));</div>
<div class="line"><a name="l00482"></a><span class="lineno">  482</span>&#160;      }</div>
<div class="line"><a name="l00483"></a><span class="lineno">  483</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;binaryDataArray&quot;</span> <span class="comment">/* &amp;&amp; in_spectrum_list_*/</span>)</div>
<div class="line"><a name="l00484"></a><span class="lineno">  484</span>&#160;      {</div>
<div class="line"><a name="l00485"></a><span class="lineno">  485</span>&#160;        data_.push_back(<a class="code" href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html">BinaryData</a>());</div>
<div class="line"><a name="l00486"></a><span class="lineno">  486</span>&#160;</div>
<div class="line"><a name="l00487"></a><span class="lineno">  487</span>&#160;        <span class="comment">//array length</span></div>
<div class="line"><a name="l00488"></a><span class="lineno">  488</span>&#160;        <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> array_length = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>) default_array_length_;</div>
<div class="line"><a name="l00489"></a><span class="lineno">  489</span>&#160;        optionalAttributeAsInt_(array_length, attributes, s_array_length);</div>
<div class="line"><a name="l00490"></a><span class="lineno">  490</span>&#160;        data_.back().size = array_length;</div>
<div class="line"><a name="l00491"></a><span class="lineno">  491</span>&#160;</div>
<div class="line"><a name="l00492"></a><span class="lineno">  492</span>&#160;        <span class="comment">//data processing</span></div>
<div class="line"><a name="l00493"></a><span class="lineno">  493</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref;</div>
<div class="line"><a name="l00494"></a><span class="lineno">  494</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(data_processing_ref, attributes, s_data_processing_ref))</div>
<div class="line"><a name="l00495"></a><span class="lineno">  495</span>&#160;        {</div>
<div class="line"><a name="l00496"></a><span class="lineno">  496</span>&#160;          data_.back().meta.setDataProcessing(processing_[data_processing_ref]);</div>
<div class="line"><a name="l00497"></a><span class="lineno">  497</span>&#160;        }</div>
<div class="line"><a name="l00498"></a><span class="lineno">  498</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00499"></a><span class="lineno">  499</span>&#160;        {</div>
<div class="line"><a name="l00500"></a><span class="lineno">  500</span>&#160;          data_.back().meta.setDataProcessing(processing_[data_processing_ref]);</div>
<div class="line"><a name="l00501"></a><span class="lineno">  501</span>&#160;        }</div>
<div class="line"><a name="l00502"></a><span class="lineno">  502</span>&#160;      }</div>
<div class="line"><a name="l00503"></a><span class="lineno">  503</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;cvParam&quot;</span>)</div>
<div class="line"><a name="l00504"></a><span class="lineno">  504</span>&#160;      {</div>
<div class="line"><a name="l00505"></a><span class="lineno">  505</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> value = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00506"></a><span class="lineno">  506</span>&#160;        optionalAttributeAsString_(value, attributes, s_value);</div>
<div class="line"><a name="l00507"></a><span class="lineno">  507</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> unit_accession = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00508"></a><span class="lineno">  508</span>&#160;        optionalAttributeAsString_(unit_accession, attributes, s_unit_accession);</div>
<div class="line"><a name="l00509"></a><span class="lineno">  509</span>&#160;        handleCVParam_(parent_parent_tag, parent_tag, <span class="comment">/* attributeAsString_(attributes, s_cvref), */</span> attributeAsString_(attributes, s_accession), attributeAsString_(attributes, s_name), value, unit_accession);</div>
<div class="line"><a name="l00510"></a><span class="lineno">  510</span>&#160;      }</div>
<div class="line"><a name="l00511"></a><span class="lineno">  511</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;userParam&quot;</span>)</div>
<div class="line"><a name="l00512"></a><span class="lineno">  512</span>&#160;      {</div>
<div class="line"><a name="l00513"></a><span class="lineno">  513</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> type = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00514"></a><span class="lineno">  514</span>&#160;        optionalAttributeAsString_(type, attributes, s_type);</div>
<div class="line"><a name="l00515"></a><span class="lineno">  515</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> value = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00516"></a><span class="lineno">  516</span>&#160;        optionalAttributeAsString_(value, attributes, s_value);</div>
<div class="line"><a name="l00517"></a><span class="lineno">  517</span>&#160;        handleUserParam_(parent_parent_tag, parent_tag, attributeAsString_(attributes, s_name), type, value);</div>
<div class="line"><a name="l00518"></a><span class="lineno">  518</span>&#160;      }</div>
<div class="line"><a name="l00519"></a><span class="lineno">  519</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;referenceableParamGroup&quot;</span>)</div>
<div class="line"><a name="l00520"></a><span class="lineno">  520</span>&#160;      {</div>
<div class="line"><a name="l00521"></a><span class="lineno">  521</span>&#160;        current_id_ = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00522"></a><span class="lineno">  522</span>&#160;      }</div>
<div class="line"><a name="l00523"></a><span class="lineno">  523</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;sourceFile&quot;</span>)</div>
<div class="line"><a name="l00524"></a><span class="lineno">  524</span>&#160;      {</div>
<div class="line"><a name="l00525"></a><span class="lineno">  525</span>&#160;        current_id_ = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00526"></a><span class="lineno">  526</span>&#160;        source_files_[current_id_].setNameOfFile(attributeAsString_(attributes, s_name));</div>
<div class="line"><a name="l00527"></a><span class="lineno">  527</span>&#160;        source_files_[current_id_].setPathToFile(attributeAsString_(attributes, s_location));</div>
<div class="line"><a name="l00528"></a><span class="lineno">  528</span>&#160;      }</div>
<div class="line"><a name="l00529"></a><span class="lineno">  529</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;referenceableParamGroupRef&quot;</span>)</div>
<div class="line"><a name="l00530"></a><span class="lineno">  530</span>&#160;      {</div>
<div class="line"><a name="l00531"></a><span class="lineno">  531</span>&#160;        <span class="comment">//call handleCVParam_ with the parent tag for each parameter in the group</span></div>
<div class="line"><a name="l00532"></a><span class="lineno">  532</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> ref = attributeAsString_(attributes, s_ref);</div>
<div class="line"><a name="l00533"></a><span class="lineno">  533</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; ref_param_[ref].size(); ++i)</div>
<div class="line"><a name="l00534"></a><span class="lineno">  534</span>&#160;        {</div>
<div class="line"><a name="l00535"></a><span class="lineno">  535</span>&#160;          handleCVParam_(parent_parent_tag, parent_tag, <span class="comment">/* attributeAsString_(attributes, s_cvref), */</span> ref_param_[ref][i].accession, ref_param_[ref][i].name, ref_param_[ref][i].value, ref_param_[ref][i].unit_accession);</div>
<div class="line"><a name="l00536"></a><span class="lineno">  536</span>&#160;        }</div>
<div class="line"><a name="l00537"></a><span class="lineno">  537</span>&#160;      }</div>
<div class="line"><a name="l00538"></a><span class="lineno">  538</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;scan&quot;</span>)</div>
<div class="line"><a name="l00539"></a><span class="lineno">  539</span>&#160;      {</div>
<div class="line"><a name="l00540"></a><span class="lineno">  540</span>&#160;        <a class="code" href="classOpenMS_1_1Acquisition.html">Acquisition</a> tmp;</div>
<div class="line"><a name="l00541"></a><span class="lineno">  541</span>&#160;        <span class="comment">//source file =&gt; meta data</span></div>
<div class="line"><a name="l00542"></a><span class="lineno">  542</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> source_file_ref;</div>
<div class="line"><a name="l00543"></a><span class="lineno">  543</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(source_file_ref, attributes, s_source_file_ref))</div>
<div class="line"><a name="l00544"></a><span class="lineno">  544</span>&#160;        {</div>
<div class="line"><a name="l00545"></a><span class="lineno">  545</span>&#160;          tmp.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;source_file_name&quot;</span>, source_files_[source_file_ref].getNameOfFile());</div>
<div class="line"><a name="l00546"></a><span class="lineno">  546</span>&#160;          tmp.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;source_file_path&quot;</span>, source_files_[source_file_ref].getPathToFile());</div>
<div class="line"><a name="l00547"></a><span class="lineno">  547</span>&#160;        }</div>
<div class="line"><a name="l00548"></a><span class="lineno">  548</span>&#160;        <span class="comment">//external spectrum id =&gt; meta data</span></div>
<div class="line"><a name="l00549"></a><span class="lineno">  549</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> external_spectrum_id;</div>
<div class="line"><a name="l00550"></a><span class="lineno">  550</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(external_spectrum_id, attributes, s_external_spectrum_id))</div>
<div class="line"><a name="l00551"></a><span class="lineno">  551</span>&#160;        {</div>
<div class="line"><a name="l00552"></a><span class="lineno">  552</span>&#160;          tmp.<a class="code" href="classOpenMS_1_1Acquisition.html#a3ea2e9a83b6b409b673cac018f5099ab">setIdentifier</a>(external_spectrum_id);</div>
<div class="line"><a name="l00553"></a><span class="lineno">  553</span>&#160;        }</div>
<div class="line"><a name="l00554"></a><span class="lineno">  554</span>&#160;</div>
<div class="line"><a name="l00555"></a><span class="lineno">  555</span>&#160;        <span class="comment">//spectrumRef - not really needed</span></div>
<div class="line"><a name="l00556"></a><span class="lineno">  556</span>&#160;</div>
<div class="line"><a name="l00557"></a><span class="lineno">  557</span>&#160;        <span class="comment">//instrumentConfigurationRef - not really needed: why should a scan have a different instrument?</span></div>
<div class="line"><a name="l00558"></a><span class="lineno">  558</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> instrument_configuration_ref;</div>
<div class="line"><a name="l00559"></a><span class="lineno">  559</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(instrument_configuration_ref, attributes, s_instrument_configuration_ref))</div>
<div class="line"><a name="l00560"></a><span class="lineno">  560</span>&#160;        {</div>
<div class="line"><a name="l00561"></a><span class="lineno">  561</span>&#160;          warning(LOAD, <span class="stringliteral">&quot;Unhandled attribute &#39;instrumentConfigurationRef&#39; in &#39;scan&#39; tag.&quot;</span>);</div>
<div class="line"><a name="l00562"></a><span class="lineno">  562</span>&#160;        }</div>
<div class="line"><a name="l00563"></a><span class="lineno">  563</span>&#160;</div>
<div class="line"><a name="l00564"></a><span class="lineno">  564</span>&#160;        spec_.getAcquisitionInfo().push_back(tmp);</div>
<div class="line"><a name="l00565"></a><span class="lineno">  565</span>&#160;      }</div>
<div class="line"><a name="l00566"></a><span class="lineno">  566</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;mzML&quot;</span>)</div>
<div class="line"><a name="l00567"></a><span class="lineno">  567</span>&#160;      {</div>
<div class="line"><a name="l00568"></a><span class="lineno">  568</span>&#160;        <span class="comment">//check file version against schema version</span></div>
<div class="line"><a name="l00569"></a><span class="lineno">  569</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> file_version = attributeAsString_(attributes, s_version);</div>
<div class="line"><a name="l00570"></a><span class="lineno">  570</span>&#160;</div>
<div class="line"><a name="l00571"></a><span class="lineno">  571</span>&#160;        <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html">VersionInfo::VersionDetails</a> current_version = <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a43f7f28c650b47c685b8b059a716f35c">VersionInfo::VersionDetails::create</a>(file_version);</div>
<div class="line"><a name="l00572"></a><span class="lineno">  572</span>&#160;        <span class="keyword">static</span> <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html">VersionInfo::VersionDetails</a> mzML_min_version = <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a43f7f28c650b47c685b8b059a716f35c">VersionInfo::VersionDetails::create</a>(<span class="stringliteral">&quot;1.1.0&quot;</span>);</div>
<div class="line"><a name="l00573"></a><span class="lineno">  573</span>&#160;</div>
<div class="line"><a name="l00574"></a><span class="lineno">  574</span>&#160;        <span class="keywordflow">if</span> (current_version == <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a8c1650d1d281b01a53b669240c70a4ab">VersionInfo::VersionDetails::EMPTY</a>)</div>
<div class="line"><a name="l00575"></a><span class="lineno">  575</span>&#160;        {</div>
<div class="line"><a name="l00576"></a><span class="lineno">  576</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Invalid mzML version string &#39;&quot;</span>) + file_version + <span class="stringliteral">&quot;&#39;. Assuming mzML version &quot;</span> + version_ + <span class="stringliteral">&quot;!&quot;</span>);</div>
<div class="line"><a name="l00577"></a><span class="lineno">  577</span>&#160;        }</div>
<div class="line"><a name="l00578"></a><span class="lineno">  578</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00579"></a><span class="lineno">  579</span>&#160;        {</div>
<div class="line"><a name="l00580"></a><span class="lineno">  580</span>&#160;          <span class="keywordflow">if</span> (current_version &lt; mzML_min_version)</div>
<div class="line"><a name="l00581"></a><span class="lineno">  581</span>&#160;          {</div>
<div class="line"><a name="l00582"></a><span class="lineno">  582</span>&#160;            fatalError(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Only mzML 1.1.0 or higher is supported! This file has version &#39;&quot;</span>) + file_version + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l00583"></a><span class="lineno">  583</span>&#160;          }</div>
<div class="line"><a name="l00584"></a><span class="lineno">  584</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_version &gt; <a class="code" href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a43f7f28c650b47c685b8b059a716f35c">VersionInfo::VersionDetails::create</a>(version_))</div>
<div class="line"><a name="l00585"></a><span class="lineno">  585</span>&#160;          {</div>
<div class="line"><a name="l00586"></a><span class="lineno">  586</span>&#160;            warning(LOAD, <span class="stringliteral">&quot;The mzML file version (&quot;</span> + file_version + <span class="stringliteral">&quot;) is newer than the parser version (&quot;</span> + version_ + <span class="stringliteral">&quot;). This might lead to undefined behavior.&quot;</span>);</div>
<div class="line"><a name="l00587"></a><span class="lineno">  587</span>&#160;          }</div>
<div class="line"><a name="l00588"></a><span class="lineno">  588</span>&#160;        }</div>
<div class="line"><a name="l00589"></a><span class="lineno">  589</span>&#160;</div>
<div class="line"><a name="l00590"></a><span class="lineno">  590</span>&#160;        <span class="comment">//handle file accession</span></div>
<div class="line"><a name="l00591"></a><span class="lineno">  591</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> accession;</div>
<div class="line"><a name="l00592"></a><span class="lineno">  592</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(accession, attributes, s_accession))</div>
<div class="line"><a name="l00593"></a><span class="lineno">  593</span>&#160;        {</div>
<div class="line"><a name="l00594"></a><span class="lineno">  594</span>&#160;          exp_-&gt;setIdentifier(accession);</div>
<div class="line"><a name="l00595"></a><span class="lineno">  595</span>&#160;        }</div>
<div class="line"><a name="l00596"></a><span class="lineno">  596</span>&#160;        <span class="comment">//handle file id</span></div>
<div class="line"><a name="l00597"></a><span class="lineno">  597</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> id;</div>
<div class="line"><a name="l00598"></a><span class="lineno">  598</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(<span class="keywordtype">id</span>, attributes, s_id))</div>
<div class="line"><a name="l00599"></a><span class="lineno">  599</span>&#160;        {</div>
<div class="line"><a name="l00600"></a><span class="lineno">  600</span>&#160;          exp_-&gt;setMetaValue(<span class="stringliteral">&quot;mzml_id&quot;</span>, <span class="keywordtype">id</span>);</div>
<div class="line"><a name="l00601"></a><span class="lineno">  601</span>&#160;        }</div>
<div class="line"><a name="l00602"></a><span class="lineno">  602</span>&#160;      }</div>
<div class="line"><a name="l00603"></a><span class="lineno">  603</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;contact&quot;</span>)</div>
<div class="line"><a name="l00604"></a><span class="lineno">  604</span>&#160;      {</div>
<div class="line"><a name="l00605"></a><span class="lineno">  605</span>&#160;        exp_-&gt;getContacts().push_back(<a class="code" href="classOpenMS_1_1ContactPerson.html">ContactPerson</a>());</div>
<div class="line"><a name="l00606"></a><span class="lineno">  606</span>&#160;      }</div>
<div class="line"><a name="l00607"></a><span class="lineno">  607</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;sample&quot;</span>)</div>
<div class="line"><a name="l00608"></a><span class="lineno">  608</span>&#160;      {</div>
<div class="line"><a name="l00609"></a><span class="lineno">  609</span>&#160;        current_id_ = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00610"></a><span class="lineno">  610</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> name;</div>
<div class="line"><a name="l00611"></a><span class="lineno">  611</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(name, attributes, s_name))</div>
<div class="line"><a name="l00612"></a><span class="lineno">  612</span>&#160;        {</div>
<div class="line"><a name="l00613"></a><span class="lineno">  613</span>&#160;          samples_[current_id_].setName(name);</div>
<div class="line"><a name="l00614"></a><span class="lineno">  614</span>&#160;        }</div>
<div class="line"><a name="l00615"></a><span class="lineno">  615</span>&#160;      }</div>
<div class="line"><a name="l00616"></a><span class="lineno">  616</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;run&quot;</span>)</div>
<div class="line"><a name="l00617"></a><span class="lineno">  617</span>&#160;      {</div>
<div class="line"><a name="l00618"></a><span class="lineno">  618</span>&#160;        <span class="comment">//sample</span></div>
<div class="line"><a name="l00619"></a><span class="lineno">  619</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> sample_ref;</div>
<div class="line"><a name="l00620"></a><span class="lineno">  620</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(sample_ref, attributes, s_sample_ref))</div>
<div class="line"><a name="l00621"></a><span class="lineno">  621</span>&#160;        {</div>
<div class="line"><a name="l00622"></a><span class="lineno">  622</span>&#160;          exp_-&gt;setSample(samples_[sample_ref]);</div>
<div class="line"><a name="l00623"></a><span class="lineno">  623</span>&#160;        }</div>
<div class="line"><a name="l00624"></a><span class="lineno">  624</span>&#160;        <span class="comment">//instrument</span></div>
<div class="line"><a name="l00625"></a><span class="lineno">  625</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> instrument_ref = attributeAsString_(attributes, s_default_instrument_configuration_ref);</div>
<div class="line"><a name="l00626"></a><span class="lineno">  626</span>&#160;        exp_-&gt;setInstrument(instruments_[instrument_ref]);</div>
<div class="line"><a name="l00627"></a><span class="lineno">  627</span>&#160;        <span class="comment">//start time</span></div>
<div class="line"><a name="l00628"></a><span class="lineno">  628</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> start_time;</div>
<div class="line"><a name="l00629"></a><span class="lineno">  629</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(start_time, attributes, s_start_time_stamp))</div>
<div class="line"><a name="l00630"></a><span class="lineno">  630</span>&#160;        {</div>
<div class="line"><a name="l00631"></a><span class="lineno">  631</span>&#160;          exp_-&gt;setDateTime(asDateTime_(start_time));</div>
<div class="line"><a name="l00632"></a><span class="lineno">  632</span>&#160;        }</div>
<div class="line"><a name="l00633"></a><span class="lineno">  633</span>&#160;        <span class="comment">//defaultSourceFileRef</span></div>
<div class="line"><a name="l00634"></a><span class="lineno">  634</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> default_source_file_ref;</div>
<div class="line"><a name="l00635"></a><span class="lineno">  635</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(default_source_file_ref, attributes, s_default_source_file_ref))</div>
<div class="line"><a name="l00636"></a><span class="lineno">  636</span>&#160;        {</div>
<div class="line"><a name="l00637"></a><span class="lineno">  637</span>&#160;          exp_-&gt;getSourceFiles().push_back(source_files_[default_source_file_ref]);</div>
<div class="line"><a name="l00638"></a><span class="lineno">  638</span>&#160;        }</div>
<div class="line"><a name="l00639"></a><span class="lineno">  639</span>&#160;      }</div>
<div class="line"><a name="l00640"></a><span class="lineno">  640</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;software&quot;</span>)</div>
<div class="line"><a name="l00641"></a><span class="lineno">  641</span>&#160;      {</div>
<div class="line"><a name="l00642"></a><span class="lineno">  642</span>&#160;        current_id_ = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00643"></a><span class="lineno">  643</span>&#160;        software_[current_id_].setVersion(attributeAsString_(attributes, s_version));</div>
<div class="line"><a name="l00644"></a><span class="lineno">  644</span>&#160;      }</div>
<div class="line"><a name="l00645"></a><span class="lineno">  645</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;dataProcessing&quot;</span>)</div>
<div class="line"><a name="l00646"></a><span class="lineno">  646</span>&#160;      {</div>
<div class="line"><a name="l00647"></a><span class="lineno">  647</span>&#160;        current_id_ = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00648"></a><span class="lineno">  648</span>&#160;      }</div>
<div class="line"><a name="l00649"></a><span class="lineno">  649</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;processingMethod&quot;</span>)</div>
<div class="line"><a name="l00650"></a><span class="lineno">  650</span>&#160;      {</div>
<div class="line"><a name="l00651"></a><span class="lineno">  651</span>&#160;        <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> dp;</div>
<div class="line"><a name="l00652"></a><span class="lineno">  652</span>&#160;        <span class="comment">// See ticket 452: Do NOT remove  this try/catch block until foreign</span></div>
<div class="line"><a name="l00653"></a><span class="lineno">  653</span>&#160;        <span class="comment">// software (e.g. ProteoWizard msconvert.exe) produces valid mzML.</span></div>
<div class="line"><a name="l00654"></a><span class="lineno">  654</span>&#160;        <span class="keywordflow">try</span></div>
<div class="line"><a name="l00655"></a><span class="lineno">  655</span>&#160;        {</div>
<div class="line"><a name="l00656"></a><span class="lineno">  656</span>&#160;          dp.<a class="code" href="classOpenMS_1_1DataProcessing.html#a8ff34073a7ed3fabe3f5deff96c0282e">setSoftware</a>(software_[attributeAsString_(attributes, s_software_ref)]);</div>
<div class="line"><a name="l00657"></a><span class="lineno">  657</span>&#160;        }</div>
<div class="line"><a name="l00658"></a><span class="lineno">  658</span>&#160;        <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>&amp; <span class="comment">/*e*/</span>)</div>
<div class="line"><a name="l00659"></a><span class="lineno">  659</span>&#160;        {</div>
<div class="line"><a name="l00660"></a><span class="lineno">  660</span>&#160;          <a class="code" href="LogStream_8h.html#aced66975c154ea0e2a8ec3bc818b4e08">LOG_ERROR</a> &lt;&lt; <span class="stringliteral">&quot;Warning: Parsing error, \&quot;processingMethod\&quot; is missing the required attribute \&quot;softwareRef\&quot;.\n&quot;</span> &lt;&lt;</div>
<div class="line"><a name="l00661"></a><span class="lineno">  661</span>&#160;            <span class="stringliteral">&quot;The software tool which generated this mzML should be fixed. Please notify the maintainers.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00662"></a><span class="lineno">  662</span>&#160;        }</div>
<div class="line"><a name="l00663"></a><span class="lineno">  663</span>&#160;        processing_[current_id_].push_back(dp);</div>
<div class="line"><a name="l00664"></a><span class="lineno">  664</span>&#160;        <span class="comment">//The order of processing methods is currently ignored</span></div>
<div class="line"><a name="l00665"></a><span class="lineno">  665</span>&#160;      }</div>
<div class="line"><a name="l00666"></a><span class="lineno">  666</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;instrumentConfiguration&quot;</span>)</div>
<div class="line"><a name="l00667"></a><span class="lineno">  667</span>&#160;      {</div>
<div class="line"><a name="l00668"></a><span class="lineno">  668</span>&#160;        current_id_ = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00669"></a><span class="lineno">  669</span>&#160;</div>
<div class="line"><a name="l00670"></a><span class="lineno">  670</span>&#160;        <span class="comment">//scan settings</span></div>
<div class="line"><a name="l00671"></a><span class="lineno">  671</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> scan_settings_ref;</div>
<div class="line"><a name="l00672"></a><span class="lineno">  672</span>&#160;        <span class="keywordflow">if</span> (optionalAttributeAsString_(scan_settings_ref, attributes, s_scan_settings_ref))</div>
<div class="line"><a name="l00673"></a><span class="lineno">  673</span>&#160;        {</div>
<div class="line"><a name="l00674"></a><span class="lineno">  674</span>&#160;          warning(LOAD, <span class="stringliteral">&quot;Unhandled attribute &#39;scanSettingsRef&#39; in &#39;instrumentConfiguration&#39; tag.&quot;</span>);</div>
<div class="line"><a name="l00675"></a><span class="lineno">  675</span>&#160;        }</div>
<div class="line"><a name="l00676"></a><span class="lineno">  676</span>&#160;      }</div>
<div class="line"><a name="l00677"></a><span class="lineno">  677</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;softwareRef&quot;</span>)</div>
<div class="line"><a name="l00678"></a><span class="lineno">  678</span>&#160;      {</div>
<div class="line"><a name="l00679"></a><span class="lineno">  679</span>&#160;        <span class="comment">//Set the software of the instrument</span></div>
<div class="line"><a name="l00680"></a><span class="lineno">  680</span>&#160;        instruments_[current_id_].setSoftware(software_[attributeAsString_(attributes, s_ref)]);</div>
<div class="line"><a name="l00681"></a><span class="lineno">  681</span>&#160;      }</div>
<div class="line"><a name="l00682"></a><span class="lineno">  682</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;source&quot;</span>)</div>
<div class="line"><a name="l00683"></a><span class="lineno">  683</span>&#160;      {</div>
<div class="line"><a name="l00684"></a><span class="lineno">  684</span>&#160;        instruments_[current_id_].getIonSources().push_back(<a class="code" href="classOpenMS_1_1IonSource.html">IonSource</a>());</div>
<div class="line"><a name="l00685"></a><span class="lineno">  685</span>&#160;        instruments_[current_id_].getIonSources().back().setOrder(attributeAsInt_(attributes, s_order));</div>
<div class="line"><a name="l00686"></a><span class="lineno">  686</span>&#160;      }</div>
<div class="line"><a name="l00687"></a><span class="lineno">  687</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;analyzer&quot;</span>)</div>
<div class="line"><a name="l00688"></a><span class="lineno">  688</span>&#160;      {</div>
<div class="line"><a name="l00689"></a><span class="lineno">  689</span>&#160;        instruments_[current_id_].getMassAnalyzers().push_back(<a class="code" href="classOpenMS_1_1MassAnalyzer.html">MassAnalyzer</a>());</div>
<div class="line"><a name="l00690"></a><span class="lineno">  690</span>&#160;        instruments_[current_id_].getMassAnalyzers().back().setOrder(attributeAsInt_(attributes, s_order));</div>
<div class="line"><a name="l00691"></a><span class="lineno">  691</span>&#160;      }</div>
<div class="line"><a name="l00692"></a><span class="lineno">  692</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;detector&quot;</span>)</div>
<div class="line"><a name="l00693"></a><span class="lineno">  693</span>&#160;      {</div>
<div class="line"><a name="l00694"></a><span class="lineno">  694</span>&#160;        instruments_[current_id_].getIonDetectors().push_back(<a class="code" href="classOpenMS_1_1IonDetector.html">IonDetector</a>());</div>
<div class="line"><a name="l00695"></a><span class="lineno">  695</span>&#160;        instruments_[current_id_].getIonDetectors().back().setOrder(attributeAsInt_(attributes, s_order));</div>
<div class="line"><a name="l00696"></a><span class="lineno">  696</span>&#160;      }</div>
<div class="line"><a name="l00697"></a><span class="lineno">  697</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;precursor&quot;</span>)</div>
<div class="line"><a name="l00698"></a><span class="lineno">  698</span>&#160;      {</div>
<div class="line"><a name="l00699"></a><span class="lineno">  699</span>&#160;        <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l00700"></a><span class="lineno">  700</span>&#160;        {</div>
<div class="line"><a name="l00701"></a><span class="lineno">  701</span>&#160;          <span class="comment">//initialize</span></div>
<div class="line"><a name="l00702"></a><span class="lineno">  702</span>&#160;          spec_.getPrecursors().push_back(<a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>());</div>
<div class="line"><a name="l00703"></a><span class="lineno">  703</span>&#160;</div>
<div class="line"><a name="l00704"></a><span class="lineno">  704</span>&#160;          <span class="comment">//source file =&gt; meta data</span></div>
<div class="line"><a name="l00705"></a><span class="lineno">  705</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> source_file_ref;</div>
<div class="line"><a name="l00706"></a><span class="lineno">  706</span>&#160;          <span class="keywordflow">if</span> (optionalAttributeAsString_(source_file_ref, attributes, s_source_file_ref))</div>
<div class="line"><a name="l00707"></a><span class="lineno">  707</span>&#160;          {</div>
<div class="line"><a name="l00708"></a><span class="lineno">  708</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;source_file_name&quot;</span>, source_files_[source_file_ref].getNameOfFile());</div>
<div class="line"><a name="l00709"></a><span class="lineno">  709</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;source_file_path&quot;</span>, source_files_[source_file_ref].getPathToFile());</div>
<div class="line"><a name="l00710"></a><span class="lineno">  710</span>&#160;          }</div>
<div class="line"><a name="l00711"></a><span class="lineno">  711</span>&#160;          <span class="comment">//external spectrum id =&gt; meta data</span></div>
<div class="line"><a name="l00712"></a><span class="lineno">  712</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> external_spectrum_id;</div>
<div class="line"><a name="l00713"></a><span class="lineno">  713</span>&#160;          <span class="keywordflow">if</span> (optionalAttributeAsString_(external_spectrum_id, attributes, s_external_spectrum_id))</div>
<div class="line"><a name="l00714"></a><span class="lineno">  714</span>&#160;          {</div>
<div class="line"><a name="l00715"></a><span class="lineno">  715</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;external_spectrum_id&quot;</span>, external_spectrum_id);</div>
<div class="line"><a name="l00716"></a><span class="lineno">  716</span>&#160;          }</div>
<div class="line"><a name="l00717"></a><span class="lineno">  717</span>&#160;          <span class="comment">//reset selected ion count</span></div>
<div class="line"><a name="l00718"></a><span class="lineno">  718</span>&#160;          selected_ion_count_ = 0;</div>
<div class="line"><a name="l00719"></a><span class="lineno">  719</span>&#160;        }</div>
<div class="line"><a name="l00720"></a><span class="lineno">  720</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00721"></a><span class="lineno">  721</span>&#160;        {</div>
<div class="line"><a name="l00722"></a><span class="lineno">  722</span>&#160;          chromatogram_.setPrecursor(<a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>());</div>
<div class="line"><a name="l00723"></a><span class="lineno">  723</span>&#160;</div>
<div class="line"><a name="l00724"></a><span class="lineno">  724</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> source_file_ref;</div>
<div class="line"><a name="l00725"></a><span class="lineno">  725</span>&#160;          <span class="keywordflow">if</span> (optionalAttributeAsString_(source_file_ref, attributes, s_source_file_ref))</div>
<div class="line"><a name="l00726"></a><span class="lineno">  726</span>&#160;          {</div>
<div class="line"><a name="l00727"></a><span class="lineno">  727</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;source_file_name&quot;</span>, source_files_[source_file_ref].getNameOfFile());</div>
<div class="line"><a name="l00728"></a><span class="lineno">  728</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;source_file_path&quot;</span>, source_files_[source_file_ref].getPathToFile());</div>
<div class="line"><a name="l00729"></a><span class="lineno">  729</span>&#160;          }</div>
<div class="line"><a name="l00730"></a><span class="lineno">  730</span>&#160;</div>
<div class="line"><a name="l00731"></a><span class="lineno">  731</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> external_spectrum_id;</div>
<div class="line"><a name="l00732"></a><span class="lineno">  732</span>&#160;          <span class="keywordflow">if</span> (optionalAttributeAsString_(external_spectrum_id, attributes, s_external_spectrum_id))</div>
<div class="line"><a name="l00733"></a><span class="lineno">  733</span>&#160;          {</div>
<div class="line"><a name="l00734"></a><span class="lineno">  734</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;external_spectrum_id&quot;</span>, external_spectrum_id);</div>
<div class="line"><a name="l00735"></a><span class="lineno">  735</span>&#160;          }</div>
<div class="line"><a name="l00736"></a><span class="lineno">  736</span>&#160;          selected_ion_count_ = 0;</div>
<div class="line"><a name="l00737"></a><span class="lineno">  737</span>&#160;        }</div>
<div class="line"><a name="l00738"></a><span class="lineno">  738</span>&#160;      }</div>
<div class="line"><a name="l00739"></a><span class="lineno">  739</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;product&quot;</span>)</div>
<div class="line"><a name="l00740"></a><span class="lineno">  740</span>&#160;      {</div>
<div class="line"><a name="l00741"></a><span class="lineno">  741</span>&#160;        <span class="comment">//initialize</span></div>
<div class="line"><a name="l00742"></a><span class="lineno">  742</span>&#160;        <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l00743"></a><span class="lineno">  743</span>&#160;        {</div>
<div class="line"><a name="l00744"></a><span class="lineno">  744</span>&#160;          spec_.getProducts().push_back(<a class="code" href="classOpenMS_1_1Product.html">Product</a>());</div>
<div class="line"><a name="l00745"></a><span class="lineno">  745</span>&#160;        }</div>
<div class="line"><a name="l00746"></a><span class="lineno">  746</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00747"></a><span class="lineno">  747</span>&#160;        {</div>
<div class="line"><a name="l00748"></a><span class="lineno">  748</span>&#160;          chromatogram_.setProduct(<a class="code" href="classOpenMS_1_1Product.html">Product</a>());</div>
<div class="line"><a name="l00749"></a><span class="lineno">  749</span>&#160;        }</div>
<div class="line"><a name="l00750"></a><span class="lineno">  750</span>&#160;      }</div>
<div class="line"><a name="l00751"></a><span class="lineno">  751</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;selectedIon&quot;</span>)</div>
<div class="line"><a name="l00752"></a><span class="lineno">  752</span>&#160;      {</div>
<div class="line"><a name="l00753"></a><span class="lineno">  753</span>&#160;        <span class="comment">//increase selected ion count</span></div>
<div class="line"><a name="l00754"></a><span class="lineno">  754</span>&#160;        ++selected_ion_count_;</div>
<div class="line"><a name="l00755"></a><span class="lineno">  755</span>&#160;      }</div>
<div class="line"><a name="l00756"></a><span class="lineno">  756</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;selectedIonList&quot;</span>)</div>
<div class="line"><a name="l00757"></a><span class="lineno">  757</span>&#160;      {</div>
<div class="line"><a name="l00758"></a><span class="lineno">  758</span>&#160;        <span class="comment">//Warn if more than one selected ion is present</span></div>
<div class="line"><a name="l00759"></a><span class="lineno">  759</span>&#160;        <span class="keywordflow">if</span> (attributeAsInt_(attributes, s_count) &gt; 1)</div>
<div class="line"><a name="l00760"></a><span class="lineno">  760</span>&#160;        {</div>
<div class="line"><a name="l00761"></a><span class="lineno">  761</span>&#160;          warning(LOAD, <span class="stringliteral">&quot;OpenMS can currently handle only one selection ion per precursor! Only the first ion is loaded!&quot;</span>);</div>
<div class="line"><a name="l00762"></a><span class="lineno">  762</span>&#160;        }</div>
<div class="line"><a name="l00763"></a><span class="lineno">  763</span>&#160;      }</div>
<div class="line"><a name="l00764"></a><span class="lineno">  764</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">&quot;scanWindow&quot;</span>)</div>
<div class="line"><a name="l00765"></a><span class="lineno">  765</span>&#160;      {</div>
<div class="line"><a name="l00766"></a><span class="lineno">  766</span>&#160;        spec_.getInstrumentSettings().getScanWindows().push_back(<a class="code" href="structOpenMS_1_1ScanWindow.html">ScanWindow</a>());</div>
<div class="line"><a name="l00767"></a><span class="lineno">  767</span>&#160;      }</div>
<div class="line"><a name="l00768"></a><span class="lineno">  768</span>&#160;    }</div>
<div class="line"><a name="l00769"></a><span class="lineno">  769</span>&#160;</div>
<div class="line"><a name="l00770"></a><span class="lineno">  770</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00771"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9028634d022a74d1fc8db852d99984d6">  771</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9028634d022a74d1fc8db852d99984d6">MzMLHandler&lt;MapType&gt;::endElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname)</div>
<div class="line"><a name="l00772"></a><span class="lineno">  772</span>&#160;    {</div>
<div class="line"><a name="l00773"></a><span class="lineno">  773</span>&#160;      <span class="keyword">static</span> <a class="code" href="classunsigned_01int.html">UInt</a> scan_count = 0;</div>
<div class="line"><a name="l00774"></a><span class="lineno">  774</span>&#160;      <span class="keyword">static</span> <a class="code" href="classunsigned_01int.html">UInt</a> chromatogram_count = 0;</div>
<div class="line"><a name="l00775"></a><span class="lineno">  775</span>&#160;</div>
<div class="line"><a name="l00776"></a><span class="lineno">  776</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_spectrum = xercesc::XMLString::transcode(<span class="stringliteral">&quot;spectrum&quot;</span>);</div>
<div class="line"><a name="l00777"></a><span class="lineno">  777</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_chromatogram = xercesc::XMLString::transcode(<span class="stringliteral">&quot;chromatogram&quot;</span>);</div>
<div class="line"><a name="l00778"></a><span class="lineno">  778</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_spectrum_list = xercesc::XMLString::transcode(<span class="stringliteral">&quot;spectrumList&quot;</span>);</div>
<div class="line"><a name="l00779"></a><span class="lineno">  779</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_chromatogram_list = xercesc::XMLString::transcode(<span class="stringliteral">&quot;chromatogramList&quot;</span>);</div>
<div class="line"><a name="l00780"></a><span class="lineno">  780</span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_mzml = xercesc::XMLString::transcode(<span class="stringliteral">&quot;mzML&quot;</span>);</div>
<div class="line"><a name="l00781"></a><span class="lineno">  781</span>&#160;</div>
<div class="line"><a name="l00782"></a><span class="lineno">  782</span>&#160;      open_tags_.pop_back();</div>
<div class="line"><a name="l00783"></a><span class="lineno">  783</span>&#160;</div>
<div class="line"><a name="l00784"></a><span class="lineno">  784</span>&#160;      <span class="keywordflow">if</span> (equal_(qname, s_spectrum))</div>
<div class="line"><a name="l00785"></a><span class="lineno">  785</span>&#160;      {</div>
<div class="line"><a name="l00786"></a><span class="lineno">  786</span>&#160;        <span class="keywordflow">if</span> (!skip_spectrum_)</div>
<div class="line"><a name="l00787"></a><span class="lineno">  787</span>&#160;        {</div>
<div class="line"><a name="l00788"></a><span class="lineno">  788</span>&#160;</div>
<div class="line"><a name="l00789"></a><span class="lineno">  789</span>&#160;          <span class="comment">// catch errors stemming from confusion about elution time and scan time</span></div>
<div class="line"><a name="l00790"></a><span class="lineno">  790</span>&#160;          <span class="keywordflow">if</span> (spec_.getRT() == -1.0 &amp;&amp; spec_.metaValueExists(<span class="stringliteral">&quot;elution time (seconds)&quot;</span>))</div>
<div class="line"><a name="l00791"></a><span class="lineno">  791</span>&#160;          {</div>
<div class="line"><a name="l00792"></a><span class="lineno">  792</span>&#160;            spec_.setRT(spec_.getMetaValue(<span class="stringliteral">&quot;elution time (seconds)&quot;</span>));</div>
<div class="line"><a name="l00793"></a><span class="lineno">  793</span>&#160;          }</div>
<div class="line"><a name="l00794"></a><span class="lineno">  794</span>&#160;          <span class="comment">/* this is too hot (could be SRM as well? -- check!):</span></div>
<div class="line"><a name="l00795"></a><span class="lineno">  795</span>&#160;<span class="comment">             // correct spectrum type if possible (i.e., make it more specific)</span></div>
<div class="line"><a name="l00796"></a><span class="lineno">  796</span>&#160;<span class="comment">          if (spec_.getInstrumentSettings().getScanMode() == InstrumentSettings::MASSSPECTRUM)</span></div>
<div class="line"><a name="l00797"></a><span class="lineno">  797</span>&#160;<span class="comment">          {</span></div>
<div class="line"><a name="l00798"></a><span class="lineno">  798</span>&#160;<span class="comment">            if (spec_.getMSLevel() &lt;= 1) spec_.getInstrumentSettings().setScanMode(InstrumentSettings::MS1SPECTRUM);</span></div>
<div class="line"><a name="l00799"></a><span class="lineno">  799</span>&#160;<span class="comment">            else                         spec_.getInstrumentSettings().setScanMode(InstrumentSettings::MSNSPECTRUM);</span></div>
<div class="line"><a name="l00800"></a><span class="lineno">  800</span>&#160;<span class="comment">          }</span></div>
<div class="line"><a name="l00801"></a><span class="lineno">  801</span>&#160;<span class="comment">          */</span></div>
<div class="line"><a name="l00802"></a><span class="lineno">  802</span>&#160;</div>
<div class="line"><a name="l00803"></a><span class="lineno">  803</span>&#160;          fillData_();</div>
<div class="line"><a name="l00804"></a><span class="lineno">  804</span>&#160;          exp_-&gt;addSpectrum(spec_);</div>
<div class="line"><a name="l00805"></a><span class="lineno">  805</span>&#160;</div>
<div class="line"><a name="l00806"></a><span class="lineno">  806</span>&#160;        }</div>
<div class="line"><a name="l00807"></a><span class="lineno">  807</span>&#160;        skip_spectrum_ = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00808"></a><span class="lineno">  808</span>&#160;        logger_.setProgress(++scan_count);</div>
<div class="line"><a name="l00809"></a><span class="lineno">  809</span>&#160;        data_.clear();</div>
<div class="line"><a name="l00810"></a><span class="lineno">  810</span>&#160;        default_array_length_ = 0;</div>
<div class="line"><a name="l00811"></a><span class="lineno">  811</span>&#160;      }</div>
<div class="line"><a name="l00812"></a><span class="lineno">  812</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (equal_(qname, s_chromatogram))</div>
<div class="line"><a name="l00813"></a><span class="lineno">  813</span>&#160;      {</div>
<div class="line"><a name="l00814"></a><span class="lineno">  814</span>&#160;        fillChromatogramData_();</div>
<div class="line"><a name="l00815"></a><span class="lineno">  815</span>&#160;        exp_-&gt;addChromatogram(chromatogram_);</div>
<div class="line"><a name="l00816"></a><span class="lineno">  816</span>&#160;        logger_.setProgress(++chromatogram_count);</div>
<div class="line"><a name="l00817"></a><span class="lineno">  817</span>&#160;        data_.clear();</div>
<div class="line"><a name="l00818"></a><span class="lineno">  818</span>&#160;        default_array_length_ = 0;</div>
<div class="line"><a name="l00819"></a><span class="lineno">  819</span>&#160;      }</div>
<div class="line"><a name="l00820"></a><span class="lineno">  820</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (equal_(qname, s_spectrum_list))</div>
<div class="line"><a name="l00821"></a><span class="lineno">  821</span>&#160;      {</div>
<div class="line"><a name="l00822"></a><span class="lineno">  822</span>&#160;        in_spectrum_list_ = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00823"></a><span class="lineno">  823</span>&#160;        logger_.endProgress();</div>
<div class="line"><a name="l00824"></a><span class="lineno">  824</span>&#160;      }</div>
<div class="line"><a name="l00825"></a><span class="lineno">  825</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (equal_(qname, s_chromatogram_list))</div>
<div class="line"><a name="l00826"></a><span class="lineno">  826</span>&#160;      {</div>
<div class="line"><a name="l00827"></a><span class="lineno">  827</span>&#160;        in_spectrum_list_ = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00828"></a><span class="lineno">  828</span>&#160;        logger_.endProgress();</div>
<div class="line"><a name="l00829"></a><span class="lineno">  829</span>&#160;      }</div>
<div class="line"><a name="l00830"></a><span class="lineno">  830</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (equal_(qname, s_mzml))</div>
<div class="line"><a name="l00831"></a><span class="lineno">  831</span>&#160;      {</div>
<div class="line"><a name="l00832"></a><span class="lineno">  832</span>&#160;        scan_count = 0;</div>
<div class="line"><a name="l00833"></a><span class="lineno">  833</span>&#160;        chromatogram_count = 0;</div>
<div class="line"><a name="l00834"></a><span class="lineno">  834</span>&#160;        ref_param_.clear();</div>
<div class="line"><a name="l00835"></a><span class="lineno">  835</span>&#160;        current_id_ = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00836"></a><span class="lineno">  836</span>&#160;        source_files_.clear();</div>
<div class="line"><a name="l00837"></a><span class="lineno">  837</span>&#160;        samples_.clear();</div>
<div class="line"><a name="l00838"></a><span class="lineno">  838</span>&#160;        software_.clear();</div>
<div class="line"><a name="l00839"></a><span class="lineno">  839</span>&#160;        instruments_.clear();</div>
<div class="line"><a name="l00840"></a><span class="lineno">  840</span>&#160;        processing_.clear();</div>
<div class="line"><a name="l00841"></a><span class="lineno">  841</span>&#160;      }</div>
<div class="line"><a name="l00842"></a><span class="lineno">  842</span>&#160;</div>
<div class="line"><a name="l00843"></a><span class="lineno">  843</span>&#160;      sm_.clear();</div>
<div class="line"><a name="l00844"></a><span class="lineno">  844</span>&#160;    }</div>
<div class="line"><a name="l00845"></a><span class="lineno">  845</span>&#160;</div>
<div class="line"><a name="l00846"></a><span class="lineno">  846</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l00847"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add1bc02b038fe1abde05c0352577f1df">  847</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add1bc02b038fe1abde05c0352577f1df">MzMLHandler&lt;MapType&gt;::fillData_</a>()</div>
<div class="line"><a name="l00848"></a><span class="lineno">  848</span>&#160;    {</div>
<div class="line"><a name="l00849"></a><span class="lineno">  849</span>&#160;      <span class="comment">//decode all base64 arrays</span></div>
<div class="line"><a name="l00850"></a><span class="lineno">  850</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l00851"></a><span class="lineno">  851</span>&#160;      {</div>
<div class="line"><a name="l00852"></a><span class="lineno">  852</span>&#160;        <span class="comment">//remove whitespaces from binary data</span></div>
<div class="line"><a name="l00853"></a><span class="lineno">  853</span>&#160;        <span class="comment">//this should not be necessary, but linebreaks inside the base64 data are unfortunately no exception</span></div>
<div class="line"><a name="l00854"></a><span class="lineno">  854</span>&#160;        data_[i].base64.removeWhitespaces();</div>
<div class="line"><a name="l00855"></a><span class="lineno">  855</span>&#160;</div>
<div class="line"><a name="l00856"></a><span class="lineno">  856</span>&#160;        <span class="comment">//decode data and check if the length of the decoded data matches the expected length</span></div>
<div class="line"><a name="l00857"></a><span class="lineno">  857</span>&#160;        <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_FLOAT)</div>
<div class="line"><a name="l00858"></a><span class="lineno">  858</span>&#160;        {</div>
<div class="line"><a name="l00859"></a><span class="lineno">  859</span>&#160;          <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_64)</div>
<div class="line"><a name="l00860"></a><span class="lineno">  860</span>&#160;          {</div>
<div class="line"><a name="l00861"></a><span class="lineno">  861</span>&#160;            decoder_.decode(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].floats_64, data_[i].compression);</div>
<div class="line"><a name="l00862"></a><span class="lineno">  862</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].floats_64.size())</div>
<div class="line"><a name="l00863"></a><span class="lineno">  863</span>&#160;            {</div>
<div class="line"><a name="l00864"></a><span class="lineno">  864</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Float binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of spectrum &#39;&quot;</span> + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].floats_64.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00865"></a><span class="lineno">  865</span>&#160;              data_[i].size = data_[i].floats_64.size();</div>
<div class="line"><a name="l00866"></a><span class="lineno">  866</span>&#160;            }</div>
<div class="line"><a name="l00867"></a><span class="lineno">  867</span>&#160;          }</div>
<div class="line"><a name="l00868"></a><span class="lineno">  868</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_32)</div>
<div class="line"><a name="l00869"></a><span class="lineno">  869</span>&#160;          {</div>
<div class="line"><a name="l00870"></a><span class="lineno">  870</span>&#160;            decoder_.decode(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].floats_32, data_[i].compression);</div>
<div class="line"><a name="l00871"></a><span class="lineno">  871</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].floats_32.size())</div>
<div class="line"><a name="l00872"></a><span class="lineno">  872</span>&#160;            {</div>
<div class="line"><a name="l00873"></a><span class="lineno">  873</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Float binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of spectrum &#39;&quot;</span> + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].floats_32.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00874"></a><span class="lineno">  874</span>&#160;              data_[i].size = data_[i].floats_32.size();</div>
<div class="line"><a name="l00875"></a><span class="lineno">  875</span>&#160;            }</div>
<div class="line"><a name="l00876"></a><span class="lineno">  876</span>&#160;          }</div>
<div class="line"><a name="l00877"></a><span class="lineno">  877</span>&#160;        }</div>
<div class="line"><a name="l00878"></a><span class="lineno">  878</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_INT)</div>
<div class="line"><a name="l00879"></a><span class="lineno">  879</span>&#160;        {</div>
<div class="line"><a name="l00880"></a><span class="lineno">  880</span>&#160;          <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_64)</div>
<div class="line"><a name="l00881"></a><span class="lineno">  881</span>&#160;          {</div>
<div class="line"><a name="l00882"></a><span class="lineno">  882</span>&#160;            decoder_.decodeIntegers(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].ints_64, data_[i].compression);</div>
<div class="line"><a name="l00883"></a><span class="lineno">  883</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].ints_64.size())</div>
<div class="line"><a name="l00884"></a><span class="lineno">  884</span>&#160;            {</div>
<div class="line"><a name="l00885"></a><span class="lineno">  885</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Integer binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of spectrum &#39;&quot;</span> + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].ints_64.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00886"></a><span class="lineno">  886</span>&#160;              data_[i].size = data_[i].ints_64.size();</div>
<div class="line"><a name="l00887"></a><span class="lineno">  887</span>&#160;            }</div>
<div class="line"><a name="l00888"></a><span class="lineno">  888</span>&#160;          }</div>
<div class="line"><a name="l00889"></a><span class="lineno">  889</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_32)</div>
<div class="line"><a name="l00890"></a><span class="lineno">  890</span>&#160;          {</div>
<div class="line"><a name="l00891"></a><span class="lineno">  891</span>&#160;            decoder_.decodeIntegers(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].ints_32, data_[i].compression);</div>
<div class="line"><a name="l00892"></a><span class="lineno">  892</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].ints_32.size())</div>
<div class="line"><a name="l00893"></a><span class="lineno">  893</span>&#160;            {</div>
<div class="line"><a name="l00894"></a><span class="lineno">  894</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Integer binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of spectrum &#39;&quot;</span> + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].ints_32.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00895"></a><span class="lineno">  895</span>&#160;              data_[i].size = data_[i].ints_32.size();</div>
<div class="line"><a name="l00896"></a><span class="lineno">  896</span>&#160;            }</div>
<div class="line"><a name="l00897"></a><span class="lineno">  897</span>&#160;          }</div>
<div class="line"><a name="l00898"></a><span class="lineno">  898</span>&#160;        }</div>
<div class="line"><a name="l00899"></a><span class="lineno">  899</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_STRING)</div>
<div class="line"><a name="l00900"></a><span class="lineno">  900</span>&#160;        {</div>
<div class="line"><a name="l00901"></a><span class="lineno">  901</span>&#160;          decoder_.decodeStrings(data_[i].base64, data_[i].decoded_char, data_[i].compression);</div>
<div class="line"><a name="l00902"></a><span class="lineno">  902</span>&#160;          <span class="keywordflow">if</span> (data_[i].size != data_[i].decoded_char.size())</div>
<div class="line"><a name="l00903"></a><span class="lineno">  903</span>&#160;          {</div>
<div class="line"><a name="l00904"></a><span class="lineno">  904</span>&#160;            warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;String binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of spectrum &#39;&quot;</span> + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].decoded_char.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00905"></a><span class="lineno">  905</span>&#160;            data_[i].size = data_[i].decoded_char.size();</div>
<div class="line"><a name="l00906"></a><span class="lineno">  906</span>&#160;          }</div>
<div class="line"><a name="l00907"></a><span class="lineno">  907</span>&#160;        }</div>
<div class="line"><a name="l00908"></a><span class="lineno">  908</span>&#160;      }</div>
<div class="line"><a name="l00909"></a><span class="lineno">  909</span>&#160;</div>
<div class="line"><a name="l00910"></a><span class="lineno">  910</span>&#160;      <span class="comment">//look up the precision and the index of the intensity and m/z array</span></div>
<div class="line"><a name="l00911"></a><span class="lineno">  911</span>&#160;      <span class="keywordtype">bool</span> mz_precision_64 = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00912"></a><span class="lineno">  912</span>&#160;      <span class="keywordtype">bool</span> int_precision_64 = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00913"></a><span class="lineno">  913</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> mz_index = -1;</div>
<div class="line"><a name="l00914"></a><span class="lineno">  914</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> int_index = -1;</div>
<div class="line"><a name="l00915"></a><span class="lineno">  915</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l00916"></a><span class="lineno">  916</span>&#160;      {</div>
<div class="line"><a name="l00917"></a><span class="lineno">  917</span>&#160;        <span class="keywordflow">if</span> (data_[i].meta.getName() == <span class="stringliteral">&quot;m/z array&quot;</span>)</div>
<div class="line"><a name="l00918"></a><span class="lineno">  918</span>&#160;        {</div>
<div class="line"><a name="l00919"></a><span class="lineno">  919</span>&#160;          mz_index = i;</div>
<div class="line"><a name="l00920"></a><span class="lineno">  920</span>&#160;          mz_precision_64 = (data_[i].precision == BinaryData::PRE_64);</div>
<div class="line"><a name="l00921"></a><span class="lineno">  921</span>&#160;        }</div>
<div class="line"><a name="l00922"></a><span class="lineno">  922</span>&#160;        <span class="keywordflow">if</span> (data_[i].meta.getName() == <span class="stringliteral">&quot;intensity array&quot;</span>)</div>
<div class="line"><a name="l00923"></a><span class="lineno">  923</span>&#160;        {</div>
<div class="line"><a name="l00924"></a><span class="lineno">  924</span>&#160;          int_index = i;</div>
<div class="line"><a name="l00925"></a><span class="lineno">  925</span>&#160;          int_precision_64 = (data_[i].precision == BinaryData::PRE_64);</div>
<div class="line"><a name="l00926"></a><span class="lineno">  926</span>&#160;        }</div>
<div class="line"><a name="l00927"></a><span class="lineno">  927</span>&#160;      }</div>
<div class="line"><a name="l00928"></a><span class="lineno">  928</span>&#160;</div>
<div class="line"><a name="l00929"></a><span class="lineno">  929</span>&#160;      <span class="comment">//Abort if no m/z or intensity array is present</span></div>
<div class="line"><a name="l00930"></a><span class="lineno">  930</span>&#160;      <span class="keywordflow">if</span> (int_index == -1 || mz_index == -1)</div>
<div class="line"><a name="l00931"></a><span class="lineno">  931</span>&#160;      {</div>
<div class="line"><a name="l00932"></a><span class="lineno">  932</span>&#160;        <span class="comment">//if defaultArrayLength &gt; 0 : warn that no m/z or int arrays is present</span></div>
<div class="line"><a name="l00933"></a><span class="lineno">  933</span>&#160;        <span class="keywordflow">if</span> (default_array_length_ != 0)</div>
<div class="line"><a name="l00934"></a><span class="lineno">  934</span>&#160;        {</div>
<div class="line"><a name="l00935"></a><span class="lineno">  935</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The m/z or intensity array of spectrum &#39;&quot;</span>) + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; is missing and default_array_length_ is &quot;</span> + default_array_length_ + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00936"></a><span class="lineno">  936</span>&#160;        }</div>
<div class="line"><a name="l00937"></a><span class="lineno">  937</span>&#160;        <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00938"></a><span class="lineno">  938</span>&#160;      }</div>
<div class="line"><a name="l00939"></a><span class="lineno">  939</span>&#160;</div>
<div class="line"><a name="l00940"></a><span class="lineno">  940</span>&#160;</div>
<div class="line"><a name="l00941"></a><span class="lineno">  941</span>&#160;      <span class="comment">// Error if intensity or m/z is encoded as int32|64 - they should be float32|64!</span></div>
<div class="line"><a name="l00942"></a><span class="lineno">  942</span>&#160;      <span class="keywordflow">if</span> ((data_[mz_index].ints_32.size() &gt; 0) || (data_[mz_index].ints_64.size() &gt; 0))</div>
<div class="line"><a name="l00943"></a><span class="lineno">  943</span>&#160;      {</div>
<div class="line"><a name="l00944"></a><span class="lineno">  944</span>&#160;        fatalError(LOAD, <span class="stringliteral">&quot;Encoding m/z array as integer is not allowed!&quot;</span>);</div>
<div class="line"><a name="l00945"></a><span class="lineno">  945</span>&#160;      }</div>
<div class="line"><a name="l00946"></a><span class="lineno">  946</span>&#160;      <span class="keywordflow">if</span> ((data_[int_index].ints_32.size() &gt; 0) || (data_[int_index].ints_64.size() &gt; 0))</div>
<div class="line"><a name="l00947"></a><span class="lineno">  947</span>&#160;      {</div>
<div class="line"><a name="l00948"></a><span class="lineno">  948</span>&#160;        fatalError(LOAD, <span class="stringliteral">&quot;Encoding intensity array as integer is not allowed!&quot;</span>);</div>
<div class="line"><a name="l00949"></a><span class="lineno">  949</span>&#160;      }</div>
<div class="line"><a name="l00950"></a><span class="lineno">  950</span>&#160;</div>
<div class="line"><a name="l00951"></a><span class="lineno">  951</span>&#160;      <span class="comment">// Warn if the decoded data has a different size than the the defaultArrayLength</span></div>
<div class="line"><a name="l00952"></a><span class="lineno">  952</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> mz_size = mz_precision_64 ? data_[mz_index].floats_64.size() : data_[mz_index].floats_32.size();</div>
<div class="line"><a name="l00953"></a><span class="lineno">  953</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> int_size = int_precision_64 ? data_[int_index].floats_64.size() : data_[int_index].floats_32.size();</div>
<div class="line"><a name="l00954"></a><span class="lineno">  954</span>&#160;      <span class="comment">// Check if int-size and mz-size are equal</span></div>
<div class="line"><a name="l00955"></a><span class="lineno">  955</span>&#160;      <span class="keywordflow">if</span> (mz_size != int_size)</div>
<div class="line"><a name="l00956"></a><span class="lineno">  956</span>&#160;      {</div>
<div class="line"><a name="l00957"></a><span class="lineno">  957</span>&#160;        fatalError(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The length of m/z and integer values of spectrum &#39;&quot;</span>) + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; differ (mz-size: &quot;</span> + mz_size + <span class="stringliteral">&quot;, int-size: &quot;</span> + int_size + <span class="stringliteral">&quot;! Not reading spectrum!&quot;</span>);</div>
<div class="line"><a name="l00958"></a><span class="lineno">  958</span>&#160;      }</div>
<div class="line"><a name="l00959"></a><span class="lineno">  959</span>&#160;      <span class="keywordtype">bool</span> repair_array_length = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00960"></a><span class="lineno">  960</span>&#160;      <span class="keywordflow">if</span> (default_array_length_ != mz_size)</div>
<div class="line"><a name="l00961"></a><span class="lineno">  961</span>&#160;      {</div>
<div class="line"><a name="l00962"></a><span class="lineno">  962</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The m/z array of spectrum &#39;&quot;</span>) + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has the size &quot;</span> + mz_size + <span class="stringliteral">&quot;, but it should have size &quot;</span> + default_array_length_ + <span class="stringliteral">&quot; (defaultArrayLength).&quot;</span>);</div>
<div class="line"><a name="l00963"></a><span class="lineno">  963</span>&#160;        repair_array_length = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00964"></a><span class="lineno">  964</span>&#160;      }</div>
<div class="line"><a name="l00965"></a><span class="lineno">  965</span>&#160;      <span class="keywordflow">if</span> (default_array_length_ != int_size)</div>
<div class="line"><a name="l00966"></a><span class="lineno">  966</span>&#160;      {</div>
<div class="line"><a name="l00967"></a><span class="lineno">  967</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The intensity array of spectrum &#39;&quot;</span>) + spec_.getNativeID() + <span class="stringliteral">&quot;&#39; has the size &quot;</span> + int_size + <span class="stringliteral">&quot;, but it should have size &quot;</span> + default_array_length_ + <span class="stringliteral">&quot; (defaultArrayLength).&quot;</span>);</div>
<div class="line"><a name="l00968"></a><span class="lineno">  968</span>&#160;        repair_array_length = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00969"></a><span class="lineno">  969</span>&#160;      }</div>
<div class="line"><a name="l00970"></a><span class="lineno">  970</span>&#160;      <span class="keywordflow">if</span> (repair_array_length)</div>
<div class="line"><a name="l00971"></a><span class="lineno">  971</span>&#160;      {</div>
<div class="line"><a name="l00972"></a><span class="lineno">  972</span>&#160;        default_array_length_ = int_size;</div>
<div class="line"><a name="l00973"></a><span class="lineno">  973</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Fixing faulty defaultArrayLength to &quot;</span>) + default_array_length_ + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00974"></a><span class="lineno">  974</span>&#160;      }</div>
<div class="line"><a name="l00975"></a><span class="lineno">  975</span>&#160;</div>
<div class="line"><a name="l00976"></a><span class="lineno">  976</span>&#160;      <span class="comment">//create meta data arrays and reserve enough space for the content</span></div>
<div class="line"><a name="l00977"></a><span class="lineno">  977</span>&#160;      <span class="keywordflow">if</span> (data_.size() &gt; 2)</div>
<div class="line"><a name="l00978"></a><span class="lineno">  978</span>&#160;      {</div>
<div class="line"><a name="l00979"></a><span class="lineno">  979</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l00980"></a><span class="lineno">  980</span>&#160;        {</div>
<div class="line"><a name="l00981"></a><span class="lineno">  981</span>&#160;          <span class="keywordflow">if</span> (data_[i].meta.getName() != <span class="stringliteral">&quot;m/z array&quot;</span> &amp;&amp; data_[i].meta.getName() != <span class="stringliteral">&quot;intensity array&quot;</span>)</div>
<div class="line"><a name="l00982"></a><span class="lineno">  982</span>&#160;          {</div>
<div class="line"><a name="l00983"></a><span class="lineno">  983</span>&#160;            <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_FLOAT)</div>
<div class="line"><a name="l00984"></a><span class="lineno">  984</span>&#160;            {</div>
<div class="line"><a name="l00985"></a><span class="lineno">  985</span>&#160;              <span class="comment">//create new array</span></div>
<div class="line"><a name="l00986"></a><span class="lineno">  986</span>&#160;              spec_.getFloatDataArrays().resize(spec_.getFloatDataArrays().size() + 1);</div>
<div class="line"><a name="l00987"></a><span class="lineno">  987</span>&#160;              <span class="comment">//reserve space in the array</span></div>
<div class="line"><a name="l00988"></a><span class="lineno">  988</span>&#160;              spec_.getFloatDataArrays().back().reserve(data_[i].size);</div>
<div class="line"><a name="l00989"></a><span class="lineno">  989</span>&#160;              <span class="comment">//copy meta info into MetaInfoDescription</span></div>
<div class="line"><a name="l00990"></a><span class="lineno">  990</span>&#160;              spec_.getFloatDataArrays().back().MetaInfoDescription::operator=(data_[i].meta);</div>
<div class="line"><a name="l00991"></a><span class="lineno">  991</span>&#160;            }</div>
<div class="line"><a name="l00992"></a><span class="lineno">  992</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_INT)</div>
<div class="line"><a name="l00993"></a><span class="lineno">  993</span>&#160;            {</div>
<div class="line"><a name="l00994"></a><span class="lineno">  994</span>&#160;              <span class="comment">//create new array</span></div>
<div class="line"><a name="l00995"></a><span class="lineno">  995</span>&#160;              spec_.getIntegerDataArrays().resize(spec_.getIntegerDataArrays().size() + 1);</div>
<div class="line"><a name="l00996"></a><span class="lineno">  996</span>&#160;              <span class="comment">//reserve space in the array</span></div>
<div class="line"><a name="l00997"></a><span class="lineno">  997</span>&#160;              spec_.getIntegerDataArrays().back().reserve(data_[i].size);</div>
<div class="line"><a name="l00998"></a><span class="lineno">  998</span>&#160;              <span class="comment">//copy meta info into MetaInfoDescription</span></div>
<div class="line"><a name="l00999"></a><span class="lineno">  999</span>&#160;              spec_.getIntegerDataArrays().back().MetaInfoDescription::operator=(data_[i].meta);</div>
<div class="line"><a name="l01000"></a><span class="lineno"> 1000</span>&#160;            }</div>
<div class="line"><a name="l01001"></a><span class="lineno"> 1001</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_STRING)</div>
<div class="line"><a name="l01002"></a><span class="lineno"> 1002</span>&#160;            {</div>
<div class="line"><a name="l01003"></a><span class="lineno"> 1003</span>&#160;              <span class="comment">//create new array</span></div>
<div class="line"><a name="l01004"></a><span class="lineno"> 1004</span>&#160;              spec_.getStringDataArrays().resize(spec_.getStringDataArrays().size() + 1);</div>
<div class="line"><a name="l01005"></a><span class="lineno"> 1005</span>&#160;              <span class="comment">//reserve space in the array</span></div>
<div class="line"><a name="l01006"></a><span class="lineno"> 1006</span>&#160;              spec_.getStringDataArrays().back().reserve(data_[i].decoded_char.size());</div>
<div class="line"><a name="l01007"></a><span class="lineno"> 1007</span>&#160;              <span class="comment">//copy meta info into MetaInfoDescription</span></div>
<div class="line"><a name="l01008"></a><span class="lineno"> 1008</span>&#160;              spec_.getStringDataArrays().back().MetaInfoDescription::operator=(data_[i].meta);</div>
<div class="line"><a name="l01009"></a><span class="lineno"> 1009</span>&#160;            }</div>
<div class="line"><a name="l01010"></a><span class="lineno"> 1010</span>&#160;          }</div>
<div class="line"><a name="l01011"></a><span class="lineno"> 1011</span>&#160;        }</div>
<div class="line"><a name="l01012"></a><span class="lineno"> 1012</span>&#160;      }</div>
<div class="line"><a name="l01013"></a><span class="lineno"> 1013</span>&#160;</div>
<div class="line"><a name="l01014"></a><span class="lineno"> 1014</span>&#160;      <span class="comment">// Copy meta data from m/z and intensity binary</span></div>
<div class="line"><a name="l01015"></a><span class="lineno"> 1015</span>&#160;      <span class="comment">// We don&#39;t have this as a separate location =&gt; store it in spectrum</span></div>
<div class="line"><a name="l01016"></a><span class="lineno"> 1016</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l01017"></a><span class="lineno"> 1017</span>&#160;      {</div>
<div class="line"><a name="l01018"></a><span class="lineno"> 1018</span>&#160;        <span class="keywordflow">if</span> (data_[i].meta.getName() == <span class="stringliteral">&quot;m/z array&quot;</span> || data_[i].meta.getName() == <span class="stringliteral">&quot;intensity array&quot;</span>)</div>
<div class="line"><a name="l01019"></a><span class="lineno"> 1019</span>&#160;        {</div>
<div class="line"><a name="l01020"></a><span class="lineno"> 1020</span>&#160;          std::vector&lt;UInt&gt; keys;</div>
<div class="line"><a name="l01021"></a><span class="lineno"> 1021</span>&#160;          data_[i].meta.getKeys(keys);</div>
<div class="line"><a name="l01022"></a><span class="lineno"> 1022</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> &lt; keys.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l01023"></a><span class="lineno"> 1023</span>&#160;          {</div>
<div class="line"><a name="l01024"></a><span class="lineno"> 1024</span>&#160;            spec_.setMetaValue(keys[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>], data_[i].meta.getMetaValue(keys[k]));</div>
<div class="line"><a name="l01025"></a><span class="lineno"> 1025</span>&#160;          }</div>
<div class="line"><a name="l01026"></a><span class="lineno"> 1026</span>&#160;        }</div>
<div class="line"><a name="l01027"></a><span class="lineno"> 1027</span>&#160;      }</div>
<div class="line"><a name="l01028"></a><span class="lineno"> 1028</span>&#160;</div>
<div class="line"><a name="l01029"></a><span class="lineno"> 1029</span>&#160;      <span class="comment">//add the peaks and the meta data to the container (if they pass the restrictions)</span></div>
<div class="line"><a name="l01030"></a><span class="lineno"> 1030</span>&#160;      spec_.reserve(default_array_length_);</div>
<div class="line"><a name="l01031"></a><span class="lineno"> 1031</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n = 0; n &lt; default_array_length_; n++)</div>
<div class="line"><a name="l01032"></a><span class="lineno"> 1032</span>&#160;      {</div>
<div class="line"><a name="l01033"></a><span class="lineno"> 1033</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> mz = mz_precision_64 ? data_[mz_index].floats_64[n] : data_[mz_index].floats_32[n];</div>
<div class="line"><a name="l01034"></a><span class="lineno"> 1034</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> intensity = int_precision_64 ? data_[int_index].floats_64[n] : data_[int_index].floats_32[n];</div>
<div class="line"><a name="l01035"></a><span class="lineno"> 1035</span>&#160;        <span class="keywordflow">if</span> ((!options_.hasMZRange() || options_.getMZRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(mz)))</div>
<div class="line"><a name="l01036"></a><span class="lineno"> 1036</span>&#160;           &amp;&amp; (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(intensity))))</div>
<div class="line"><a name="l01037"></a><span class="lineno"> 1037</span>&#160;        {</div>
<div class="line"><a name="l01038"></a><span class="lineno"> 1038</span>&#160;          <span class="comment">//add peak</span></div>
<div class="line"><a name="l01039"></a><span class="lineno"> 1039</span>&#160;          <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a> tmp;</div>
<div class="line"><a name="l01040"></a><span class="lineno"> 1040</span>&#160;          tmp.setIntensity(intensity);</div>
<div class="line"><a name="l01041"></a><span class="lineno"> 1041</span>&#160;          tmp.setMZ(mz);</div>
<div class="line"><a name="l01042"></a><span class="lineno"> 1042</span>&#160;          spec_.push_back(tmp);</div>
<div class="line"><a name="l01043"></a><span class="lineno"> 1043</span>&#160;</div>
<div class="line"><a name="l01044"></a><span class="lineno"> 1044</span>&#160;          <span class="comment">//add meta data</span></div>
<div class="line"><a name="l01045"></a><span class="lineno"> 1045</span>&#160;          <a class="code" href="classunsigned_01int.html">UInt</a> meta_float_array_index = 0;</div>
<div class="line"><a name="l01046"></a><span class="lineno"> 1046</span>&#160;          <a class="code" href="classunsigned_01int.html">UInt</a> meta_int_array_index = 0;</div>
<div class="line"><a name="l01047"></a><span class="lineno"> 1047</span>&#160;          <a class="code" href="classunsigned_01int.html">UInt</a> meta_string_array_index = 0;</div>
<div class="line"><a name="l01048"></a><span class="lineno"> 1048</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++) <span class="comment">//loop over all binary data arrays</span></div>
<div class="line"><a name="l01049"></a><span class="lineno"> 1049</span>&#160;          {</div>
<div class="line"><a name="l01050"></a><span class="lineno"> 1050</span>&#160;            <span class="keywordflow">if</span> (data_[i].meta.getName() != <span class="stringliteral">&quot;m/z array&quot;</span> &amp;&amp; data_[i].meta.getName() != <span class="stringliteral">&quot;intensity array&quot;</span>) <span class="comment">// is meta data array?</span></div>
<div class="line"><a name="l01051"></a><span class="lineno"> 1051</span>&#160;            {</div>
<div class="line"><a name="l01052"></a><span class="lineno"> 1052</span>&#160;              <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_FLOAT)</div>
<div class="line"><a name="l01053"></a><span class="lineno"> 1053</span>&#160;              {</div>
<div class="line"><a name="l01054"></a><span class="lineno"> 1054</span>&#160;                <span class="keywordflow">if</span> (n &lt; data_[i].size)</div>
<div class="line"><a name="l01055"></a><span class="lineno"> 1055</span>&#160;                {</div>
<div class="line"><a name="l01056"></a><span class="lineno"> 1056</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> value = (data_[i].precision == BinaryData::PRE_64) ? data_[i].floats_64[n] : data_[i].floats_32[n];</div>
<div class="line"><a name="l01057"></a><span class="lineno"> 1057</span>&#160;                  spec_.getFloatDataArrays()[meta_float_array_index].push_back(value);</div>
<div class="line"><a name="l01058"></a><span class="lineno"> 1058</span>&#160;                }</div>
<div class="line"><a name="l01059"></a><span class="lineno"> 1059</span>&#160;                ++meta_float_array_index;</div>
<div class="line"><a name="l01060"></a><span class="lineno"> 1060</span>&#160;              }</div>
<div class="line"><a name="l01061"></a><span class="lineno"> 1061</span>&#160;              <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_INT)</div>
<div class="line"><a name="l01062"></a><span class="lineno"> 1062</span>&#160;              {</div>
<div class="line"><a name="l01063"></a><span class="lineno"> 1063</span>&#160;                <span class="keywordflow">if</span> (n &lt; data_[i].size)</div>
<div class="line"><a name="l01064"></a><span class="lineno"> 1064</span>&#160;                {</div>
<div class="line"><a name="l01065"></a><span class="lineno"> 1065</span>&#160;                  <a class="code" href="group__Concept.html#ga84f5fc936107ae0a002c345694c41dcd">Int64</a> value = (data_[i].precision == BinaryData::PRE_64) ? data_[i].ints_64[n] : data_[i].ints_32[n];</div>
<div class="line"><a name="l01066"></a><span class="lineno"> 1066</span>&#160;                  spec_.getIntegerDataArrays()[meta_int_array_index].push_back(value);</div>
<div class="line"><a name="l01067"></a><span class="lineno"> 1067</span>&#160;                }</div>
<div class="line"><a name="l01068"></a><span class="lineno"> 1068</span>&#160;                ++meta_int_array_index;</div>
<div class="line"><a name="l01069"></a><span class="lineno"> 1069</span>&#160;              }</div>
<div class="line"><a name="l01070"></a><span class="lineno"> 1070</span>&#160;              <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_STRING)</div>
<div class="line"><a name="l01071"></a><span class="lineno"> 1071</span>&#160;              {</div>
<div class="line"><a name="l01072"></a><span class="lineno"> 1072</span>&#160;                <span class="keywordflow">if</span> (n &lt; data_[i].decoded_char.size())</div>
<div class="line"><a name="l01073"></a><span class="lineno"> 1073</span>&#160;                {</div>
<div class="line"><a name="l01074"></a><span class="lineno"> 1074</span>&#160;                  <a class="code" href="classOpenMS_1_1String.html">String</a> value = data_[i].decoded_char[n];</div>
<div class="line"><a name="l01075"></a><span class="lineno"> 1075</span>&#160;                  spec_.getStringDataArrays()[meta_string_array_index].push_back(value);</div>
<div class="line"><a name="l01076"></a><span class="lineno"> 1076</span>&#160;                }</div>
<div class="line"><a name="l01077"></a><span class="lineno"> 1077</span>&#160;                ++meta_string_array_index;</div>
<div class="line"><a name="l01078"></a><span class="lineno"> 1078</span>&#160;              }</div>
<div class="line"><a name="l01079"></a><span class="lineno"> 1079</span>&#160;            }</div>
<div class="line"><a name="l01080"></a><span class="lineno"> 1080</span>&#160;          }</div>
<div class="line"><a name="l01081"></a><span class="lineno"> 1081</span>&#160;        }</div>
<div class="line"><a name="l01082"></a><span class="lineno"> 1082</span>&#160;      }</div>
<div class="line"><a name="l01083"></a><span class="lineno"> 1083</span>&#160;    }</div>
<div class="line"><a name="l01084"></a><span class="lineno"> 1084</span>&#160;</div>
<div class="line"><a name="l01085"></a><span class="lineno"> 1085</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l01086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a96e4bd823df13baa5f500b1776d463ea"> 1086</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a96e4bd823df13baa5f500b1776d463ea">MzMLHandler&lt;MapType&gt;::fillChromatogramData_</a>()</div>
<div class="line"><a name="l01087"></a><span class="lineno"> 1087</span>&#160;    {</div>
<div class="line"><a name="l01088"></a><span class="lineno"> 1088</span>&#160;      <span class="comment">//decode all base64 arrays</span></div>
<div class="line"><a name="l01089"></a><span class="lineno"> 1089</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l01090"></a><span class="lineno"> 1090</span>&#160;      {</div>
<div class="line"><a name="l01091"></a><span class="lineno"> 1091</span>&#160;        <span class="comment">//remove whitespaces from binary data</span></div>
<div class="line"><a name="l01092"></a><span class="lineno"> 1092</span>&#160;        <span class="comment">//this should not be necessary, but linebreaks inside the base64 data are unfortunately no exception</span></div>
<div class="line"><a name="l01093"></a><span class="lineno"> 1093</span>&#160;        data_[i].base64.removeWhitespaces();</div>
<div class="line"><a name="l01094"></a><span class="lineno"> 1094</span>&#160;</div>
<div class="line"><a name="l01095"></a><span class="lineno"> 1095</span>&#160;        <span class="comment">//decode data and check if the length of the decoded data matches the expected length</span></div>
<div class="line"><a name="l01096"></a><span class="lineno"> 1096</span>&#160;        <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_FLOAT)</div>
<div class="line"><a name="l01097"></a><span class="lineno"> 1097</span>&#160;        {</div>
<div class="line"><a name="l01098"></a><span class="lineno"> 1098</span>&#160;          <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_64)</div>
<div class="line"><a name="l01099"></a><span class="lineno"> 1099</span>&#160;          {</div>
<div class="line"><a name="l01100"></a><span class="lineno"> 1100</span>&#160;            decoder_.decode(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].floats_64, data_[i].compression);</div>
<div class="line"><a name="l01101"></a><span class="lineno"> 1101</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].floats_64.size())</div>
<div class="line"><a name="l01102"></a><span class="lineno"> 1102</span>&#160;            {</div>
<div class="line"><a name="l01103"></a><span class="lineno"> 1103</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Float binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of chromatogram &#39;&quot;</span> + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].floats_64.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l01104"></a><span class="lineno"> 1104</span>&#160;            }</div>
<div class="line"><a name="l01105"></a><span class="lineno"> 1105</span>&#160;          }</div>
<div class="line"><a name="l01106"></a><span class="lineno"> 1106</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_32)</div>
<div class="line"><a name="l01107"></a><span class="lineno"> 1107</span>&#160;          {</div>
<div class="line"><a name="l01108"></a><span class="lineno"> 1108</span>&#160;            decoder_.decode(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].floats_32, data_[i].compression);</div>
<div class="line"><a name="l01109"></a><span class="lineno"> 1109</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].floats_32.size())</div>
<div class="line"><a name="l01110"></a><span class="lineno"> 1110</span>&#160;            {</div>
<div class="line"><a name="l01111"></a><span class="lineno"> 1111</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Float binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of chromatogram &#39;&quot;</span> + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].floats_32.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l01112"></a><span class="lineno"> 1112</span>&#160;            }</div>
<div class="line"><a name="l01113"></a><span class="lineno"> 1113</span>&#160;          }</div>
<div class="line"><a name="l01114"></a><span class="lineno"> 1114</span>&#160;        }</div>
<div class="line"><a name="l01115"></a><span class="lineno"> 1115</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_INT)</div>
<div class="line"><a name="l01116"></a><span class="lineno"> 1116</span>&#160;        {</div>
<div class="line"><a name="l01117"></a><span class="lineno"> 1117</span>&#160;          <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_64)</div>
<div class="line"><a name="l01118"></a><span class="lineno"> 1118</span>&#160;          {</div>
<div class="line"><a name="l01119"></a><span class="lineno"> 1119</span>&#160;            decoder_.decodeIntegers(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].ints_64, data_[i].compression);</div>
<div class="line"><a name="l01120"></a><span class="lineno"> 1120</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].ints_64.size())</div>
<div class="line"><a name="l01121"></a><span class="lineno"> 1121</span>&#160;            {</div>
<div class="line"><a name="l01122"></a><span class="lineno"> 1122</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Integer binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of chromatogram &#39;&quot;</span> + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].ints_64.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l01123"></a><span class="lineno"> 1123</span>&#160;            }</div>
<div class="line"><a name="l01124"></a><span class="lineno"> 1124</span>&#160;          }</div>
<div class="line"><a name="l01125"></a><span class="lineno"> 1125</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].precision == BinaryData::PRE_32)</div>
<div class="line"><a name="l01126"></a><span class="lineno"> 1126</span>&#160;          {</div>
<div class="line"><a name="l01127"></a><span class="lineno"> 1127</span>&#160;            decoder_.decodeIntegers(data_[i].base64, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, data_[i].ints_32, data_[i].compression);</div>
<div class="line"><a name="l01128"></a><span class="lineno"> 1128</span>&#160;            <span class="keywordflow">if</span> (data_[i].size != data_[i].ints_32.size())</div>
<div class="line"><a name="l01129"></a><span class="lineno"> 1129</span>&#160;            {</div>
<div class="line"><a name="l01130"></a><span class="lineno"> 1130</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Integer binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of chromatogram &#39;&quot;</span> + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].ints_32.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l01131"></a><span class="lineno"> 1131</span>&#160;            }</div>
<div class="line"><a name="l01132"></a><span class="lineno"> 1132</span>&#160;          }</div>
<div class="line"><a name="l01133"></a><span class="lineno"> 1133</span>&#160;        }</div>
<div class="line"><a name="l01134"></a><span class="lineno"> 1134</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_STRING)</div>
<div class="line"><a name="l01135"></a><span class="lineno"> 1135</span>&#160;        {</div>
<div class="line"><a name="l01136"></a><span class="lineno"> 1136</span>&#160;          decoder_.decodeStrings(data_[i].base64, data_[i].decoded_char, data_[i].compression);</div>
<div class="line"><a name="l01137"></a><span class="lineno"> 1137</span>&#160;          <span class="keywordflow">if</span> (data_[i].size != data_[i].decoded_char.size())</div>
<div class="line"><a name="l01138"></a><span class="lineno"> 1138</span>&#160;          {</div>
<div class="line"><a name="l01139"></a><span class="lineno"> 1139</span>&#160;            warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;String binary data array &#39;&quot;</span>) + data_[i].meta.getName() + <span class="stringliteral">&quot;&#39; of chromatogram &#39;&quot;</span> + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has length &quot;</span> + data_[i].decoded_char.size() + <span class="stringliteral">&quot;, but should have length &quot;</span> + data_[i].size + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l01140"></a><span class="lineno"> 1140</span>&#160;          }</div>
<div class="line"><a name="l01141"></a><span class="lineno"> 1141</span>&#160;        }</div>
<div class="line"><a name="l01142"></a><span class="lineno"> 1142</span>&#160;      }</div>
<div class="line"><a name="l01143"></a><span class="lineno"> 1143</span>&#160;</div>
<div class="line"><a name="l01144"></a><span class="lineno"> 1144</span>&#160;      <span class="comment">//look up the precision and the index of the intensity and m/z array</span></div>
<div class="line"><a name="l01145"></a><span class="lineno"> 1145</span>&#160;      <span class="keywordtype">bool</span> int_precision_64 = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01146"></a><span class="lineno"> 1146</span>&#160;      <span class="keywordtype">bool</span> rt_precision_64 = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01147"></a><span class="lineno"> 1147</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> int_index = -1;</div>
<div class="line"><a name="l01148"></a><span class="lineno"> 1148</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> rt_index = -1;</div>
<div class="line"><a name="l01149"></a><span class="lineno"> 1149</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l01150"></a><span class="lineno"> 1150</span>&#160;      {</div>
<div class="line"><a name="l01151"></a><span class="lineno"> 1151</span>&#160;        <span class="keywordflow">if</span> (data_[i].meta.getName() == <span class="stringliteral">&quot;intensity array&quot;</span>)</div>
<div class="line"><a name="l01152"></a><span class="lineno"> 1152</span>&#160;        {</div>
<div class="line"><a name="l01153"></a><span class="lineno"> 1153</span>&#160;          int_index = i;</div>
<div class="line"><a name="l01154"></a><span class="lineno"> 1154</span>&#160;          int_precision_64 = (data_[i].precision == BinaryData::PRE_64);</div>
<div class="line"><a name="l01155"></a><span class="lineno"> 1155</span>&#160;        }</div>
<div class="line"><a name="l01156"></a><span class="lineno"> 1156</span>&#160;        <span class="keywordflow">if</span> (data_[i].meta.getName() == <span class="stringliteral">&quot;time array&quot;</span>)</div>
<div class="line"><a name="l01157"></a><span class="lineno"> 1157</span>&#160;        {</div>
<div class="line"><a name="l01158"></a><span class="lineno"> 1158</span>&#160;          rt_index = i;</div>
<div class="line"><a name="l01159"></a><span class="lineno"> 1159</span>&#160;          rt_precision_64 = (data_[i].precision == BinaryData::PRE_64);</div>
<div class="line"><a name="l01160"></a><span class="lineno"> 1160</span>&#160;        }</div>
<div class="line"><a name="l01161"></a><span class="lineno"> 1161</span>&#160;      }</div>
<div class="line"><a name="l01162"></a><span class="lineno"> 1162</span>&#160;</div>
<div class="line"><a name="l01163"></a><span class="lineno"> 1163</span>&#160;      <span class="comment">//Abort if no m/z or intensity array is present</span></div>
<div class="line"><a name="l01164"></a><span class="lineno"> 1164</span>&#160;      <span class="keywordflow">if</span> (int_index == -1 || rt_index == -1)</div>
<div class="line"><a name="l01165"></a><span class="lineno"> 1165</span>&#160;      {</div>
<div class="line"><a name="l01166"></a><span class="lineno"> 1166</span>&#160;        <span class="comment">//if defaultArrayLength &gt; 0 : warn that no m/z or int arrays is present</span></div>
<div class="line"><a name="l01167"></a><span class="lineno"> 1167</span>&#160;        <span class="keywordflow">if</span> (default_array_length_ != 0)</div>
<div class="line"><a name="l01168"></a><span class="lineno"> 1168</span>&#160;        {</div>
<div class="line"><a name="l01169"></a><span class="lineno"> 1169</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The m/z or intensity array of chromatogram &#39;&quot;</span>) + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; is missing and default_array_length_ is &quot;</span> + default_array_length_ + <span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l01170"></a><span class="lineno"> 1170</span>&#160;        }</div>
<div class="line"><a name="l01171"></a><span class="lineno"> 1171</span>&#160;        <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01172"></a><span class="lineno"> 1172</span>&#160;      }</div>
<div class="line"><a name="l01173"></a><span class="lineno"> 1173</span>&#160;</div>
<div class="line"><a name="l01174"></a><span class="lineno"> 1174</span>&#160;      <span class="comment">//Warn if the decoded data has a different size than the the defaultArrayLength</span></div>
<div class="line"><a name="l01175"></a><span class="lineno"> 1175</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> rt_size = rt_precision_64 ? data_[rt_index].floats_64.size() : data_[rt_index].floats_32.size();</div>
<div class="line"><a name="l01176"></a><span class="lineno"> 1176</span>&#160;      <span class="keywordflow">if</span> (default_array_length_ != rt_size)</div>
<div class="line"><a name="l01177"></a><span class="lineno"> 1177</span>&#160;      {</div>
<div class="line"><a name="l01178"></a><span class="lineno"> 1178</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The base64-decoded rt array of chromatogram &#39;&quot;</span>) + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has the size &quot;</span> + rt_size + <span class="stringliteral">&quot;, but it should have size &quot;</span> + default_array_length_ + <span class="stringliteral">&quot; (defaultArrayLength).&quot;</span>);</div>
<div class="line"><a name="l01179"></a><span class="lineno"> 1179</span>&#160;      }</div>
<div class="line"><a name="l01180"></a><span class="lineno"> 1180</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> int_size = int_precision_64 ? data_[int_index].floats_64.size() : data_[int_index].floats_32.size();</div>
<div class="line"><a name="l01181"></a><span class="lineno"> 1181</span>&#160;      <span class="keywordflow">if</span> (default_array_length_ != int_size)</div>
<div class="line"><a name="l01182"></a><span class="lineno"> 1182</span>&#160;      {</div>
<div class="line"><a name="l01183"></a><span class="lineno"> 1183</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The base64-decoded intensity array of chromatogram &#39;&quot;</span>) + chromatogram_.getNativeID() + <span class="stringliteral">&quot;&#39; has the size &quot;</span> + int_size + <span class="stringliteral">&quot;, but it should have size &quot;</span> + default_array_length_ + <span class="stringliteral">&quot; (defaultArrayLength).&quot;</span>);</div>
<div class="line"><a name="l01184"></a><span class="lineno"> 1184</span>&#160;      }</div>
<div class="line"><a name="l01185"></a><span class="lineno"> 1185</span>&#160;</div>
<div class="line"><a name="l01186"></a><span class="lineno"> 1186</span>&#160;      <span class="comment">//create meta data arrays and reserve enough space for the content</span></div>
<div class="line"><a name="l01187"></a><span class="lineno"> 1187</span>&#160;      <span class="keywordflow">if</span> (data_.size() &gt; 2)</div>
<div class="line"><a name="l01188"></a><span class="lineno"> 1188</span>&#160;      {</div>
<div class="line"><a name="l01189"></a><span class="lineno"> 1189</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l01190"></a><span class="lineno"> 1190</span>&#160;        {</div>
<div class="line"><a name="l01191"></a><span class="lineno"> 1191</span>&#160;          <span class="keywordflow">if</span> (data_[i].meta.getName() != <span class="stringliteral">&quot;intensity array&quot;</span> &amp;&amp; data_[i].meta.getName() != <span class="stringliteral">&quot;time array&quot;</span>)</div>
<div class="line"><a name="l01192"></a><span class="lineno"> 1192</span>&#160;          {</div>
<div class="line"><a name="l01193"></a><span class="lineno"> 1193</span>&#160;            <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_FLOAT)</div>
<div class="line"><a name="l01194"></a><span class="lineno"> 1194</span>&#160;            {</div>
<div class="line"><a name="l01195"></a><span class="lineno"> 1195</span>&#160;              <span class="comment">//create new array</span></div>
<div class="line"><a name="l01196"></a><span class="lineno"> 1196</span>&#160;              chromatogram_.getFloatDataArrays().resize(chromatogram_.getFloatDataArrays().size() + 1);</div>
<div class="line"><a name="l01197"></a><span class="lineno"> 1197</span>&#160;              <span class="comment">//reserve space in the array</span></div>
<div class="line"><a name="l01198"></a><span class="lineno"> 1198</span>&#160;              chromatogram_.getFloatDataArrays().back().reserve(data_[i].size);</div>
<div class="line"><a name="l01199"></a><span class="lineno"> 1199</span>&#160;              <span class="comment">//copy meta info into MetaInfoDescription</span></div>
<div class="line"><a name="l01200"></a><span class="lineno"> 1200</span>&#160;              chromatogram_.getFloatDataArrays().back().MetaInfoDescription::operator=(data_[i].meta);</div>
<div class="line"><a name="l01201"></a><span class="lineno"> 1201</span>&#160;            }</div>
<div class="line"><a name="l01202"></a><span class="lineno"> 1202</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_INT)</div>
<div class="line"><a name="l01203"></a><span class="lineno"> 1203</span>&#160;            {</div>
<div class="line"><a name="l01204"></a><span class="lineno"> 1204</span>&#160;              <span class="comment">//create new array</span></div>
<div class="line"><a name="l01205"></a><span class="lineno"> 1205</span>&#160;              chromatogram_.getIntegerDataArrays().resize(chromatogram_.getIntegerDataArrays().size() + 1);</div>
<div class="line"><a name="l01206"></a><span class="lineno"> 1206</span>&#160;              <span class="comment">//reserve space in the array</span></div>
<div class="line"><a name="l01207"></a><span class="lineno"> 1207</span>&#160;              chromatogram_.getIntegerDataArrays().back().reserve(data_[i].size);</div>
<div class="line"><a name="l01208"></a><span class="lineno"> 1208</span>&#160;              <span class="comment">//copy meta info into MetaInfoDescription</span></div>
<div class="line"><a name="l01209"></a><span class="lineno"> 1209</span>&#160;              chromatogram_.getIntegerDataArrays().back().MetaInfoDescription::operator=(data_[i].meta);</div>
<div class="line"><a name="l01210"></a><span class="lineno"> 1210</span>&#160;            }</div>
<div class="line"><a name="l01211"></a><span class="lineno"> 1211</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_STRING)</div>
<div class="line"><a name="l01212"></a><span class="lineno"> 1212</span>&#160;            {</div>
<div class="line"><a name="l01213"></a><span class="lineno"> 1213</span>&#160;              <span class="comment">//create new array</span></div>
<div class="line"><a name="l01214"></a><span class="lineno"> 1214</span>&#160;              chromatogram_.getStringDataArrays().resize(chromatogram_.getStringDataArrays().size() + 1);</div>
<div class="line"><a name="l01215"></a><span class="lineno"> 1215</span>&#160;              <span class="comment">//reserve space in the array</span></div>
<div class="line"><a name="l01216"></a><span class="lineno"> 1216</span>&#160;              chromatogram_.getStringDataArrays().back().reserve(data_[i].decoded_char.size());</div>
<div class="line"><a name="l01217"></a><span class="lineno"> 1217</span>&#160;              <span class="comment">//copy meta info into MetaInfoDescription</span></div>
<div class="line"><a name="l01218"></a><span class="lineno"> 1218</span>&#160;              chromatogram_.getStringDataArrays().back().MetaInfoDescription::operator=(data_[i].meta);</div>
<div class="line"><a name="l01219"></a><span class="lineno"> 1219</span>&#160;            }</div>
<div class="line"><a name="l01220"></a><span class="lineno"> 1220</span>&#160;          }</div>
<div class="line"><a name="l01221"></a><span class="lineno"> 1221</span>&#160;        }</div>
<div class="line"><a name="l01222"></a><span class="lineno"> 1222</span>&#160;      }</div>
<div class="line"><a name="l01223"></a><span class="lineno"> 1223</span>&#160;</div>
<div class="line"><a name="l01224"></a><span class="lineno"> 1224</span>&#160;      <span class="comment">//copy meta data from time and intensity binary</span></div>
<div class="line"><a name="l01225"></a><span class="lineno"> 1225</span>&#160;      <span class="comment">//We don&#39;t have this as a separate location =&gt; store it in spectrum</span></div>
<div class="line"><a name="l01226"></a><span class="lineno"> 1226</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++)</div>
<div class="line"><a name="l01227"></a><span class="lineno"> 1227</span>&#160;      {</div>
<div class="line"><a name="l01228"></a><span class="lineno"> 1228</span>&#160;        <span class="keywordflow">if</span> (data_[i].meta.getName() == <span class="stringliteral">&quot;time array&quot;</span> || data_[i].meta.getName() == <span class="stringliteral">&quot;intensity array&quot;</span>)</div>
<div class="line"><a name="l01229"></a><span class="lineno"> 1229</span>&#160;        {</div>
<div class="line"><a name="l01230"></a><span class="lineno"> 1230</span>&#160;          std::vector&lt;UInt&gt; keys;</div>
<div class="line"><a name="l01231"></a><span class="lineno"> 1231</span>&#160;          data_[i].meta.getKeys(keys);</div>
<div class="line"><a name="l01232"></a><span class="lineno"> 1232</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> &lt; keys.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l01233"></a><span class="lineno"> 1233</span>&#160;          {</div>
<div class="line"><a name="l01234"></a><span class="lineno"> 1234</span>&#160;            chromatogram_.setMetaValue(keys[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>], data_[i].meta.getMetaValue(keys[k]));</div>
<div class="line"><a name="l01235"></a><span class="lineno"> 1235</span>&#160;          }</div>
<div class="line"><a name="l01236"></a><span class="lineno"> 1236</span>&#160;        }</div>
<div class="line"><a name="l01237"></a><span class="lineno"> 1237</span>&#160;      }</div>
<div class="line"><a name="l01238"></a><span class="lineno"> 1238</span>&#160;</div>
<div class="line"><a name="l01239"></a><span class="lineno"> 1239</span>&#160;      <span class="comment">//add the peaks and the meta data to the container (if they pass the restrictions)</span></div>
<div class="line"><a name="l01240"></a><span class="lineno"> 1240</span>&#160;      chromatogram_.reserve(default_array_length_);</div>
<div class="line"><a name="l01241"></a><span class="lineno"> 1241</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n = 0; n &lt; default_array_length_; n++)</div>
<div class="line"><a name="l01242"></a><span class="lineno"> 1242</span>&#160;      {</div>
<div class="line"><a name="l01243"></a><span class="lineno"> 1243</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> rt = rt_precision_64 ? data_[rt_index].floats_64[n] : data_[rt_index].floats_32[n];</div>
<div class="line"><a name="l01244"></a><span class="lineno"> 1244</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> intensity = int_precision_64 ? data_[int_index].floats_64[n] : data_[int_index].floats_32[n];</div>
<div class="line"><a name="l01245"></a><span class="lineno"> 1245</span>&#160;        <span class="keywordflow">if</span> ((!options_.hasRTRange() || options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(rt)))</div>
<div class="line"><a name="l01246"></a><span class="lineno"> 1246</span>&#160;           &amp;&amp; (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(intensity))))</div>
<div class="line"><a name="l01247"></a><span class="lineno"> 1247</span>&#160;        {</div>
<div class="line"><a name="l01248"></a><span class="lineno"> 1248</span>&#160;          <span class="comment">//add peak</span></div>
<div class="line"><a name="l01249"></a><span class="lineno"> 1249</span>&#160;          <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#af50693f3924366b3c157bea5dcbe4355">ChromatogramPeakType</a> tmp;</div>
<div class="line"><a name="l01250"></a><span class="lineno"> 1250</span>&#160;          tmp.setIntensity(intensity);</div>
<div class="line"><a name="l01251"></a><span class="lineno"> 1251</span>&#160;          tmp.setRT(rt);</div>
<div class="line"><a name="l01252"></a><span class="lineno"> 1252</span>&#160;          chromatogram_.push_back(tmp);</div>
<div class="line"><a name="l01253"></a><span class="lineno"> 1253</span>&#160;</div>
<div class="line"><a name="l01254"></a><span class="lineno"> 1254</span>&#160;          <span class="comment">//add meta data</span></div>
<div class="line"><a name="l01255"></a><span class="lineno"> 1255</span>&#160;          <a class="code" href="classunsigned_01int.html">UInt</a> meta_float_array_index = 0;</div>
<div class="line"><a name="l01256"></a><span class="lineno"> 1256</span>&#160;          <a class="code" href="classunsigned_01int.html">UInt</a> meta_int_array_index = 0;</div>
<div class="line"><a name="l01257"></a><span class="lineno"> 1257</span>&#160;          <a class="code" href="classunsigned_01int.html">UInt</a> meta_string_array_index = 0;</div>
<div class="line"><a name="l01258"></a><span class="lineno"> 1258</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; data_.size(); i++) <span class="comment">//loop over all binary data arrays</span></div>
<div class="line"><a name="l01259"></a><span class="lineno"> 1259</span>&#160;          {</div>
<div class="line"><a name="l01260"></a><span class="lineno"> 1260</span>&#160;            <span class="keywordflow">if</span> (data_[i].meta.getName() != <span class="stringliteral">&quot;intensity array&quot;</span> &amp;&amp; data_[i].meta.getName() != <span class="stringliteral">&quot;time array&quot;</span>) <span class="comment">// is meta data array?</span></div>
<div class="line"><a name="l01261"></a><span class="lineno"> 1261</span>&#160;            {</div>
<div class="line"><a name="l01262"></a><span class="lineno"> 1262</span>&#160;              <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_FLOAT)</div>
<div class="line"><a name="l01263"></a><span class="lineno"> 1263</span>&#160;              {</div>
<div class="line"><a name="l01264"></a><span class="lineno"> 1264</span>&#160;                <span class="keywordflow">if</span> (n &lt; data_[i].size)</div>
<div class="line"><a name="l01265"></a><span class="lineno"> 1265</span>&#160;                {</div>
<div class="line"><a name="l01266"></a><span class="lineno"> 1266</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> value = (data_[i].precision == BinaryData::PRE_64) ? data_[i].floats_64[n] : data_[i].floats_32[n];</div>
<div class="line"><a name="l01267"></a><span class="lineno"> 1267</span>&#160;                  chromatogram_.getFloatDataArrays()[meta_float_array_index].push_back(value);</div>
<div class="line"><a name="l01268"></a><span class="lineno"> 1268</span>&#160;                }</div>
<div class="line"><a name="l01269"></a><span class="lineno"> 1269</span>&#160;                ++meta_float_array_index;</div>
<div class="line"><a name="l01270"></a><span class="lineno"> 1270</span>&#160;              }</div>
<div class="line"><a name="l01271"></a><span class="lineno"> 1271</span>&#160;              <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_INT)</div>
<div class="line"><a name="l01272"></a><span class="lineno"> 1272</span>&#160;              {</div>
<div class="line"><a name="l01273"></a><span class="lineno"> 1273</span>&#160;                <span class="keywordflow">if</span> (n &lt; data_[i].size)</div>
<div class="line"><a name="l01274"></a><span class="lineno"> 1274</span>&#160;                {</div>
<div class="line"><a name="l01275"></a><span class="lineno"> 1275</span>&#160;                  <a class="code" href="group__Concept.html#ga84f5fc936107ae0a002c345694c41dcd">Int64</a> value = (data_[i].precision == BinaryData::PRE_64) ? data_[i].ints_64[n] : data_[i].ints_32[n];</div>
<div class="line"><a name="l01276"></a><span class="lineno"> 1276</span>&#160;                  chromatogram_.getIntegerDataArrays()[meta_int_array_index].push_back(value);</div>
<div class="line"><a name="l01277"></a><span class="lineno"> 1277</span>&#160;                }</div>
<div class="line"><a name="l01278"></a><span class="lineno"> 1278</span>&#160;                ++meta_int_array_index;</div>
<div class="line"><a name="l01279"></a><span class="lineno"> 1279</span>&#160;              }</div>
<div class="line"><a name="l01280"></a><span class="lineno"> 1280</span>&#160;              <span class="keywordflow">else</span> <span class="keywordflow">if</span> (data_[i].data_type == BinaryData::DT_STRING)</div>
<div class="line"><a name="l01281"></a><span class="lineno"> 1281</span>&#160;              {</div>
<div class="line"><a name="l01282"></a><span class="lineno"> 1282</span>&#160;                <span class="keywordflow">if</span> (n &lt; data_[i].decoded_char.size())</div>
<div class="line"><a name="l01283"></a><span class="lineno"> 1283</span>&#160;                {</div>
<div class="line"><a name="l01284"></a><span class="lineno"> 1284</span>&#160;                  <a class="code" href="classOpenMS_1_1String.html">String</a> value = data_[i].decoded_char[n];</div>
<div class="line"><a name="l01285"></a><span class="lineno"> 1285</span>&#160;                  chromatogram_.getStringDataArrays()[meta_string_array_index].push_back(value);</div>
<div class="line"><a name="l01286"></a><span class="lineno"> 1286</span>&#160;                }</div>
<div class="line"><a name="l01287"></a><span class="lineno"> 1287</span>&#160;                ++meta_string_array_index;</div>
<div class="line"><a name="l01288"></a><span class="lineno"> 1288</span>&#160;              }</div>
<div class="line"><a name="l01289"></a><span class="lineno"> 1289</span>&#160;            }</div>
<div class="line"><a name="l01290"></a><span class="lineno"> 1290</span>&#160;          }</div>
<div class="line"><a name="l01291"></a><span class="lineno"> 1291</span>&#160;        }</div>
<div class="line"><a name="l01292"></a><span class="lineno"> 1292</span>&#160;      }</div>
<div class="line"><a name="l01293"></a><span class="lineno"> 1293</span>&#160;    }</div>
<div class="line"><a name="l01294"></a><span class="lineno"> 1294</span>&#160;</div>
<div class="line"><a name="l01295"></a><span class="lineno"> 1295</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l01296"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aaf3831bc627f95286afdf5c6b91c731b"> 1296</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aaf3831bc627f95286afdf5c6b91c731b">MzMLHandler&lt;MapType&gt;::handleCVParam_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_tag, <span class="comment">/* const String &amp; cvref,  */</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; unit_accession)</div>
<div class="line"><a name="l01297"></a><span class="lineno"> 1297</span>&#160;    {</div>
<div class="line"><a name="l01298"></a><span class="lineno"> 1298</span>&#160;      <span class="comment">// the actual value stored in the CVParam</span></div>
<div class="line"><a name="l01299"></a><span class="lineno"> 1299</span>&#160;      <span class="comment">// we assume for now that it is a string value, we update the type later on</span></div>
<div class="line"><a name="l01300"></a><span class="lineno"> 1300</span>&#160;      <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a> termValue = value;</div>
<div class="line"><a name="l01301"></a><span class="lineno"> 1301</span>&#160;</div>
<div class="line"><a name="l01302"></a><span class="lineno"> 1302</span>&#160;      <span class="comment">//Abort on unknown terms</span></div>
<div class="line"><a name="l01303"></a><span class="lineno"> 1303</span>&#160;      <span class="keywordflow">if</span> (!cv_.exists(accession))</div>
<div class="line"><a name="l01304"></a><span class="lineno"> 1304</span>&#160;      {</div>
<div class="line"><a name="l01305"></a><span class="lineno"> 1305</span>&#160;        <span class="comment">//in &#39;sample&#39; several external CVs are used (Brenda, GO, ...). Do not warn then.</span></div>
<div class="line"><a name="l01306"></a><span class="lineno"> 1306</span>&#160;        <span class="keywordflow">if</span> (parent_tag != <span class="stringliteral">&quot;sample&quot;</span>)</div>
<div class="line"><a name="l01307"></a><span class="lineno"> 1307</span>&#160;        {</div>
<div class="line"><a name="l01308"></a><span class="lineno"> 1308</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unknown cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01309"></a><span class="lineno"> 1309</span>&#160;          <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01310"></a><span class="lineno"> 1310</span>&#160;        }</div>
<div class="line"><a name="l01311"></a><span class="lineno"> 1311</span>&#160;      }</div>
<div class="line"><a name="l01312"></a><span class="lineno"> 1312</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l01313"></a><span class="lineno"> 1313</span>&#160;      {</div>
<div class="line"><a name="l01314"></a><span class="lineno"> 1314</span>&#160;        <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a>&amp; term = cv_.getTerm(accession);</div>
<div class="line"><a name="l01315"></a><span class="lineno"> 1315</span>&#160;</div>
<div class="line"><a name="l01316"></a><span class="lineno"> 1316</span>&#160;        <span class="comment">//obsolete CV terms</span></div>
<div class="line"><a name="l01317"></a><span class="lineno"> 1317</span>&#160;        <span class="keywordflow">if</span> (term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a89015d9d8ecc70d84c1eeb2d6c983c03">obsolete</a>)</div>
<div class="line"><a name="l01318"></a><span class="lineno"> 1318</span>&#160;        {</div>
<div class="line"><a name="l01319"></a><span class="lineno"> 1319</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Obsolete CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01320"></a><span class="lineno"> 1320</span>&#160;        }</div>
<div class="line"><a name="l01321"></a><span class="lineno"> 1321</span>&#160;        <span class="comment">//check if term name and parsed name match</span></div>
<div class="line"><a name="l01322"></a><span class="lineno"> 1322</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> parsed_name = name;</div>
<div class="line"><a name="l01323"></a><span class="lineno"> 1323</span>&#160;        parsed_name.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l01324"></a><span class="lineno"> 1324</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> correct_name = term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a>;</div>
<div class="line"><a name="l01325"></a><span class="lineno"> 1325</span>&#160;        correct_name.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l01326"></a><span class="lineno"> 1326</span>&#160;        <span class="keywordflow">if</span> (parsed_name != correct_name)</div>
<div class="line"><a name="l01327"></a><span class="lineno"> 1327</span>&#160;        {</div>
<div class="line"><a name="l01328"></a><span class="lineno"> 1328</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Name of CV term not correct: &#39;&quot;</span>) + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> + <span class="stringliteral">&quot; - &quot;</span> + parsed_name + <span class="stringliteral">&quot;&#39; should be &#39;&quot;</span> + correct_name + <span class="stringliteral">&quot;&#39;&quot;</span>);</div>
<div class="line"><a name="l01329"></a><span class="lineno"> 1329</span>&#160;        }</div>
<div class="line"><a name="l01330"></a><span class="lineno"> 1330</span>&#160;        <span class="keywordflow">if</span> (term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a89015d9d8ecc70d84c1eeb2d6c983c03">obsolete</a>)</div>
<div class="line"><a name="l01331"></a><span class="lineno"> 1331</span>&#160;        {</div>
<div class="line"><a name="l01332"></a><span class="lineno"> 1332</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Obsolete CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01333"></a><span class="lineno"> 1333</span>&#160;        }</div>
<div class="line"><a name="l01334"></a><span class="lineno"> 1334</span>&#160;        <span class="comment">//values used in wrong places and wrong value types</span></div>
<div class="line"><a name="l01335"></a><span class="lineno"> 1335</span>&#160;        <span class="keywordflow">if</span> (value != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l01336"></a><span class="lineno"> 1336</span>&#160;        {</div>
<div class="line"><a name="l01337"></a><span class="lineno"> 1337</span>&#160;          <span class="keywordflow">if</span> (term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#aa730524a83fc19c0ba3a466fb9c62f95">xref_type</a> == <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09ac157bdf0b85a40d2619cbc8bc1ae5fe2">ControlledVocabulary::CVTerm::NONE</a>)</div>
<div class="line"><a name="l01338"></a><span class="lineno"> 1338</span>&#160;          {</div>
<div class="line"><a name="l01339"></a><span class="lineno"> 1339</span>&#160;            <span class="comment">//Quality CV does not state value type :(</span></div>
<div class="line"><a name="l01340"></a><span class="lineno"> 1340</span>&#160;            <span class="keywordflow">if</span> (!accession.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">&quot;PATO:&quot;</span>))</div>
<div class="line"><a name="l01341"></a><span class="lineno"> 1341</span>&#160;            {</div>
<div class="line"><a name="l01342"></a><span class="lineno"> 1342</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39; must not have a value. The value is &#39;&quot;</span> + value + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01343"></a><span class="lineno"> 1343</span>&#160;            }</div>
<div class="line"><a name="l01344"></a><span class="lineno"> 1344</span>&#160;          }</div>
<div class="line"><a name="l01345"></a><span class="lineno"> 1345</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01346"></a><span class="lineno"> 1346</span>&#160;          {</div>
<div class="line"><a name="l01347"></a><span class="lineno"> 1347</span>&#160;            <span class="keywordflow">switch</span> (term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#aa730524a83fc19c0ba3a466fb9c62f95">xref_type</a>)</div>
<div class="line"><a name="l01348"></a><span class="lineno"> 1348</span>&#160;            {</div>
<div class="line"><a name="l01349"></a><span class="lineno"> 1349</span>&#160;            <span class="comment">//string value can be anything</span></div>
<div class="line"><a name="l01350"></a><span class="lineno"> 1350</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a869ef254cbf763367b5f618642d94242">ControlledVocabulary::CVTerm::XSD_STRING</a>:</div>
<div class="line"><a name="l01351"></a><span class="lineno"> 1351</span>&#160;              <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01352"></a><span class="lineno"> 1352</span>&#160;</div>
<div class="line"><a name="l01353"></a><span class="lineno"> 1353</span>&#160;            <span class="comment">//int value =&gt; try casting</span></div>
<div class="line"><a name="l01354"></a><span class="lineno"> 1354</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09ae39436e89ac71af5243d896a4acd6496">ControlledVocabulary::CVTerm::XSD_INTEGER</a>:</div>
<div class="line"><a name="l01355"></a><span class="lineno"> 1355</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a38d413e2b31af5d67c4c71f17f5f63d0">ControlledVocabulary::CVTerm::XSD_NEGATIVE_INTEGER</a>:</div>
<div class="line"><a name="l01356"></a><span class="lineno"> 1356</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a4452061824c767b63771c808ac8db712">ControlledVocabulary::CVTerm::XSD_POSITIVE_INTEGER</a>:</div>
<div class="line"><a name="l01357"></a><span class="lineno"> 1357</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09aab6ed9fc0d339bd90c445e066f13fd67">ControlledVocabulary::CVTerm::XSD_NON_NEGATIVE_INTEGER</a>:</div>
<div class="line"><a name="l01358"></a><span class="lineno"> 1358</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a6606dea51053a6eb746ba4ccaa37a1f3">ControlledVocabulary::CVTerm::XSD_NON_POSITIVE_INTEGER</a>:</div>
<div class="line"><a name="l01359"></a><span class="lineno"> 1359</span>&#160;              <span class="keywordflow">try</span></div>
<div class="line"><a name="l01360"></a><span class="lineno"> 1360</span>&#160;              {</div>
<div class="line"><a name="l01361"></a><span class="lineno"> 1361</span>&#160;                termValue = value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01362"></a><span class="lineno"> 1362</span>&#160;              }</div>
<div class="line"><a name="l01363"></a><span class="lineno"> 1363</span>&#160;              <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ConversionError.html">Exception::ConversionError</a>&amp;)</div>
<div class="line"><a name="l01364"></a><span class="lineno"> 1364</span>&#160;              {</div>
<div class="line"><a name="l01365"></a><span class="lineno"> 1365</span>&#160;                warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39; must have an integer value. The value is &#39;&quot;</span> + value + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01366"></a><span class="lineno"> 1366</span>&#160;                <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01367"></a><span class="lineno"> 1367</span>&#160;              }</div>
<div class="line"><a name="l01368"></a><span class="lineno"> 1368</span>&#160;              <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01369"></a><span class="lineno"> 1369</span>&#160;</div>
<div class="line"><a name="l01370"></a><span class="lineno"> 1370</span>&#160;            <span class="comment">//double value =&gt; try casting</span></div>
<div class="line"><a name="l01371"></a><span class="lineno"> 1371</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a9936481d5130ac6611cf2eff629207f3">ControlledVocabulary::CVTerm::XSD_DECIMAL</a>:</div>
<div class="line"><a name="l01372"></a><span class="lineno"> 1372</span>&#160;              <span class="keywordflow">try</span></div>
<div class="line"><a name="l01373"></a><span class="lineno"> 1373</span>&#160;              {</div>
<div class="line"><a name="l01374"></a><span class="lineno"> 1374</span>&#160;                termValue = value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>();</div>
<div class="line"><a name="l01375"></a><span class="lineno"> 1375</span>&#160;              }</div>
<div class="line"><a name="l01376"></a><span class="lineno"> 1376</span>&#160;              <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ConversionError.html">Exception::ConversionError</a>&amp;)</div>
<div class="line"><a name="l01377"></a><span class="lineno"> 1377</span>&#160;              {</div>
<div class="line"><a name="l01378"></a><span class="lineno"> 1378</span>&#160;                warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39; must have a floating-point value. The value is &#39;&quot;</span> + value + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01379"></a><span class="lineno"> 1379</span>&#160;                <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01380"></a><span class="lineno"> 1380</span>&#160;              }</div>
<div class="line"><a name="l01381"></a><span class="lineno"> 1381</span>&#160;              <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01382"></a><span class="lineno"> 1382</span>&#160;</div>
<div class="line"><a name="l01383"></a><span class="lineno"> 1383</span>&#160;            <span class="comment">//date string =&gt; try conversion</span></div>
<div class="line"><a name="l01384"></a><span class="lineno"> 1384</span>&#160;            <span class="keywordflow">case</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a38016896f280e9e0f3481f8c96bbf3ff">ControlledVocabulary::CVTerm::XSD_DATE</a>:</div>
<div class="line"><a name="l01385"></a><span class="lineno"> 1385</span>&#160;              <span class="keywordflow">try</span></div>
<div class="line"><a name="l01386"></a><span class="lineno"> 1386</span>&#160;              {</div>
<div class="line"><a name="l01387"></a><span class="lineno"> 1387</span>&#160;                <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a> tmp;</div>
<div class="line"><a name="l01388"></a><span class="lineno"> 1388</span>&#160;                tmp.<a class="code" href="classOpenMS_1_1DateTime.html#afb2353cf7399e53aa4b59ce122c6fc49">set</a>(value);</div>
<div class="line"><a name="l01389"></a><span class="lineno"> 1389</span>&#160;              }</div>
<div class="line"><a name="l01390"></a><span class="lineno"> 1390</span>&#160;              <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>&amp;)</div>
<div class="line"><a name="l01391"></a><span class="lineno"> 1391</span>&#160;              {</div>
<div class="line"><a name="l01392"></a><span class="lineno"> 1392</span>&#160;                warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39; must be a valid date. The value is &#39;&quot;</span> + value + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01393"></a><span class="lineno"> 1393</span>&#160;                <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01394"></a><span class="lineno"> 1394</span>&#160;              }</div>
<div class="line"><a name="l01395"></a><span class="lineno"> 1395</span>&#160;              <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01396"></a><span class="lineno"> 1396</span>&#160;</div>
<div class="line"><a name="l01397"></a><span class="lineno"> 1397</span>&#160;            <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l01398"></a><span class="lineno"> 1398</span>&#160;              warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39; has the unknown value type &#39;&quot;</span> + <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a8b19d98c71f9926a1a2ff8822c0722c3">ControlledVocabulary::CVTerm::getXRefTypeName</a>(term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#aa730524a83fc19c0ba3a466fb9c62f95">xref_type</a>) + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01399"></a><span class="lineno"> 1399</span>&#160;              <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01400"></a><span class="lineno"> 1400</span>&#160;            }</div>
<div class="line"><a name="l01401"></a><span class="lineno"> 1401</span>&#160;          }</div>
<div class="line"><a name="l01402"></a><span class="lineno"> 1402</span>&#160;        }</div>
<div class="line"><a name="l01403"></a><span class="lineno"> 1403</span>&#160;        <span class="comment">//no value, although there should be a numerical value</span></div>
<div class="line"><a name="l01404"></a><span class="lineno"> 1404</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#aa730524a83fc19c0ba3a466fb9c62f95">xref_type</a> != <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09ac157bdf0b85a40d2619cbc8bc1ae5fe2">ControlledVocabulary::CVTerm::NONE</a> &amp;&amp; term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#aa730524a83fc19c0ba3a466fb9c62f95">xref_type</a> != <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a869ef254cbf763367b5f618642d94242">ControlledVocabulary::CVTerm::XSD_STRING</a>)</div>
<div class="line"><a name="l01405"></a><span class="lineno"> 1405</span>&#160;        {</div>
<div class="line"><a name="l01406"></a><span class="lineno"> 1406</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;The CV term &#39;&quot;</span>) + accession + <span class="stringliteral">&quot; - &quot;</span> + term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;&#39; used in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39; should have a numerical value. The value is &#39;&quot;</span> + value + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01407"></a><span class="lineno"> 1407</span>&#160;          <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01408"></a><span class="lineno"> 1408</span>&#160;        }</div>
<div class="line"><a name="l01409"></a><span class="lineno"> 1409</span>&#160;      }</div>
<div class="line"><a name="l01410"></a><span class="lineno"> 1410</span>&#160;</div>
<div class="line"><a name="l01411"></a><span class="lineno"> 1411</span>&#160;      <span class="keywordflow">if</span> (unit_accession != <span class="stringliteral">&quot;&quot;</span>) termValue.<a class="code" href="classOpenMS_1_1DataValue.html#a1ade56fdfbde5b31702cfbbab985f619">setUnit</a>(unit_accession);</div>
<div class="line"><a name="l01412"></a><span class="lineno"> 1412</span>&#160;</div>
<div class="line"><a name="l01413"></a><span class="lineno"> 1413</span>&#160;      <span class="comment">//------------------------- run ----------------------------</span></div>
<div class="line"><a name="l01414"></a><span class="lineno"> 1414</span>&#160;      <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;run&quot;</span>)</div>
<div class="line"><a name="l01415"></a><span class="lineno"> 1415</span>&#160;      {</div>
<div class="line"><a name="l01416"></a><span class="lineno"> 1416</span>&#160;        <span class="comment">//MS:1000857 ! run attribute</span></div>
<div class="line"><a name="l01417"></a><span class="lineno"> 1417</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000858&quot;</span>) <span class="comment">//fraction identifier</span></div>
<div class="line"><a name="l01418"></a><span class="lineno"> 1418</span>&#160;        {</div>
<div class="line"><a name="l01419"></a><span class="lineno"> 1419</span>&#160;          exp_-&gt;setFractionIdentifier(value);</div>
<div class="line"><a name="l01420"></a><span class="lineno"> 1420</span>&#160;        }</div>
<div class="line"><a name="l01421"></a><span class="lineno"> 1421</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01422"></a><span class="lineno"> 1422</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01423"></a><span class="lineno"> 1423</span>&#160;      }</div>
<div class="line"><a name="l01424"></a><span class="lineno"> 1424</span>&#160;      <span class="comment">//------------------------- binaryDataArray ----------------------------</span></div>
<div class="line"><a name="l01425"></a><span class="lineno"> 1425</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;binaryDataArray&quot;</span>)</div>
<div class="line"><a name="l01426"></a><span class="lineno"> 1426</span>&#160;      {</div>
<div class="line"><a name="l01427"></a><span class="lineno"> 1427</span>&#160;        <span class="comment">//MS:1000518 ! binary data type</span></div>
<div class="line"><a name="l01428"></a><span class="lineno"> 1428</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000523&quot;</span>) <span class="comment">//64-bit float</span></div>
<div class="line"><a name="l01429"></a><span class="lineno"> 1429</span>&#160;        {</div>
<div class="line"><a name="l01430"></a><span class="lineno"> 1430</span>&#160;          data_.back().precision = BinaryData::PRE_64;</div>
<div class="line"><a name="l01431"></a><span class="lineno"> 1431</span>&#160;          data_.back().data_type = BinaryData::DT_FLOAT;</div>
<div class="line"><a name="l01432"></a><span class="lineno"> 1432</span>&#160;        }</div>
<div class="line"><a name="l01433"></a><span class="lineno"> 1433</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000521&quot;</span>) <span class="comment">//32-bit float</span></div>
<div class="line"><a name="l01434"></a><span class="lineno"> 1434</span>&#160;        {</div>
<div class="line"><a name="l01435"></a><span class="lineno"> 1435</span>&#160;          data_.back().precision = BinaryData::PRE_32;</div>
<div class="line"><a name="l01436"></a><span class="lineno"> 1436</span>&#160;          data_.back().data_type = BinaryData::DT_FLOAT;</div>
<div class="line"><a name="l01437"></a><span class="lineno"> 1437</span>&#160;        }</div>
<div class="line"><a name="l01438"></a><span class="lineno"> 1438</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000519&quot;</span>) <span class="comment">//32-bit integer</span></div>
<div class="line"><a name="l01439"></a><span class="lineno"> 1439</span>&#160;        {</div>
<div class="line"><a name="l01440"></a><span class="lineno"> 1440</span>&#160;          data_.back().precision = BinaryData::PRE_32;</div>
<div class="line"><a name="l01441"></a><span class="lineno"> 1441</span>&#160;          data_.back().data_type = BinaryData::DT_INT;</div>
<div class="line"><a name="l01442"></a><span class="lineno"> 1442</span>&#160;        }</div>
<div class="line"><a name="l01443"></a><span class="lineno"> 1443</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000522&quot;</span>) <span class="comment">//64-bit integer</span></div>
<div class="line"><a name="l01444"></a><span class="lineno"> 1444</span>&#160;        {</div>
<div class="line"><a name="l01445"></a><span class="lineno"> 1445</span>&#160;          data_.back().precision = BinaryData::PRE_64;</div>
<div class="line"><a name="l01446"></a><span class="lineno"> 1446</span>&#160;          data_.back().data_type = BinaryData::DT_INT;</div>
<div class="line"><a name="l01447"></a><span class="lineno"> 1447</span>&#160;        }</div>
<div class="line"><a name="l01448"></a><span class="lineno"> 1448</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001479&quot;</span>)</div>
<div class="line"><a name="l01449"></a><span class="lineno"> 1449</span>&#160;        {</div>
<div class="line"><a name="l01450"></a><span class="lineno"> 1450</span>&#160;          data_.back().precision = BinaryData::PRE_NONE;</div>
<div class="line"><a name="l01451"></a><span class="lineno"> 1451</span>&#160;          data_.back().data_type = BinaryData::DT_STRING;</div>
<div class="line"><a name="l01452"></a><span class="lineno"> 1452</span>&#160;        }</div>
<div class="line"><a name="l01453"></a><span class="lineno"> 1453</span>&#160;        <span class="comment">//MS:1000513 ! binary data array</span></div>
<div class="line"><a name="l01454"></a><span class="lineno"> 1454</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000786&quot;</span>) <span class="comment">// non-standard binary data array (with name as value)</span></div>
<div class="line"><a name="l01455"></a><span class="lineno"> 1455</span>&#160;        {</div>
<div class="line"><a name="l01456"></a><span class="lineno"> 1456</span>&#160;          data_.back().meta.setName(value);</div>
<div class="line"><a name="l01457"></a><span class="lineno"> 1457</span>&#160;        }</div>
<div class="line"><a name="l01458"></a><span class="lineno"> 1458</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000513&quot;</span>)) <span class="comment">//other array names as string</span></div>
<div class="line"><a name="l01459"></a><span class="lineno"> 1459</span>&#160;        {</div>
<div class="line"><a name="l01460"></a><span class="lineno"> 1460</span>&#160;          data_.back().meta.setName(cv_.getTerm(accession).name);</div>
<div class="line"><a name="l01461"></a><span class="lineno"> 1461</span>&#160;        }</div>
<div class="line"><a name="l01462"></a><span class="lineno"> 1462</span>&#160;        <span class="comment">//MS:1000572 ! binary data compression type</span></div>
<div class="line"><a name="l01463"></a><span class="lineno"> 1463</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000574&quot;</span>) <span class="comment">//zlib compression</span></div>
<div class="line"><a name="l01464"></a><span class="lineno"> 1464</span>&#160;        {</div>
<div class="line"><a name="l01465"></a><span class="lineno"> 1465</span>&#160;          data_.back().compression = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01466"></a><span class="lineno"> 1466</span>&#160;        }</div>
<div class="line"><a name="l01467"></a><span class="lineno"> 1467</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000576&quot;</span>) <span class="comment">// no compression</span></div>
<div class="line"><a name="l01468"></a><span class="lineno"> 1468</span>&#160;        {</div>
<div class="line"><a name="l01469"></a><span class="lineno"> 1469</span>&#160;          data_.back().compression = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01470"></a><span class="lineno"> 1470</span>&#160;        }</div>
<div class="line"><a name="l01471"></a><span class="lineno"> 1471</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01472"></a><span class="lineno"> 1472</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01473"></a><span class="lineno"> 1473</span>&#160;      }</div>
<div class="line"><a name="l01474"></a><span class="lineno"> 1474</span>&#160;      <span class="comment">//------------------------- spectrum ----------------------------</span></div>
<div class="line"><a name="l01475"></a><span class="lineno"> 1475</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;spectrum&quot;</span>)</div>
<div class="line"><a name="l01476"></a><span class="lineno"> 1476</span>&#160;      {</div>
<div class="line"><a name="l01477"></a><span class="lineno"> 1477</span>&#160;        <span class="comment">//spectrum type</span></div>
<div class="line"><a name="l01478"></a><span class="lineno"> 1478</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000294&quot;</span>) <span class="comment">//mass spectrum</span></div>
<div class="line"><a name="l01479"></a><span class="lineno"> 1479</span>&#160;        {</div>
<div class="line"><a name="l01480"></a><span class="lineno"> 1480</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l01481"></a><span class="lineno"> 1481</span>&#160;        }</div>
<div class="line"><a name="l01482"></a><span class="lineno"> 1482</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000579&quot;</span>) <span class="comment">//MS1 spectrum</span></div>
<div class="line"><a name="l01483"></a><span class="lineno"> 1483</span>&#160;        {</div>
<div class="line"><a name="l01484"></a><span class="lineno"> 1484</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">InstrumentSettings::MS1SPECTRUM</a>);</div>
<div class="line"><a name="l01485"></a><span class="lineno"> 1485</span>&#160;        }</div>
<div class="line"><a name="l01486"></a><span class="lineno"> 1486</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000580&quot;</span>) <span class="comment">//MSn spectrum</span></div>
<div class="line"><a name="l01487"></a><span class="lineno"> 1487</span>&#160;        {</div>
<div class="line"><a name="l01488"></a><span class="lineno"> 1488</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>);</div>
<div class="line"><a name="l01489"></a><span class="lineno"> 1489</span>&#160;        }</div>
<div class="line"><a name="l01490"></a><span class="lineno"> 1490</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000581&quot;</span>) <span class="comment">//CRM spectrum</span></div>
<div class="line"><a name="l01491"></a><span class="lineno"> 1491</span>&#160;        {</div>
<div class="line"><a name="l01492"></a><span class="lineno"> 1492</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>);</div>
<div class="line"><a name="l01493"></a><span class="lineno"> 1493</span>&#160;        }</div>
<div class="line"><a name="l01494"></a><span class="lineno"> 1494</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000582&quot;</span>) <span class="comment">//SIM spectrum</span></div>
<div class="line"><a name="l01495"></a><span class="lineno"> 1495</span>&#160;        {</div>
<div class="line"><a name="l01496"></a><span class="lineno"> 1496</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>);</div>
<div class="line"><a name="l01497"></a><span class="lineno"> 1497</span>&#160;        }</div>
<div class="line"><a name="l01498"></a><span class="lineno"> 1498</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000583&quot;</span>) <span class="comment">//SRM spectrum</span></div>
<div class="line"><a name="l01499"></a><span class="lineno"> 1499</span>&#160;        {</div>
<div class="line"><a name="l01500"></a><span class="lineno"> 1500</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>);</div>
<div class="line"><a name="l01501"></a><span class="lineno"> 1501</span>&#160;        }</div>
<div class="line"><a name="l01502"></a><span class="lineno"> 1502</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000804&quot;</span>) <span class="comment">//electromagnetic radiation spectrum</span></div>
<div class="line"><a name="l01503"></a><span class="lineno"> 1503</span>&#160;        {</div>
<div class="line"><a name="l01504"></a><span class="lineno"> 1504</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a45cd2a1ea065b4909b86190b372ed7da">InstrumentSettings::EMR</a>);</div>
<div class="line"><a name="l01505"></a><span class="lineno"> 1505</span>&#160;        }</div>
<div class="line"><a name="l01506"></a><span class="lineno"> 1506</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000805&quot;</span>) <span class="comment">//emission spectrum</span></div>
<div class="line"><a name="l01507"></a><span class="lineno"> 1507</span>&#160;        {</div>
<div class="line"><a name="l01508"></a><span class="lineno"> 1508</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6b66c706c4bc43ff1a3b5a0044fdfa18">InstrumentSettings::EMISSION</a>);</div>
<div class="line"><a name="l01509"></a><span class="lineno"> 1509</span>&#160;        }</div>
<div class="line"><a name="l01510"></a><span class="lineno"> 1510</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000806&quot;</span>) <span class="comment">//absorption spectrum</span></div>
<div class="line"><a name="l01511"></a><span class="lineno"> 1511</span>&#160;        {</div>
<div class="line"><a name="l01512"></a><span class="lineno"> 1512</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac1923f59816bf846e2a62d41cfb91b2f">InstrumentSettings::ABSORBTION</a>);</div>
<div class="line"><a name="l01513"></a><span class="lineno"> 1513</span>&#160;        }</div>
<div class="line"><a name="l01514"></a><span class="lineno"> 1514</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000325&quot;</span>) <span class="comment">//constant neutral gain spectrum</span></div>
<div class="line"><a name="l01515"></a><span class="lineno"> 1515</span>&#160;        {</div>
<div class="line"><a name="l01516"></a><span class="lineno"> 1516</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f">InstrumentSettings::CNG</a>);</div>
<div class="line"><a name="l01517"></a><span class="lineno"> 1517</span>&#160;        }</div>
<div class="line"><a name="l01518"></a><span class="lineno"> 1518</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000326&quot;</span>) <span class="comment">//constant neutral loss spectrum</span></div>
<div class="line"><a name="l01519"></a><span class="lineno"> 1519</span>&#160;        {</div>
<div class="line"><a name="l01520"></a><span class="lineno"> 1520</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca">InstrumentSettings::CNL</a>);</div>
<div class="line"><a name="l01521"></a><span class="lineno"> 1521</span>&#160;        }</div>
<div class="line"><a name="l01522"></a><span class="lineno"> 1522</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000341&quot;</span>) <span class="comment">//precursor ion spectrum</span></div>
<div class="line"><a name="l01523"></a><span class="lineno"> 1523</span>&#160;        {</div>
<div class="line"><a name="l01524"></a><span class="lineno"> 1524</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f">InstrumentSettings::PRECURSOR</a>);</div>
<div class="line"><a name="l01525"></a><span class="lineno"> 1525</span>&#160;        }</div>
<div class="line"><a name="l01526"></a><span class="lineno"> 1526</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000789&quot;</span>) <span class="comment">//enhanced multiply charged spectrum</span></div>
<div class="line"><a name="l01527"></a><span class="lineno"> 1527</span>&#160;        {</div>
<div class="line"><a name="l01528"></a><span class="lineno"> 1528</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac21206f76146b8913723119f609be907">InstrumentSettings::EMC</a>);</div>
<div class="line"><a name="l01529"></a><span class="lineno"> 1529</span>&#160;        }</div>
<div class="line"><a name="l01530"></a><span class="lineno"> 1530</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000790&quot;</span>) <span class="comment">//time-delayed fragmentation spectrum</span></div>
<div class="line"><a name="l01531"></a><span class="lineno"> 1531</span>&#160;        {</div>
<div class="line"><a name="l01532"></a><span class="lineno"> 1532</span>&#160;          spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a5980df92dcce7a0e1e8bc482e4f07aa6">InstrumentSettings::TDF</a>);</div>
<div class="line"><a name="l01533"></a><span class="lineno"> 1533</span>&#160;        }</div>
<div class="line"><a name="l01534"></a><span class="lineno"> 1534</span>&#160;        <span class="comment">//spectrum representation</span></div>
<div class="line"><a name="l01535"></a><span class="lineno"> 1535</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000127&quot;</span>) <span class="comment">//centroid spectrum</span></div>
<div class="line"><a name="l01536"></a><span class="lineno"> 1536</span>&#160;        {</div>
<div class="line"><a name="l01537"></a><span class="lineno"> 1537</span>&#160;          spec_.setType(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>);</div>
<div class="line"><a name="l01538"></a><span class="lineno"> 1538</span>&#160;        }</div>
<div class="line"><a name="l01539"></a><span class="lineno"> 1539</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000128&quot;</span>) <span class="comment">//profile spectrum</span></div>
<div class="line"><a name="l01540"></a><span class="lineno"> 1540</span>&#160;        {</div>
<div class="line"><a name="l01541"></a><span class="lineno"> 1541</span>&#160;          spec_.setType(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533">SpectrumSettings::RAWDATA</a>);</div>
<div class="line"><a name="l01542"></a><span class="lineno"> 1542</span>&#160;        }</div>
<div class="line"><a name="l01543"></a><span class="lineno"> 1543</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000525&quot;</span>) <span class="comment">//spectrum representation</span></div>
<div class="line"><a name="l01544"></a><span class="lineno"> 1544</span>&#160;        {</div>
<div class="line"><a name="l01545"></a><span class="lineno"> 1545</span>&#160;          spec_.setType(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a6ce26a62afab55d7606ad4e92428b30c">SpectrumSettings::UNKNOWN</a>);</div>
<div class="line"><a name="l01546"></a><span class="lineno"> 1546</span>&#160;        }</div>
<div class="line"><a name="l01547"></a><span class="lineno"> 1547</span>&#160;        <span class="comment">//spectrum attribute</span></div>
<div class="line"><a name="l01548"></a><span class="lineno"> 1548</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000511&quot;</span>) <span class="comment">//ms level</span></div>
<div class="line"><a name="l01549"></a><span class="lineno"> 1549</span>&#160;        {</div>
<div class="line"><a name="l01550"></a><span class="lineno"> 1550</span>&#160;          spec_.setMSLevel(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l01551"></a><span class="lineno"> 1551</span>&#160;</div>
<div class="line"><a name="l01552"></a><span class="lineno"> 1552</span>&#160;          <span class="keywordflow">if</span> (options_.hasMSLevels() &amp;&amp; !options_.containsMSLevel(spec_.getMSLevel()))</div>
<div class="line"><a name="l01553"></a><span class="lineno"> 1553</span>&#160;          {</div>
<div class="line"><a name="l01554"></a><span class="lineno"> 1554</span>&#160;            skip_spectrum_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01555"></a><span class="lineno"> 1555</span>&#160;          }</div>
<div class="line"><a name="l01556"></a><span class="lineno"> 1556</span>&#160;        }</div>
<div class="line"><a name="l01557"></a><span class="lineno"> 1557</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000497&quot;</span>) <span class="comment">//zoom scan</span></div>
<div class="line"><a name="l01558"></a><span class="lineno"> 1558</span>&#160;        {</div>
<div class="line"><a name="l01559"></a><span class="lineno"> 1559</span>&#160;          spec_.getInstrumentSettings().setZoomScan(<span class="keyword">true</span>);</div>
<div class="line"><a name="l01560"></a><span class="lineno"> 1560</span>&#160;        }</div>
<div class="line"><a name="l01561"></a><span class="lineno"> 1561</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000285&quot;</span>) <span class="comment">//total ion current</span></div>
<div class="line"><a name="l01562"></a><span class="lineno"> 1562</span>&#160;        {</div>
<div class="line"><a name="l01563"></a><span class="lineno"> 1563</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01564"></a><span class="lineno"> 1564</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;total ion current&quot;</span>, termValue);</div>
<div class="line"><a name="l01565"></a><span class="lineno"> 1565</span>&#160;        }</div>
<div class="line"><a name="l01566"></a><span class="lineno"> 1566</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000504&quot;</span>) <span class="comment">//base peak m/z</span></div>
<div class="line"><a name="l01567"></a><span class="lineno"> 1567</span>&#160;        {</div>
<div class="line"><a name="l01568"></a><span class="lineno"> 1568</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01569"></a><span class="lineno"> 1569</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;base peak m/z&quot;</span>, termValue);</div>
<div class="line"><a name="l01570"></a><span class="lineno"> 1570</span>&#160;        }</div>
<div class="line"><a name="l01571"></a><span class="lineno"> 1571</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000505&quot;</span>) <span class="comment">//base peak intensity</span></div>
<div class="line"><a name="l01572"></a><span class="lineno"> 1572</span>&#160;        {</div>
<div class="line"><a name="l01573"></a><span class="lineno"> 1573</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01574"></a><span class="lineno"> 1574</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;base peak intensity&quot;</span>, termValue);</div>
<div class="line"><a name="l01575"></a><span class="lineno"> 1575</span>&#160;        }</div>
<div class="line"><a name="l01576"></a><span class="lineno"> 1576</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000527&quot;</span>) <span class="comment">//highest observed m/z</span></div>
<div class="line"><a name="l01577"></a><span class="lineno"> 1577</span>&#160;        {</div>
<div class="line"><a name="l01578"></a><span class="lineno"> 1578</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01579"></a><span class="lineno"> 1579</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;highest observed m/z&quot;</span>, termValue);</div>
<div class="line"><a name="l01580"></a><span class="lineno"> 1580</span>&#160;        }</div>
<div class="line"><a name="l01581"></a><span class="lineno"> 1581</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000528&quot;</span>) <span class="comment">//lowest observed m/z</span></div>
<div class="line"><a name="l01582"></a><span class="lineno"> 1582</span>&#160;        {</div>
<div class="line"><a name="l01583"></a><span class="lineno"> 1583</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01584"></a><span class="lineno"> 1584</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;lowest observed m/z&quot;</span>, termValue);</div>
<div class="line"><a name="l01585"></a><span class="lineno"> 1585</span>&#160;        }</div>
<div class="line"><a name="l01586"></a><span class="lineno"> 1586</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000618&quot;</span>) <span class="comment">//highest observed wavelength</span></div>
<div class="line"><a name="l01587"></a><span class="lineno"> 1587</span>&#160;        {</div>
<div class="line"><a name="l01588"></a><span class="lineno"> 1588</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01589"></a><span class="lineno"> 1589</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;highest observed wavelength&quot;</span>, termValue);</div>
<div class="line"><a name="l01590"></a><span class="lineno"> 1590</span>&#160;        }</div>
<div class="line"><a name="l01591"></a><span class="lineno"> 1591</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000619&quot;</span>) <span class="comment">//lowest observed wavelength</span></div>
<div class="line"><a name="l01592"></a><span class="lineno"> 1592</span>&#160;        {</div>
<div class="line"><a name="l01593"></a><span class="lineno"> 1593</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01594"></a><span class="lineno"> 1594</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;lowest observed wavelength&quot;</span>, termValue);</div>
<div class="line"><a name="l01595"></a><span class="lineno"> 1595</span>&#160;        }</div>
<div class="line"><a name="l01596"></a><span class="lineno"> 1596</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000796&quot;</span>) <span class="comment">//spectrum title</span></div>
<div class="line"><a name="l01597"></a><span class="lineno"> 1597</span>&#160;        {</div>
<div class="line"><a name="l01598"></a><span class="lineno"> 1598</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01599"></a><span class="lineno"> 1599</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;spectrum title&quot;</span>, termValue);</div>
<div class="line"><a name="l01600"></a><span class="lineno"> 1600</span>&#160;        }</div>
<div class="line"><a name="l01601"></a><span class="lineno"> 1601</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000797&quot;</span>) <span class="comment">//peak list scans</span></div>
<div class="line"><a name="l01602"></a><span class="lineno"> 1602</span>&#160;        {</div>
<div class="line"><a name="l01603"></a><span class="lineno"> 1603</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01604"></a><span class="lineno"> 1604</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;peak list scans&quot;</span>, termValue);</div>
<div class="line"><a name="l01605"></a><span class="lineno"> 1605</span>&#160;        }</div>
<div class="line"><a name="l01606"></a><span class="lineno"> 1606</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000798&quot;</span>) <span class="comment">//peak list raw scans</span></div>
<div class="line"><a name="l01607"></a><span class="lineno"> 1607</span>&#160;        {</div>
<div class="line"><a name="l01608"></a><span class="lineno"> 1608</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01609"></a><span class="lineno"> 1609</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;peak list raw scans&quot;</span>, termValue);</div>
<div class="line"><a name="l01610"></a><span class="lineno"> 1610</span>&#160;        }</div>
<div class="line"><a name="l01611"></a><span class="lineno"> 1611</span>&#160;        <span class="comment">//scan polarity</span></div>
<div class="line"><a name="l01612"></a><span class="lineno"> 1612</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000129&quot;</span>) <span class="comment">//negative scan</span></div>
<div class="line"><a name="l01613"></a><span class="lineno"> 1613</span>&#160;        {</div>
<div class="line"><a name="l01614"></a><span class="lineno"> 1614</span>&#160;          spec_.getInstrumentSettings().setPolarity(<a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">IonSource::NEGATIVE</a>);</div>
<div class="line"><a name="l01615"></a><span class="lineno"> 1615</span>&#160;        }</div>
<div class="line"><a name="l01616"></a><span class="lineno"> 1616</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000130&quot;</span>) <span class="comment">//positive scan</span></div>
<div class="line"><a name="l01617"></a><span class="lineno"> 1617</span>&#160;        {</div>
<div class="line"><a name="l01618"></a><span class="lineno"> 1618</span>&#160;          spec_.getInstrumentSettings().setPolarity(<a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5">IonSource::POSITIVE</a>);</div>
<div class="line"><a name="l01619"></a><span class="lineno"> 1619</span>&#160;        }</div>
<div class="line"><a name="l01620"></a><span class="lineno"> 1620</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01621"></a><span class="lineno"> 1621</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01622"></a><span class="lineno"> 1622</span>&#160;      }</div>
<div class="line"><a name="l01623"></a><span class="lineno"> 1623</span>&#160;      <span class="comment">//------------------------- scanWindow ----------------------------</span></div>
<div class="line"><a name="l01624"></a><span class="lineno"> 1624</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;scanWindow&quot;</span>)</div>
<div class="line"><a name="l01625"></a><span class="lineno"> 1625</span>&#160;      {</div>
<div class="line"><a name="l01626"></a><span class="lineno"> 1626</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000501&quot;</span>) <span class="comment">//scan window lower limit</span></div>
<div class="line"><a name="l01627"></a><span class="lineno"> 1627</span>&#160;        {</div>
<div class="line"><a name="l01628"></a><span class="lineno"> 1628</span>&#160;          spec_.getInstrumentSettings().getScanWindows().back().begin = value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>();</div>
<div class="line"><a name="l01629"></a><span class="lineno"> 1629</span>&#160;        }</div>
<div class="line"><a name="l01630"></a><span class="lineno"> 1630</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000500&quot;</span>) <span class="comment">//scan window upper limit</span></div>
<div class="line"><a name="l01631"></a><span class="lineno"> 1631</span>&#160;        {</div>
<div class="line"><a name="l01632"></a><span class="lineno"> 1632</span>&#160;          spec_.getInstrumentSettings().getScanWindows().back().end = value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>();</div>
<div class="line"><a name="l01633"></a><span class="lineno"> 1633</span>&#160;        }</div>
<div class="line"><a name="l01634"></a><span class="lineno"> 1634</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01635"></a><span class="lineno"> 1635</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01636"></a><span class="lineno"> 1636</span>&#160;      }</div>
<div class="line"><a name="l01637"></a><span class="lineno"> 1637</span>&#160;      <span class="comment">//------------------------- referenceableParamGroup ----------------------------</span></div>
<div class="line"><a name="l01638"></a><span class="lineno"> 1638</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;referenceableParamGroup&quot;</span>)</div>
<div class="line"><a name="l01639"></a><span class="lineno"> 1639</span>&#160;      {</div>
<div class="line"><a name="l01640"></a><span class="lineno"> 1640</span>&#160;        <a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html">SemanticValidator::CVTerm</a> term;</div>
<div class="line"><a name="l01641"></a><span class="lineno"> 1641</span>&#160;        term.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#aa4b705e9e4267f64630cacd7fc55fc5d">accession</a> = accession;</div>
<div class="line"><a name="l01642"></a><span class="lineno"> 1642</span>&#160;        term.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> = name;</div>
<div class="line"><a name="l01643"></a><span class="lineno"> 1643</span>&#160;        term.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a32147dacf0dd0bda3c39144c67347bf3">value</a> = value;</div>
<div class="line"><a name="l01644"></a><span class="lineno"> 1644</span>&#160;        term.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a6d07a35e88f53d1b49ddc99f84163312">unit_accession</a> = unit_accession;</div>
<div class="line"><a name="l01645"></a><span class="lineno"> 1645</span>&#160;        ref_param_[current_id_].push_back(term);</div>
<div class="line"><a name="l01646"></a><span class="lineno"> 1646</span>&#160;      }</div>
<div class="line"><a name="l01647"></a><span class="lineno"> 1647</span>&#160;      <span class="comment">//------------------------- selectedIon ----------------------------</span></div>
<div class="line"><a name="l01648"></a><span class="lineno"> 1648</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;selectedIon&quot;</span>)</div>
<div class="line"><a name="l01649"></a><span class="lineno"> 1649</span>&#160;      {</div>
<div class="line"><a name="l01650"></a><span class="lineno"> 1650</span>&#160;        <span class="comment">//parse only the first selected ion</span></div>
<div class="line"><a name="l01651"></a><span class="lineno"> 1651</span>&#160;        <span class="keywordflow">if</span> (selected_ion_count_ &gt; 1)</div>
<div class="line"><a name="l01652"></a><span class="lineno"> 1652</span>&#160;          <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01653"></a><span class="lineno"> 1653</span>&#160;</div>
<div class="line"><a name="l01654"></a><span class="lineno"> 1654</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000744&quot;</span>) <span class="comment">//selected ion m/z</span></div>
<div class="line"><a name="l01655"></a><span class="lineno"> 1655</span>&#160;        {</div>
<div class="line"><a name="l01656"></a><span class="lineno"> 1656</span>&#160;          <span class="comment">//this overwrites the m/z of the isolation window, as it is probably more accurate</span></div>
<div class="line"><a name="l01657"></a><span class="lineno"> 1657</span>&#160;          <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01658"></a><span class="lineno"> 1658</span>&#160;          {</div>
<div class="line"><a name="l01659"></a><span class="lineno"> 1659</span>&#160;            spec_.getPrecursors().back().setMZ(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01660"></a><span class="lineno"> 1660</span>&#160;          }</div>
<div class="line"><a name="l01661"></a><span class="lineno"> 1661</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01662"></a><span class="lineno"> 1662</span>&#160;          {</div>
<div class="line"><a name="l01663"></a><span class="lineno"> 1663</span>&#160;            chromatogram_.getPrecursor().setMZ(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01664"></a><span class="lineno"> 1664</span>&#160;          }</div>
<div class="line"><a name="l01665"></a><span class="lineno"> 1665</span>&#160;        }</div>
<div class="line"><a name="l01666"></a><span class="lineno"> 1666</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000041&quot;</span>) <span class="comment">//charge state</span></div>
<div class="line"><a name="l01667"></a><span class="lineno"> 1667</span>&#160;        {</div>
<div class="line"><a name="l01668"></a><span class="lineno"> 1668</span>&#160;          <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01669"></a><span class="lineno"> 1669</span>&#160;          {</div>
<div class="line"><a name="l01670"></a><span class="lineno"> 1670</span>&#160;            spec_.getPrecursors().back().setCharge(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l01671"></a><span class="lineno"> 1671</span>&#160;          }</div>
<div class="line"><a name="l01672"></a><span class="lineno"> 1672</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01673"></a><span class="lineno"> 1673</span>&#160;          {</div>
<div class="line"><a name="l01674"></a><span class="lineno"> 1674</span>&#160;            chromatogram_.getPrecursor().setCharge(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l01675"></a><span class="lineno"> 1675</span>&#160;          }</div>
<div class="line"><a name="l01676"></a><span class="lineno"> 1676</span>&#160;        }</div>
<div class="line"><a name="l01677"></a><span class="lineno"> 1677</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000042&quot;</span>) <span class="comment">//peak intensity</span></div>
<div class="line"><a name="l01678"></a><span class="lineno"> 1678</span>&#160;        {</div>
<div class="line"><a name="l01679"></a><span class="lineno"> 1679</span>&#160;          <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01680"></a><span class="lineno"> 1680</span>&#160;          {</div>
<div class="line"><a name="l01681"></a><span class="lineno"> 1681</span>&#160;            spec_.getPrecursors().back().setIntensity(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01682"></a><span class="lineno"> 1682</span>&#160;          }</div>
<div class="line"><a name="l01683"></a><span class="lineno"> 1683</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01684"></a><span class="lineno"> 1684</span>&#160;          {</div>
<div class="line"><a name="l01685"></a><span class="lineno"> 1685</span>&#160;            chromatogram_.getPrecursor().setIntensity(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01686"></a><span class="lineno"> 1686</span>&#160;          }</div>
<div class="line"><a name="l01687"></a><span class="lineno"> 1687</span>&#160;        }</div>
<div class="line"><a name="l01688"></a><span class="lineno"> 1688</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000633&quot;</span>) <span class="comment">//possible charge state</span></div>
<div class="line"><a name="l01689"></a><span class="lineno"> 1689</span>&#160;        {</div>
<div class="line"><a name="l01690"></a><span class="lineno"> 1690</span>&#160;          <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01691"></a><span class="lineno"> 1691</span>&#160;          {</div>
<div class="line"><a name="l01692"></a><span class="lineno"> 1692</span>&#160;            spec_.getPrecursors().back().getPossibleChargeStates().push_back(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l01693"></a><span class="lineno"> 1693</span>&#160;          }</div>
<div class="line"><a name="l01694"></a><span class="lineno"> 1694</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01695"></a><span class="lineno"> 1695</span>&#160;          {</div>
<div class="line"><a name="l01696"></a><span class="lineno"> 1696</span>&#160;            chromatogram_.getPrecursor().getPossibleChargeStates().push_back(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l01697"></a><span class="lineno"> 1697</span>&#160;          }</div>
<div class="line"><a name="l01698"></a><span class="lineno"> 1698</span>&#160;        }</div>
<div class="line"><a name="l01699"></a><span class="lineno"> 1699</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01700"></a><span class="lineno"> 1700</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01701"></a><span class="lineno"> 1701</span>&#160;      }</div>
<div class="line"><a name="l01702"></a><span class="lineno"> 1702</span>&#160;      <span class="comment">//------------------------- activation ----------------------------</span></div>
<div class="line"><a name="l01703"></a><span class="lineno"> 1703</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;activation&quot;</span>)</div>
<div class="line"><a name="l01704"></a><span class="lineno"> 1704</span>&#160;      {</div>
<div class="line"><a name="l01705"></a><span class="lineno"> 1705</span>&#160;        <span class="comment">//precursor activation attribute</span></div>
<div class="line"><a name="l01706"></a><span class="lineno"> 1706</span>&#160;        <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01707"></a><span class="lineno"> 1707</span>&#160;        {</div>
<div class="line"><a name="l01708"></a><span class="lineno"> 1708</span>&#160;          <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000245&quot;</span>) <span class="comment">//charge stripping</span></div>
<div class="line"><a name="l01709"></a><span class="lineno"> 1709</span>&#160;          {</div>
<div class="line"><a name="l01710"></a><span class="lineno"> 1710</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01711"></a><span class="lineno"> 1711</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;charge stripping&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;true&quot;</span>));</div>
<div class="line"><a name="l01712"></a><span class="lineno"> 1712</span>&#160;          }</div>
<div class="line"><a name="l01713"></a><span class="lineno"> 1713</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000045&quot;</span>) <span class="comment">//collision energy (ev)</span></div>
<div class="line"><a name="l01714"></a><span class="lineno"> 1714</span>&#160;          {</div>
<div class="line"><a name="l01715"></a><span class="lineno"> 1715</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01716"></a><span class="lineno"> 1716</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;collision energy&quot;</span>, termValue);</div>
<div class="line"><a name="l01717"></a><span class="lineno"> 1717</span>&#160;          }</div>
<div class="line"><a name="l01718"></a><span class="lineno"> 1718</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000412&quot;</span>) <span class="comment">//buffer gas</span></div>
<div class="line"><a name="l01719"></a><span class="lineno"> 1719</span>&#160;          {</div>
<div class="line"><a name="l01720"></a><span class="lineno"> 1720</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01721"></a><span class="lineno"> 1721</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;buffer gas&quot;</span>, termValue);</div>
<div class="line"><a name="l01722"></a><span class="lineno"> 1722</span>&#160;          }</div>
<div class="line"><a name="l01723"></a><span class="lineno"> 1723</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000419&quot;</span>) <span class="comment">//collision gas</span></div>
<div class="line"><a name="l01724"></a><span class="lineno"> 1724</span>&#160;          {</div>
<div class="line"><a name="l01725"></a><span class="lineno"> 1725</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01726"></a><span class="lineno"> 1726</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;collision gas&quot;</span>, termValue);</div>
<div class="line"><a name="l01727"></a><span class="lineno"> 1727</span>&#160;          }</div>
<div class="line"><a name="l01728"></a><span class="lineno"> 1728</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000509&quot;</span>) <span class="comment">//activation energy (ev)</span></div>
<div class="line"><a name="l01729"></a><span class="lineno"> 1729</span>&#160;          {</div>
<div class="line"><a name="l01730"></a><span class="lineno"> 1730</span>&#160;            spec_.getPrecursors().back().setActivationEnergy(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01731"></a><span class="lineno"> 1731</span>&#160;          }</div>
<div class="line"><a name="l01732"></a><span class="lineno"> 1732</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000138&quot;</span>) <span class="comment">//percent collision energy</span></div>
<div class="line"><a name="l01733"></a><span class="lineno"> 1733</span>&#160;          {</div>
<div class="line"><a name="l01734"></a><span class="lineno"> 1734</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01735"></a><span class="lineno"> 1735</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;percent collision energy&quot;</span>, termValue);</div>
<div class="line"><a name="l01736"></a><span class="lineno"> 1736</span>&#160;          }</div>
<div class="line"><a name="l01737"></a><span class="lineno"> 1737</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000869&quot;</span>) <span class="comment">//collision gas pressure</span></div>
<div class="line"><a name="l01738"></a><span class="lineno"> 1738</span>&#160;          {</div>
<div class="line"><a name="l01739"></a><span class="lineno"> 1739</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01740"></a><span class="lineno"> 1740</span>&#160;            spec_.getPrecursors().back().setMetaValue(<span class="stringliteral">&quot;collision gas pressure&quot;</span>, termValue);</div>
<div class="line"><a name="l01741"></a><span class="lineno"> 1741</span>&#160;          }</div>
<div class="line"><a name="l01742"></a><span class="lineno"> 1742</span>&#160;          <span class="comment">//dissociation method</span></div>
<div class="line"><a name="l01743"></a><span class="lineno"> 1743</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000044&quot;</span>) <span class="comment">//dissociation method</span></div>
<div class="line"><a name="l01744"></a><span class="lineno"> 1744</span>&#160;          {</div>
<div class="line"><a name="l01745"></a><span class="lineno"> 1745</span>&#160;            <span class="comment">//nothing to do here</span></div>
<div class="line"><a name="l01746"></a><span class="lineno"> 1746</span>&#160;          }</div>
<div class="line"><a name="l01747"></a><span class="lineno"> 1747</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000133&quot;</span>) <span class="comment">//collision-induced dissociation</span></div>
<div class="line"><a name="l01748"></a><span class="lineno"> 1748</span>&#160;          {</div>
<div class="line"><a name="l01749"></a><span class="lineno"> 1749</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab20b009dfccc7838ba06622a9d53daff">Precursor::CID</a>);</div>
<div class="line"><a name="l01750"></a><span class="lineno"> 1750</span>&#160;          }</div>
<div class="line"><a name="l01751"></a><span class="lineno"> 1751</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000134&quot;</span>) <span class="comment">//plasma desorption</span></div>
<div class="line"><a name="l01752"></a><span class="lineno"> 1752</span>&#160;          {</div>
<div class="line"><a name="l01753"></a><span class="lineno"> 1753</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1aefbc069e0ac4cd293f3ba527bec2befe">Precursor::PD</a>);</div>
<div class="line"><a name="l01754"></a><span class="lineno"> 1754</span>&#160;          }</div>
<div class="line"><a name="l01755"></a><span class="lineno"> 1755</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000135&quot;</span>) <span class="comment">//post-source decay</span></div>
<div class="line"><a name="l01756"></a><span class="lineno"> 1756</span>&#160;          {</div>
<div class="line"><a name="l01757"></a><span class="lineno"> 1757</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a7d2afca1f43e915528abd513b30b7a55">Precursor::PSD</a>);</div>
<div class="line"><a name="l01758"></a><span class="lineno"> 1758</span>&#160;          }</div>
<div class="line"><a name="l01759"></a><span class="lineno"> 1759</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000136&quot;</span>) <span class="comment">//surface-induced dissociation</span></div>
<div class="line"><a name="l01760"></a><span class="lineno"> 1760</span>&#160;          {</div>
<div class="line"><a name="l01761"></a><span class="lineno"> 1761</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab2fca50c5baefb10e5ecdc553e372586">Precursor::SID</a>);</div>
<div class="line"><a name="l01762"></a><span class="lineno"> 1762</span>&#160;          }</div>
<div class="line"><a name="l01763"></a><span class="lineno"> 1763</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000242&quot;</span>) <span class="comment">//blackbody infrared radiative dissociation</span></div>
<div class="line"><a name="l01764"></a><span class="lineno"> 1764</span>&#160;          {</div>
<div class="line"><a name="l01765"></a><span class="lineno"> 1765</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a3901fa9d6f534ab0c36a34a0850dffa0">Precursor::BIRD</a>);</div>
<div class="line"><a name="l01766"></a><span class="lineno"> 1766</span>&#160;          }</div>
<div class="line"><a name="l01767"></a><span class="lineno"> 1767</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000250&quot;</span>) <span class="comment">//electron capture dissociation</span></div>
<div class="line"><a name="l01768"></a><span class="lineno"> 1768</span>&#160;          {</div>
<div class="line"><a name="l01769"></a><span class="lineno"> 1769</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a2634661cb45dc1d0f135daebb5fa118b">Precursor::ECD</a>);</div>
<div class="line"><a name="l01770"></a><span class="lineno"> 1770</span>&#160;          }</div>
<div class="line"><a name="l01771"></a><span class="lineno"> 1771</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000262&quot;</span>) <span class="comment">//infrared multiphoton dissociation</span></div>
<div class="line"><a name="l01772"></a><span class="lineno"> 1772</span>&#160;          {</div>
<div class="line"><a name="l01773"></a><span class="lineno"> 1773</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a8c41c05a63a15c5d188d02f6f4db4303">Precursor::IMD</a>);</div>
<div class="line"><a name="l01774"></a><span class="lineno"> 1774</span>&#160;          }</div>
<div class="line"><a name="l01775"></a><span class="lineno"> 1775</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000282&quot;</span>) <span class="comment">//sustained off-resonance irradiation</span></div>
<div class="line"><a name="l01776"></a><span class="lineno"> 1776</span>&#160;          {</div>
<div class="line"><a name="l01777"></a><span class="lineno"> 1777</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a0ce1e0457af4bc9ab4bd841128c6ea84">Precursor::SORI</a>);</div>
<div class="line"><a name="l01778"></a><span class="lineno"> 1778</span>&#160;          }</div>
<div class="line"><a name="l01779"></a><span class="lineno"> 1779</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000422&quot;</span>) <span class="comment">//high-energy collision-induced dissociation</span></div>
<div class="line"><a name="l01780"></a><span class="lineno"> 1780</span>&#160;          {</div>
<div class="line"><a name="l01781"></a><span class="lineno"> 1781</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a1bf627bed7951e975a31ba7033786d05">Precursor::HCID</a>);</div>
<div class="line"><a name="l01782"></a><span class="lineno"> 1782</span>&#160;          }</div>
<div class="line"><a name="l01783"></a><span class="lineno"> 1783</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000433&quot;</span>) <span class="comment">//low-energy collision-induced dissociation</span></div>
<div class="line"><a name="l01784"></a><span class="lineno"> 1784</span>&#160;          {</div>
<div class="line"><a name="l01785"></a><span class="lineno"> 1785</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4437a3dbac928dd5e3ee699f931bd355">Precursor::LCID</a>);</div>
<div class="line"><a name="l01786"></a><span class="lineno"> 1786</span>&#160;          }</div>
<div class="line"><a name="l01787"></a><span class="lineno"> 1787</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000435&quot;</span>) <span class="comment">//photodissociation</span></div>
<div class="line"><a name="l01788"></a><span class="lineno"> 1788</span>&#160;          {</div>
<div class="line"><a name="l01789"></a><span class="lineno"> 1789</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4187f6dae406f24b70e3c34a7448b15f">Precursor::PHD</a>);</div>
<div class="line"><a name="l01790"></a><span class="lineno"> 1790</span>&#160;          }</div>
<div class="line"><a name="l01791"></a><span class="lineno"> 1791</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000598&quot;</span>) <span class="comment">//electron transfer dissociation</span></div>
<div class="line"><a name="l01792"></a><span class="lineno"> 1792</span>&#160;          {</div>
<div class="line"><a name="l01793"></a><span class="lineno"> 1793</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a56a28ad07746c6bae402cc7d7ec0839a">Precursor::ETD</a>);</div>
<div class="line"><a name="l01794"></a><span class="lineno"> 1794</span>&#160;          }</div>
<div class="line"><a name="l01795"></a><span class="lineno"> 1795</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000599&quot;</span>) <span class="comment">//pulsed q dissociation</span></div>
<div class="line"><a name="l01796"></a><span class="lineno"> 1796</span>&#160;          {</div>
<div class="line"><a name="l01797"></a><span class="lineno"> 1797</span>&#160;            spec_.getPrecursors().back().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a22a843b242764a6b3b320c1b26274433">Precursor::PQD</a>);</div>
<div class="line"><a name="l01798"></a><span class="lineno"> 1798</span>&#160;          }</div>
<div class="line"><a name="l01799"></a><span class="lineno"> 1799</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01800"></a><span class="lineno"> 1800</span>&#160;            warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01801"></a><span class="lineno"> 1801</span>&#160;        }</div>
<div class="line"><a name="l01802"></a><span class="lineno"> 1802</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01803"></a><span class="lineno"> 1803</span>&#160;        {</div>
<div class="line"><a name="l01804"></a><span class="lineno"> 1804</span>&#160;          <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000245&quot;</span>) <span class="comment">//charge stripping</span></div>
<div class="line"><a name="l01805"></a><span class="lineno"> 1805</span>&#160;          {</div>
<div class="line"><a name="l01806"></a><span class="lineno"> 1806</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01807"></a><span class="lineno"> 1807</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;charge stripping&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;true&quot;</span>));</div>
<div class="line"><a name="l01808"></a><span class="lineno"> 1808</span>&#160;          }</div>
<div class="line"><a name="l01809"></a><span class="lineno"> 1809</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000045&quot;</span>) <span class="comment">//collision energy (ev)</span></div>
<div class="line"><a name="l01810"></a><span class="lineno"> 1810</span>&#160;          {</div>
<div class="line"><a name="l01811"></a><span class="lineno"> 1811</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01812"></a><span class="lineno"> 1812</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;collision energy&quot;</span>, termValue);</div>
<div class="line"><a name="l01813"></a><span class="lineno"> 1813</span>&#160;          }</div>
<div class="line"><a name="l01814"></a><span class="lineno"> 1814</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000412&quot;</span>) <span class="comment">//buffer gas</span></div>
<div class="line"><a name="l01815"></a><span class="lineno"> 1815</span>&#160;          {</div>
<div class="line"><a name="l01816"></a><span class="lineno"> 1816</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01817"></a><span class="lineno"> 1817</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;buffer gas&quot;</span>, termValue);</div>
<div class="line"><a name="l01818"></a><span class="lineno"> 1818</span>&#160;          }</div>
<div class="line"><a name="l01819"></a><span class="lineno"> 1819</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000419&quot;</span>) <span class="comment">//collision gas</span></div>
<div class="line"><a name="l01820"></a><span class="lineno"> 1820</span>&#160;          {</div>
<div class="line"><a name="l01821"></a><span class="lineno"> 1821</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01822"></a><span class="lineno"> 1822</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;collision gas&quot;</span>, termValue);</div>
<div class="line"><a name="l01823"></a><span class="lineno"> 1823</span>&#160;          }</div>
<div class="line"><a name="l01824"></a><span class="lineno"> 1824</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000509&quot;</span>) <span class="comment">//activation energy (ev)</span></div>
<div class="line"><a name="l01825"></a><span class="lineno"> 1825</span>&#160;          {</div>
<div class="line"><a name="l01826"></a><span class="lineno"> 1826</span>&#160;            chromatogram_.getPrecursor().setActivationEnergy(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01827"></a><span class="lineno"> 1827</span>&#160;          }</div>
<div class="line"><a name="l01828"></a><span class="lineno"> 1828</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000138&quot;</span>) <span class="comment">//percent collision energy</span></div>
<div class="line"><a name="l01829"></a><span class="lineno"> 1829</span>&#160;          {</div>
<div class="line"><a name="l01830"></a><span class="lineno"> 1830</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01831"></a><span class="lineno"> 1831</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;percent collision energy&quot;</span>, termValue);</div>
<div class="line"><a name="l01832"></a><span class="lineno"> 1832</span>&#160;          }</div>
<div class="line"><a name="l01833"></a><span class="lineno"> 1833</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000869&quot;</span>) <span class="comment">//collision gas pressure</span></div>
<div class="line"><a name="l01834"></a><span class="lineno"> 1834</span>&#160;          {</div>
<div class="line"><a name="l01835"></a><span class="lineno"> 1835</span>&#160;            <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01836"></a><span class="lineno"> 1836</span>&#160;            chromatogram_.getPrecursor().setMetaValue(<span class="stringliteral">&quot;collision gas pressure&quot;</span>, termValue);</div>
<div class="line"><a name="l01837"></a><span class="lineno"> 1837</span>&#160;          }</div>
<div class="line"><a name="l01838"></a><span class="lineno"> 1838</span>&#160;          <span class="comment">//dissociation method</span></div>
<div class="line"><a name="l01839"></a><span class="lineno"> 1839</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000044&quot;</span>) <span class="comment">//dissociation method</span></div>
<div class="line"><a name="l01840"></a><span class="lineno"> 1840</span>&#160;          {</div>
<div class="line"><a name="l01841"></a><span class="lineno"> 1841</span>&#160;            <span class="comment">//nothing to do here</span></div>
<div class="line"><a name="l01842"></a><span class="lineno"> 1842</span>&#160;          }</div>
<div class="line"><a name="l01843"></a><span class="lineno"> 1843</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000133&quot;</span>) <span class="comment">//collision-induced dissociation</span></div>
<div class="line"><a name="l01844"></a><span class="lineno"> 1844</span>&#160;          {</div>
<div class="line"><a name="l01845"></a><span class="lineno"> 1845</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab20b009dfccc7838ba06622a9d53daff">Precursor::CID</a>);</div>
<div class="line"><a name="l01846"></a><span class="lineno"> 1846</span>&#160;          }</div>
<div class="line"><a name="l01847"></a><span class="lineno"> 1847</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000134&quot;</span>) <span class="comment">//plasma desorption</span></div>
<div class="line"><a name="l01848"></a><span class="lineno"> 1848</span>&#160;          {</div>
<div class="line"><a name="l01849"></a><span class="lineno"> 1849</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1aefbc069e0ac4cd293f3ba527bec2befe">Precursor::PD</a>);</div>
<div class="line"><a name="l01850"></a><span class="lineno"> 1850</span>&#160;          }</div>
<div class="line"><a name="l01851"></a><span class="lineno"> 1851</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000135&quot;</span>) <span class="comment">//post-source decay</span></div>
<div class="line"><a name="l01852"></a><span class="lineno"> 1852</span>&#160;          {</div>
<div class="line"><a name="l01853"></a><span class="lineno"> 1853</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a7d2afca1f43e915528abd513b30b7a55">Precursor::PSD</a>);</div>
<div class="line"><a name="l01854"></a><span class="lineno"> 1854</span>&#160;          }</div>
<div class="line"><a name="l01855"></a><span class="lineno"> 1855</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000136&quot;</span>) <span class="comment">//surface-induced dissociation</span></div>
<div class="line"><a name="l01856"></a><span class="lineno"> 1856</span>&#160;          {</div>
<div class="line"><a name="l01857"></a><span class="lineno"> 1857</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab2fca50c5baefb10e5ecdc553e372586">Precursor::SID</a>);</div>
<div class="line"><a name="l01858"></a><span class="lineno"> 1858</span>&#160;          }</div>
<div class="line"><a name="l01859"></a><span class="lineno"> 1859</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000242&quot;</span>) <span class="comment">//blackbody infrared radiative dissociation</span></div>
<div class="line"><a name="l01860"></a><span class="lineno"> 1860</span>&#160;          {</div>
<div class="line"><a name="l01861"></a><span class="lineno"> 1861</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a3901fa9d6f534ab0c36a34a0850dffa0">Precursor::BIRD</a>);</div>
<div class="line"><a name="l01862"></a><span class="lineno"> 1862</span>&#160;          }</div>
<div class="line"><a name="l01863"></a><span class="lineno"> 1863</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000250&quot;</span>) <span class="comment">//electron capture dissociation</span></div>
<div class="line"><a name="l01864"></a><span class="lineno"> 1864</span>&#160;          {</div>
<div class="line"><a name="l01865"></a><span class="lineno"> 1865</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a2634661cb45dc1d0f135daebb5fa118b">Precursor::ECD</a>);</div>
<div class="line"><a name="l01866"></a><span class="lineno"> 1866</span>&#160;          }</div>
<div class="line"><a name="l01867"></a><span class="lineno"> 1867</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000262&quot;</span>) <span class="comment">//infrared multiphoton dissociation</span></div>
<div class="line"><a name="l01868"></a><span class="lineno"> 1868</span>&#160;          {</div>
<div class="line"><a name="l01869"></a><span class="lineno"> 1869</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a8c41c05a63a15c5d188d02f6f4db4303">Precursor::IMD</a>);</div>
<div class="line"><a name="l01870"></a><span class="lineno"> 1870</span>&#160;          }</div>
<div class="line"><a name="l01871"></a><span class="lineno"> 1871</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000282&quot;</span>) <span class="comment">//sustained off-resonance irradiation</span></div>
<div class="line"><a name="l01872"></a><span class="lineno"> 1872</span>&#160;          {</div>
<div class="line"><a name="l01873"></a><span class="lineno"> 1873</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a0ce1e0457af4bc9ab4bd841128c6ea84">Precursor::SORI</a>);</div>
<div class="line"><a name="l01874"></a><span class="lineno"> 1874</span>&#160;          }</div>
<div class="line"><a name="l01875"></a><span class="lineno"> 1875</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000422&quot;</span>) <span class="comment">//high-energy collision-induced dissociation</span></div>
<div class="line"><a name="l01876"></a><span class="lineno"> 1876</span>&#160;          {</div>
<div class="line"><a name="l01877"></a><span class="lineno"> 1877</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a1bf627bed7951e975a31ba7033786d05">Precursor::HCID</a>);</div>
<div class="line"><a name="l01878"></a><span class="lineno"> 1878</span>&#160;          }</div>
<div class="line"><a name="l01879"></a><span class="lineno"> 1879</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000433&quot;</span>) <span class="comment">//low-energy collision-induced dissociation</span></div>
<div class="line"><a name="l01880"></a><span class="lineno"> 1880</span>&#160;          {</div>
<div class="line"><a name="l01881"></a><span class="lineno"> 1881</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4437a3dbac928dd5e3ee699f931bd355">Precursor::LCID</a>);</div>
<div class="line"><a name="l01882"></a><span class="lineno"> 1882</span>&#160;          }</div>
<div class="line"><a name="l01883"></a><span class="lineno"> 1883</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000435&quot;</span>) <span class="comment">//photodissociation</span></div>
<div class="line"><a name="l01884"></a><span class="lineno"> 1884</span>&#160;          {</div>
<div class="line"><a name="l01885"></a><span class="lineno"> 1885</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4187f6dae406f24b70e3c34a7448b15f">Precursor::PHD</a>);</div>
<div class="line"><a name="l01886"></a><span class="lineno"> 1886</span>&#160;          }</div>
<div class="line"><a name="l01887"></a><span class="lineno"> 1887</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000598&quot;</span>) <span class="comment">//electron transfer dissociation</span></div>
<div class="line"><a name="l01888"></a><span class="lineno"> 1888</span>&#160;          {</div>
<div class="line"><a name="l01889"></a><span class="lineno"> 1889</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a56a28ad07746c6bae402cc7d7ec0839a">Precursor::ETD</a>);</div>
<div class="line"><a name="l01890"></a><span class="lineno"> 1890</span>&#160;          }</div>
<div class="line"><a name="l01891"></a><span class="lineno"> 1891</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000599&quot;</span>) <span class="comment">//pulsed q dissociation</span></div>
<div class="line"><a name="l01892"></a><span class="lineno"> 1892</span>&#160;          {</div>
<div class="line"><a name="l01893"></a><span class="lineno"> 1893</span>&#160;            chromatogram_.getPrecursor().getActivationMethods().insert(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a22a843b242764a6b3b320c1b26274433">Precursor::PQD</a>);</div>
<div class="line"><a name="l01894"></a><span class="lineno"> 1894</span>&#160;          }</div>
<div class="line"><a name="l01895"></a><span class="lineno"> 1895</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01896"></a><span class="lineno"> 1896</span>&#160;            warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01897"></a><span class="lineno"> 1897</span>&#160;        }</div>
<div class="line"><a name="l01898"></a><span class="lineno"> 1898</span>&#160;      }</div>
<div class="line"><a name="l01899"></a><span class="lineno"> 1899</span>&#160;      <span class="comment">//------------------------- isolationWindow ----------------------------</span></div>
<div class="line"><a name="l01900"></a><span class="lineno"> 1900</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;isolationWindow&quot;</span>)</div>
<div class="line"><a name="l01901"></a><span class="lineno"> 1901</span>&#160;      {</div>
<div class="line"><a name="l01902"></a><span class="lineno"> 1902</span>&#160;        <span class="keywordflow">if</span> (parent_parent_tag == <span class="stringliteral">&quot;precursor&quot;</span>)</div>
<div class="line"><a name="l01903"></a><span class="lineno"> 1903</span>&#160;        {</div>
<div class="line"><a name="l01904"></a><span class="lineno"> 1904</span>&#160;          <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000827&quot;</span>) <span class="comment">//isolation window target m/z</span></div>
<div class="line"><a name="l01905"></a><span class="lineno"> 1905</span>&#160;          {</div>
<div class="line"><a name="l01906"></a><span class="lineno"> 1906</span>&#160;            <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01907"></a><span class="lineno"> 1907</span>&#160;            {</div>
<div class="line"><a name="l01908"></a><span class="lineno"> 1908</span>&#160;              spec_.getPrecursors().back().setMZ(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01909"></a><span class="lineno"> 1909</span>&#160;            }</div>
<div class="line"><a name="l01910"></a><span class="lineno"> 1910</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01911"></a><span class="lineno"> 1911</span>&#160;            {</div>
<div class="line"><a name="l01912"></a><span class="lineno"> 1912</span>&#160;              chromatogram_.getPrecursor().setMZ(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01913"></a><span class="lineno"> 1913</span>&#160;            }</div>
<div class="line"><a name="l01914"></a><span class="lineno"> 1914</span>&#160;          }</div>
<div class="line"><a name="l01915"></a><span class="lineno"> 1915</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000828&quot;</span>) <span class="comment">//isolation window lower offset</span></div>
<div class="line"><a name="l01916"></a><span class="lineno"> 1916</span>&#160;          {</div>
<div class="line"><a name="l01917"></a><span class="lineno"> 1917</span>&#160;            <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01918"></a><span class="lineno"> 1918</span>&#160;            {</div>
<div class="line"><a name="l01919"></a><span class="lineno"> 1919</span>&#160;              spec_.getPrecursors().back().setIsolationWindowLowerOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01920"></a><span class="lineno"> 1920</span>&#160;            }</div>
<div class="line"><a name="l01921"></a><span class="lineno"> 1921</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01922"></a><span class="lineno"> 1922</span>&#160;            {</div>
<div class="line"><a name="l01923"></a><span class="lineno"> 1923</span>&#160;              chromatogram_.getPrecursor().setIsolationWindowLowerOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01924"></a><span class="lineno"> 1924</span>&#160;            }</div>
<div class="line"><a name="l01925"></a><span class="lineno"> 1925</span>&#160;          }</div>
<div class="line"><a name="l01926"></a><span class="lineno"> 1926</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000829&quot;</span>) <span class="comment">//isolation window upper offset</span></div>
<div class="line"><a name="l01927"></a><span class="lineno"> 1927</span>&#160;          {</div>
<div class="line"><a name="l01928"></a><span class="lineno"> 1928</span>&#160;            <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01929"></a><span class="lineno"> 1929</span>&#160;            {</div>
<div class="line"><a name="l01930"></a><span class="lineno"> 1930</span>&#160;              spec_.getPrecursors().back().setIsolationWindowUpperOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01931"></a><span class="lineno"> 1931</span>&#160;            }</div>
<div class="line"><a name="l01932"></a><span class="lineno"> 1932</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01933"></a><span class="lineno"> 1933</span>&#160;            {</div>
<div class="line"><a name="l01934"></a><span class="lineno"> 1934</span>&#160;              chromatogram_.getPrecursor().setIsolationWindowUpperOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01935"></a><span class="lineno"> 1935</span>&#160;            }</div>
<div class="line"><a name="l01936"></a><span class="lineno"> 1936</span>&#160;          }</div>
<div class="line"><a name="l01937"></a><span class="lineno"> 1937</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01938"></a><span class="lineno"> 1938</span>&#160;            warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01939"></a><span class="lineno"> 1939</span>&#160;        }</div>
<div class="line"><a name="l01940"></a><span class="lineno"> 1940</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_parent_tag == <span class="stringliteral">&quot;product&quot;</span>)</div>
<div class="line"><a name="l01941"></a><span class="lineno"> 1941</span>&#160;        {</div>
<div class="line"><a name="l01942"></a><span class="lineno"> 1942</span>&#160;          <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000827&quot;</span>) <span class="comment">//isolation window target m/z</span></div>
<div class="line"><a name="l01943"></a><span class="lineno"> 1943</span>&#160;          {</div>
<div class="line"><a name="l01944"></a><span class="lineno"> 1944</span>&#160;            <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01945"></a><span class="lineno"> 1945</span>&#160;            {</div>
<div class="line"><a name="l01946"></a><span class="lineno"> 1946</span>&#160;              spec_.getProducts().back().setMZ(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01947"></a><span class="lineno"> 1947</span>&#160;            }</div>
<div class="line"><a name="l01948"></a><span class="lineno"> 1948</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01949"></a><span class="lineno"> 1949</span>&#160;            {</div>
<div class="line"><a name="l01950"></a><span class="lineno"> 1950</span>&#160;              chromatogram_.getProduct().setMZ(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01951"></a><span class="lineno"> 1951</span>&#160;            }</div>
<div class="line"><a name="l01952"></a><span class="lineno"> 1952</span>&#160;          }</div>
<div class="line"><a name="l01953"></a><span class="lineno"> 1953</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000829&quot;</span>) <span class="comment">//isolation window upper offset</span></div>
<div class="line"><a name="l01954"></a><span class="lineno"> 1954</span>&#160;          {</div>
<div class="line"><a name="l01955"></a><span class="lineno"> 1955</span>&#160;            <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01956"></a><span class="lineno"> 1956</span>&#160;            {</div>
<div class="line"><a name="l01957"></a><span class="lineno"> 1957</span>&#160;              spec_.getProducts().back().setIsolationWindowUpperOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01958"></a><span class="lineno"> 1958</span>&#160;            }</div>
<div class="line"><a name="l01959"></a><span class="lineno"> 1959</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01960"></a><span class="lineno"> 1960</span>&#160;            {</div>
<div class="line"><a name="l01961"></a><span class="lineno"> 1961</span>&#160;              chromatogram_.getProduct().setIsolationWindowUpperOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01962"></a><span class="lineno"> 1962</span>&#160;            }</div>
<div class="line"><a name="l01963"></a><span class="lineno"> 1963</span>&#160;          }</div>
<div class="line"><a name="l01964"></a><span class="lineno"> 1964</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000828&quot;</span>) <span class="comment">//isolation window lower offset</span></div>
<div class="line"><a name="l01965"></a><span class="lineno"> 1965</span>&#160;          {</div>
<div class="line"><a name="l01966"></a><span class="lineno"> 1966</span>&#160;            <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l01967"></a><span class="lineno"> 1967</span>&#160;            {</div>
<div class="line"><a name="l01968"></a><span class="lineno"> 1968</span>&#160;              spec_.getProducts().back().setIsolationWindowLowerOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01969"></a><span class="lineno"> 1969</span>&#160;            }</div>
<div class="line"><a name="l01970"></a><span class="lineno"> 1970</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01971"></a><span class="lineno"> 1971</span>&#160;            {</div>
<div class="line"><a name="l01972"></a><span class="lineno"> 1972</span>&#160;              chromatogram_.getProduct().setIsolationWindowLowerOffset(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l01973"></a><span class="lineno"> 1973</span>&#160;            }</div>
<div class="line"><a name="l01974"></a><span class="lineno"> 1974</span>&#160;          }</div>
<div class="line"><a name="l01975"></a><span class="lineno"> 1975</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l01976"></a><span class="lineno"> 1976</span>&#160;            warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01977"></a><span class="lineno"> 1977</span>&#160;        }</div>
<div class="line"><a name="l01978"></a><span class="lineno"> 1978</span>&#160;      }</div>
<div class="line"><a name="l01979"></a><span class="lineno"> 1979</span>&#160;      <span class="comment">//------------------------- scanList ----------------------------</span></div>
<div class="line"><a name="l01980"></a><span class="lineno"> 1980</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;scanList&quot;</span>)</div>
<div class="line"><a name="l01981"></a><span class="lineno"> 1981</span>&#160;      {</div>
<div class="line"><a name="l01982"></a><span class="lineno"> 1982</span>&#160;        <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000570&quot;</span>)) <span class="comment">//method of combination as string</span></div>
<div class="line"><a name="l01983"></a><span class="lineno"> 1983</span>&#160;        {</div>
<div class="line"><a name="l01984"></a><span class="lineno"> 1984</span>&#160;          spec_.getAcquisitionInfo().setMethodOfCombination(cv_.getTerm(accession).name);</div>
<div class="line"><a name="l01985"></a><span class="lineno"> 1985</span>&#160;        }</div>
<div class="line"><a name="l01986"></a><span class="lineno"> 1986</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01987"></a><span class="lineno"> 1987</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l01988"></a><span class="lineno"> 1988</span>&#160;      }</div>
<div class="line"><a name="l01989"></a><span class="lineno"> 1989</span>&#160;      <span class="comment">//------------------------- scan ----------------------------</span></div>
<div class="line"><a name="l01990"></a><span class="lineno"> 1990</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;scan&quot;</span>)</div>
<div class="line"><a name="l01991"></a><span class="lineno"> 1991</span>&#160;      {</div>
<div class="line"><a name="l01992"></a><span class="lineno"> 1992</span>&#160;        <span class="comment">//scan attributes</span></div>
<div class="line"><a name="l01993"></a><span class="lineno"> 1993</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000502&quot;</span>) <span class="comment">//dwell time</span></div>
<div class="line"><a name="l01994"></a><span class="lineno"> 1994</span>&#160;        {</div>
<div class="line"><a name="l01995"></a><span class="lineno"> 1995</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l01996"></a><span class="lineno"> 1996</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;dwell time&quot;</span>, termValue);</div>
<div class="line"><a name="l01997"></a><span class="lineno"> 1997</span>&#160;        }</div>
<div class="line"><a name="l01998"></a><span class="lineno"> 1998</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000011&quot;</span>) <span class="comment">//mass resolution</span></div>
<div class="line"><a name="l01999"></a><span class="lineno"> 1999</span>&#160;        {</div>
<div class="line"><a name="l02000"></a><span class="lineno"> 2000</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02001"></a><span class="lineno"> 2001</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;mass resolution&quot;</span>, termValue);</div>
<div class="line"><a name="l02002"></a><span class="lineno"> 2002</span>&#160;        }</div>
<div class="line"><a name="l02003"></a><span class="lineno"> 2003</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000015&quot;</span>) <span class="comment">//scan rate</span></div>
<div class="line"><a name="l02004"></a><span class="lineno"> 2004</span>&#160;        {</div>
<div class="line"><a name="l02005"></a><span class="lineno"> 2005</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02006"></a><span class="lineno"> 2006</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;scan rate&quot;</span>, termValue);</div>
<div class="line"><a name="l02007"></a><span class="lineno"> 2007</span>&#160;        }</div>
<div class="line"><a name="l02008"></a><span class="lineno"> 2008</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000016&quot;</span>) <span class="comment">//scan start time</span></div>
<div class="line"><a name="l02009"></a><span class="lineno"> 2009</span>&#160;        {</div>
<div class="line"><a name="l02010"></a><span class="lineno"> 2010</span>&#160;          <span class="keywordflow">if</span> (unit_accession == <span class="stringliteral">&quot;UO:0000031&quot;</span>) <span class="comment">//minutes</span></div>
<div class="line"><a name="l02011"></a><span class="lineno"> 2011</span>&#160;          {</div>
<div class="line"><a name="l02012"></a><span class="lineno"> 2012</span>&#160;            spec_.setRT(60.0 * value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02013"></a><span class="lineno"> 2013</span>&#160;          }</div>
<div class="line"><a name="l02014"></a><span class="lineno"> 2014</span>&#160;          <span class="keywordflow">else</span> <span class="comment">//seconds</span></div>
<div class="line"><a name="l02015"></a><span class="lineno"> 2015</span>&#160;          {</div>
<div class="line"><a name="l02016"></a><span class="lineno"> 2016</span>&#160;            spec_.setRT(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02017"></a><span class="lineno"> 2017</span>&#160;          }</div>
<div class="line"><a name="l02018"></a><span class="lineno"> 2018</span>&#160;          <span class="keywordflow">if</span> (options_.hasRTRange() &amp;&amp; !options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;1&gt;</a>(spec_.getRT())))</div>
<div class="line"><a name="l02019"></a><span class="lineno"> 2019</span>&#160;          {</div>
<div class="line"><a name="l02020"></a><span class="lineno"> 2020</span>&#160;            skip_spectrum_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l02021"></a><span class="lineno"> 2021</span>&#160;          }</div>
<div class="line"><a name="l02022"></a><span class="lineno"> 2022</span>&#160;        }</div>
<div class="line"><a name="l02023"></a><span class="lineno"> 2023</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000826&quot;</span>) <span class="comment">//elution time</span></div>
<div class="line"><a name="l02024"></a><span class="lineno"> 2024</span>&#160;        {</div>
<div class="line"><a name="l02025"></a><span class="lineno"> 2025</span>&#160;          <span class="keywordflow">if</span> (unit_accession == <span class="stringliteral">&quot;UO:0000031&quot;</span>) <span class="comment">//minutes</span></div>
<div class="line"><a name="l02026"></a><span class="lineno"> 2026</span>&#160;          {</div>
<div class="line"><a name="l02027"></a><span class="lineno"> 2027</span>&#160;            spec_.setMetaValue(<span class="stringliteral">&quot;elution time (seconds)&quot;</span>, 60.0 * value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02028"></a><span class="lineno"> 2028</span>&#160;          }</div>
<div class="line"><a name="l02029"></a><span class="lineno"> 2029</span>&#160;          <span class="keywordflow">else</span> <span class="comment">//seconds</span></div>
<div class="line"><a name="l02030"></a><span class="lineno"> 2030</span>&#160;          {</div>
<div class="line"><a name="l02031"></a><span class="lineno"> 2031</span>&#160;            spec_.setMetaValue(<span class="stringliteral">&quot;elution time (seconds)&quot;</span>, value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02032"></a><span class="lineno"> 2032</span>&#160;          }</div>
<div class="line"><a name="l02033"></a><span class="lineno"> 2033</span>&#160;        }</div>
<div class="line"><a name="l02034"></a><span class="lineno"> 2034</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000512&quot;</span>) <span class="comment">//filter string</span></div>
<div class="line"><a name="l02035"></a><span class="lineno"> 2035</span>&#160;        {</div>
<div class="line"><a name="l02036"></a><span class="lineno"> 2036</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02037"></a><span class="lineno"> 2037</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;filter string&quot;</span>, termValue);</div>
<div class="line"><a name="l02038"></a><span class="lineno"> 2038</span>&#160;        }</div>
<div class="line"><a name="l02039"></a><span class="lineno"> 2039</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000803&quot;</span>) <span class="comment">//analyzer scan offset</span></div>
<div class="line"><a name="l02040"></a><span class="lineno"> 2040</span>&#160;        {</div>
<div class="line"><a name="l02041"></a><span class="lineno"> 2041</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02042"></a><span class="lineno"> 2042</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;analyzer scan offset&quot;</span>, termValue);</div>
<div class="line"><a name="l02043"></a><span class="lineno"> 2043</span>&#160;        }</div>
<div class="line"><a name="l02044"></a><span class="lineno"> 2044</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000616&quot;</span>) <span class="comment">//preset scan configuration</span></div>
<div class="line"><a name="l02045"></a><span class="lineno"> 2045</span>&#160;        {</div>
<div class="line"><a name="l02046"></a><span class="lineno"> 2046</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02047"></a><span class="lineno"> 2047</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;preset scan configuration&quot;</span>, termValue);</div>
<div class="line"><a name="l02048"></a><span class="lineno"> 2048</span>&#160;        }</div>
<div class="line"><a name="l02049"></a><span class="lineno"> 2049</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000800&quot;</span>) <span class="comment">//mass resolving power</span></div>
<div class="line"><a name="l02050"></a><span class="lineno"> 2050</span>&#160;        {</div>
<div class="line"><a name="l02051"></a><span class="lineno"> 2051</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02052"></a><span class="lineno"> 2052</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;mass resolving power&quot;</span>, termValue);</div>
<div class="line"><a name="l02053"></a><span class="lineno"> 2053</span>&#160;        }</div>
<div class="line"><a name="l02054"></a><span class="lineno"> 2054</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000880&quot;</span>) <span class="comment">//interchannel delay</span></div>
<div class="line"><a name="l02055"></a><span class="lineno"> 2055</span>&#160;        {</div>
<div class="line"><a name="l02056"></a><span class="lineno"> 2056</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02057"></a><span class="lineno"> 2057</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;interchannel delay&quot;</span>, termValue);</div>
<div class="line"><a name="l02058"></a><span class="lineno"> 2058</span>&#160;        }</div>
<div class="line"><a name="l02059"></a><span class="lineno"> 2059</span>&#160;        <span class="comment">//scan direction</span></div>
<div class="line"><a name="l02060"></a><span class="lineno"> 2060</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000092&quot;</span>) <span class="comment">//decreasing m/z scan</span></div>
<div class="line"><a name="l02061"></a><span class="lineno"> 2061</span>&#160;        {</div>
<div class="line"><a name="l02062"></a><span class="lineno"> 2062</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02063"></a><span class="lineno"> 2063</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;scan direction&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;decreasing&quot;</span>));</div>
<div class="line"><a name="l02064"></a><span class="lineno"> 2064</span>&#160;        }</div>
<div class="line"><a name="l02065"></a><span class="lineno"> 2065</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000093&quot;</span>) <span class="comment">//increasing m/z scan</span></div>
<div class="line"><a name="l02066"></a><span class="lineno"> 2066</span>&#160;        {</div>
<div class="line"><a name="l02067"></a><span class="lineno"> 2067</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02068"></a><span class="lineno"> 2068</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;scan direction&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;increasing&quot;</span>));</div>
<div class="line"><a name="l02069"></a><span class="lineno"> 2069</span>&#160;        }</div>
<div class="line"><a name="l02070"></a><span class="lineno"> 2070</span>&#160;        <span class="comment">//scan law</span></div>
<div class="line"><a name="l02071"></a><span class="lineno"> 2071</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000094&quot;</span>) <span class="comment">//scan law: exponential</span></div>
<div class="line"><a name="l02072"></a><span class="lineno"> 2072</span>&#160;        {</div>
<div class="line"><a name="l02073"></a><span class="lineno"> 2073</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02074"></a><span class="lineno"> 2074</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;scan law&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;exponential&quot;</span>));</div>
<div class="line"><a name="l02075"></a><span class="lineno"> 2075</span>&#160;        }</div>
<div class="line"><a name="l02076"></a><span class="lineno"> 2076</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000095&quot;</span>) <span class="comment">//scan law: linear</span></div>
<div class="line"><a name="l02077"></a><span class="lineno"> 2077</span>&#160;        {</div>
<div class="line"><a name="l02078"></a><span class="lineno"> 2078</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02079"></a><span class="lineno"> 2079</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;scan law&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;linear&quot;</span>));</div>
<div class="line"><a name="l02080"></a><span class="lineno"> 2080</span>&#160;        }</div>
<div class="line"><a name="l02081"></a><span class="lineno"> 2081</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000096&quot;</span>) <span class="comment">//scan law: quadratic</span></div>
<div class="line"><a name="l02082"></a><span class="lineno"> 2082</span>&#160;        {</div>
<div class="line"><a name="l02083"></a><span class="lineno"> 2083</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02084"></a><span class="lineno"> 2084</span>&#160;          spec_.setMetaValue(<span class="stringliteral">&quot;scan law&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;quadratic&quot;</span>));</div>
<div class="line"><a name="l02085"></a><span class="lineno"> 2085</span>&#160;        }</div>
<div class="line"><a name="l02086"></a><span class="lineno"> 2086</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02087"></a><span class="lineno"> 2087</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02088"></a><span class="lineno"> 2088</span>&#160;      }</div>
<div class="line"><a name="l02089"></a><span class="lineno"> 2089</span>&#160;      <span class="comment">//------------------------- contact ----------------------------</span></div>
<div class="line"><a name="l02090"></a><span class="lineno"> 2090</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;contact&quot;</span>)</div>
<div class="line"><a name="l02091"></a><span class="lineno"> 2091</span>&#160;      {</div>
<div class="line"><a name="l02092"></a><span class="lineno"> 2092</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000586&quot;</span>) <span class="comment">//contact name</span></div>
<div class="line"><a name="l02093"></a><span class="lineno"> 2093</span>&#160;        {</div>
<div class="line"><a name="l02094"></a><span class="lineno"> 2094</span>&#160;          exp_-&gt;getContacts().back().setName(value);</div>
<div class="line"><a name="l02095"></a><span class="lineno"> 2095</span>&#160;        }</div>
<div class="line"><a name="l02096"></a><span class="lineno"> 2096</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000587&quot;</span>) <span class="comment">//contact address</span></div>
<div class="line"><a name="l02097"></a><span class="lineno"> 2097</span>&#160;        {</div>
<div class="line"><a name="l02098"></a><span class="lineno"> 2098</span>&#160;          exp_-&gt;getContacts().back().setAddress(value);</div>
<div class="line"><a name="l02099"></a><span class="lineno"> 2099</span>&#160;        }</div>
<div class="line"><a name="l02100"></a><span class="lineno"> 2100</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000588&quot;</span>) <span class="comment">//contact URL</span></div>
<div class="line"><a name="l02101"></a><span class="lineno"> 2101</span>&#160;        {</div>
<div class="line"><a name="l02102"></a><span class="lineno"> 2102</span>&#160;          exp_-&gt;getContacts().back().setURL(value);</div>
<div class="line"><a name="l02103"></a><span class="lineno"> 2103</span>&#160;        }</div>
<div class="line"><a name="l02104"></a><span class="lineno"> 2104</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000589&quot;</span>) <span class="comment">//contact email</span></div>
<div class="line"><a name="l02105"></a><span class="lineno"> 2105</span>&#160;        {</div>
<div class="line"><a name="l02106"></a><span class="lineno"> 2106</span>&#160;          exp_-&gt;getContacts().back().setEmail(value);</div>
<div class="line"><a name="l02107"></a><span class="lineno"> 2107</span>&#160;        }</div>
<div class="line"><a name="l02108"></a><span class="lineno"> 2108</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000590&quot;</span>) <span class="comment">//contact organization</span></div>
<div class="line"><a name="l02109"></a><span class="lineno"> 2109</span>&#160;        {</div>
<div class="line"><a name="l02110"></a><span class="lineno"> 2110</span>&#160;          exp_-&gt;getContacts().back().setInstitution(value);</div>
<div class="line"><a name="l02111"></a><span class="lineno"> 2111</span>&#160;        }</div>
<div class="line"><a name="l02112"></a><span class="lineno"> 2112</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02113"></a><span class="lineno"> 2113</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02114"></a><span class="lineno"> 2114</span>&#160;      }</div>
<div class="line"><a name="l02115"></a><span class="lineno"> 2115</span>&#160;      <span class="comment">//------------------------- sourceFile ----------------------------</span></div>
<div class="line"><a name="l02116"></a><span class="lineno"> 2116</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;sourceFile&quot;</span>)</div>
<div class="line"><a name="l02117"></a><span class="lineno"> 2117</span>&#160;      {</div>
<div class="line"><a name="l02118"></a><span class="lineno"> 2118</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000569&quot;</span>) <span class="comment">//SHA-1 checksum</span></div>
<div class="line"><a name="l02119"></a><span class="lineno"> 2119</span>&#160;        {</div>
<div class="line"><a name="l02120"></a><span class="lineno"> 2120</span>&#160;          source_files_[current_id_].setChecksum(value, <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">SourceFile::SHA1</a>);</div>
<div class="line"><a name="l02121"></a><span class="lineno"> 2121</span>&#160;        }</div>
<div class="line"><a name="l02122"></a><span class="lineno"> 2122</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000568&quot;</span>) <span class="comment">//MD5 checksum</span></div>
<div class="line"><a name="l02123"></a><span class="lineno"> 2123</span>&#160;        {</div>
<div class="line"><a name="l02124"></a><span class="lineno"> 2124</span>&#160;          source_files_[current_id_].setChecksum(value, <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5ad37464787fa5104b0ae6bea524eec264">SourceFile::MD5</a>);</div>
<div class="line"><a name="l02125"></a><span class="lineno"> 2125</span>&#160;        }</div>
<div class="line"><a name="l02126"></a><span class="lineno"> 2126</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000560&quot;</span>)) <span class="comment">//source file type as string</span></div>
<div class="line"><a name="l02127"></a><span class="lineno"> 2127</span>&#160;        {</div>
<div class="line"><a name="l02128"></a><span class="lineno"> 2128</span>&#160;          source_files_[current_id_].setFileType(cv_.getTerm(accession).name);</div>
<div class="line"><a name="l02129"></a><span class="lineno"> 2129</span>&#160;        }</div>
<div class="line"><a name="l02130"></a><span class="lineno"> 2130</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000767&quot;</span>)) <span class="comment">//native spectrum identifier format as string</span></div>
<div class="line"><a name="l02131"></a><span class="lineno"> 2131</span>&#160;        {</div>
<div class="line"><a name="l02132"></a><span class="lineno"> 2132</span>&#160;          source_files_[current_id_].setNativeIDType(cv_.getTerm(accession).name);</div>
<div class="line"><a name="l02133"></a><span class="lineno"> 2133</span>&#160;        }</div>
<div class="line"><a name="l02134"></a><span class="lineno"> 2134</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02135"></a><span class="lineno"> 2135</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02136"></a><span class="lineno"> 2136</span>&#160;      }</div>
<div class="line"><a name="l02137"></a><span class="lineno"> 2137</span>&#160;      <span class="comment">//------------------------- sample ----------------------------</span></div>
<div class="line"><a name="l02138"></a><span class="lineno"> 2138</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;sample&quot;</span>)</div>
<div class="line"><a name="l02139"></a><span class="lineno"> 2139</span>&#160;      {</div>
<div class="line"><a name="l02140"></a><span class="lineno"> 2140</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000004&quot;</span>) <span class="comment">//sample mass (gram)</span></div>
<div class="line"><a name="l02141"></a><span class="lineno"> 2141</span>&#160;        {</div>
<div class="line"><a name="l02142"></a><span class="lineno"> 2142</span>&#160;          samples_[current_id_].setMass(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02143"></a><span class="lineno"> 2143</span>&#160;        }</div>
<div class="line"><a name="l02144"></a><span class="lineno"> 2144</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000001&quot;</span>) <span class="comment">//sample number</span></div>
<div class="line"><a name="l02145"></a><span class="lineno"> 2145</span>&#160;        {</div>
<div class="line"><a name="l02146"></a><span class="lineno"> 2146</span>&#160;          samples_[current_id_].setNumber(value);</div>
<div class="line"><a name="l02147"></a><span class="lineno"> 2147</span>&#160;        }</div>
<div class="line"><a name="l02148"></a><span class="lineno"> 2148</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000005&quot;</span>) <span class="comment">//sample volume (milliliter)</span></div>
<div class="line"><a name="l02149"></a><span class="lineno"> 2149</span>&#160;        {</div>
<div class="line"><a name="l02150"></a><span class="lineno"> 2150</span>&#160;          samples_[current_id_].setVolume(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02151"></a><span class="lineno"> 2151</span>&#160;        }</div>
<div class="line"><a name="l02152"></a><span class="lineno"> 2152</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000006&quot;</span>) <span class="comment">//sample concentration (gram per liter)</span></div>
<div class="line"><a name="l02153"></a><span class="lineno"> 2153</span>&#160;        {</div>
<div class="line"><a name="l02154"></a><span class="lineno"> 2154</span>&#160;          samples_[current_id_].setConcentration(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02155"></a><span class="lineno"> 2155</span>&#160;        }</div>
<div class="line"><a name="l02156"></a><span class="lineno"> 2156</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000053&quot;</span>) <span class="comment">//sample batch</span></div>
<div class="line"><a name="l02157"></a><span class="lineno"> 2157</span>&#160;        {</div>
<div class="line"><a name="l02158"></a><span class="lineno"> 2158</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02159"></a><span class="lineno"> 2159</span>&#160;          samples_[current_id_].setMetaValue(<span class="stringliteral">&quot;sample batch&quot;</span>, termValue);</div>
<div class="line"><a name="l02160"></a><span class="lineno"> 2160</span>&#160;        }</div>
<div class="line"><a name="l02161"></a><span class="lineno"> 2161</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000047&quot;</span>) <span class="comment">//emulsion</span></div>
<div class="line"><a name="l02162"></a><span class="lineno"> 2162</span>&#160;        {</div>
<div class="line"><a name="l02163"></a><span class="lineno"> 2163</span>&#160;          samples_[current_id_].setState(<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a6c36859458a3b2652671a36349914666">Sample::EMULSION</a>);</div>
<div class="line"><a name="l02164"></a><span class="lineno"> 2164</span>&#160;        }</div>
<div class="line"><a name="l02165"></a><span class="lineno"> 2165</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000048&quot;</span>) <span class="comment">//gas</span></div>
<div class="line"><a name="l02166"></a><span class="lineno"> 2166</span>&#160;        {</div>
<div class="line"><a name="l02167"></a><span class="lineno"> 2167</span>&#160;          samples_[current_id_].setState(<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a9584dc4fcb96c51dda36a881a6dbb212">Sample::GAS</a>);</div>
<div class="line"><a name="l02168"></a><span class="lineno"> 2168</span>&#160;        }</div>
<div class="line"><a name="l02169"></a><span class="lineno"> 2169</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000049&quot;</span>) <span class="comment">//liquid</span></div>
<div class="line"><a name="l02170"></a><span class="lineno"> 2170</span>&#160;        {</div>
<div class="line"><a name="l02171"></a><span class="lineno"> 2171</span>&#160;          samples_[current_id_].setState(<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71aa87f9501ff2b390be1ea7d261b0d7cce">Sample::LIQUID</a>);</div>
<div class="line"><a name="l02172"></a><span class="lineno"> 2172</span>&#160;        }</div>
<div class="line"><a name="l02173"></a><span class="lineno"> 2173</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000050&quot;</span>) <span class="comment">//solid</span></div>
<div class="line"><a name="l02174"></a><span class="lineno"> 2174</span>&#160;        {</div>
<div class="line"><a name="l02175"></a><span class="lineno"> 2175</span>&#160;          samples_[current_id_].setState(<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a1b45f84e1f6603b52e5ef442836df9af">Sample::SOLID</a>);</div>
<div class="line"><a name="l02176"></a><span class="lineno"> 2176</span>&#160;        }</div>
<div class="line"><a name="l02177"></a><span class="lineno"> 2177</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000051&quot;</span>) <span class="comment">//solution</span></div>
<div class="line"><a name="l02178"></a><span class="lineno"> 2178</span>&#160;        {</div>
<div class="line"><a name="l02179"></a><span class="lineno"> 2179</span>&#160;          samples_[current_id_].setState(<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a0a57d2bc6d4da43c5fdb8c9293764d8d">Sample::SOLUTION</a>);</div>
<div class="line"><a name="l02180"></a><span class="lineno"> 2180</span>&#160;        }</div>
<div class="line"><a name="l02181"></a><span class="lineno"> 2181</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000052&quot;</span>) <span class="comment">//suspension</span></div>
<div class="line"><a name="l02182"></a><span class="lineno"> 2182</span>&#160;        {</div>
<div class="line"><a name="l02183"></a><span class="lineno"> 2183</span>&#160;          samples_[current_id_].setState(<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a67a73d64984460ab1251bea87b873aab">Sample::SUSPENSION</a>);</div>
<div class="line"><a name="l02184"></a><span class="lineno"> 2184</span>&#160;        }</div>
<div class="line"><a name="l02185"></a><span class="lineno"> 2185</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">&quot;PATO:&quot;</span>)) <span class="comment">//quality of an object</span></div>
<div class="line"><a name="l02186"></a><span class="lineno"> 2186</span>&#160;        {</div>
<div class="line"><a name="l02187"></a><span class="lineno"> 2187</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02188"></a><span class="lineno"> 2188</span>&#160;          samples_[current_id_].setMetaValue(<a class="code" href="classOpenMS_1_1String.html">String</a>(name), termValue);</div>
<div class="line"><a name="l02189"></a><span class="lineno"> 2189</span>&#160;        }</div>
<div class="line"><a name="l02190"></a><span class="lineno"> 2190</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">&quot;GO:&quot;</span>)) <span class="comment">//cellular_component</span></div>
<div class="line"><a name="l02191"></a><span class="lineno"> 2191</span>&#160;        {</div>
<div class="line"><a name="l02192"></a><span class="lineno"> 2192</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02193"></a><span class="lineno"> 2193</span>&#160;          samples_[current_id_].setMetaValue(<span class="stringliteral">&quot;GO cellular component&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(name));</div>
<div class="line"><a name="l02194"></a><span class="lineno"> 2194</span>&#160;        }</div>
<div class="line"><a name="l02195"></a><span class="lineno"> 2195</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">&quot;BTO:&quot;</span>)) <span class="comment">//brenda source tissue ontology</span></div>
<div class="line"><a name="l02196"></a><span class="lineno"> 2196</span>&#160;        {</div>
<div class="line"><a name="l02197"></a><span class="lineno"> 2197</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02198"></a><span class="lineno"> 2198</span>&#160;          samples_[current_id_].setMetaValue(<span class="stringliteral">&quot;brenda source tissue&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(name));</div>
<div class="line"><a name="l02199"></a><span class="lineno"> 2199</span>&#160;        }</div>
<div class="line"><a name="l02200"></a><span class="lineno"> 2200</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02201"></a><span class="lineno"> 2201</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02202"></a><span class="lineno"> 2202</span>&#160;      }</div>
<div class="line"><a name="l02203"></a><span class="lineno"> 2203</span>&#160;      <span class="comment">//------------------------- instrumentConfiguration ----------------------------</span></div>
<div class="line"><a name="l02204"></a><span class="lineno"> 2204</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;instrumentConfiguration&quot;</span>)</div>
<div class="line"><a name="l02205"></a><span class="lineno"> 2205</span>&#160;      {</div>
<div class="line"><a name="l02206"></a><span class="lineno"> 2206</span>&#160;        <span class="comment">//instrument model</span></div>
<div class="line"><a name="l02207"></a><span class="lineno"> 2207</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000031&quot;</span>)</div>
<div class="line"><a name="l02208"></a><span class="lineno"> 2208</span>&#160;        {</div>
<div class="line"><a name="l02209"></a><span class="lineno"> 2209</span>&#160;          <span class="comment">//unknown instrument =&gt; notthing to do</span></div>
<div class="line"><a name="l02210"></a><span class="lineno"> 2210</span>&#160;        }</div>
<div class="line"><a name="l02211"></a><span class="lineno"> 2211</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000031&quot;</span>)) <span class="comment">//instrument name as string</span></div>
<div class="line"><a name="l02212"></a><span class="lineno"> 2212</span>&#160;        {</div>
<div class="line"><a name="l02213"></a><span class="lineno"> 2213</span>&#160;          instruments_[current_id_].setName(cv_.getTerm(accession).name);</div>
<div class="line"><a name="l02214"></a><span class="lineno"> 2214</span>&#160;        }</div>
<div class="line"><a name="l02215"></a><span class="lineno"> 2215</span>&#160;        <span class="comment">//instrument attribute</span></div>
<div class="line"><a name="l02216"></a><span class="lineno"> 2216</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000529&quot;</span>) <span class="comment">//instrument serial number</span></div>
<div class="line"><a name="l02217"></a><span class="lineno"> 2217</span>&#160;        {</div>
<div class="line"><a name="l02218"></a><span class="lineno"> 2218</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02219"></a><span class="lineno"> 2219</span>&#160;          instruments_[current_id_].setMetaValue(<span class="stringliteral">&quot;instrument serial number&quot;</span>, termValue);</div>
<div class="line"><a name="l02220"></a><span class="lineno"> 2220</span>&#160;        }</div>
<div class="line"><a name="l02221"></a><span class="lineno"> 2221</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000032&quot;</span>) <span class="comment">//customization</span></div>
<div class="line"><a name="l02222"></a><span class="lineno"> 2222</span>&#160;        {</div>
<div class="line"><a name="l02223"></a><span class="lineno"> 2223</span>&#160;          instruments_[current_id_].setCustomizations(value);</div>
<div class="line"><a name="l02224"></a><span class="lineno"> 2224</span>&#160;        }</div>
<div class="line"><a name="l02225"></a><span class="lineno"> 2225</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000236&quot;</span>) <span class="comment">//transmission</span></div>
<div class="line"><a name="l02226"></a><span class="lineno"> 2226</span>&#160;        {</div>
<div class="line"><a name="l02227"></a><span class="lineno"> 2227</span>&#160;          <span class="comment">//No member =&gt; metadata</span></div>
<div class="line"><a name="l02228"></a><span class="lineno"> 2228</span>&#160;          instruments_[current_id_].setMetaValue(<span class="stringliteral">&quot;transmission&quot;</span>, termValue);</div>
<div class="line"><a name="l02229"></a><span class="lineno"> 2229</span>&#160;        }</div>
<div class="line"><a name="l02230"></a><span class="lineno"> 2230</span>&#160;        <span class="comment">//ion optics type</span></div>
<div class="line"><a name="l02231"></a><span class="lineno"> 2231</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000246&quot;</span>) <span class="comment">//delayed extraction</span></div>
<div class="line"><a name="l02232"></a><span class="lineno"> 2232</span>&#160;        {</div>
<div class="line"><a name="l02233"></a><span class="lineno"> 2233</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea9f31dbfcc7e3828fea80213c74fa76e2">Instrument::DELAYED_EXTRACTION</a>);</div>
<div class="line"><a name="l02234"></a><span class="lineno"> 2234</span>&#160;        }</div>
<div class="line"><a name="l02235"></a><span class="lineno"> 2235</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000221&quot;</span>) <span class="comment">//magnetic deflection</span></div>
<div class="line"><a name="l02236"></a><span class="lineno"> 2236</span>&#160;        {</div>
<div class="line"><a name="l02237"></a><span class="lineno"> 2237</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea78e072856cb37e4c51c595d8236347d7">Instrument::MAGNETIC_DEFLECTION</a>);</div>
<div class="line"><a name="l02238"></a><span class="lineno"> 2238</span>&#160;        }</div>
<div class="line"><a name="l02239"></a><span class="lineno"> 2239</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000275&quot;</span>) <span class="comment">//collision quadrupole</span></div>
<div class="line"><a name="l02240"></a><span class="lineno"> 2240</span>&#160;        {</div>
<div class="line"><a name="l02241"></a><span class="lineno"> 2241</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea2573b581168afac70eeffa4a02e4ac66">Instrument::COLLISION_QUADRUPOLE</a>);</div>
<div class="line"><a name="l02242"></a><span class="lineno"> 2242</span>&#160;        }</div>
<div class="line"><a name="l02243"></a><span class="lineno"> 2243</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000281&quot;</span>) <span class="comment">//selected ion flow tube</span></div>
<div class="line"><a name="l02244"></a><span class="lineno"> 2244</span>&#160;        {</div>
<div class="line"><a name="l02245"></a><span class="lineno"> 2245</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825eaad34ce194cef545b3decfad97565ea17">Instrument::SELECTED_ION_FLOW_TUBE</a>);</div>
<div class="line"><a name="l02246"></a><span class="lineno"> 2246</span>&#160;        }</div>
<div class="line"><a name="l02247"></a><span class="lineno"> 2247</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000286&quot;</span>) <span class="comment">//time lag focusing</span></div>
<div class="line"><a name="l02248"></a><span class="lineno"> 2248</span>&#160;        {</div>
<div class="line"><a name="l02249"></a><span class="lineno"> 2249</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea1a077c77350bebae4e5a37f5ef2d4d98">Instrument::TIME_LAG_FOCUSING</a>);</div>
<div class="line"><a name="l02250"></a><span class="lineno"> 2250</span>&#160;        }</div>
<div class="line"><a name="l02251"></a><span class="lineno"> 2251</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000300&quot;</span>) <span class="comment">//reflectron</span></div>
<div class="line"><a name="l02252"></a><span class="lineno"> 2252</span>&#160;        {</div>
<div class="line"><a name="l02253"></a><span class="lineno"> 2253</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea00c6731b4cbe1c7f48610afb10686c9c">Instrument::REFLECTRON</a>);</div>
<div class="line"><a name="l02254"></a><span class="lineno"> 2254</span>&#160;        }</div>
<div class="line"><a name="l02255"></a><span class="lineno"> 2255</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000307&quot;</span>) <span class="comment">//einzel lens</span></div>
<div class="line"><a name="l02256"></a><span class="lineno"> 2256</span>&#160;        {</div>
<div class="line"><a name="l02257"></a><span class="lineno"> 2257</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825eabac1358aab1b37a968f2dc90facf110e">Instrument::EINZEL_LENS</a>);</div>
<div class="line"><a name="l02258"></a><span class="lineno"> 2258</span>&#160;        }</div>
<div class="line"><a name="l02259"></a><span class="lineno"> 2259</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000309&quot;</span>) <span class="comment">//first stability region</span></div>
<div class="line"><a name="l02260"></a><span class="lineno"> 2260</span>&#160;        {</div>
<div class="line"><a name="l02261"></a><span class="lineno"> 2261</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea02fb42fb91d78f40b3280cec43ff67a9">Instrument::FIRST_STABILITY_REGION</a>);</div>
<div class="line"><a name="l02262"></a><span class="lineno"> 2262</span>&#160;        }</div>
<div class="line"><a name="l02263"></a><span class="lineno"> 2263</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000310&quot;</span>) <span class="comment">//fringing field</span></div>
<div class="line"><a name="l02264"></a><span class="lineno"> 2264</span>&#160;        {</div>
<div class="line"><a name="l02265"></a><span class="lineno"> 2265</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea9503ab7efe8e81ba7b6ec9e11a4aec86">Instrument::FRINGING_FIELD</a>);</div>
<div class="line"><a name="l02266"></a><span class="lineno"> 2266</span>&#160;        }</div>
<div class="line"><a name="l02267"></a><span class="lineno"> 2267</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000311&quot;</span>) <span class="comment">//kinetic energy analyzer</span></div>
<div class="line"><a name="l02268"></a><span class="lineno"> 2268</span>&#160;        {</div>
<div class="line"><a name="l02269"></a><span class="lineno"> 2269</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea17e86bcc9b8f78ff8c458d7b9253699d">Instrument::KINETIC_ENERGY_ANALYZER</a>);</div>
<div class="line"><a name="l02270"></a><span class="lineno"> 2270</span>&#160;        }</div>
<div class="line"><a name="l02271"></a><span class="lineno"> 2271</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000320&quot;</span>) <span class="comment">//static field</span></div>
<div class="line"><a name="l02272"></a><span class="lineno"> 2272</span>&#160;        {</div>
<div class="line"><a name="l02273"></a><span class="lineno"> 2273</span>&#160;          instruments_[current_id_].setIonOptics(<a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea15567a4ebc7d975ae3be35e3efd7daae">Instrument::STATIC_FIELD</a>);</div>
<div class="line"><a name="l02274"></a><span class="lineno"> 2274</span>&#160;        }</div>
<div class="line"><a name="l02275"></a><span class="lineno"> 2275</span>&#160;        <span class="comment">//ion optics attribute</span></div>
<div class="line"><a name="l02276"></a><span class="lineno"> 2276</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000304&quot;</span>) <span class="comment">//accelerating voltage</span></div>
<div class="line"><a name="l02277"></a><span class="lineno"> 2277</span>&#160;        {</div>
<div class="line"><a name="l02278"></a><span class="lineno"> 2278</span>&#160;          <span class="comment">//No member =&gt; metadata</span></div>
<div class="line"><a name="l02279"></a><span class="lineno"> 2279</span>&#160;          instruments_[current_id_].setMetaValue(<span class="stringliteral">&quot;accelerating voltage&quot;</span>, termValue);</div>
<div class="line"><a name="l02280"></a><span class="lineno"> 2280</span>&#160;        }</div>
<div class="line"><a name="l02281"></a><span class="lineno"> 2281</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000216&quot;</span>) <span class="comment">//field-free region</span></div>
<div class="line"><a name="l02282"></a><span class="lineno"> 2282</span>&#160;        {</div>
<div class="line"><a name="l02283"></a><span class="lineno"> 2283</span>&#160;          <span class="comment">//No member =&gt; metadata</span></div>
<div class="line"><a name="l02284"></a><span class="lineno"> 2284</span>&#160;          instruments_[current_id_].setMetaValue(<span class="stringliteral">&quot;field-free region&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;true&quot;</span>));</div>
<div class="line"><a name="l02285"></a><span class="lineno"> 2285</span>&#160;        }</div>
<div class="line"><a name="l02286"></a><span class="lineno"> 2286</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000308&quot;</span>) <span class="comment">//electric field strength</span></div>
<div class="line"><a name="l02287"></a><span class="lineno"> 2287</span>&#160;        {</div>
<div class="line"><a name="l02288"></a><span class="lineno"> 2288</span>&#160;          <span class="comment">//No member =&gt; metadata</span></div>
<div class="line"><a name="l02289"></a><span class="lineno"> 2289</span>&#160;          instruments_[current_id_].setMetaValue(<span class="stringliteral">&quot;electric field strength&quot;</span>, termValue);</div>
<div class="line"><a name="l02290"></a><span class="lineno"> 2290</span>&#160;        }</div>
<div class="line"><a name="l02291"></a><span class="lineno"> 2291</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000319&quot;</span>) <span class="comment">//space charge effect</span></div>
<div class="line"><a name="l02292"></a><span class="lineno"> 2292</span>&#160;        {</div>
<div class="line"><a name="l02293"></a><span class="lineno"> 2293</span>&#160;          <span class="comment">//No member =&gt; metadata</span></div>
<div class="line"><a name="l02294"></a><span class="lineno"> 2294</span>&#160;          instruments_[current_id_].setMetaValue(<span class="stringliteral">&quot;space charge effect&quot;</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;true&quot;</span>));</div>
<div class="line"><a name="l02295"></a><span class="lineno"> 2295</span>&#160;        }</div>
<div class="line"><a name="l02296"></a><span class="lineno"> 2296</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02297"></a><span class="lineno"> 2297</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02298"></a><span class="lineno"> 2298</span>&#160;      }</div>
<div class="line"><a name="l02299"></a><span class="lineno"> 2299</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;source&quot;</span>)</div>
<div class="line"><a name="l02300"></a><span class="lineno"> 2300</span>&#160;      {</div>
<div class="line"><a name="l02301"></a><span class="lineno"> 2301</span>&#160;        <span class="comment">//inlet type</span></div>
<div class="line"><a name="l02302"></a><span class="lineno"> 2302</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000055&quot;</span>) <span class="comment">//continuous flow fast atom bombardment</span></div>
<div class="line"><a name="l02303"></a><span class="lineno"> 2303</span>&#160;        {</div>
<div class="line"><a name="l02304"></a><span class="lineno"> 2304</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fab6d52778aef5ed31ac17025f4bffd8f4">IonSource::CONTINUOUSFLOWFASTATOMBOMBARDMENT</a>);</div>
<div class="line"><a name="l02305"></a><span class="lineno"> 2305</span>&#160;        }</div>
<div class="line"><a name="l02306"></a><span class="lineno"> 2306</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000056&quot;</span>) <span class="comment">//direct inlet</span></div>
<div class="line"><a name="l02307"></a><span class="lineno"> 2307</span>&#160;        {</div>
<div class="line"><a name="l02308"></a><span class="lineno"> 2308</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa1ea328a644e627283a35716a54108248">IonSource::DIRECT</a>);</div>
<div class="line"><a name="l02309"></a><span class="lineno"> 2309</span>&#160;        }</div>
<div class="line"><a name="l02310"></a><span class="lineno"> 2310</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000057&quot;</span>) <span class="comment">//electrospray inlet</span></div>
<div class="line"><a name="l02311"></a><span class="lineno"> 2311</span>&#160;        {</div>
<div class="line"><a name="l02312"></a><span class="lineno"> 2312</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa9c897c6cdabbcc5b84159ac533e72f32">IonSource::ELECTROSPRAYINLET</a>);</div>
<div class="line"><a name="l02313"></a><span class="lineno"> 2313</span>&#160;        }</div>
<div class="line"><a name="l02314"></a><span class="lineno"> 2314</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000058&quot;</span>) <span class="comment">//flow injection analysis</span></div>
<div class="line"><a name="l02315"></a><span class="lineno"> 2315</span>&#160;        {</div>
<div class="line"><a name="l02316"></a><span class="lineno"> 2316</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa6c48ed9c4442494fd5f122c94860447d">IonSource::FLOWINJECTIONANALYSIS</a>);</div>
<div class="line"><a name="l02317"></a><span class="lineno"> 2317</span>&#160;        }</div>
<div class="line"><a name="l02318"></a><span class="lineno"> 2318</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000059&quot;</span>) <span class="comment">//inductively coupled plasma</span></div>
<div class="line"><a name="l02319"></a><span class="lineno"> 2319</span>&#160;        {</div>
<div class="line"><a name="l02320"></a><span class="lineno"> 2320</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa8f610db6e93fa153152a1c46b49539b2">IonSource::INDUCTIVELYCOUPLEDPLASMA</a>);</div>
<div class="line"><a name="l02321"></a><span class="lineno"> 2321</span>&#160;        }</div>
<div class="line"><a name="l02322"></a><span class="lineno"> 2322</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000060&quot;</span>) <span class="comment">//infusion</span></div>
<div class="line"><a name="l02323"></a><span class="lineno"> 2323</span>&#160;        {</div>
<div class="line"><a name="l02324"></a><span class="lineno"> 2324</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa27dcc04b8d9859dfe2ea21b888c26189">IonSource::INFUSION</a>);</div>
<div class="line"><a name="l02325"></a><span class="lineno"> 2325</span>&#160;        }</div>
<div class="line"><a name="l02326"></a><span class="lineno"> 2326</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000061&quot;</span>) <span class="comment">//jet separator</span></div>
<div class="line"><a name="l02327"></a><span class="lineno"> 2327</span>&#160;        {</div>
<div class="line"><a name="l02328"></a><span class="lineno"> 2328</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa0598d1c2cd7107bff01eb8de6ff74f94">IonSource::JETSEPARATOR</a>);</div>
<div class="line"><a name="l02329"></a><span class="lineno"> 2329</span>&#160;        }</div>
<div class="line"><a name="l02330"></a><span class="lineno"> 2330</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000062&quot;</span>) <span class="comment">//membrane separator</span></div>
<div class="line"><a name="l02331"></a><span class="lineno"> 2331</span>&#160;        {</div>
<div class="line"><a name="l02332"></a><span class="lineno"> 2332</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa19ff98c123f82fd251780c91d5d52f13">IonSource::MEMBRANESEPARATOR</a>);</div>
<div class="line"><a name="l02333"></a><span class="lineno"> 2333</span>&#160;        }</div>
<div class="line"><a name="l02334"></a><span class="lineno"> 2334</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000063&quot;</span>) <span class="comment">//moving belt</span></div>
<div class="line"><a name="l02335"></a><span class="lineno"> 2335</span>&#160;        {</div>
<div class="line"><a name="l02336"></a><span class="lineno"> 2336</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fafc825adbdcb19797aad0ed340db940c3">IonSource::MOVINGBELT</a>);</div>
<div class="line"><a name="l02337"></a><span class="lineno"> 2337</span>&#160;        }</div>
<div class="line"><a name="l02338"></a><span class="lineno"> 2338</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000064&quot;</span>) <span class="comment">//moving wire</span></div>
<div class="line"><a name="l02339"></a><span class="lineno"> 2339</span>&#160;        {</div>
<div class="line"><a name="l02340"></a><span class="lineno"> 2340</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa3c5780d8602eb19c5c2d688498c29de8">IonSource::MOVINGWIRE</a>);</div>
<div class="line"><a name="l02341"></a><span class="lineno"> 2341</span>&#160;        }</div>
<div class="line"><a name="l02342"></a><span class="lineno"> 2342</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000065&quot;</span>) <span class="comment">//open split</span></div>
<div class="line"><a name="l02343"></a><span class="lineno"> 2343</span>&#160;        {</div>
<div class="line"><a name="l02344"></a><span class="lineno"> 2344</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa884aab0e62a0e1db261a95022a6ef25d">IonSource::OPENSPLIT</a>);</div>
<div class="line"><a name="l02345"></a><span class="lineno"> 2345</span>&#160;        }</div>
<div class="line"><a name="l02346"></a><span class="lineno"> 2346</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000066&quot;</span>) <span class="comment">//particle beam</span></div>
<div class="line"><a name="l02347"></a><span class="lineno"> 2347</span>&#160;        {</div>
<div class="line"><a name="l02348"></a><span class="lineno"> 2348</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa564313b42cf82a9be19c95050133911b">IonSource::PARTICLEBEAM</a>);</div>
<div class="line"><a name="l02349"></a><span class="lineno"> 2349</span>&#160;        }</div>
<div class="line"><a name="l02350"></a><span class="lineno"> 2350</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000067&quot;</span>) <span class="comment">//reservoir</span></div>
<div class="line"><a name="l02351"></a><span class="lineno"> 2351</span>&#160;        {</div>
<div class="line"><a name="l02352"></a><span class="lineno"> 2352</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa73dded3a91104b5de02f9f408023ef18">IonSource::RESERVOIR</a>);</div>
<div class="line"><a name="l02353"></a><span class="lineno"> 2353</span>&#160;        }</div>
<div class="line"><a name="l02354"></a><span class="lineno"> 2354</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000068&quot;</span>) <span class="comment">//septum</span></div>
<div class="line"><a name="l02355"></a><span class="lineno"> 2355</span>&#160;        {</div>
<div class="line"><a name="l02356"></a><span class="lineno"> 2356</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fad7f5a34d7e508de209ade5decea9e80c">IonSource::SEPTUM</a>);</div>
<div class="line"><a name="l02357"></a><span class="lineno"> 2357</span>&#160;        }</div>
<div class="line"><a name="l02358"></a><span class="lineno"> 2358</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000069&quot;</span>) <span class="comment">//thermospray inlet</span></div>
<div class="line"><a name="l02359"></a><span class="lineno"> 2359</span>&#160;        {</div>
<div class="line"><a name="l02360"></a><span class="lineno"> 2360</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675faf72472484541d6de7bfe8151b04b7417">IonSource::THERMOSPRAYINLET</a>);</div>
<div class="line"><a name="l02361"></a><span class="lineno"> 2361</span>&#160;        }</div>
<div class="line"><a name="l02362"></a><span class="lineno"> 2362</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000248&quot;</span>) <span class="comment">//direct insertion probe</span></div>
<div class="line"><a name="l02363"></a><span class="lineno"> 2363</span>&#160;        {</div>
<div class="line"><a name="l02364"></a><span class="lineno"> 2364</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fabc04848b2d94351b99f92127e29bb075">IonSource::BATCH</a>);</div>
<div class="line"><a name="l02365"></a><span class="lineno"> 2365</span>&#160;        }</div>
<div class="line"><a name="l02366"></a><span class="lineno"> 2366</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000249&quot;</span>) <span class="comment">//direct liquid introduction</span></div>
<div class="line"><a name="l02367"></a><span class="lineno"> 2367</span>&#160;        {</div>
<div class="line"><a name="l02368"></a><span class="lineno"> 2368</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa066def527c3472b49e0d152c392ee0d7">IonSource::CHROMATOGRAPHY</a>);</div>
<div class="line"><a name="l02369"></a><span class="lineno"> 2369</span>&#160;        }</div>
<div class="line"><a name="l02370"></a><span class="lineno"> 2370</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000396&quot;</span>) <span class="comment">//membrane inlet</span></div>
<div class="line"><a name="l02371"></a><span class="lineno"> 2371</span>&#160;        {</div>
<div class="line"><a name="l02372"></a><span class="lineno"> 2372</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa14dec9ac85c4c53db9e1fa17d0bffeea">IonSource::MEMBRANE</a>);</div>
<div class="line"><a name="l02373"></a><span class="lineno"> 2373</span>&#160;        }</div>
<div class="line"><a name="l02374"></a><span class="lineno"> 2374</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000485&quot;</span>) <span class="comment">//nanospray inlet</span></div>
<div class="line"><a name="l02375"></a><span class="lineno"> 2375</span>&#160;        {</div>
<div class="line"><a name="l02376"></a><span class="lineno"> 2376</span>&#160;          instruments_[current_id_].getIonSources().back().setInletType(<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa2328ee396a2ca9e44bd7a8459bcfef28">IonSource::NANOSPRAY</a>);</div>
<div class="line"><a name="l02377"></a><span class="lineno"> 2377</span>&#160;        }</div>
<div class="line"><a name="l02378"></a><span class="lineno"> 2378</span>&#160;        <span class="comment">//ionization type</span></div>
<div class="line"><a name="l02379"></a><span class="lineno"> 2379</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000071&quot;</span>) <span class="comment">//chemical ionization</span></div>
<div class="line"><a name="l02380"></a><span class="lineno"> 2380</span>&#160;        {</div>
<div class="line"><a name="l02381"></a><span class="lineno"> 2381</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aed87f9b08a003dc2ef4c4920060eae14">IonSource::CI</a>);</div>
<div class="line"><a name="l02382"></a><span class="lineno"> 2382</span>&#160;        }</div>
<div class="line"><a name="l02383"></a><span class="lineno"> 2383</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000073&quot;</span>) <span class="comment">//electrospray ionization</span></div>
<div class="line"><a name="l02384"></a><span class="lineno"> 2384</span>&#160;        {</div>
<div class="line"><a name="l02385"></a><span class="lineno"> 2385</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a4ce1f413b646020308281e301ce1e4ec">IonSource::ESI</a>);</div>
<div class="line"><a name="l02386"></a><span class="lineno"> 2386</span>&#160;        }</div>
<div class="line"><a name="l02387"></a><span class="lineno"> 2387</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000074&quot;</span>) <span class="comment">//fast atom bombardment ionization</span></div>
<div class="line"><a name="l02388"></a><span class="lineno"> 2388</span>&#160;        {</div>
<div class="line"><a name="l02389"></a><span class="lineno"> 2389</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4abccdeef60efaa51840b2bda65c374e7e">IonSource::FAB</a>);</div>
<div class="line"><a name="l02390"></a><span class="lineno"> 2390</span>&#160;        }</div>
<div class="line"><a name="l02391"></a><span class="lineno"> 2391</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000227&quot;</span>) <span class="comment">//multiphoton ionization</span></div>
<div class="line"><a name="l02392"></a><span class="lineno"> 2392</span>&#160;        {</div>
<div class="line"><a name="l02393"></a><span class="lineno"> 2393</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aece8c4cb0f2685308261ef5409676a18">IonSource::MPI</a>);</div>
<div class="line"><a name="l02394"></a><span class="lineno"> 2394</span>&#160;        }</div>
<div class="line"><a name="l02395"></a><span class="lineno"> 2395</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000240&quot;</span>) <span class="comment">//atmospheric pressure ionization</span></div>
<div class="line"><a name="l02396"></a><span class="lineno"> 2396</span>&#160;        {</div>
<div class="line"><a name="l02397"></a><span class="lineno"> 2397</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a7fd5f3a93cf5139877f23acb316f99c0">IonSource::API</a>);</div>
<div class="line"><a name="l02398"></a><span class="lineno"> 2398</span>&#160;        }</div>
<div class="line"><a name="l02399"></a><span class="lineno"> 2399</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000247&quot;</span>) <span class="comment">//desorption ionization</span></div>
<div class="line"><a name="l02400"></a><span class="lineno"> 2400</span>&#160;        {</div>
<div class="line"><a name="l02401"></a><span class="lineno"> 2401</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a527f7ffe8e4e1d4cd85dd9e61eed9795">IonSource::DI</a>);</div>
<div class="line"><a name="l02402"></a><span class="lineno"> 2402</span>&#160;        }</div>
<div class="line"><a name="l02403"></a><span class="lineno"> 2403</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000255&quot;</span>) <span class="comment">//flowing afterglow</span></div>
<div class="line"><a name="l02404"></a><span class="lineno"> 2404</span>&#160;        {</div>
<div class="line"><a name="l02405"></a><span class="lineno"> 2405</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a587607b9ab280181a8b20a9fb147bad3">IonSource::FA</a>);</div>
<div class="line"><a name="l02406"></a><span class="lineno"> 2406</span>&#160;        }</div>
<div class="line"><a name="l02407"></a><span class="lineno"> 2407</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000258&quot;</span>) <span class="comment">//field ionization</span></div>
<div class="line"><a name="l02408"></a><span class="lineno"> 2408</span>&#160;        {</div>
<div class="line"><a name="l02409"></a><span class="lineno"> 2409</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a83fe4091c0761e944734545d162259a9">IonSource::FII</a>);</div>
<div class="line"><a name="l02410"></a><span class="lineno"> 2410</span>&#160;        }</div>
<div class="line"><a name="l02411"></a><span class="lineno"> 2411</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000259&quot;</span>) <span class="comment">//glow discharge ionization</span></div>
<div class="line"><a name="l02412"></a><span class="lineno"> 2412</span>&#160;        {</div>
<div class="line"><a name="l02413"></a><span class="lineno"> 2413</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a535e49bf5eee5561caead0a39995a48b">IonSource::GD_MS</a>);</div>
<div class="line"><a name="l02414"></a><span class="lineno"> 2414</span>&#160;        }</div>
<div class="line"><a name="l02415"></a><span class="lineno"> 2415</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000271&quot;</span>) <span class="comment">//Negative ion chemical ionization</span></div>
<div class="line"><a name="l02416"></a><span class="lineno"> 2416</span>&#160;        {</div>
<div class="line"><a name="l02417"></a><span class="lineno"> 2417</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a20d56bc7900e25dc3e84f15078eefdf7">IonSource::NICI</a>);</div>
<div class="line"><a name="l02418"></a><span class="lineno"> 2418</span>&#160;        }</div>
<div class="line"><a name="l02419"></a><span class="lineno"> 2419</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000272&quot;</span>) <span class="comment">//neutralization reionization mass spectrometry</span></div>
<div class="line"><a name="l02420"></a><span class="lineno"> 2420</span>&#160;        {</div>
<div class="line"><a name="l02421"></a><span class="lineno"> 2421</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a6c146484587d495e53fe377ca0b855fe">IonSource::NRMS</a>);</div>
<div class="line"><a name="l02422"></a><span class="lineno"> 2422</span>&#160;        }</div>
<div class="line"><a name="l02423"></a><span class="lineno"> 2423</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000273&quot;</span>) <span class="comment">//photoionization</span></div>
<div class="line"><a name="l02424"></a><span class="lineno"> 2424</span>&#160;        {</div>
<div class="line"><a name="l02425"></a><span class="lineno"> 2425</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5b26cd07c89ea86afa2fa793fb7fc729">IonSource::PI</a>);</div>
<div class="line"><a name="l02426"></a><span class="lineno"> 2426</span>&#160;        }</div>
<div class="line"><a name="l02427"></a><span class="lineno"> 2427</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000274&quot;</span>) <span class="comment">//pyrolysis mass spectrometry</span></div>
<div class="line"><a name="l02428"></a><span class="lineno"> 2428</span>&#160;        {</div>
<div class="line"><a name="l02429"></a><span class="lineno"> 2429</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aae20fd962cf613d3911e5f7da51de1df">IonSource::PYMS</a>);</div>
<div class="line"><a name="l02430"></a><span class="lineno"> 2430</span>&#160;        }</div>
<div class="line"><a name="l02431"></a><span class="lineno"> 2431</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000276&quot;</span>) <span class="comment">//resonance enhanced multiphoton ionization</span></div>
<div class="line"><a name="l02432"></a><span class="lineno"> 2432</span>&#160;        {</div>
<div class="line"><a name="l02433"></a><span class="lineno"> 2433</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aae01bfe30f377fbd7d8e5f4e431eaacb">IonSource::REMPI</a>);</div>
<div class="line"><a name="l02434"></a><span class="lineno"> 2434</span>&#160;        }</div>
<div class="line"><a name="l02435"></a><span class="lineno"> 2435</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000380&quot;</span>) <span class="comment">//adiabatic ionization</span></div>
<div class="line"><a name="l02436"></a><span class="lineno"> 2436</span>&#160;        {</div>
<div class="line"><a name="l02437"></a><span class="lineno"> 2437</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a9c74caa56a3c05723eb1dbad44bc9bc3">IonSource::AI</a>);</div>
<div class="line"><a name="l02438"></a><span class="lineno"> 2438</span>&#160;        }</div>
<div class="line"><a name="l02439"></a><span class="lineno"> 2439</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000381&quot;</span>) <span class="comment">//associative ionization</span></div>
<div class="line"><a name="l02440"></a><span class="lineno"> 2440</span>&#160;        {</div>
<div class="line"><a name="l02441"></a><span class="lineno"> 2441</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ad534995d8fa8bd372ad247e16ff746fa">IonSource::ASI</a>);</div>
<div class="line"><a name="l02442"></a><span class="lineno"> 2442</span>&#160;        }</div>
<div class="line"><a name="l02443"></a><span class="lineno"> 2443</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000383&quot;</span>) <span class="comment">//autodetachment</span></div>
<div class="line"><a name="l02444"></a><span class="lineno"> 2444</span>&#160;        {</div>
<div class="line"><a name="l02445"></a><span class="lineno"> 2445</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ae63d77c61a2a5b9777024af082a36719">IonSource::AD</a>);</div>
<div class="line"><a name="l02446"></a><span class="lineno"> 2446</span>&#160;        }</div>
<div class="line"><a name="l02447"></a><span class="lineno"> 2447</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000384&quot;</span>) <span class="comment">//autoionization</span></div>
<div class="line"><a name="l02448"></a><span class="lineno"> 2448</span>&#160;        {</div>
<div class="line"><a name="l02449"></a><span class="lineno"> 2449</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a3306da16fbcb1fde30d4ec351db99285">IonSource::AUI</a>);</div>
<div class="line"><a name="l02450"></a><span class="lineno"> 2450</span>&#160;        }</div>
<div class="line"><a name="l02451"></a><span class="lineno"> 2451</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000385&quot;</span>) <span class="comment">//charge exchange ionization</span></div>
<div class="line"><a name="l02452"></a><span class="lineno"> 2452</span>&#160;        {</div>
<div class="line"><a name="l02453"></a><span class="lineno"> 2453</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a32e4cb82b586a059c77128a1cdcd3282">IonSource::CEI</a>);</div>
<div class="line"><a name="l02454"></a><span class="lineno"> 2454</span>&#160;        }</div>
<div class="line"><a name="l02455"></a><span class="lineno"> 2455</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000386&quot;</span>) <span class="comment">//chemi-ionization</span></div>
<div class="line"><a name="l02456"></a><span class="lineno"> 2456</span>&#160;        {</div>
<div class="line"><a name="l02457"></a><span class="lineno"> 2457</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ae3a31f903a1ebacac4aa4de2409c80ff">IonSource::CHEMI</a>);</div>
<div class="line"><a name="l02458"></a><span class="lineno"> 2458</span>&#160;        }</div>
<div class="line"><a name="l02459"></a><span class="lineno"> 2459</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000388&quot;</span>) <span class="comment">//dissociative ionization</span></div>
<div class="line"><a name="l02460"></a><span class="lineno"> 2460</span>&#160;        {</div>
<div class="line"><a name="l02461"></a><span class="lineno"> 2461</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4affe4bbe037c9af162387d453f90e129a">IonSource::DISSI</a>);</div>
<div class="line"><a name="l02462"></a><span class="lineno"> 2462</span>&#160;        }</div>
<div class="line"><a name="l02463"></a><span class="lineno"> 2463</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000389&quot;</span>) <span class="comment">//electron ionization</span></div>
<div class="line"><a name="l02464"></a><span class="lineno"> 2464</span>&#160;        {</div>
<div class="line"><a name="l02465"></a><span class="lineno"> 2465</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a3158578f2cc1fb7fbd261b4094e7f5fd">IonSource::EI</a>);</div>
<div class="line"><a name="l02466"></a><span class="lineno"> 2466</span>&#160;        }</div>
<div class="line"><a name="l02467"></a><span class="lineno"> 2467</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000395&quot;</span>) <span class="comment">//liquid secondary ionization</span></div>
<div class="line"><a name="l02468"></a><span class="lineno"> 2468</span>&#160;        {</div>
<div class="line"><a name="l02469"></a><span class="lineno"> 2469</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ac59b221b111954833c988555d5972f88">IonSource::LSI</a>);</div>
<div class="line"><a name="l02470"></a><span class="lineno"> 2470</span>&#160;        }</div>
<div class="line"><a name="l02471"></a><span class="lineno"> 2471</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000399&quot;</span>) <span class="comment">//penning ionization</span></div>
<div class="line"><a name="l02472"></a><span class="lineno"> 2472</span>&#160;        {</div>
<div class="line"><a name="l02473"></a><span class="lineno"> 2473</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a0525c6afa4d96f74d29bbe7511a204db">IonSource::PEI</a>);</div>
<div class="line"><a name="l02474"></a><span class="lineno"> 2474</span>&#160;        }</div>
<div class="line"><a name="l02475"></a><span class="lineno"> 2475</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000400&quot;</span>) <span class="comment">//plasma desorption ionization</span></div>
<div class="line"><a name="l02476"></a><span class="lineno"> 2476</span>&#160;        {</div>
<div class="line"><a name="l02477"></a><span class="lineno"> 2477</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aefbc069e0ac4cd293f3ba527bec2befe">IonSource::PD</a>);</div>
<div class="line"><a name="l02478"></a><span class="lineno"> 2478</span>&#160;        }</div>
<div class="line"><a name="l02479"></a><span class="lineno"> 2479</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000402&quot;</span>) <span class="comment">//secondary ionization</span></div>
<div class="line"><a name="l02480"></a><span class="lineno"> 2480</span>&#160;        {</div>
<div class="line"><a name="l02481"></a><span class="lineno"> 2481</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a6cbe5ff42f143903e1c67abf94613791">IonSource::SI</a>);</div>
<div class="line"><a name="l02482"></a><span class="lineno"> 2482</span>&#160;        }</div>
<div class="line"><a name="l02483"></a><span class="lineno"> 2483</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000403&quot;</span>) <span class="comment">//soft ionization</span></div>
<div class="line"><a name="l02484"></a><span class="lineno"> 2484</span>&#160;        {</div>
<div class="line"><a name="l02485"></a><span class="lineno"> 2485</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a90291956e102c1e1aa6e642164751197">IonSource::SOI</a>);</div>
<div class="line"><a name="l02486"></a><span class="lineno"> 2486</span>&#160;        }</div>
<div class="line"><a name="l02487"></a><span class="lineno"> 2487</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000404&quot;</span>) <span class="comment">//spark ionization</span></div>
<div class="line"><a name="l02488"></a><span class="lineno"> 2488</span>&#160;        {</div>
<div class="line"><a name="l02489"></a><span class="lineno"> 2489</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aefea9eb0772378037221a3f1fe759a76">IonSource::SPI</a>);</div>
<div class="line"><a name="l02490"></a><span class="lineno"> 2490</span>&#160;        }</div>
<div class="line"><a name="l02491"></a><span class="lineno"> 2491</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000406&quot;</span>) <span class="comment">//surface ionization</span></div>
<div class="line"><a name="l02492"></a><span class="lineno"> 2492</span>&#160;        {</div>
<div class="line"><a name="l02493"></a><span class="lineno"> 2493</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5de3914c3b308664d35967f1a5ffc142">IonSource::SUI</a>);</div>
<div class="line"><a name="l02494"></a><span class="lineno"> 2494</span>&#160;        }</div>
<div class="line"><a name="l02495"></a><span class="lineno"> 2495</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000407&quot;</span>) <span class="comment">//thermal ionization</span></div>
<div class="line"><a name="l02496"></a><span class="lineno"> 2496</span>&#160;        {</div>
<div class="line"><a name="l02497"></a><span class="lineno"> 2497</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a205ce9325a3a2b1ca71be96bee9d7f89">IonSource::TI</a>);</div>
<div class="line"><a name="l02498"></a><span class="lineno"> 2498</span>&#160;        }</div>
<div class="line"><a name="l02499"></a><span class="lineno"> 2499</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000408&quot;</span>) <span class="comment">//vertical ionization</span></div>
<div class="line"><a name="l02500"></a><span class="lineno"> 2500</span>&#160;        {</div>
<div class="line"><a name="l02501"></a><span class="lineno"> 2501</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a97bce951e4585a39601c04d86bb14ffd">IonSource::VI</a>);</div>
<div class="line"><a name="l02502"></a><span class="lineno"> 2502</span>&#160;        }</div>
<div class="line"><a name="l02503"></a><span class="lineno"> 2503</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000446&quot;</span>) <span class="comment">//fast ion bombardment</span></div>
<div class="line"><a name="l02504"></a><span class="lineno"> 2504</span>&#160;        {</div>
<div class="line"><a name="l02505"></a><span class="lineno"> 2505</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aecf7855b0a44ab470fabcb44277200d7">IonSource::FIB</a>);</div>
<div class="line"><a name="l02506"></a><span class="lineno"> 2506</span>&#160;        }</div>
<div class="line"><a name="l02507"></a><span class="lineno"> 2507</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000070&quot;</span>) <span class="comment">//atmospheric pressure chemical ionization</span></div>
<div class="line"><a name="l02508"></a><span class="lineno"> 2508</span>&#160;        {</div>
<div class="line"><a name="l02509"></a><span class="lineno"> 2509</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aa45f628d1930ccc096fd37583145fccb">IonSource::APCI</a>);</div>
<div class="line"><a name="l02510"></a><span class="lineno"> 2510</span>&#160;        }</div>
<div class="line"><a name="l02511"></a><span class="lineno"> 2511</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000239&quot;</span>) <span class="comment">//atmospheric pressure matrix-assisted laser desorption ionization</span></div>
<div class="line"><a name="l02512"></a><span class="lineno"> 2512</span>&#160;        {</div>
<div class="line"><a name="l02513"></a><span class="lineno"> 2513</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4adfcd7e7c05c5dda54aa06c36077abab0">IonSource::AP_MALDI</a>);</div>
<div class="line"><a name="l02514"></a><span class="lineno"> 2514</span>&#160;        }</div>
<div class="line"><a name="l02515"></a><span class="lineno"> 2515</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000382&quot;</span>) <span class="comment">//atmospheric pressure photoionization</span></div>
<div class="line"><a name="l02516"></a><span class="lineno"> 2516</span>&#160;        {</div>
<div class="line"><a name="l02517"></a><span class="lineno"> 2517</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5c60e3178bb8db38b3970316b0c5aae8">IonSource::APPI</a>);</div>
<div class="line"><a name="l02518"></a><span class="lineno"> 2518</span>&#160;        }</div>
<div class="line"><a name="l02519"></a><span class="lineno"> 2519</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000075&quot;</span>) <span class="comment">//matrix-assisted laser desorption ionization</span></div>
<div class="line"><a name="l02520"></a><span class="lineno"> 2520</span>&#160;        {</div>
<div class="line"><a name="l02521"></a><span class="lineno"> 2521</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4af44dbf64796c3c09b804546061c39258">IonSource::MALDI</a>);</div>
<div class="line"><a name="l02522"></a><span class="lineno"> 2522</span>&#160;        }</div>
<div class="line"><a name="l02523"></a><span class="lineno"> 2523</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000257&quot;</span>) <span class="comment">//field desorption</span></div>
<div class="line"><a name="l02524"></a><span class="lineno"> 2524</span>&#160;        {</div>
<div class="line"><a name="l02525"></a><span class="lineno"> 2525</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4af6cb3036978c564d260f5016cac04f85">IonSource::FD</a>);</div>
<div class="line"><a name="l02526"></a><span class="lineno"> 2526</span>&#160;        }</div>
<div class="line"><a name="l02527"></a><span class="lineno"> 2527</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000387&quot;</span>) <span class="comment">//desorption/ionization on silicon</span></div>
<div class="line"><a name="l02528"></a><span class="lineno"> 2528</span>&#160;        {</div>
<div class="line"><a name="l02529"></a><span class="lineno"> 2529</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4afda196677d08ccd458e96fe74597d638">IonSource::SILI</a>);</div>
<div class="line"><a name="l02530"></a><span class="lineno"> 2530</span>&#160;        }</div>
<div class="line"><a name="l02531"></a><span class="lineno"> 2531</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000393&quot;</span>) <span class="comment">//laser desorption ionization</span></div>
<div class="line"><a name="l02532"></a><span class="lineno"> 2532</span>&#160;        {</div>
<div class="line"><a name="l02533"></a><span class="lineno"> 2533</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a24a5a956f8abcaacbde751c49c7d5001">IonSource::LD</a>);</div>
<div class="line"><a name="l02534"></a><span class="lineno"> 2534</span>&#160;        }</div>
<div class="line"><a name="l02535"></a><span class="lineno"> 2535</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000405&quot;</span>) <span class="comment">//surface-assisted laser desorption ionization</span></div>
<div class="line"><a name="l02536"></a><span class="lineno"> 2536</span>&#160;        {</div>
<div class="line"><a name="l02537"></a><span class="lineno"> 2537</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aaade3182d7ec0b4c0ef7a60392ed72b9">IonSource::SALDI</a>);</div>
<div class="line"><a name="l02538"></a><span class="lineno"> 2538</span>&#160;        }</div>
<div class="line"><a name="l02539"></a><span class="lineno"> 2539</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000397&quot;</span>) <span class="comment">//microelectrospray</span></div>
<div class="line"><a name="l02540"></a><span class="lineno"> 2540</span>&#160;        {</div>
<div class="line"><a name="l02541"></a><span class="lineno"> 2541</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a626c8167a1599535349b7288be3895d1">IonSource::MESI</a>);</div>
<div class="line"><a name="l02542"></a><span class="lineno"> 2542</span>&#160;        }</div>
<div class="line"><a name="l02543"></a><span class="lineno"> 2543</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000398&quot;</span>) <span class="comment">//nanoelectrospray</span></div>
<div class="line"><a name="l02544"></a><span class="lineno"> 2544</span>&#160;        {</div>
<div class="line"><a name="l02545"></a><span class="lineno"> 2545</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a07b393b769a687470db848e3eb98f578">IonSource::NESI</a>);</div>
<div class="line"><a name="l02546"></a><span class="lineno"> 2546</span>&#160;        }</div>
<div class="line"><a name="l02547"></a><span class="lineno"> 2547</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000278&quot;</span>) <span class="comment">//surface enhanced laser desorption ionization</span></div>
<div class="line"><a name="l02548"></a><span class="lineno"> 2548</span>&#160;        {</div>
<div class="line"><a name="l02549"></a><span class="lineno"> 2549</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a259eb726b6a08b2a08164df4e14db708">IonSource::SELDI</a>);</div>
<div class="line"><a name="l02550"></a><span class="lineno"> 2550</span>&#160;        }</div>
<div class="line"><a name="l02551"></a><span class="lineno"> 2551</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000279&quot;</span>) <span class="comment">//surface enhanced neat desorption</span></div>
<div class="line"><a name="l02552"></a><span class="lineno"> 2552</span>&#160;        {</div>
<div class="line"><a name="l02553"></a><span class="lineno"> 2553</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a67be7a5f47004345047b32fff72a2230">IonSource::SEND</a>);</div>
<div class="line"><a name="l02554"></a><span class="lineno"> 2554</span>&#160;        }</div>
<div class="line"><a name="l02555"></a><span class="lineno"> 2555</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000008&quot;</span>) <span class="comment">//ionization type (base term)</span></div>
<div class="line"><a name="l02556"></a><span class="lineno"> 2556</span>&#160;        {</div>
<div class="line"><a name="l02557"></a><span class="lineno"> 2557</span>&#160;          instruments_[current_id_].getIonSources().back().setIonizationMethod(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a4443b16a744c30d496e4b5bcb834b029">IonSource::IONMETHODNULL</a>);</div>
<div class="line"><a name="l02558"></a><span class="lineno"> 2558</span>&#160;        }</div>
<div class="line"><a name="l02559"></a><span class="lineno"> 2559</span>&#160;        <span class="comment">//source attribute</span></div>
<div class="line"><a name="l02560"></a><span class="lineno"> 2560</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000392&quot;</span>) <span class="comment">//ionization efficiency</span></div>
<div class="line"><a name="l02561"></a><span class="lineno"> 2561</span>&#160;        {</div>
<div class="line"><a name="l02562"></a><span class="lineno"> 2562</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02563"></a><span class="lineno"> 2563</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;ionization efficiency&quot;</span>, termValue);</div>
<div class="line"><a name="l02564"></a><span class="lineno"> 2564</span>&#160;        }</div>
<div class="line"><a name="l02565"></a><span class="lineno"> 2565</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000486&quot;</span>) <span class="comment">//source potential</span></div>
<div class="line"><a name="l02566"></a><span class="lineno"> 2566</span>&#160;        {</div>
<div class="line"><a name="l02567"></a><span class="lineno"> 2567</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02568"></a><span class="lineno"> 2568</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;source potential&quot;</span>, termValue);</div>
<div class="line"><a name="l02569"></a><span class="lineno"> 2569</span>&#160;        }</div>
<div class="line"><a name="l02570"></a><span class="lineno"> 2570</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000875&quot;</span>) <span class="comment">// declustering potential</span></div>
<div class="line"><a name="l02571"></a><span class="lineno"> 2571</span>&#160;        {</div>
<div class="line"><a name="l02572"></a><span class="lineno"> 2572</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02573"></a><span class="lineno"> 2573</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;declustering potential&quot;</span>, termValue);</div>
<div class="line"><a name="l02574"></a><span class="lineno"> 2574</span>&#160;        }</div>
<div class="line"><a name="l02575"></a><span class="lineno"> 2575</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000876&quot;</span>) <span class="comment">// cone voltage</span></div>
<div class="line"><a name="l02576"></a><span class="lineno"> 2576</span>&#160;        {</div>
<div class="line"><a name="l02577"></a><span class="lineno"> 2577</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02578"></a><span class="lineno"> 2578</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;cone voltage&quot;</span>, termValue);</div>
<div class="line"><a name="l02579"></a><span class="lineno"> 2579</span>&#160;        }</div>
<div class="line"><a name="l02580"></a><span class="lineno"> 2580</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000877&quot;</span>) <span class="comment">// tube lens</span></div>
<div class="line"><a name="l02581"></a><span class="lineno"> 2581</span>&#160;        {</div>
<div class="line"><a name="l02582"></a><span class="lineno"> 2582</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02583"></a><span class="lineno"> 2583</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;tube lens&quot;</span>, termValue);</div>
<div class="line"><a name="l02584"></a><span class="lineno"> 2584</span>&#160;        }</div>
<div class="line"><a name="l02585"></a><span class="lineno"> 2585</span>&#160;        <span class="comment">//laser attribute</span></div>
<div class="line"><a name="l02586"></a><span class="lineno"> 2586</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000843&quot;</span>) <span class="comment">// wavelength</span></div>
<div class="line"><a name="l02587"></a><span class="lineno"> 2587</span>&#160;        {</div>
<div class="line"><a name="l02588"></a><span class="lineno"> 2588</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02589"></a><span class="lineno"> 2589</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;wavelength&quot;</span>, termValue);</div>
<div class="line"><a name="l02590"></a><span class="lineno"> 2590</span>&#160;        }</div>
<div class="line"><a name="l02591"></a><span class="lineno"> 2591</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000844&quot;</span>) <span class="comment">// focus diameter x</span></div>
<div class="line"><a name="l02592"></a><span class="lineno"> 2592</span>&#160;        {</div>
<div class="line"><a name="l02593"></a><span class="lineno"> 2593</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02594"></a><span class="lineno"> 2594</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;focus diameter x&quot;</span>, termValue);</div>
<div class="line"><a name="l02595"></a><span class="lineno"> 2595</span>&#160;        }</div>
<div class="line"><a name="l02596"></a><span class="lineno"> 2596</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000845&quot;</span>) <span class="comment">// focus diameter y</span></div>
<div class="line"><a name="l02597"></a><span class="lineno"> 2597</span>&#160;        {</div>
<div class="line"><a name="l02598"></a><span class="lineno"> 2598</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02599"></a><span class="lineno"> 2599</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;focus diameter y&quot;</span>, termValue);</div>
<div class="line"><a name="l02600"></a><span class="lineno"> 2600</span>&#160;        }</div>
<div class="line"><a name="l02601"></a><span class="lineno"> 2601</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000846&quot;</span>) <span class="comment">// pulse energy</span></div>
<div class="line"><a name="l02602"></a><span class="lineno"> 2602</span>&#160;        {</div>
<div class="line"><a name="l02603"></a><span class="lineno"> 2603</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02604"></a><span class="lineno"> 2604</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;pulse energy&quot;</span>, termValue);</div>
<div class="line"><a name="l02605"></a><span class="lineno"> 2605</span>&#160;        }</div>
<div class="line"><a name="l02606"></a><span class="lineno"> 2606</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000847&quot;</span>) <span class="comment">// pulse duration</span></div>
<div class="line"><a name="l02607"></a><span class="lineno"> 2607</span>&#160;        {</div>
<div class="line"><a name="l02608"></a><span class="lineno"> 2608</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02609"></a><span class="lineno"> 2609</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;pulse duration&quot;</span>, termValue);</div>
<div class="line"><a name="l02610"></a><span class="lineno"> 2610</span>&#160;        }</div>
<div class="line"><a name="l02611"></a><span class="lineno"> 2611</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000848&quot;</span>) <span class="comment">// attenuation</span></div>
<div class="line"><a name="l02612"></a><span class="lineno"> 2612</span>&#160;        {</div>
<div class="line"><a name="l02613"></a><span class="lineno"> 2613</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02614"></a><span class="lineno"> 2614</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;attenuation&quot;</span>, termValue);</div>
<div class="line"><a name="l02615"></a><span class="lineno"> 2615</span>&#160;        }</div>
<div class="line"><a name="l02616"></a><span class="lineno"> 2616</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000849&quot;</span>) <span class="comment">// impact angle</span></div>
<div class="line"><a name="l02617"></a><span class="lineno"> 2617</span>&#160;        {</div>
<div class="line"><a name="l02618"></a><span class="lineno"> 2618</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02619"></a><span class="lineno"> 2619</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;impact angle&quot;</span>, termValue);</div>
<div class="line"><a name="l02620"></a><span class="lineno"> 2620</span>&#160;        }</div>
<div class="line"><a name="l02621"></a><span class="lineno"> 2621</span>&#160;        <span class="comment">//laser type</span></div>
<div class="line"><a name="l02622"></a><span class="lineno"> 2622</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000850&quot;</span>) <span class="comment">// gas laser</span></div>
<div class="line"><a name="l02623"></a><span class="lineno"> 2623</span>&#160;        {</div>
<div class="line"><a name="l02624"></a><span class="lineno"> 2624</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02625"></a><span class="lineno"> 2625</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;laser type&quot;</span>, <span class="stringliteral">&quot;gas laser&quot;</span>);</div>
<div class="line"><a name="l02626"></a><span class="lineno"> 2626</span>&#160;        }</div>
<div class="line"><a name="l02627"></a><span class="lineno"> 2627</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000851&quot;</span>) <span class="comment">// solid-state laser</span></div>
<div class="line"><a name="l02628"></a><span class="lineno"> 2628</span>&#160;        {</div>
<div class="line"><a name="l02629"></a><span class="lineno"> 2629</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02630"></a><span class="lineno"> 2630</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;laser type&quot;</span>, <span class="stringliteral">&quot;solid-state laser&quot;</span>);</div>
<div class="line"><a name="l02631"></a><span class="lineno"> 2631</span>&#160;        }</div>
<div class="line"><a name="l02632"></a><span class="lineno"> 2632</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000852&quot;</span>) <span class="comment">// dye-laser</span></div>
<div class="line"><a name="l02633"></a><span class="lineno"> 2633</span>&#160;        {</div>
<div class="line"><a name="l02634"></a><span class="lineno"> 2634</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02635"></a><span class="lineno"> 2635</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;laser type&quot;</span>, <span class="stringliteral">&quot;dye-laser&quot;</span>);</div>
<div class="line"><a name="l02636"></a><span class="lineno"> 2636</span>&#160;        }</div>
<div class="line"><a name="l02637"></a><span class="lineno"> 2637</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000853&quot;</span>) <span class="comment">// free electron laser</span></div>
<div class="line"><a name="l02638"></a><span class="lineno"> 2638</span>&#160;        {</div>
<div class="line"><a name="l02639"></a><span class="lineno"> 2639</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02640"></a><span class="lineno"> 2640</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;laser type&quot;</span>, <span class="stringliteral">&quot;free electron laser&quot;</span>);</div>
<div class="line"><a name="l02641"></a><span class="lineno"> 2641</span>&#160;        }</div>
<div class="line"><a name="l02642"></a><span class="lineno"> 2642</span>&#160;        <span class="comment">//MALDI matrix application</span></div>
<div class="line"><a name="l02643"></a><span class="lineno"> 2643</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000834&quot;</span>) <span class="comment">// matrix solution</span></div>
<div class="line"><a name="l02644"></a><span class="lineno"> 2644</span>&#160;        {</div>
<div class="line"><a name="l02645"></a><span class="lineno"> 2645</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02646"></a><span class="lineno"> 2646</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;matrix solution&quot;</span>, termValue);</div>
<div class="line"><a name="l02647"></a><span class="lineno"> 2647</span>&#160;        }</div>
<div class="line"><a name="l02648"></a><span class="lineno"> 2648</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000835&quot;</span>) <span class="comment">// matrix solution concentration</span></div>
<div class="line"><a name="l02649"></a><span class="lineno"> 2649</span>&#160;        {</div>
<div class="line"><a name="l02650"></a><span class="lineno"> 2650</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02651"></a><span class="lineno"> 2651</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;matrix solution concentration&quot;</span>, termValue);</div>
<div class="line"><a name="l02652"></a><span class="lineno"> 2652</span>&#160;        }</div>
<div class="line"><a name="l02653"></a><span class="lineno"> 2653</span>&#160;        <span class="comment">// matrix application type</span></div>
<div class="line"><a name="l02654"></a><span class="lineno"> 2654</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000836&quot;</span>) <span class="comment">// dried dropplet</span></div>
<div class="line"><a name="l02655"></a><span class="lineno"> 2655</span>&#160;        {</div>
<div class="line"><a name="l02656"></a><span class="lineno"> 2656</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02657"></a><span class="lineno"> 2657</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;matrix application type&quot;</span>, <span class="stringliteral">&quot;dried dropplet&quot;</span>);</div>
<div class="line"><a name="l02658"></a><span class="lineno"> 2658</span>&#160;        }</div>
<div class="line"><a name="l02659"></a><span class="lineno"> 2659</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000837&quot;</span>) <span class="comment">// printed</span></div>
<div class="line"><a name="l02660"></a><span class="lineno"> 2660</span>&#160;        {</div>
<div class="line"><a name="l02661"></a><span class="lineno"> 2661</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02662"></a><span class="lineno"> 2662</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;matrix application type&quot;</span>, <span class="stringliteral">&quot;printed&quot;</span>);</div>
<div class="line"><a name="l02663"></a><span class="lineno"> 2663</span>&#160;        }</div>
<div class="line"><a name="l02664"></a><span class="lineno"> 2664</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000838&quot;</span>) <span class="comment">// sprayed</span></div>
<div class="line"><a name="l02665"></a><span class="lineno"> 2665</span>&#160;        {</div>
<div class="line"><a name="l02666"></a><span class="lineno"> 2666</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02667"></a><span class="lineno"> 2667</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;matrix application type&quot;</span>, <span class="stringliteral">&quot;sprayed&quot;</span>);</div>
<div class="line"><a name="l02668"></a><span class="lineno"> 2668</span>&#160;        }</div>
<div class="line"><a name="l02669"></a><span class="lineno"> 2669</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000839&quot;</span>) <span class="comment">//  precoated plate</span></div>
<div class="line"><a name="l02670"></a><span class="lineno"> 2670</span>&#160;        {</div>
<div class="line"><a name="l02671"></a><span class="lineno"> 2671</span>&#160;          <span class="comment">//No member =&gt; meta data</span></div>
<div class="line"><a name="l02672"></a><span class="lineno"> 2672</span>&#160;          instruments_[current_id_].getIonSources().back().setMetaValue(<span class="stringliteral">&quot;matrix application type&quot;</span>, <span class="stringliteral">&quot; precoated plate&quot;</span>);</div>
<div class="line"><a name="l02673"></a><span class="lineno"> 2673</span>&#160;        }</div>
<div class="line"><a name="l02674"></a><span class="lineno"> 2674</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02675"></a><span class="lineno"> 2675</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02676"></a><span class="lineno"> 2676</span>&#160;      }</div>
<div class="line"><a name="l02677"></a><span class="lineno"> 2677</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;analyzer&quot;</span>)</div>
<div class="line"><a name="l02678"></a><span class="lineno"> 2678</span>&#160;      {</div>
<div class="line"><a name="l02679"></a><span class="lineno"> 2679</span>&#160;        <span class="comment">//mass analyzer type</span></div>
<div class="line"><a name="l02680"></a><span class="lineno"> 2680</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000079&quot;</span>) <span class="comment">//fourier transform ion cyclotron resonance mass spectrometer</span></div>
<div class="line"><a name="l02681"></a><span class="lineno"> 2681</span>&#160;        {</div>
<div class="line"><a name="l02682"></a><span class="lineno"> 2682</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a30b4d649b3cd56fb7e6aa514b67dc75a">MassAnalyzer::FOURIERTRANSFORM</a>);</div>
<div class="line"><a name="l02683"></a><span class="lineno"> 2683</span>&#160;        }</div>
<div class="line"><a name="l02684"></a><span class="lineno"> 2684</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000080&quot;</span>) <span class="comment">//magnetic sector</span></div>
<div class="line"><a name="l02685"></a><span class="lineno"> 2685</span>&#160;        {</div>
<div class="line"><a name="l02686"></a><span class="lineno"> 2686</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a805264162c317eb0e81b8aa508726725">MassAnalyzer::SECTOR</a>);</div>
<div class="line"><a name="l02687"></a><span class="lineno"> 2687</span>&#160;        }</div>
<div class="line"><a name="l02688"></a><span class="lineno"> 2688</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000081&quot;</span>) <span class="comment">//quadrupole</span></div>
<div class="line"><a name="l02689"></a><span class="lineno"> 2689</span>&#160;        {</div>
<div class="line"><a name="l02690"></a><span class="lineno"> 2690</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ad9bdaac4d0e7c5cb182ae5da106a75c1">MassAnalyzer::QUADRUPOLE</a>);</div>
<div class="line"><a name="l02691"></a><span class="lineno"> 2691</span>&#160;        }</div>
<div class="line"><a name="l02692"></a><span class="lineno"> 2692</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000084&quot;</span>) <span class="comment">//time-of-flight</span></div>
<div class="line"><a name="l02693"></a><span class="lineno"> 2693</span>&#160;        {</div>
<div class="line"><a name="l02694"></a><span class="lineno"> 2694</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ac18e0fdb830eeb3a7f657a75000744db">MassAnalyzer::TOF</a>);</div>
<div class="line"><a name="l02695"></a><span class="lineno"> 2695</span>&#160;        }</div>
<div class="line"><a name="l02696"></a><span class="lineno"> 2696</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000254&quot;</span>) <span class="comment">//electrostatic energy analyzer</span></div>
<div class="line"><a name="l02697"></a><span class="lineno"> 2697</span>&#160;        {</div>
<div class="line"><a name="l02698"></a><span class="lineno"> 2698</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ab7a09aace4e7aa91599309ab8b613bb4">MassAnalyzer::ESA</a>);</div>
<div class="line"><a name="l02699"></a><span class="lineno"> 2699</span>&#160;        }</div>
<div class="line"><a name="l02700"></a><span class="lineno"> 2700</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000264&quot;</span>) <span class="comment">//ion trap</span></div>
<div class="line"><a name="l02701"></a><span class="lineno"> 2701</span>&#160;        {</div>
<div class="line"><a name="l02702"></a><span class="lineno"> 2702</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ae9e2537cbd38bd116d7bdb8b634f991a">MassAnalyzer::IT</a>);</div>
<div class="line"><a name="l02703"></a><span class="lineno"> 2703</span>&#160;        }</div>
<div class="line"><a name="l02704"></a><span class="lineno"> 2704</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000284&quot;</span>) <span class="comment">//stored waveform inverse fourier transform</span></div>
<div class="line"><a name="l02705"></a><span class="lineno"> 2705</span>&#160;        {</div>
<div class="line"><a name="l02706"></a><span class="lineno"> 2706</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a1cd375d755f36023b93bbd8afd1316f3">MassAnalyzer::SWIFT</a>);</div>
<div class="line"><a name="l02707"></a><span class="lineno"> 2707</span>&#160;        }</div>
<div class="line"><a name="l02708"></a><span class="lineno"> 2708</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000288&quot;</span>) <span class="comment">//cyclotron</span></div>
<div class="line"><a name="l02709"></a><span class="lineno"> 2709</span>&#160;        {</div>
<div class="line"><a name="l02710"></a><span class="lineno"> 2710</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ac59fe43006f5fee91317753c98fb6fb3">MassAnalyzer::CYCLOTRON</a>);</div>
<div class="line"><a name="l02711"></a><span class="lineno"> 2711</span>&#160;        }</div>
<div class="line"><a name="l02712"></a><span class="lineno"> 2712</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000484&quot;</span>) <span class="comment">//orbitrap</span></div>
<div class="line"><a name="l02713"></a><span class="lineno"> 2713</span>&#160;        {</div>
<div class="line"><a name="l02714"></a><span class="lineno"> 2714</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a5d02c7b244115a39bcb42170c21d0a58">MassAnalyzer::ORBITRAP</a>);</div>
<div class="line"><a name="l02715"></a><span class="lineno"> 2715</span>&#160;        }</div>
<div class="line"><a name="l02716"></a><span class="lineno"> 2716</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000078&quot;</span>) <span class="comment">//axial ejection linear ion trap</span></div>
<div class="line"><a name="l02717"></a><span class="lineno"> 2717</span>&#160;        {</div>
<div class="line"><a name="l02718"></a><span class="lineno"> 2718</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ace4c2a8d1433baa487103cbcd83bbb01">MassAnalyzer::AXIALEJECTIONLINEARIONTRAP</a>);</div>
<div class="line"><a name="l02719"></a><span class="lineno"> 2719</span>&#160;        }</div>
<div class="line"><a name="l02720"></a><span class="lineno"> 2720</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000082&quot;</span>) <span class="comment">//quadrupole ion trap</span></div>
<div class="line"><a name="l02721"></a><span class="lineno"> 2721</span>&#160;        {</div>
<div class="line"><a name="l02722"></a><span class="lineno"> 2722</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a1a7f597d623d72306c8adbdbfaaa350d">MassAnalyzer::PAULIONTRAP</a>);</div>
<div class="line"><a name="l02723"></a><span class="lineno"> 2723</span>&#160;        }</div>
<div class="line"><a name="l02724"></a><span class="lineno"> 2724</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000083&quot;</span>) <span class="comment">//radial ejection linear ion trap</span></div>
<div class="line"><a name="l02725"></a><span class="lineno"> 2725</span>&#160;        {</div>
<div class="line"><a name="l02726"></a><span class="lineno"> 2726</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a3da723842841c3ff4194d0d71b0da0fd">MassAnalyzer::RADIALEJECTIONLINEARIONTRAP</a>);</div>
<div class="line"><a name="l02727"></a><span class="lineno"> 2727</span>&#160;        }</div>
<div class="line"><a name="l02728"></a><span class="lineno"> 2728</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000291&quot;</span>) <span class="comment">//linear ion trap</span></div>
<div class="line"><a name="l02729"></a><span class="lineno"> 2729</span>&#160;        {</div>
<div class="line"><a name="l02730"></a><span class="lineno"> 2730</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a3b759690471ed29ecd243a8f36b93f60">MassAnalyzer::LIT</a>);</div>
<div class="line"><a name="l02731"></a><span class="lineno"> 2731</span>&#160;        }</div>
<div class="line"><a name="l02732"></a><span class="lineno"> 2732</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000443&quot;</span>) <span class="comment">//mass analyzer type (base term)</span></div>
<div class="line"><a name="l02733"></a><span class="lineno"> 2733</span>&#160;        {</div>
<div class="line"><a name="l02734"></a><span class="lineno"> 2734</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setType(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a39869181b0414af3507c53e260851151">MassAnalyzer::ANALYZERNULL</a>);</div>
<div class="line"><a name="l02735"></a><span class="lineno"> 2735</span>&#160;        }</div>
<div class="line"><a name="l02736"></a><span class="lineno"> 2736</span>&#160;        <span class="comment">//mass analyzer attribute</span></div>
<div class="line"><a name="l02737"></a><span class="lineno"> 2737</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000014&quot;</span>) <span class="comment">//accuracy (ppm)</span></div>
<div class="line"><a name="l02738"></a><span class="lineno"> 2738</span>&#160;        {</div>
<div class="line"><a name="l02739"></a><span class="lineno"> 2739</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setAccuracy(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02740"></a><span class="lineno"> 2740</span>&#160;        }</div>
<div class="line"><a name="l02741"></a><span class="lineno"> 2741</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000022&quot;</span>) <span class="comment">//TOF Total Path Length (meter)</span></div>
<div class="line"><a name="l02742"></a><span class="lineno"> 2742</span>&#160;        {</div>
<div class="line"><a name="l02743"></a><span class="lineno"> 2743</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setTOFTotalPathLength(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02744"></a><span class="lineno"> 2744</span>&#160;        }</div>
<div class="line"><a name="l02745"></a><span class="lineno"> 2745</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000024&quot;</span>) <span class="comment">//final MS exponent</span></div>
<div class="line"><a name="l02746"></a><span class="lineno"> 2746</span>&#160;        {</div>
<div class="line"><a name="l02747"></a><span class="lineno"> 2747</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setFinalMSExponent(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l02748"></a><span class="lineno"> 2748</span>&#160;        }</div>
<div class="line"><a name="l02749"></a><span class="lineno"> 2749</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000025&quot;</span>) <span class="comment">//magnetic field strength (tesla)</span></div>
<div class="line"><a name="l02750"></a><span class="lineno"> 2750</span>&#160;        {</div>
<div class="line"><a name="l02751"></a><span class="lineno"> 2751</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setMagneticFieldStrength(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02752"></a><span class="lineno"> 2752</span>&#160;        }</div>
<div class="line"><a name="l02753"></a><span class="lineno"> 2753</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000105&quot;</span>) <span class="comment">//reflectron off</span></div>
<div class="line"><a name="l02754"></a><span class="lineno"> 2754</span>&#160;        {</div>
<div class="line"><a name="l02755"></a><span class="lineno"> 2755</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setReflectronState(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52faac132f2982b98bcaa3445e535a03ff75">MassAnalyzer::OFF</a>);</div>
<div class="line"><a name="l02756"></a><span class="lineno"> 2756</span>&#160;        }</div>
<div class="line"><a name="l02757"></a><span class="lineno"> 2757</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000106&quot;</span>) <span class="comment">//reflectron on</span></div>
<div class="line"><a name="l02758"></a><span class="lineno"> 2758</span>&#160;        {</div>
<div class="line"><a name="l02759"></a><span class="lineno"> 2759</span>&#160;          instruments_[current_id_].getMassAnalyzers().back().setReflectronState(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52fa977d478dacaae531f95695750d1e9d03">MassAnalyzer::ON</a>);</div>
<div class="line"><a name="l02760"></a><span class="lineno"> 2760</span>&#160;        }</div>
<div class="line"><a name="l02761"></a><span class="lineno"> 2761</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02762"></a><span class="lineno"> 2762</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02763"></a><span class="lineno"> 2763</span>&#160;      }</div>
<div class="line"><a name="l02764"></a><span class="lineno"> 2764</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;detector&quot;</span>)</div>
<div class="line"><a name="l02765"></a><span class="lineno"> 2765</span>&#160;      {</div>
<div class="line"><a name="l02766"></a><span class="lineno"> 2766</span>&#160;        <span class="comment">//detector type</span></div>
<div class="line"><a name="l02767"></a><span class="lineno"> 2767</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000107&quot;</span>) <span class="comment">//channeltron</span></div>
<div class="line"><a name="l02768"></a><span class="lineno"> 2768</span>&#160;        {</div>
<div class="line"><a name="l02769"></a><span class="lineno"> 2769</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7acf7c454254df079071463f080099b4b3">IonDetector::CHANNELTRON</a>);</div>
<div class="line"><a name="l02770"></a><span class="lineno"> 2770</span>&#160;        }</div>
<div class="line"><a name="l02771"></a><span class="lineno"> 2771</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000110&quot;</span>) <span class="comment">//daly detector</span></div>
<div class="line"><a name="l02772"></a><span class="lineno"> 2772</span>&#160;        {</div>
<div class="line"><a name="l02773"></a><span class="lineno"> 2773</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ac251cfb1e58eccf7b508c730505ea75e">IonDetector::DALYDETECTOR</a>);</div>
<div class="line"><a name="l02774"></a><span class="lineno"> 2774</span>&#160;        }</div>
<div class="line"><a name="l02775"></a><span class="lineno"> 2775</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000112&quot;</span>) <span class="comment">//faraday cup</span></div>
<div class="line"><a name="l02776"></a><span class="lineno"> 2776</span>&#160;        {</div>
<div class="line"><a name="l02777"></a><span class="lineno"> 2777</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a1019d3d05762a5ea12ffec336dd45c35">IonDetector::FARADAYCUP</a>);</div>
<div class="line"><a name="l02778"></a><span class="lineno"> 2778</span>&#160;        }</div>
<div class="line"><a name="l02779"></a><span class="lineno"> 2779</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000114&quot;</span>) <span class="comment">//microchannel plate detector</span></div>
<div class="line"><a name="l02780"></a><span class="lineno"> 2780</span>&#160;        {</div>
<div class="line"><a name="l02781"></a><span class="lineno"> 2781</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a8e54f1259bd67fbaa579f32b73b34482">IonDetector::MICROCHANNELPLATEDETECTOR</a>);</div>
<div class="line"><a name="l02782"></a><span class="lineno"> 2782</span>&#160;        }</div>
<div class="line"><a name="l02783"></a><span class="lineno"> 2783</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000115&quot;</span>) <span class="comment">//multi-collector</span></div>
<div class="line"><a name="l02784"></a><span class="lineno"> 2784</span>&#160;        {</div>
<div class="line"><a name="l02785"></a><span class="lineno"> 2785</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7aa6af6570fb6cf6172b241f4230d0bd9f">IonDetector::MULTICOLLECTOR</a>);</div>
<div class="line"><a name="l02786"></a><span class="lineno"> 2786</span>&#160;        }</div>
<div class="line"><a name="l02787"></a><span class="lineno"> 2787</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000116&quot;</span>) <span class="comment">//photomultiplier</span></div>
<div class="line"><a name="l02788"></a><span class="lineno"> 2788</span>&#160;        {</div>
<div class="line"><a name="l02789"></a><span class="lineno"> 2789</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a80abf032317ac0521e7ea0c601e3b387">IonDetector::PHOTOMULTIPLIER</a>);</div>
<div class="line"><a name="l02790"></a><span class="lineno"> 2790</span>&#160;        }</div>
<div class="line"><a name="l02791"></a><span class="lineno"> 2791</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000253&quot;</span>) <span class="comment">//electron multiplier</span></div>
<div class="line"><a name="l02792"></a><span class="lineno"> 2792</span>&#160;        {</div>
<div class="line"><a name="l02793"></a><span class="lineno"> 2793</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a5fd9b4a1925c08d12d8d0d3a43b0ab8c">IonDetector::ELECTRONMULTIPLIER</a>);</div>
<div class="line"><a name="l02794"></a><span class="lineno"> 2794</span>&#160;        }</div>
<div class="line"><a name="l02795"></a><span class="lineno"> 2795</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000345&quot;</span>) <span class="comment">//array detector</span></div>
<div class="line"><a name="l02796"></a><span class="lineno"> 2796</span>&#160;        {</div>
<div class="line"><a name="l02797"></a><span class="lineno"> 2797</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a04a49f0fe9b8b9be26628d0bd8ee0882">IonDetector::ARRAYDETECTOR</a>);</div>
<div class="line"><a name="l02798"></a><span class="lineno"> 2798</span>&#160;        }</div>
<div class="line"><a name="l02799"></a><span class="lineno"> 2799</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000346&quot;</span>) <span class="comment">//conversion dynode</span></div>
<div class="line"><a name="l02800"></a><span class="lineno"> 2800</span>&#160;        {</div>
<div class="line"><a name="l02801"></a><span class="lineno"> 2801</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a671a0183b391575bccbe91a826e831a2">IonDetector::CONVERSIONDYNODE</a>);</div>
<div class="line"><a name="l02802"></a><span class="lineno"> 2802</span>&#160;        }</div>
<div class="line"><a name="l02803"></a><span class="lineno"> 2803</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000347&quot;</span>) <span class="comment">//dynode</span></div>
<div class="line"><a name="l02804"></a><span class="lineno"> 2804</span>&#160;        {</div>
<div class="line"><a name="l02805"></a><span class="lineno"> 2805</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a54d74359f2cede6481a434f8634be324">IonDetector::DYNODE</a>);</div>
<div class="line"><a name="l02806"></a><span class="lineno"> 2806</span>&#160;        }</div>
<div class="line"><a name="l02807"></a><span class="lineno"> 2807</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000348&quot;</span>) <span class="comment">//focal plane collector</span></div>
<div class="line"><a name="l02808"></a><span class="lineno"> 2808</span>&#160;        {</div>
<div class="line"><a name="l02809"></a><span class="lineno"> 2809</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a27064596541d23c1b3040817e417d39c">IonDetector::FOCALPLANECOLLECTOR</a>);</div>
<div class="line"><a name="l02810"></a><span class="lineno"> 2810</span>&#160;        }</div>
<div class="line"><a name="l02811"></a><span class="lineno"> 2811</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000349&quot;</span>) <span class="comment">//ion-to-photon detector</span></div>
<div class="line"><a name="l02812"></a><span class="lineno"> 2812</span>&#160;        {</div>
<div class="line"><a name="l02813"></a><span class="lineno"> 2813</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ac49f262a3810cbb127ca53b2a804b719">IonDetector::IONTOPHOTONDETECTOR</a>);</div>
<div class="line"><a name="l02814"></a><span class="lineno"> 2814</span>&#160;        }</div>
<div class="line"><a name="l02815"></a><span class="lineno"> 2815</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000350&quot;</span>) <span class="comment">//point collector</span></div>
<div class="line"><a name="l02816"></a><span class="lineno"> 2816</span>&#160;        {</div>
<div class="line"><a name="l02817"></a><span class="lineno"> 2817</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a74d32454593ae69307e86dbca912a605">IonDetector::POINTCOLLECTOR</a>);</div>
<div class="line"><a name="l02818"></a><span class="lineno"> 2818</span>&#160;        }</div>
<div class="line"><a name="l02819"></a><span class="lineno"> 2819</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000351&quot;</span>) <span class="comment">//postacceleration detector</span></div>
<div class="line"><a name="l02820"></a><span class="lineno"> 2820</span>&#160;        {</div>
<div class="line"><a name="l02821"></a><span class="lineno"> 2821</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ab853daddf114acf995e3486fe604e849">IonDetector::POSTACCELERATIONDETECTOR</a>);</div>
<div class="line"><a name="l02822"></a><span class="lineno"> 2822</span>&#160;        }</div>
<div class="line"><a name="l02823"></a><span class="lineno"> 2823</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000621&quot;</span>) <span class="comment">//photodiode array detector</span></div>
<div class="line"><a name="l02824"></a><span class="lineno"> 2824</span>&#160;        {</div>
<div class="line"><a name="l02825"></a><span class="lineno"> 2825</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a2b44c2af82a0218d3cb5faa3d163fa1f">IonDetector::PHOTODIODEARRAYDETECTOR</a>);</div>
<div class="line"><a name="l02826"></a><span class="lineno"> 2826</span>&#160;        }</div>
<div class="line"><a name="l02827"></a><span class="lineno"> 2827</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000624&quot;</span>) <span class="comment">//inductive detector</span></div>
<div class="line"><a name="l02828"></a><span class="lineno"> 2828</span>&#160;        {</div>
<div class="line"><a name="l02829"></a><span class="lineno"> 2829</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a0f812ecbbe9fffeec4cee4ad92c5a2ce">IonDetector::INDUCTIVEDETECTOR</a>);</div>
<div class="line"><a name="l02830"></a><span class="lineno"> 2830</span>&#160;        }</div>
<div class="line"><a name="l02831"></a><span class="lineno"> 2831</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000108&quot;</span>) <span class="comment">//conversion dynode electron multiplier</span></div>
<div class="line"><a name="l02832"></a><span class="lineno"> 2832</span>&#160;        {</div>
<div class="line"><a name="l02833"></a><span class="lineno"> 2833</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a7ab83a85e2b66a4d8c4e0a6ccac159c7">IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER</a>);</div>
<div class="line"><a name="l02834"></a><span class="lineno"> 2834</span>&#160;        }</div>
<div class="line"><a name="l02835"></a><span class="lineno"> 2835</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000109&quot;</span>) <span class="comment">//conversion dynode photomultiplier</span></div>
<div class="line"><a name="l02836"></a><span class="lineno"> 2836</span>&#160;        {</div>
<div class="line"><a name="l02837"></a><span class="lineno"> 2837</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a2a909086473828f229ef69ee60230fd2">IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER</a>);</div>
<div class="line"><a name="l02838"></a><span class="lineno"> 2838</span>&#160;        }</div>
<div class="line"><a name="l02839"></a><span class="lineno"> 2839</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000111&quot;</span>) <span class="comment">//electron multiplier tube</span></div>
<div class="line"><a name="l02840"></a><span class="lineno"> 2840</span>&#160;        {</div>
<div class="line"><a name="l02841"></a><span class="lineno"> 2841</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7acfbc26fbfdecb47353d1ef9712c4b86d">IonDetector::ELECTRONMULTIPLIERTUBE</a>);</div>
<div class="line"><a name="l02842"></a><span class="lineno"> 2842</span>&#160;        }</div>
<div class="line"><a name="l02843"></a><span class="lineno"> 2843</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000113&quot;</span>) <span class="comment">//focal plane array</span></div>
<div class="line"><a name="l02844"></a><span class="lineno"> 2844</span>&#160;        {</div>
<div class="line"><a name="l02845"></a><span class="lineno"> 2845</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7af12c576ac46ce5b814f2613b1aebedc8">IonDetector::FOCALPLANEARRAY</a>);</div>
<div class="line"><a name="l02846"></a><span class="lineno"> 2846</span>&#160;        }</div>
<div class="line"><a name="l02847"></a><span class="lineno"> 2847</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000026&quot;</span>) <span class="comment">//detector type (base term)</span></div>
<div class="line"><a name="l02848"></a><span class="lineno"> 2848</span>&#160;        {</div>
<div class="line"><a name="l02849"></a><span class="lineno"> 2849</span>&#160;          instruments_[current_id_].getIonDetectors().back().setType(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a7d066f30823d68dafa1f1746027390b5">IonDetector::TYPENULL</a>);</div>
<div class="line"><a name="l02850"></a><span class="lineno"> 2850</span>&#160;        }</div>
<div class="line"><a name="l02851"></a><span class="lineno"> 2851</span>&#160;        <span class="comment">//detector attribute</span></div>
<div class="line"><a name="l02852"></a><span class="lineno"> 2852</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000028&quot;</span>) <span class="comment">//detector resolution</span></div>
<div class="line"><a name="l02853"></a><span class="lineno"> 2853</span>&#160;        {</div>
<div class="line"><a name="l02854"></a><span class="lineno"> 2854</span>&#160;          instruments_[current_id_].getIonDetectors().back().setResolution(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02855"></a><span class="lineno"> 2855</span>&#160;        }</div>
<div class="line"><a name="l02856"></a><span class="lineno"> 2856</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000029&quot;</span>) <span class="comment">//sampling frequency</span></div>
<div class="line"><a name="l02857"></a><span class="lineno"> 2857</span>&#160;        {</div>
<div class="line"><a name="l02858"></a><span class="lineno"> 2858</span>&#160;          instruments_[current_id_].getIonDetectors().back().setADCSamplingFrequency(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l02859"></a><span class="lineno"> 2859</span>&#160;        }</div>
<div class="line"><a name="l02860"></a><span class="lineno"> 2860</span>&#160;        <span class="comment">//dectector acquisition mode</span></div>
<div class="line"><a name="l02861"></a><span class="lineno"> 2861</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000117&quot;</span>) <span class="comment">//analog-digital converter</span></div>
<div class="line"><a name="l02862"></a><span class="lineno"> 2862</span>&#160;        {</div>
<div class="line"><a name="l02863"></a><span class="lineno"> 2863</span>&#160;          instruments_[current_id_].getIonDetectors().back().setAcquisitionMode(<a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a5ec0e8ce4c96673614190a8852261f4f">IonDetector::ADC</a>);</div>
<div class="line"><a name="l02864"></a><span class="lineno"> 2864</span>&#160;        }</div>
<div class="line"><a name="l02865"></a><span class="lineno"> 2865</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000118&quot;</span>) <span class="comment">//pulse counting</span></div>
<div class="line"><a name="l02866"></a><span class="lineno"> 2866</span>&#160;        {</div>
<div class="line"><a name="l02867"></a><span class="lineno"> 2867</span>&#160;          instruments_[current_id_].getIonDetectors().back().setAcquisitionMode(<a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a1b9d0cc39dc3d1de4db442674ca8761b">IonDetector::PULSECOUNTING</a>);</div>
<div class="line"><a name="l02868"></a><span class="lineno"> 2868</span>&#160;        }</div>
<div class="line"><a name="l02869"></a><span class="lineno"> 2869</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000119&quot;</span>) <span class="comment">//time-digital converter</span></div>
<div class="line"><a name="l02870"></a><span class="lineno"> 2870</span>&#160;        {</div>
<div class="line"><a name="l02871"></a><span class="lineno"> 2871</span>&#160;          instruments_[current_id_].getIonDetectors().back().setAcquisitionMode(<a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a09970273b87198398bb9192b84b8eea7">IonDetector::TDC</a>);</div>
<div class="line"><a name="l02872"></a><span class="lineno"> 2872</span>&#160;        }</div>
<div class="line"><a name="l02873"></a><span class="lineno"> 2873</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000120&quot;</span>) <span class="comment">//transient recorder</span></div>
<div class="line"><a name="l02874"></a><span class="lineno"> 2874</span>&#160;        {</div>
<div class="line"><a name="l02875"></a><span class="lineno"> 2875</span>&#160;          instruments_[current_id_].getIonDetectors().back().setAcquisitionMode(<a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a7caeaaac284597b2a217cbd43f8c7233">IonDetector::TRANSIENTRECORDER</a>);</div>
<div class="line"><a name="l02876"></a><span class="lineno"> 2876</span>&#160;        }</div>
<div class="line"><a name="l02877"></a><span class="lineno"> 2877</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02878"></a><span class="lineno"> 2878</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02879"></a><span class="lineno"> 2879</span>&#160;      }</div>
<div class="line"><a name="l02880"></a><span class="lineno"> 2880</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;processingMethod&quot;</span>)</div>
<div class="line"><a name="l02881"></a><span class="lineno"> 2881</span>&#160;      {</div>
<div class="line"><a name="l02882"></a><span class="lineno"> 2882</span>&#160;        <span class="comment">//data processing parameter</span></div>
<div class="line"><a name="l02883"></a><span class="lineno"> 2883</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000629&quot;</span>) <span class="comment">//low intensity threshold (ion count)</span></div>
<div class="line"><a name="l02884"></a><span class="lineno"> 2884</span>&#160;        {</div>
<div class="line"><a name="l02885"></a><span class="lineno"> 2885</span>&#160;          processing_[current_id_].back().setMetaValue(<span class="stringliteral">&quot;low_intensity_threshold&quot;</span>, termValue);</div>
<div class="line"><a name="l02886"></a><span class="lineno"> 2886</span>&#160;        }</div>
<div class="line"><a name="l02887"></a><span class="lineno"> 2887</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000631&quot;</span>) <span class="comment">//high intensity threshold (ion count)</span></div>
<div class="line"><a name="l02888"></a><span class="lineno"> 2888</span>&#160;        {</div>
<div class="line"><a name="l02889"></a><span class="lineno"> 2889</span>&#160;          processing_[current_id_].back().setMetaValue(<span class="stringliteral">&quot;high_intensity_threshold&quot;</span>, termValue);</div>
<div class="line"><a name="l02890"></a><span class="lineno"> 2890</span>&#160;        }</div>
<div class="line"><a name="l02891"></a><span class="lineno"> 2891</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000787&quot;</span>) <span class="comment">//inclusive low intensity threshold</span></div>
<div class="line"><a name="l02892"></a><span class="lineno"> 2892</span>&#160;        {</div>
<div class="line"><a name="l02893"></a><span class="lineno"> 2893</span>&#160;          processing_[current_id_].back().setMetaValue(<span class="stringliteral">&quot;inclusive_low_intensity_threshold&quot;</span>, termValue);</div>
<div class="line"><a name="l02894"></a><span class="lineno"> 2894</span>&#160;        }</div>
<div class="line"><a name="l02895"></a><span class="lineno"> 2895</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000788&quot;</span>) <span class="comment">//inclusive high intensity threshold</span></div>
<div class="line"><a name="l02896"></a><span class="lineno"> 2896</span>&#160;        {</div>
<div class="line"><a name="l02897"></a><span class="lineno"> 2897</span>&#160;          processing_[current_id_].back().setMetaValue(<span class="stringliteral">&quot;inclusive_high_intensity_threshold&quot;</span>, termValue);</div>
<div class="line"><a name="l02898"></a><span class="lineno"> 2898</span>&#160;        }</div>
<div class="line"><a name="l02899"></a><span class="lineno"> 2899</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000747&quot;</span>) <span class="comment">//completion time</span></div>
<div class="line"><a name="l02900"></a><span class="lineno"> 2900</span>&#160;        {</div>
<div class="line"><a name="l02901"></a><span class="lineno"> 2901</span>&#160;          processing_[current_id_].back().setCompletionTime(asDateTime_(value));</div>
<div class="line"><a name="l02902"></a><span class="lineno"> 2902</span>&#160;        }</div>
<div class="line"><a name="l02903"></a><span class="lineno"> 2903</span>&#160;        <span class="comment">//file format conversion</span></div>
<div class="line"><a name="l02904"></a><span class="lineno"> 2904</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000530&quot;</span>) <span class="comment">//file format conversion</span></div>
<div class="line"><a name="l02905"></a><span class="lineno"> 2905</span>&#160;        {</div>
<div class="line"><a name="l02906"></a><span class="lineno"> 2906</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ab269e4bf446e6556e4f49a5737931643">DataProcessing::FORMAT_CONVERSION</a>);</div>
<div class="line"><a name="l02907"></a><span class="lineno"> 2907</span>&#160;        }</div>
<div class="line"><a name="l02908"></a><span class="lineno"> 2908</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000544&quot;</span>) <span class="comment">//Conversion to mzML</span></div>
<div class="line"><a name="l02909"></a><span class="lineno"> 2909</span>&#160;        {</div>
<div class="line"><a name="l02910"></a><span class="lineno"> 2910</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9abb654c12968c8c4c658d61af4a6e0765">DataProcessing::CONVERSION_MZML</a>);</div>
<div class="line"><a name="l02911"></a><span class="lineno"> 2911</span>&#160;        }</div>
<div class="line"><a name="l02912"></a><span class="lineno"> 2912</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000545&quot;</span>) <span class="comment">//Conversion to mzXML</span></div>
<div class="line"><a name="l02913"></a><span class="lineno"> 2913</span>&#160;        {</div>
<div class="line"><a name="l02914"></a><span class="lineno"> 2914</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ac6602550db94324f2d4b712d8962c4cd">DataProcessing::CONVERSION_MZXML</a>);</div>
<div class="line"><a name="l02915"></a><span class="lineno"> 2915</span>&#160;        }</div>
<div class="line"><a name="l02916"></a><span class="lineno"> 2916</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000546&quot;</span>) <span class="comment">//Conversion to mzData</span></div>
<div class="line"><a name="l02917"></a><span class="lineno"> 2917</span>&#160;        {</div>
<div class="line"><a name="l02918"></a><span class="lineno"> 2918</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ac7b870e1adfeb8747214d4ef5144376c">DataProcessing::CONVERSION_MZDATA</a>);</div>
<div class="line"><a name="l02919"></a><span class="lineno"> 2919</span>&#160;        }</div>
<div class="line"><a name="l02920"></a><span class="lineno"> 2920</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000741&quot;</span>) <span class="comment">//Conversion to DTA</span></div>
<div class="line"><a name="l02921"></a><span class="lineno"> 2921</span>&#160;        {</div>
<div class="line"><a name="l02922"></a><span class="lineno"> 2922</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9aa20c95ae75ff9c98d471a6e0c30b1f88">DataProcessing::CONVERSION_DTA</a>);</div>
<div class="line"><a name="l02923"></a><span class="lineno"> 2923</span>&#160;        }</div>
<div class="line"><a name="l02924"></a><span class="lineno"> 2924</span>&#160;        <span class="comment">//data processing action</span></div>
<div class="line"><a name="l02925"></a><span class="lineno"> 2925</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000543&quot;</span>) <span class="comment">//data processing action</span></div>
<div class="line"><a name="l02926"></a><span class="lineno"> 2926</span>&#160;        {</div>
<div class="line"><a name="l02927"></a><span class="lineno"> 2927</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ae75d9344e9e326323f2b485cd4c1e003">DataProcessing::DATA_PROCESSING</a>);</div>
<div class="line"><a name="l02928"></a><span class="lineno"> 2928</span>&#160;        }</div>
<div class="line"><a name="l02929"></a><span class="lineno"> 2929</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000033&quot;</span>) <span class="comment">//deisotoping</span></div>
<div class="line"><a name="l02930"></a><span class="lineno"> 2930</span>&#160;        {</div>
<div class="line"><a name="l02931"></a><span class="lineno"> 2931</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">DataProcessing::DEISOTOPING</a>);</div>
<div class="line"><a name="l02932"></a><span class="lineno"> 2932</span>&#160;        }</div>
<div class="line"><a name="l02933"></a><span class="lineno"> 2933</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000034&quot;</span>) <span class="comment">//charge deconvolution</span></div>
<div class="line"><a name="l02934"></a><span class="lineno"> 2934</span>&#160;        {</div>
<div class="line"><a name="l02935"></a><span class="lineno"> 2935</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">DataProcessing::CHARGE_DECONVOLUTION</a>);</div>
<div class="line"><a name="l02936"></a><span class="lineno"> 2936</span>&#160;        }</div>
<div class="line"><a name="l02937"></a><span class="lineno"> 2937</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000035&quot;</span> || cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000035&quot;</span>)) <span class="comment">//peak picking (or child terms, we make no difference)</span></div>
<div class="line"><a name="l02938"></a><span class="lineno"> 2938</span>&#160;        {</div>
<div class="line"><a name="l02939"></a><span class="lineno"> 2939</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">DataProcessing::PEAK_PICKING</a>);</div>
<div class="line"><a name="l02940"></a><span class="lineno"> 2940</span>&#160;        }</div>
<div class="line"><a name="l02941"></a><span class="lineno"> 2941</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000592&quot;</span> || cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000592&quot;</span>)) <span class="comment">//smoothing (or child terms, we make no difference)</span></div>
<div class="line"><a name="l02942"></a><span class="lineno"> 2942</span>&#160;        {</div>
<div class="line"><a name="l02943"></a><span class="lineno"> 2943</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad261194a1dded675599dfdc7212b63b1">DataProcessing::SMOOTHING</a>);</div>
<div class="line"><a name="l02944"></a><span class="lineno"> 2944</span>&#160;        }</div>
<div class="line"><a name="l02945"></a><span class="lineno"> 2945</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000778&quot;</span> || cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000778&quot;</span>)) <span class="comment">//charge state calculation (or child terms, we make no difference)</span></div>
<div class="line"><a name="l02946"></a><span class="lineno"> 2946</span>&#160;        {</div>
<div class="line"><a name="l02947"></a><span class="lineno"> 2947</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9af083c14a6a074a19ac7a75066eb83866">DataProcessing::CHARGE_CALCULATION</a>);</div>
<div class="line"><a name="l02948"></a><span class="lineno"> 2948</span>&#160;        }</div>
<div class="line"><a name="l02949"></a><span class="lineno"> 2949</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000780&quot;</span> || cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000780&quot;</span>)) <span class="comment">//precursor recalculation (or child terms, we make no difference)</span></div>
<div class="line"><a name="l02950"></a><span class="lineno"> 2950</span>&#160;        {</div>
<div class="line"><a name="l02951"></a><span class="lineno"> 2951</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a2ca454d58033fd433df401a2406fb173">DataProcessing::PRECURSOR_RECALCULATION</a>);</div>
<div class="line"><a name="l02952"></a><span class="lineno"> 2952</span>&#160;        }</div>
<div class="line"><a name="l02953"></a><span class="lineno"> 2953</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000593&quot;</span>) <span class="comment">//baseline reduction</span></div>
<div class="line"><a name="l02954"></a><span class="lineno"> 2954</span>&#160;        {</div>
<div class="line"><a name="l02955"></a><span class="lineno"> 2955</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9aec300465e654790d9154eb0d64ca3267">DataProcessing::BASELINE_REDUCTION</a>);</div>
<div class="line"><a name="l02956"></a><span class="lineno"> 2956</span>&#160;        }</div>
<div class="line"><a name="l02957"></a><span class="lineno"> 2957</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000745&quot;</span>) <span class="comment">//retention time alignment</span></div>
<div class="line"><a name="l02958"></a><span class="lineno"> 2958</span>&#160;        {</div>
<div class="line"><a name="l02959"></a><span class="lineno"> 2959</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">DataProcessing::ALIGNMENT</a>);</div>
<div class="line"><a name="l02960"></a><span class="lineno"> 2960</span>&#160;        }</div>
<div class="line"><a name="l02961"></a><span class="lineno"> 2961</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001484&quot;</span>) <span class="comment">//intensity normalization</span></div>
<div class="line"><a name="l02962"></a><span class="lineno"> 2962</span>&#160;        {</div>
<div class="line"><a name="l02963"></a><span class="lineno"> 2963</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a0de981225527baadd805eabc7a029173">DataProcessing::NORMALIZATION</a>);</div>
<div class="line"><a name="l02964"></a><span class="lineno"> 2964</span>&#160;        }</div>
<div class="line"><a name="l02965"></a><span class="lineno"> 2965</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001485&quot;</span>) <span class="comment">//m/z calibration</span></div>
<div class="line"><a name="l02966"></a><span class="lineno"> 2966</span>&#160;        {</div>
<div class="line"><a name="l02967"></a><span class="lineno"> 2967</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a03940d78fb7ee5fc71b49ca87cfdfb1c">DataProcessing::CALIBRATION</a>);</div>
<div class="line"><a name="l02968"></a><span class="lineno"> 2968</span>&#160;        }</div>
<div class="line"><a name="l02969"></a><span class="lineno"> 2969</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001486&quot;</span> || cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1001486&quot;</span>)) <span class="comment">//data filtering (or child terms, we make no difference)</span></div>
<div class="line"><a name="l02970"></a><span class="lineno"> 2970</span>&#160;        {</div>
<div class="line"><a name="l02971"></a><span class="lineno"> 2971</span>&#160;          processing_[current_id_].back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a9159f47bf89a34ad71b71f283ff09cd9">DataProcessing::FILTERING</a>);</div>
<div class="line"><a name="l02972"></a><span class="lineno"> 2972</span>&#160;        }</div>
<div class="line"><a name="l02973"></a><span class="lineno"> 2973</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02974"></a><span class="lineno"> 2974</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02975"></a><span class="lineno"> 2975</span>&#160;      }</div>
<div class="line"><a name="l02976"></a><span class="lineno"> 2976</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;fileContent&quot;</span>)</div>
<div class="line"><a name="l02977"></a><span class="lineno"> 2977</span>&#160;      {</div>
<div class="line"><a name="l02978"></a><span class="lineno"> 2978</span>&#160;        <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000524&quot;</span>)) <span class="comment">//data file content</span></div>
<div class="line"><a name="l02979"></a><span class="lineno"> 2979</span>&#160;        {</div>
<div class="line"><a name="l02980"></a><span class="lineno"> 2980</span>&#160;          <span class="comment">//ignored</span></div>
<div class="line"><a name="l02981"></a><span class="lineno"> 2981</span>&#160;          <span class="comment">//exp_-&gt;setMetaValue(name, termValue);</span></div>
<div class="line"><a name="l02982"></a><span class="lineno"> 2982</span>&#160;        }</div>
<div class="line"><a name="l02983"></a><span class="lineno"> 2983</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000525&quot;</span>)) <span class="comment">//spectrum representation</span></div>
<div class="line"><a name="l02984"></a><span class="lineno"> 2984</span>&#160;        {</div>
<div class="line"><a name="l02985"></a><span class="lineno"> 2985</span>&#160;          <span class="comment">//ignored</span></div>
<div class="line"><a name="l02986"></a><span class="lineno"> 2986</span>&#160;          <span class="comment">//exp_-&gt;setMetaValue(name, termValue);</span></div>
<div class="line"><a name="l02987"></a><span class="lineno"> 2987</span>&#160;        }</div>
<div class="line"><a name="l02988"></a><span class="lineno"> 2988</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02989"></a><span class="lineno"> 2989</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l02990"></a><span class="lineno"> 2990</span>&#160;      }</div>
<div class="line"><a name="l02991"></a><span class="lineno"> 2991</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;software&quot;</span>)</div>
<div class="line"><a name="l02992"></a><span class="lineno"> 2992</span>&#160;      {</div>
<div class="line"><a name="l02993"></a><span class="lineno"> 2993</span>&#160;        <span class="keywordflow">if</span> (cv_.isChildOf(accession, <span class="stringliteral">&quot;MS:1000531&quot;</span>)) <span class="comment">//software as string</span></div>
<div class="line"><a name="l02994"></a><span class="lineno"> 2994</span>&#160;        {</div>
<div class="line"><a name="l02995"></a><span class="lineno"> 2995</span>&#160;          <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000799&quot;</span>) <span class="comment">//custom unreleased software tool =&gt; use value as name</span></div>
<div class="line"><a name="l02996"></a><span class="lineno"> 2996</span>&#160;          {</div>
<div class="line"><a name="l02997"></a><span class="lineno"> 2997</span>&#160;            software_[current_id_].setName(value);</div>
<div class="line"><a name="l02998"></a><span class="lineno"> 2998</span>&#160;          }</div>
<div class="line"><a name="l02999"></a><span class="lineno"> 2999</span>&#160;          <span class="keywordflow">else</span> <span class="comment">//use name as name</span></div>
<div class="line"><a name="l03000"></a><span class="lineno"> 3000</span>&#160;          {</div>
<div class="line"><a name="l03001"></a><span class="lineno"> 3001</span>&#160;            software_[current_id_].setName(name);</div>
<div class="line"><a name="l03002"></a><span class="lineno"> 3002</span>&#160;          }</div>
<div class="line"><a name="l03003"></a><span class="lineno"> 3003</span>&#160;        }</div>
<div class="line"><a name="l03004"></a><span class="lineno"> 3004</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l03005"></a><span class="lineno"> 3005</span>&#160;        {</div>
<div class="line"><a name="l03006"></a><span class="lineno"> 3006</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l03007"></a><span class="lineno"> 3007</span>&#160;        }</div>
<div class="line"><a name="l03008"></a><span class="lineno"> 3008</span>&#160;        <span class="comment">//~ software_[current_id_].addCVTerm(   CVTerm (accession, value, const String &amp;cv_identifier_ref, const String &amp;value, const Unit &amp;unit)   ); TODO somthing like that</span></div>
<div class="line"><a name="l03009"></a><span class="lineno"> 3009</span>&#160;      }</div>
<div class="line"><a name="l03010"></a><span class="lineno"> 3010</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;chromatogram&quot;</span>)</div>
<div class="line"><a name="l03011"></a><span class="lineno"> 3011</span>&#160;      {</div>
<div class="line"><a name="l03012"></a><span class="lineno"> 3012</span>&#160;        <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000810&quot;</span>)</div>
<div class="line"><a name="l03013"></a><span class="lineno"> 3013</span>&#160;        {</div>
<div class="line"><a name="l03014"></a><span class="lineno"> 3014</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdad97236e33b7a22bd5b44ca5404d069cb">ChromatogramSettings::MASS_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03015"></a><span class="lineno"> 3015</span>&#160;        }</div>
<div class="line"><a name="l03016"></a><span class="lineno"> 3016</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000235&quot;</span>)</div>
<div class="line"><a name="l03017"></a><span class="lineno"> 3017</span>&#160;        {</div>
<div class="line"><a name="l03018"></a><span class="lineno"> 3018</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda9761ce23aa0bea120a7d581477316953">ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03019"></a><span class="lineno"> 3019</span>&#160;        }</div>
<div class="line"><a name="l03020"></a><span class="lineno"> 3020</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000627&quot;</span>)</div>
<div class="line"><a name="l03021"></a><span class="lineno"> 3021</span>&#160;        {</div>
<div class="line"><a name="l03022"></a><span class="lineno"> 3022</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda5e1f2677edbc482d260e873a4a9660c6">ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03023"></a><span class="lineno"> 3023</span>&#160;        }</div>
<div class="line"><a name="l03024"></a><span class="lineno"> 3024</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000628&quot;</span>)</div>
<div class="line"><a name="l03025"></a><span class="lineno"> 3025</span>&#160;        {</div>
<div class="line"><a name="l03026"></a><span class="lineno"> 3026</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda6becb3aa48a0fbb4401e98e6b99a9428">ChromatogramSettings::BASEPEAK_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03027"></a><span class="lineno"> 3027</span>&#160;        }</div>
<div class="line"><a name="l03028"></a><span class="lineno"> 3028</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001472&quot;</span>)</div>
<div class="line"><a name="l03029"></a><span class="lineno"> 3029</span>&#160;        {</div>
<div class="line"><a name="l03030"></a><span class="lineno"> 3030</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa">ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03031"></a><span class="lineno"> 3031</span>&#160;        }</div>
<div class="line"><a name="l03032"></a><span class="lineno"> 3032</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001473&quot;</span>)</div>
<div class="line"><a name="l03033"></a><span class="lineno"> 3033</span>&#160;        {</div>
<div class="line"><a name="l03034"></a><span class="lineno"> 3034</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03035"></a><span class="lineno"> 3035</span>&#160;        }</div>
<div class="line"><a name="l03036"></a><span class="lineno"> 3036</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1001474&quot;</span>)</div>
<div class="line"><a name="l03037"></a><span class="lineno"> 3037</span>&#160;        {</div>
<div class="line"><a name="l03038"></a><span class="lineno"> 3038</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03039"></a><span class="lineno"> 3039</span>&#160;        }</div>
<div class="line"><a name="l03040"></a><span class="lineno"> 3040</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000811&quot;</span>)</div>
<div class="line"><a name="l03041"></a><span class="lineno"> 3041</span>&#160;        {</div>
<div class="line"><a name="l03042"></a><span class="lineno"> 3042</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdaa227021fdc2a25d98a5113afc918b75b">ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03043"></a><span class="lineno"> 3043</span>&#160;        }</div>
<div class="line"><a name="l03044"></a><span class="lineno"> 3044</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000812&quot;</span>)</div>
<div class="line"><a name="l03045"></a><span class="lineno"> 3045</span>&#160;        {</div>
<div class="line"><a name="l03046"></a><span class="lineno"> 3046</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda1a3d139c1d36a9c7462f3e1e8bbba110">ChromatogramSettings::ABSORPTION_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03047"></a><span class="lineno"> 3047</span>&#160;        }</div>
<div class="line"><a name="l03048"></a><span class="lineno"> 3048</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000813&quot;</span>)</div>
<div class="line"><a name="l03049"></a><span class="lineno"> 3049</span>&#160;        {</div>
<div class="line"><a name="l03050"></a><span class="lineno"> 3050</span>&#160;          chromatogram_.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda37ef0f7f2bed3939a8c3e135067b8705">ChromatogramSettings::EMISSION_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l03051"></a><span class="lineno"> 3051</span>&#160;        }</div>
<div class="line"><a name="l03052"></a><span class="lineno"> 3052</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">&quot;MS:1000809&quot;</span>)</div>
<div class="line"><a name="l03053"></a><span class="lineno"> 3053</span>&#160;        {</div>
<div class="line"><a name="l03054"></a><span class="lineno"> 3054</span>&#160;          chromatogram_.setName(value);</div>
<div class="line"><a name="l03055"></a><span class="lineno"> 3055</span>&#160;        }</div>
<div class="line"><a name="l03056"></a><span class="lineno"> 3056</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l03057"></a><span class="lineno"> 3057</span>&#160;          warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l03058"></a><span class="lineno"> 3058</span>&#160;      }</div>
<div class="line"><a name="l03059"></a><span class="lineno"> 3059</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;target&quot;</span>)</div>
<div class="line"><a name="l03060"></a><span class="lineno"> 3060</span>&#160;      {</div>
<div class="line"><a name="l03061"></a><span class="lineno"> 3061</span>&#160;        <span class="comment">//allowed but, not needed</span></div>
<div class="line"><a name="l03062"></a><span class="lineno"> 3062</span>&#160;      }</div>
<div class="line"><a name="l03063"></a><span class="lineno"> 3063</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l03064"></a><span class="lineno"> 3064</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled cvParam &#39;&quot;</span>) + accession + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l03065"></a><span class="lineno"> 3065</span>&#160;    }</div>
<div class="line"><a name="l03066"></a><span class="lineno"> 3066</span>&#160;</div>
<div class="line"><a name="l03067"></a><span class="lineno"> 3067</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adc972b1eb7fa347dda5ee1d46ca8df79"> 3068</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adc972b1eb7fa347dda5ee1d46ca8df79">MzMLHandler&lt;MapType&gt;::handleUserParam_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; value)</div>
<div class="line"><a name="l03069"></a><span class="lineno"> 3069</span>&#160;    {</div>
<div class="line"><a name="l03070"></a><span class="lineno"> 3070</span>&#160;      <span class="comment">//create a DataValue that contains the data in the right type</span></div>
<div class="line"><a name="l03071"></a><span class="lineno"> 3071</span>&#160;      <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a> data_value;</div>
<div class="line"><a name="l03072"></a><span class="lineno"> 3072</span>&#160;      <span class="comment">//float type</span></div>
<div class="line"><a name="l03073"></a><span class="lineno"> 3073</span>&#160;      <span class="keywordflow">if</span> (type == <span class="stringliteral">&quot;xsd:double&quot;</span> || type == <span class="stringliteral">&quot;xsd:float&quot;</span>)</div>
<div class="line"><a name="l03074"></a><span class="lineno"> 3074</span>&#160;      {</div>
<div class="line"><a name="l03075"></a><span class="lineno"> 3075</span>&#160;        data_value = <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>(value.<a class="code" href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">toDouble</a>());</div>
<div class="line"><a name="l03076"></a><span class="lineno"> 3076</span>&#160;      }</div>
<div class="line"><a name="l03077"></a><span class="lineno"> 3077</span>&#160;      <span class="comment">//integer type</span></div>
<div class="line"><a name="l03078"></a><span class="lineno"> 3078</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">&quot;xsd:byte&quot;</span> || type == <span class="stringliteral">&quot;xsd:decimal&quot;</span> || type == <span class="stringliteral">&quot;xsd:int&quot;</span> || type == <span class="stringliteral">&quot;xsd:integer&quot;</span> || type == <span class="stringliteral">&quot;xsd:long&quot;</span> || type == <span class="stringliteral">&quot;xsd:negativeInteger&quot;</span> || type == <span class="stringliteral">&quot;xsd:nonNegativeInteger&quot;</span> || type == <span class="stringliteral">&quot;xsd:nonPositiveInteger&quot;</span> || type == <span class="stringliteral">&quot;xsd:positiveInteger&quot;</span> || type == <span class="stringliteral">&quot;xsd:short&quot;</span> || type == <span class="stringliteral">&quot;xsd:unsignedByte&quot;</span> || type == <span class="stringliteral">&quot;xsd:unsignedInt&quot;</span> || type == <span class="stringliteral">&quot;xsd:unsignedLong&quot;</span> || type == <span class="stringliteral">&quot;xsd:unsignedShort&quot;</span>)</div>
<div class="line"><a name="l03079"></a><span class="lineno"> 3079</span>&#160;      {</div>
<div class="line"><a name="l03080"></a><span class="lineno"> 3080</span>&#160;        data_value = <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>(value.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>());</div>
<div class="line"><a name="l03081"></a><span class="lineno"> 3081</span>&#160;      }</div>
<div class="line"><a name="l03082"></a><span class="lineno"> 3082</span>&#160;      <span class="comment">//everything else is treated as a string</span></div>
<div class="line"><a name="l03083"></a><span class="lineno"> 3083</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l03084"></a><span class="lineno"> 3084</span>&#160;      {</div>
<div class="line"><a name="l03085"></a><span class="lineno"> 3085</span>&#160;        data_value = <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>(value);</div>
<div class="line"><a name="l03086"></a><span class="lineno"> 3086</span>&#160;      }</div>
<div class="line"><a name="l03087"></a><span class="lineno"> 3087</span>&#160;</div>
<div class="line"><a name="l03088"></a><span class="lineno"> 3088</span>&#160;      <span class="comment">//find the right MetaInfoInterface</span></div>
<div class="line"><a name="l03089"></a><span class="lineno"> 3089</span>&#160;      <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;run&quot;</span>)</div>
<div class="line"><a name="l03090"></a><span class="lineno"> 3090</span>&#160;      {</div>
<div class="line"><a name="l03091"></a><span class="lineno"> 3091</span>&#160;        exp_-&gt;setMetaValue(name, data_value);</div>
<div class="line"><a name="l03092"></a><span class="lineno"> 3092</span>&#160;      }</div>
<div class="line"><a name="l03093"></a><span class="lineno"> 3093</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;instrumentConfiguration&quot;</span>)</div>
<div class="line"><a name="l03094"></a><span class="lineno"> 3094</span>&#160;      {</div>
<div class="line"><a name="l03095"></a><span class="lineno"> 3095</span>&#160;        instruments_[current_id_].setMetaValue(name, data_value);</div>
<div class="line"><a name="l03096"></a><span class="lineno"> 3096</span>&#160;      }</div>
<div class="line"><a name="l03097"></a><span class="lineno"> 3097</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;source&quot;</span>)</div>
<div class="line"><a name="l03098"></a><span class="lineno"> 3098</span>&#160;      {</div>
<div class="line"><a name="l03099"></a><span class="lineno"> 3099</span>&#160;        instruments_[current_id_].getIonSources().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03100"></a><span class="lineno"> 3100</span>&#160;      }</div>
<div class="line"><a name="l03101"></a><span class="lineno"> 3101</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;analyzer&quot;</span>)</div>
<div class="line"><a name="l03102"></a><span class="lineno"> 3102</span>&#160;      {</div>
<div class="line"><a name="l03103"></a><span class="lineno"> 3103</span>&#160;        instruments_[current_id_].getMassAnalyzers().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03104"></a><span class="lineno"> 3104</span>&#160;      }</div>
<div class="line"><a name="l03105"></a><span class="lineno"> 3105</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;detector&quot;</span>)</div>
<div class="line"><a name="l03106"></a><span class="lineno"> 3106</span>&#160;      {</div>
<div class="line"><a name="l03107"></a><span class="lineno"> 3107</span>&#160;        instruments_[current_id_].getIonDetectors().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03108"></a><span class="lineno"> 3108</span>&#160;      }</div>
<div class="line"><a name="l03109"></a><span class="lineno"> 3109</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;sample&quot;</span>)</div>
<div class="line"><a name="l03110"></a><span class="lineno"> 3110</span>&#160;      {</div>
<div class="line"><a name="l03111"></a><span class="lineno"> 3111</span>&#160;        samples_[current_id_].setMetaValue(name, data_value);</div>
<div class="line"><a name="l03112"></a><span class="lineno"> 3112</span>&#160;      }</div>
<div class="line"><a name="l03113"></a><span class="lineno"> 3113</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;software&quot;</span>)</div>
<div class="line"><a name="l03114"></a><span class="lineno"> 3114</span>&#160;      {</div>
<div class="line"><a name="l03115"></a><span class="lineno"> 3115</span>&#160;        software_[current_id_].setMetaValue(name, data_value);</div>
<div class="line"><a name="l03116"></a><span class="lineno"> 3116</span>&#160;      }</div>
<div class="line"><a name="l03117"></a><span class="lineno"> 3117</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;contact&quot;</span>)</div>
<div class="line"><a name="l03118"></a><span class="lineno"> 3118</span>&#160;      {</div>
<div class="line"><a name="l03119"></a><span class="lineno"> 3119</span>&#160;        exp_-&gt;getContacts().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03120"></a><span class="lineno"> 3120</span>&#160;      }</div>
<div class="line"><a name="l03121"></a><span class="lineno"> 3121</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;sourceFile&quot;</span>)</div>
<div class="line"><a name="l03122"></a><span class="lineno"> 3122</span>&#160;      {</div>
<div class="line"><a name="l03123"></a><span class="lineno"> 3123</span>&#160;        source_files_[current_id_].setMetaValue(name, data_value);</div>
<div class="line"><a name="l03124"></a><span class="lineno"> 3124</span>&#160;      }</div>
<div class="line"><a name="l03125"></a><span class="lineno"> 3125</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;binaryDataArray&quot;</span>)</div>
<div class="line"><a name="l03126"></a><span class="lineno"> 3126</span>&#160;      {</div>
<div class="line"><a name="l03127"></a><span class="lineno"> 3127</span>&#160;        data_.back().meta.setMetaValue(name, data_value);</div>
<div class="line"><a name="l03128"></a><span class="lineno"> 3128</span>&#160;      }</div>
<div class="line"><a name="l03129"></a><span class="lineno"> 3129</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;spectrum&quot;</span>)</div>
<div class="line"><a name="l03130"></a><span class="lineno"> 3130</span>&#160;      {</div>
<div class="line"><a name="l03131"></a><span class="lineno"> 3131</span>&#160;        spec_.setMetaValue(name, data_value);</div>
<div class="line"><a name="l03132"></a><span class="lineno"> 3132</span>&#160;      }</div>
<div class="line"><a name="l03133"></a><span class="lineno"> 3133</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;chromatogram&quot;</span>)</div>
<div class="line"><a name="l03134"></a><span class="lineno"> 3134</span>&#160;      {</div>
<div class="line"><a name="l03135"></a><span class="lineno"> 3135</span>&#160;        chromatogram_.setMetaValue(name, data_value);</div>
<div class="line"><a name="l03136"></a><span class="lineno"> 3136</span>&#160;      }</div>
<div class="line"><a name="l03137"></a><span class="lineno"> 3137</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;scanList&quot;</span>)</div>
<div class="line"><a name="l03138"></a><span class="lineno"> 3138</span>&#160;      {</div>
<div class="line"><a name="l03139"></a><span class="lineno"> 3139</span>&#160;        spec_.getAcquisitionInfo().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03140"></a><span class="lineno"> 3140</span>&#160;      }</div>
<div class="line"><a name="l03141"></a><span class="lineno"> 3141</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;scan&quot;</span>)</div>
<div class="line"><a name="l03142"></a><span class="lineno"> 3142</span>&#160;      {</div>
<div class="line"><a name="l03143"></a><span class="lineno"> 3143</span>&#160;        spec_.getAcquisitionInfo().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03144"></a><span class="lineno"> 3144</span>&#160;      }</div>
<div class="line"><a name="l03145"></a><span class="lineno"> 3145</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;scanWindow&quot;</span>)</div>
<div class="line"><a name="l03146"></a><span class="lineno"> 3146</span>&#160;      {</div>
<div class="line"><a name="l03147"></a><span class="lineno"> 3147</span>&#160;        spec_.getInstrumentSettings().getScanWindows().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03148"></a><span class="lineno"> 3148</span>&#160;      }</div>
<div class="line"><a name="l03149"></a><span class="lineno"> 3149</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;isolationWindow&quot;</span>)</div>
<div class="line"><a name="l03150"></a><span class="lineno"> 3150</span>&#160;      {</div>
<div class="line"><a name="l03151"></a><span class="lineno"> 3151</span>&#160;        <span class="comment">//We don&#39;t have this as a separate location =&gt; store it in the precursor</span></div>
<div class="line"><a name="l03152"></a><span class="lineno"> 3152</span>&#160;        <span class="keywordflow">if</span> (parent_parent_tag == <span class="stringliteral">&quot;precursor&quot;</span>)</div>
<div class="line"><a name="l03153"></a><span class="lineno"> 3153</span>&#160;        {</div>
<div class="line"><a name="l03154"></a><span class="lineno"> 3154</span>&#160;          <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l03155"></a><span class="lineno"> 3155</span>&#160;          {</div>
<div class="line"><a name="l03156"></a><span class="lineno"> 3156</span>&#160;            spec_.getPrecursors().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03157"></a><span class="lineno"> 3157</span>&#160;          }</div>
<div class="line"><a name="l03158"></a><span class="lineno"> 3158</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l03159"></a><span class="lineno"> 3159</span>&#160;          {</div>
<div class="line"><a name="l03160"></a><span class="lineno"> 3160</span>&#160;            chromatogram_.getPrecursor().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03161"></a><span class="lineno"> 3161</span>&#160;          }</div>
<div class="line"><a name="l03162"></a><span class="lineno"> 3162</span>&#160;        }</div>
<div class="line"><a name="l03163"></a><span class="lineno"> 3163</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_parent_tag == <span class="stringliteral">&quot;product&quot;</span>)</div>
<div class="line"><a name="l03164"></a><span class="lineno"> 3164</span>&#160;        {</div>
<div class="line"><a name="l03165"></a><span class="lineno"> 3165</span>&#160;          <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l03166"></a><span class="lineno"> 3166</span>&#160;          {</div>
<div class="line"><a name="l03167"></a><span class="lineno"> 3167</span>&#160;            spec_.getProducts().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03168"></a><span class="lineno"> 3168</span>&#160;          }</div>
<div class="line"><a name="l03169"></a><span class="lineno"> 3169</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l03170"></a><span class="lineno"> 3170</span>&#160;          {</div>
<div class="line"><a name="l03171"></a><span class="lineno"> 3171</span>&#160;            chromatogram_.getProduct().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03172"></a><span class="lineno"> 3172</span>&#160;          }</div>
<div class="line"><a name="l03173"></a><span class="lineno"> 3173</span>&#160;        }</div>
<div class="line"><a name="l03174"></a><span class="lineno"> 3174</span>&#160;      }</div>
<div class="line"><a name="l03175"></a><span class="lineno"> 3175</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;selectedIon&quot;</span>)</div>
<div class="line"><a name="l03176"></a><span class="lineno"> 3176</span>&#160;      {</div>
<div class="line"><a name="l03177"></a><span class="lineno"> 3177</span>&#160;        <span class="comment">//parse only the first selected ion</span></div>
<div class="line"><a name="l03178"></a><span class="lineno"> 3178</span>&#160;        <span class="keywordflow">if</span> (selected_ion_count_ &gt; 1)</div>
<div class="line"><a name="l03179"></a><span class="lineno"> 3179</span>&#160;          <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l03180"></a><span class="lineno"> 3180</span>&#160;</div>
<div class="line"><a name="l03181"></a><span class="lineno"> 3181</span>&#160;        <span class="comment">//We don&#39;t have this as a separate location =&gt; store it in the precursor</span></div>
<div class="line"><a name="l03182"></a><span class="lineno"> 3182</span>&#160;        <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l03183"></a><span class="lineno"> 3183</span>&#160;        {</div>
<div class="line"><a name="l03184"></a><span class="lineno"> 3184</span>&#160;          spec_.getPrecursors().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03185"></a><span class="lineno"> 3185</span>&#160;        }</div>
<div class="line"><a name="l03186"></a><span class="lineno"> 3186</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l03187"></a><span class="lineno"> 3187</span>&#160;        {</div>
<div class="line"><a name="l03188"></a><span class="lineno"> 3188</span>&#160;          chromatogram_.getPrecursor().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03189"></a><span class="lineno"> 3189</span>&#160;        }</div>
<div class="line"><a name="l03190"></a><span class="lineno"> 3190</span>&#160;      }</div>
<div class="line"><a name="l03191"></a><span class="lineno"> 3191</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;activation&quot;</span>)</div>
<div class="line"><a name="l03192"></a><span class="lineno"> 3192</span>&#160;      {</div>
<div class="line"><a name="l03193"></a><span class="lineno"> 3193</span>&#160;        <span class="comment">//We don&#39;t have this as a separate location =&gt; store it in the precursor</span></div>
<div class="line"><a name="l03194"></a><span class="lineno"> 3194</span>&#160;        <span class="keywordflow">if</span> (in_spectrum_list_)</div>
<div class="line"><a name="l03195"></a><span class="lineno"> 3195</span>&#160;        {</div>
<div class="line"><a name="l03196"></a><span class="lineno"> 3196</span>&#160;          spec_.getPrecursors().back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03197"></a><span class="lineno"> 3197</span>&#160;        }</div>
<div class="line"><a name="l03198"></a><span class="lineno"> 3198</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l03199"></a><span class="lineno"> 3199</span>&#160;        {</div>
<div class="line"><a name="l03200"></a><span class="lineno"> 3200</span>&#160;          chromatogram_.getPrecursor().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03201"></a><span class="lineno"> 3201</span>&#160;        }</div>
<div class="line"><a name="l03202"></a><span class="lineno"> 3202</span>&#160;      }</div>
<div class="line"><a name="l03203"></a><span class="lineno"> 3203</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;processingMethod&quot;</span>)</div>
<div class="line"><a name="l03204"></a><span class="lineno"> 3204</span>&#160;      {</div>
<div class="line"><a name="l03205"></a><span class="lineno"> 3205</span>&#160;        processing_[current_id_].back().setMetaValue(name, data_value);</div>
<div class="line"><a name="l03206"></a><span class="lineno"> 3206</span>&#160;      }</div>
<div class="line"><a name="l03207"></a><span class="lineno"> 3207</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">&quot;fileContent&quot;</span>)</div>
<div class="line"><a name="l03208"></a><span class="lineno"> 3208</span>&#160;      {</div>
<div class="line"><a name="l03209"></a><span class="lineno"> 3209</span>&#160;        <span class="comment">//exp_-&gt;setMetaValue(name, data_value);</span></div>
<div class="line"><a name="l03210"></a><span class="lineno"> 3210</span>&#160;      }</div>
<div class="line"><a name="l03211"></a><span class="lineno"> 3211</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l03212"></a><span class="lineno"> 3212</span>&#160;        warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Unhandled userParam &#39;&quot;</span>) + name + <span class="stringliteral">&quot;&#39; in tag &#39;&quot;</span> + parent_tag + <span class="stringliteral">&quot;&#39;.&quot;</span>);</div>
<div class="line"><a name="l03213"></a><span class="lineno"> 3213</span>&#160;    }</div>
<div class="line"><a name="l03214"></a><span class="lineno"> 3214</span>&#160;</div>
<div class="line"><a name="l03215"></a><span class="lineno"> 3215</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03216"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7240976da5a0394d00fecce6fd8a7baa"> 3216</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7240976da5a0394d00fecce6fd8a7baa">MzMLHandler&lt;MapType&gt;::validateCV_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a>&amp; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; path, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)<span class="keyword"> const</span></div>
<div class="line"><a name="l03217"></a><span class="lineno"> 3217</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l03218"></a><span class="lineno"> 3218</span>&#160;      <a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html">SemanticValidator::CVTerm</a> sc;</div>
<div class="line"><a name="l03219"></a><span class="lineno"> 3219</span>&#160;</div>
<div class="line"><a name="l03220"></a><span class="lineno"> 3220</span>&#160;      sc.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#aa4b705e9e4267f64630cacd7fc55fc5d">accession</a> = c.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a>;</div>
<div class="line"><a name="l03221"></a><span class="lineno"> 3221</span>&#160;      sc.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> = c.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a>;</div>
<div class="line"><a name="l03222"></a><span class="lineno"> 3222</span>&#160;      sc.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#ad25f6dba1bbd00a3122302d7bac4beb5">has_unit_accession</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l03223"></a><span class="lineno"> 3223</span>&#160;      sc.<a class="code" href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a6f8965f74e78f28d247f2027d1089d13">has_unit_name</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l03224"></a><span class="lineno"> 3224</span>&#160;</div>
<div class="line"><a name="l03225"></a><span class="lineno"> 3225</span>&#160;      <span class="keywordflow">return</span> validator.SemanticValidator::locateTerm(path, sc);</div>
<div class="line"><a name="l03226"></a><span class="lineno"> 3226</span>&#160;    }</div>
<div class="line"><a name="l03227"></a><span class="lineno"> 3227</span>&#160;</div>
<div class="line"><a name="l03228"></a><span class="lineno"> 3228</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5f66b708512374f687a8b6598408e9e8"> 3229</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5f66b708512374f687a8b6598408e9e8">MzMLHandler&lt;MapType&gt;::writeCV_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a>&amp; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>&amp; metaValue)<span class="keyword"> const</span></div>
<div class="line"><a name="l03230"></a><span class="lineno"> 3230</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l03231"></a><span class="lineno"> 3231</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> cvTerm = <span class="stringliteral">&quot;&lt;cvParam cvRef=\&quot;&quot;</span> + c.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a>.<a class="code" href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">prefix</a>(<span class="charliteral">&#39;:&#39;</span>) + <span class="stringliteral">&quot;\&quot; accession=\&quot;&quot;</span> + c.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> + <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> + c.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a>;</div>
<div class="line"><a name="l03232"></a><span class="lineno"> 3232</span>&#160;      <span class="keywordflow">if</span> (!metaValue.<a class="code" href="classOpenMS_1_1DataValue.html#a479432127ee77145cc19d6a2d1590821">isEmpty</a>())</div>
<div class="line"><a name="l03233"></a><span class="lineno"> 3233</span>&#160;      {</div>
<div class="line"><a name="l03234"></a><span class="lineno"> 3234</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> stringMetaValue = (<a class="code" href="classOpenMS_1_1String.html">String</a>)metaValue;</div>
<div class="line"><a name="l03235"></a><span class="lineno"> 3235</span>&#160;        stringMetaValue.<a class="code" href="classOpenMS_1_1String.html#a8fca08235a25819cf09375f867815f09">substitute</a>(<span class="stringliteral">&quot;\&quot;&quot;</span>, <span class="stringliteral">&quot;&amp;quot;&quot;</span>);</div>
<div class="line"><a name="l03236"></a><span class="lineno"> 3236</span>&#160;        cvTerm += <span class="stringliteral">&quot;\&quot; value=\&quot;&quot;</span> + stringMetaValue;</div>
<div class="line"><a name="l03237"></a><span class="lineno"> 3237</span>&#160;</div>
<div class="line"><a name="l03238"></a><span class="lineno"> 3238</span>&#160;        <span class="keywordflow">if</span> (metaValue.<a class="code" href="classOpenMS_1_1DataValue.html#aaeec7621a6d5913883828bb69e50c1d9">hasUnit</a>())</div>
<div class="line"><a name="l03239"></a><span class="lineno"> 3239</span>&#160;        {</div>
<div class="line"><a name="l03240"></a><span class="lineno"> 3240</span>&#160;          <span class="comment">//  unitAccession=&quot;UO:0000021&quot; unitName=&quot;gram&quot; unitCvRef=&quot;UO&quot;</span></div>
<div class="line"><a name="l03241"></a><span class="lineno"> 3241</span>&#160;          <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> unit = cv_.getTerm(metaValue.<a class="code" href="classOpenMS_1_1DataValue.html#a1fc42efb4420deedae9f5a59d4c20190">getUnit</a>());</div>
<div class="line"><a name="l03242"></a><span class="lineno"> 3242</span>&#160;          cvTerm += <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;&quot;</span> + unit.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> + <span class="stringliteral">&quot;\&quot; unitName=\&quot;&quot;</span> + unit.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> + <span class="stringliteral">&quot;\&quot; unitCvRef=\&quot;&quot;</span> + unit.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a>.<a class="code" href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">prefix</a>(2);</div>
<div class="line"><a name="l03243"></a><span class="lineno"> 3243</span>&#160;        }</div>
<div class="line"><a name="l03244"></a><span class="lineno"> 3244</span>&#160;      }</div>
<div class="line"><a name="l03245"></a><span class="lineno"> 3245</span>&#160;      cvTerm += <span class="stringliteral">&quot;\&quot;/&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03246"></a><span class="lineno"> 3246</span>&#160;      <span class="keywordflow">return</span> cvTerm;</div>
<div class="line"><a name="l03247"></a><span class="lineno"> 3247</span>&#160;    }</div>
<div class="line"><a name="l03248"></a><span class="lineno"> 3248</span>&#160;</div>
<div class="line"><a name="l03249"></a><span class="lineno"> 3249</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03250"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adfdc00e52147d9fba0252e78b76ff477"> 3250</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adfdc00e52147d9fba0252e78b76ff477">MzMLHandler&lt;MapType&gt;::writeUserParam_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a>&amp; meta, <a class="code" href="classunsigned_01int.html">UInt</a> indent, <a class="code" href="classOpenMS_1_1String.html">String</a> path, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)<span class="keyword"> const</span></div>
<div class="line"><a name="l03251"></a><span class="lineno"> 3251</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l03252"></a><span class="lineno"> 3252</span>&#160;      std::vector&lt;String&gt; cvParams;</div>
<div class="line"><a name="l03253"></a><span class="lineno"> 3253</span>&#160;      std::vector&lt;String&gt; userParams;</div>
<div class="line"><a name="l03254"></a><span class="lineno"> 3254</span>&#160;</div>
<div class="line"><a name="l03255"></a><span class="lineno"> 3255</span>&#160;      std::vector&lt;String&gt; keys;</div>
<div class="line"><a name="l03256"></a><span class="lineno"> 3256</span>&#160;      meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aaefa2a4a5d50f899cdd82d686104d164">getKeys</a>(keys);</div>
<div class="line"><a name="l03257"></a><span class="lineno"> 3257</span>&#160;</div>
<div class="line"><a name="l03258"></a><span class="lineno"> 3258</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;String&gt;::iterator key = keys.begin(); key != keys.end(); ++key)</div>
<div class="line"><a name="l03259"></a><span class="lineno"> 3259</span>&#160;      {</div>
<div class="line"><a name="l03260"></a><span class="lineno"> 3260</span>&#160;        <span class="comment">// special treatment of GO and BTO terms</span></div>
<div class="line"><a name="l03261"></a><span class="lineno"> 3261</span>&#160;        <span class="comment">// &lt;cvParam cvRef=&quot;BTO&quot; accession=&quot;BTO:0000199&quot; name=&quot;cardiac muscle&quot;/&gt;</span></div>
<div class="line"><a name="l03262"></a><span class="lineno"> 3262</span>&#160;</div>
<div class="line"><a name="l03263"></a><span class="lineno"> 3263</span>&#160;        <span class="keywordflow">if</span> (*key == <span class="stringliteral">&quot;GO cellular component&quot;</span> || *key == <span class="stringliteral">&quot;brenda source tissue&quot;</span>)</div>
<div class="line"><a name="l03264"></a><span class="lineno"> 3264</span>&#160;        {</div>
<div class="line"><a name="l03265"></a><span class="lineno"> 3265</span>&#160;          <span class="comment">// the CVTerm info is in the value</span></div>
<div class="line"><a name="l03266"></a><span class="lineno"> 3266</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>&amp; metaValue = meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(*key);</div>
<div class="line"><a name="l03267"></a><span class="lineno"> 3267</span>&#160;</div>
<div class="line"><a name="l03268"></a><span class="lineno"> 3268</span>&#160;          <span class="keywordflow">if</span> (cv_.hasTermWithName((<a class="code" href="classOpenMS_1_1String.html">String</a>) metaValue))</div>
<div class="line"><a name="l03269"></a><span class="lineno"> 3269</span>&#160;          {</div>
<div class="line"><a name="l03270"></a><span class="lineno"> 3270</span>&#160;            <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = cv_.getTermByName((<a class="code" href="classOpenMS_1_1String.html">String</a>) metaValue);</div>
<div class="line"><a name="l03271"></a><span class="lineno"> 3271</span>&#160;</div>
<div class="line"><a name="l03272"></a><span class="lineno"> 3272</span>&#160;            <span class="comment">// TODO: validate CV, we currently cannot do this as the relations in the BTO and GO are not captured by our CV impl</span></div>
<div class="line"><a name="l03273"></a><span class="lineno"> 3273</span>&#160;            cvParams.push_back(writeCV_(c, <a class="code" href="classOpenMS_1_1DataValue.html#a078588ac6fbb817e4d04ea210c86d323">DataValue::EMPTY</a>));</div>
<div class="line"><a name="l03274"></a><span class="lineno"> 3274</span>&#160;          }</div>
<div class="line"><a name="l03275"></a><span class="lineno"> 3275</span>&#160;        }</div>
<div class="line"><a name="l03276"></a><span class="lineno"> 3276</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l03277"></a><span class="lineno"> 3277</span>&#160;        {</div>
<div class="line"><a name="l03278"></a><span class="lineno"> 3278</span>&#160;</div>
<div class="line"><a name="l03279"></a><span class="lineno"> 3279</span>&#160;          <span class="keywordtype">bool</span> writtenAsCVTerm = <span class="keyword">false</span>;</div>
<div class="line"><a name="l03280"></a><span class="lineno"> 3280</span>&#160;          <span class="keywordflow">if</span> (cv_.hasTermWithName(*key))</div>
<div class="line"><a name="l03281"></a><span class="lineno"> 3281</span>&#160;          {</div>
<div class="line"><a name="l03282"></a><span class="lineno"> 3282</span>&#160;            <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = cv_.getTermByName(*key); <span class="comment">// in cv_ write cvparam else write userparam</span></div>
<div class="line"><a name="l03283"></a><span class="lineno"> 3283</span>&#160;            <span class="keywordflow">if</span> (validateCV_(c, path, validator))</div>
<div class="line"><a name="l03284"></a><span class="lineno"> 3284</span>&#160;            {</div>
<div class="line"><a name="l03285"></a><span class="lineno"> 3285</span>&#160;              <span class="comment">// write CV</span></div>
<div class="line"><a name="l03286"></a><span class="lineno"> 3286</span>&#160;              cvParams.push_back(writeCV_(c, meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(*key)));</div>
<div class="line"><a name="l03287"></a><span class="lineno"> 3287</span>&#160;              writtenAsCVTerm = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03288"></a><span class="lineno"> 3288</span>&#160;            }</div>
<div class="line"><a name="l03289"></a><span class="lineno"> 3289</span>&#160;          }</div>
<div class="line"><a name="l03290"></a><span class="lineno"> 3290</span>&#160;</div>
<div class="line"><a name="l03291"></a><span class="lineno"> 3291</span>&#160;          <span class="comment">// if we could not write it as CVTerm we will store it at least as userParam</span></div>
<div class="line"><a name="l03292"></a><span class="lineno"> 3292</span>&#160;          <span class="keywordflow">if</span> (!writtenAsCVTerm)</div>
<div class="line"><a name="l03293"></a><span class="lineno"> 3293</span>&#160;          {</div>
<div class="line"><a name="l03294"></a><span class="lineno"> 3294</span>&#160;            <a class="code" href="classOpenMS_1_1String.html">String</a> userParam = <span class="stringliteral">&quot;&lt;userParam name=\&quot;&quot;</span> + *key + <span class="stringliteral">&quot;\&quot; type=\&quot;&quot;</span>;</div>
<div class="line"><a name="l03295"></a><span class="lineno"> 3295</span>&#160;</div>
<div class="line"><a name="l03296"></a><span class="lineno"> 3296</span>&#160;            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a>&amp; d = meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(*key);</div>
<div class="line"><a name="l03297"></a><span class="lineno"> 3297</span>&#160;            <span class="comment">//determine type</span></div>
<div class="line"><a name="l03298"></a><span class="lineno"> 3298</span>&#160;            <span class="keywordflow">if</span> (d.<a class="code" href="classOpenMS_1_1DataValue.html#abc5a85a6a61fb96964c186b0bf03e1de">valueType</a>() == <a class="code" href="classOpenMS_1_1DataValue.html#ad8ed01ff3ff33333d8e19db4d2818bb6acd1ce0b084595a6072a57781dc7738a0">DataValue::INT_VALUE</a>)</div>
<div class="line"><a name="l03299"></a><span class="lineno"> 3299</span>&#160;            {</div>
<div class="line"><a name="l03300"></a><span class="lineno"> 3300</span>&#160;              userParam += <span class="stringliteral">&quot;xsd:integer&quot;</span>;</div>
<div class="line"><a name="l03301"></a><span class="lineno"> 3301</span>&#160;            }</div>
<div class="line"><a name="l03302"></a><span class="lineno"> 3302</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (d.<a class="code" href="classOpenMS_1_1DataValue.html#abc5a85a6a61fb96964c186b0bf03e1de">valueType</a>() == <a class="code" href="classOpenMS_1_1DataValue.html#ad8ed01ff3ff33333d8e19db4d2818bb6a105ee757e9b5050b891a117266e71df0">DataValue::DOUBLE_VALUE</a>)</div>
<div class="line"><a name="l03303"></a><span class="lineno"> 3303</span>&#160;            {</div>
<div class="line"><a name="l03304"></a><span class="lineno"> 3304</span>&#160;              userParam += <span class="stringliteral">&quot;xsd:double&quot;</span>;</div>
<div class="line"><a name="l03305"></a><span class="lineno"> 3305</span>&#160;            }</div>
<div class="line"><a name="l03306"></a><span class="lineno"> 3306</span>&#160;            <span class="keywordflow">else</span> <span class="comment">//string or lists are converted to string</span></div>
<div class="line"><a name="l03307"></a><span class="lineno"> 3307</span>&#160;            {</div>
<div class="line"><a name="l03308"></a><span class="lineno"> 3308</span>&#160;              userParam += <span class="stringliteral">&quot;xsd:string&quot;</span>;</div>
<div class="line"><a name="l03309"></a><span class="lineno"> 3309</span>&#160;            }</div>
<div class="line"><a name="l03310"></a><span class="lineno"> 3310</span>&#160;            <a class="code" href="classOpenMS_1_1String.html">String</a> s = (<a class="code" href="classOpenMS_1_1String.html">String</a>)(d);</div>
<div class="line"><a name="l03311"></a><span class="lineno"> 3311</span>&#160;            s.<a class="code" href="classOpenMS_1_1String.html#a8fca08235a25819cf09375f867815f09">substitute</a>(<span class="stringliteral">&quot;\&quot;&quot;</span>, <span class="stringliteral">&quot;&amp;quot;&quot;</span>);</div>
<div class="line"><a name="l03312"></a><span class="lineno"> 3312</span>&#160;            userParam += <span class="stringliteral">&quot;\&quot; value=\&quot;&quot;</span> + s + <span class="stringliteral">&quot;\&quot;/&gt;&quot;</span> + <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l03313"></a><span class="lineno"> 3313</span>&#160;</div>
<div class="line"><a name="l03314"></a><span class="lineno"> 3314</span>&#160;            userParams.push_back(userParam);</div>
<div class="line"><a name="l03315"></a><span class="lineno"> 3315</span>&#160;          }</div>
<div class="line"><a name="l03316"></a><span class="lineno"> 3316</span>&#160;        }</div>
<div class="line"><a name="l03317"></a><span class="lineno"> 3317</span>&#160;      }</div>
<div class="line"><a name="l03318"></a><span class="lineno"> 3318</span>&#160;</div>
<div class="line"><a name="l03319"></a><span class="lineno"> 3319</span>&#160;      <span class="comment">// write out all the cvParams and userParams in correct order</span></div>
<div class="line"><a name="l03320"></a><span class="lineno"> 3320</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;String&gt;::iterator term = cvParams.begin(); term != cvParams.end(); ++term)</div>
<div class="line"><a name="l03321"></a><span class="lineno"> 3321</span>&#160;      {</div>
<div class="line"><a name="l03322"></a><span class="lineno"> 3322</span>&#160;        os &lt;&lt; <a class="code" href="classOpenMS_1_1String.html">String</a>(indent, <span class="charliteral">&#39;\t&#39;</span>) &lt;&lt; *term;</div>
<div class="line"><a name="l03323"></a><span class="lineno"> 3323</span>&#160;      }</div>
<div class="line"><a name="l03324"></a><span class="lineno"> 3324</span>&#160;</div>
<div class="line"><a name="l03325"></a><span class="lineno"> 3325</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;String&gt;::iterator term = userParams.begin(); term != userParams.end(); ++term)</div>
<div class="line"><a name="l03326"></a><span class="lineno"> 3326</span>&#160;      {</div>
<div class="line"><a name="l03327"></a><span class="lineno"> 3327</span>&#160;        os &lt;&lt; <a class="code" href="classOpenMS_1_1String.html">String</a>(indent, <span class="charliteral">&#39;\t&#39;</span>) &lt;&lt; *term;</div>
<div class="line"><a name="l03328"></a><span class="lineno"> 3328</span>&#160;      }</div>
<div class="line"><a name="l03329"></a><span class="lineno"> 3329</span>&#160;    }</div>
<div class="line"><a name="l03330"></a><span class="lineno"> 3330</span>&#160;</div>
<div class="line"><a name="l03331"></a><span class="lineno"> 3331</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03332"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1d4f3e01975ac37c2b0f5b0ed1e1d92"> 3332</a></span>&#160;    <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1d4f3e01975ac37c2b0f5b0ed1e1d92">MzMLHandler&lt;MapType&gt;::getChildWithName_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; parent_accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; name)<span class="keyword"> const</span></div>
<div class="line"><a name="l03333"></a><span class="lineno"> 3333</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l03334"></a><span class="lineno"> 3334</span>&#160;      std::set&lt;String&gt; terms;</div>
<div class="line"><a name="l03335"></a><span class="lineno"> 3335</span>&#160;      cv_.getAllChildTerms(terms, parent_accession);</div>
<div class="line"><a name="l03336"></a><span class="lineno"> 3336</span>&#160;      <span class="keywordflow">for</span> (std::set&lt;String&gt;::const_iterator it = terms.begin(); it != terms.end(); ++it)</div>
<div class="line"><a name="l03337"></a><span class="lineno"> 3337</span>&#160;      {</div>
<div class="line"><a name="l03338"></a><span class="lineno"> 3338</span>&#160;        <span class="keywordflow">if</span> (cv_.getTerm(*it).name == name)</div>
<div class="line"><a name="l03339"></a><span class="lineno"> 3339</span>&#160;        {</div>
<div class="line"><a name="l03340"></a><span class="lineno"> 3340</span>&#160;          <span class="keywordflow">return</span> cv_.getTerm(*it);</div>
<div class="line"><a name="l03341"></a><span class="lineno"> 3341</span>&#160;        }</div>
<div class="line"><a name="l03342"></a><span class="lineno"> 3342</span>&#160;      }</div>
<div class="line"><a name="l03343"></a><span class="lineno"> 3343</span>&#160;      <span class="keywordflow">return</span> <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a>();</div>
<div class="line"><a name="l03344"></a><span class="lineno"> 3344</span>&#160;    }</div>
<div class="line"><a name="l03345"></a><span class="lineno"> 3345</span>&#160;</div>
<div class="line"><a name="l03346"></a><span class="lineno"> 3346</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03347"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a78331edae256b2c5de712ed5eda26bc8"> 3347</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a78331edae256b2c5de712ed5eda26bc8">MzMLHandler&lt;MapType&gt;::writeSoftware_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Software.html">Software</a>&amp; software, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l03348"></a><span class="lineno"> 3348</span>&#160;    {</div>
<div class="line"><a name="l03349"></a><span class="lineno"> 3349</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;software id=\&quot;&quot;</span> &lt;&lt; <span class="keywordtype">id</span> &lt;&lt; <span class="stringliteral">&quot;\&quot; version=\&quot;&quot;</span> &lt;&lt; software.<a class="code" href="classOpenMS_1_1Software.html#ae6b3b4b6857bc1987282e2f29611dd41">getVersion</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; &gt;\n&quot;</span>;</div>
<div class="line"><a name="l03350"></a><span class="lineno"> 3350</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> so_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000531&quot;</span>, software.<a class="code" href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>());</div>
<div class="line"><a name="l03351"></a><span class="lineno"> 3351</span>&#160;      <span class="keywordflow">if</span> (so_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> == <span class="stringliteral">&quot;MS:1000799&quot;</span>)</div>
<div class="line"><a name="l03352"></a><span class="lineno"> 3352</span>&#160;      {</div>
<div class="line"><a name="l03353"></a><span class="lineno"> 3353</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000799\&quot; name=\&quot;custom unreleased software tool\&quot; value=\&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03354"></a><span class="lineno"> 3354</span>&#160;      }</div>
<div class="line"><a name="l03355"></a><span class="lineno"> 3355</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03356"></a><span class="lineno"> 3356</span>&#160;      {</div>
<div class="line"><a name="l03357"></a><span class="lineno"> 3357</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; so_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; so_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03358"></a><span class="lineno"> 3358</span>&#160;      }</div>
<div class="line"><a name="l03359"></a><span class="lineno"> 3359</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l03360"></a><span class="lineno"> 3360</span>&#160;      {</div>
<div class="line"><a name="l03361"></a><span class="lineno"> 3361</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000799\&quot; name=\&quot;custom unreleased software tool\&quot; value=\&quot;&quot;</span> &lt;&lt; software.<a class="code" href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03362"></a><span class="lineno"> 3362</span>&#160;      }</div>
<div class="line"><a name="l03363"></a><span class="lineno"> 3363</span>&#160;      writeUserParam_(os, software, 3, <span class="stringliteral">&quot;/mzML/Software/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03364"></a><span class="lineno"> 3364</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/software&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03365"></a><span class="lineno"> 3365</span>&#160;    }</div>
<div class="line"><a name="l03366"></a><span class="lineno"> 3366</span>&#160;</div>
<div class="line"><a name="l03367"></a><span class="lineno"> 3367</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03368"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa7d348ccbf286e2aef8b0fa27453a289"> 3368</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa7d348ccbf286e2aef8b0fa27453a289">MzMLHandler&lt;MapType&gt;::writeSourceFile_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a>&amp; source_file, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l03369"></a><span class="lineno"> 3369</span>&#160;    {</div>
<div class="line"><a name="l03370"></a><span class="lineno"> 3370</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;sourceFile id=\&quot;&quot;</span> &lt;&lt; <span class="keywordtype">id</span> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#acadddeff186604f0185315e70aab94fb">getNameOfFile</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; location=\&quot;&quot;</span> &lt;&lt; source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a43aa2dacc04339d6b2cf5eb317f6bb2e">getPathToFile</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03371"></a><span class="lineno"> 3371</span>&#160;      <span class="comment">//checksum</span></div>
<div class="line"><a name="l03372"></a><span class="lineno"> 3372</span>&#160;      <span class="keywordflow">if</span> (source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a2bf1ca8186169631f23edd67ddbd45e1">getChecksumType</a>() == <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">SourceFile::SHA1</a>)</div>
<div class="line"><a name="l03373"></a><span class="lineno"> 3373</span>&#160;      {</div>
<div class="line"><a name="l03374"></a><span class="lineno"> 3374</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000569\&quot; name=\&quot;SHA-1\&quot; value=\&quot;&quot;</span> &lt;&lt; source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">getChecksum</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03375"></a><span class="lineno"> 3375</span>&#160;      }</div>
<div class="line"><a name="l03376"></a><span class="lineno"> 3376</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a2bf1ca8186169631f23edd67ddbd45e1">getChecksumType</a>() == <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5ad37464787fa5104b0ae6bea524eec264">SourceFile::MD5</a>)</div>
<div class="line"><a name="l03377"></a><span class="lineno"> 3377</span>&#160;      {</div>
<div class="line"><a name="l03378"></a><span class="lineno"> 3378</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000568\&quot; name=\&quot;MD5\&quot; value=\&quot;&quot;</span> &lt;&lt; source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">getChecksum</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03379"></a><span class="lineno"> 3379</span>&#160;      }</div>
<div class="line"><a name="l03380"></a><span class="lineno"> 3380</span>&#160;      <span class="keywordflow">else</span> <span class="comment">//FORCED</span></div>
<div class="line"><a name="l03381"></a><span class="lineno"> 3381</span>&#160;      {</div>
<div class="line"><a name="l03382"></a><span class="lineno"> 3382</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000569\&quot; name=\&quot;SHA-1\&quot; value=\&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03383"></a><span class="lineno"> 3383</span>&#160;      }</div>
<div class="line"><a name="l03384"></a><span class="lineno"> 3384</span>&#160;      <span class="comment">//file type</span></div>
<div class="line"><a name="l03385"></a><span class="lineno"> 3385</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> ft_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000560&quot;</span>, source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#ac82b3cc3ba4c24b0ab9768fede8c3c9c">getFileType</a>());</div>
<div class="line"><a name="l03386"></a><span class="lineno"> 3386</span>&#160;      <span class="keywordflow">if</span> (ft_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03387"></a><span class="lineno"> 3387</span>&#160;      {</div>
<div class="line"><a name="l03388"></a><span class="lineno"> 3388</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; ft_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; ft_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03389"></a><span class="lineno"> 3389</span>&#160;      }</div>
<div class="line"><a name="l03390"></a><span class="lineno"> 3390</span>&#160;      <span class="keywordflow">else</span> <span class="comment">//FORCED</span></div>
<div class="line"><a name="l03391"></a><span class="lineno"> 3391</span>&#160;      {</div>
<div class="line"><a name="l03392"></a><span class="lineno"> 3392</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000564\&quot; name=\&quot;PSI mzData file\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03393"></a><span class="lineno"> 3393</span>&#160;      }</div>
<div class="line"><a name="l03394"></a><span class="lineno"> 3394</span>&#160;      <span class="comment">//native ID format</span></div>
<div class="line"><a name="l03395"></a><span class="lineno"> 3395</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> id_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000767&quot;</span>, source_file.<a class="code" href="classOpenMS_1_1SourceFile.html#af766984226f4f22572e132923218324c">getNativeIDType</a>());</div>
<div class="line"><a name="l03396"></a><span class="lineno"> 3396</span>&#160;      <span class="keywordflow">if</span> (id_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03397"></a><span class="lineno"> 3397</span>&#160;      {</div>
<div class="line"><a name="l03398"></a><span class="lineno"> 3398</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; id_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; id_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03399"></a><span class="lineno"> 3399</span>&#160;      }</div>
<div class="line"><a name="l03400"></a><span class="lineno"> 3400</span>&#160;      <span class="keywordflow">else</span> <span class="comment">//FORCED</span></div>
<div class="line"><a name="l03401"></a><span class="lineno"> 3401</span>&#160;      {</div>
<div class="line"><a name="l03402"></a><span class="lineno"> 3402</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000777\&quot; name=\&quot;spectrum identifier nativeID format\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03403"></a><span class="lineno"> 3403</span>&#160;      }</div>
<div class="line"><a name="l03404"></a><span class="lineno"> 3404</span>&#160;      writeUserParam_(os, source_file, 4, <span class="stringliteral">&quot;/mzML/fileDescription/sourceFileList/sourceFile/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03405"></a><span class="lineno"> 3405</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/sourceFile&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03406"></a><span class="lineno"> 3406</span>&#160;    }</div>
<div class="line"><a name="l03407"></a><span class="lineno"> 3407</span>&#160;</div>
<div class="line"><a name="l03408"></a><span class="lineno"> 3408</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03409"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aebeb2035d3f517fa772979211fa2d514"> 3409</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aebeb2035d3f517fa772979211fa2d514">MzMLHandler&lt;MapType&gt;::writeDataProcessing_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> std::vector&lt;DataProcessing&gt;&amp; dps, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l03410"></a><span class="lineno"> 3410</span>&#160;    {</div>
<div class="line"><a name="l03411"></a><span class="lineno"> 3411</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;dataProcessing id=\&quot;&quot;</span> &lt;&lt; <span class="keywordtype">id</span> &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03412"></a><span class="lineno"> 3412</span>&#160;</div>
<div class="line"><a name="l03413"></a><span class="lineno"> 3413</span>&#160;      <span class="comment">//FORCED</span></div>
<div class="line"><a name="l03414"></a><span class="lineno"> 3414</span>&#160;      <span class="keywordflow">if</span> (dps.empty())</div>
<div class="line"><a name="l03415"></a><span class="lineno"> 3415</span>&#160;      {</div>
<div class="line"><a name="l03416"></a><span class="lineno"> 3416</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;processingMethod order=\&quot;0\&quot; softwareRef=\&quot;so_default\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03417"></a><span class="lineno"> 3417</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000544\&quot; name=\&quot;Conversion to mzML\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03418"></a><span class="lineno"> 3418</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;userParam name=\&quot;warning\&quot; type=\&quot;xsd:string\&quot; value=\&quot;fictional processing method used to fulfill format requirements\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03419"></a><span class="lineno"> 3419</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/processingMethod&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03420"></a><span class="lineno"> 3420</span>&#160;      }</div>
<div class="line"><a name="l03421"></a><span class="lineno"> 3421</span>&#160;</div>
<div class="line"><a name="l03422"></a><span class="lineno"> 3422</span>&#160;      <span class="keywordtype">bool</span> written = <span class="keyword">false</span>;</div>
<div class="line"><a name="l03423"></a><span class="lineno"> 3423</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; dps.size(); ++i)</div>
<div class="line"><a name="l03424"></a><span class="lineno"> 3424</span>&#160;      {</div>
<div class="line"><a name="l03425"></a><span class="lineno"> 3425</span>&#160;        <span class="comment">//data processing action</span></div>
<div class="line"><a name="l03426"></a><span class="lineno"> 3426</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;processingMethod order=\&quot;0\&quot; softwareRef=\&quot;so_&quot;</span> &lt;&lt; <span class="keywordtype">id</span> &lt;&lt; <span class="stringliteral">&quot;_pm_&quot;</span> &lt;&lt; i &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03427"></a><span class="lineno"> 3427</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ae75d9344e9e326323f2b485cd4c1e003">DataProcessing::DATA_PROCESSING</a>) == 1)</div>
<div class="line"><a name="l03428"></a><span class="lineno"> 3428</span>&#160;        {</div>
<div class="line"><a name="l03429"></a><span class="lineno"> 3429</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000543\&quot; name=\&quot;data processing action\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03430"></a><span class="lineno"> 3430</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03431"></a><span class="lineno"> 3431</span>&#160;        }</div>
<div class="line"><a name="l03432"></a><span class="lineno"> 3432</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">DataProcessing::CHARGE_DECONVOLUTION</a>) == 1)</div>
<div class="line"><a name="l03433"></a><span class="lineno"> 3433</span>&#160;        {</div>
<div class="line"><a name="l03434"></a><span class="lineno"> 3434</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000034\&quot; name=\&quot;charge deconvolution\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03435"></a><span class="lineno"> 3435</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03436"></a><span class="lineno"> 3436</span>&#160;        }</div>
<div class="line"><a name="l03437"></a><span class="lineno"> 3437</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">DataProcessing::DEISOTOPING</a>) == 1)</div>
<div class="line"><a name="l03438"></a><span class="lineno"> 3438</span>&#160;        {</div>
<div class="line"><a name="l03439"></a><span class="lineno"> 3439</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000033\&quot; name=\&quot;deisotoping\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03440"></a><span class="lineno"> 3440</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03441"></a><span class="lineno"> 3441</span>&#160;        }</div>
<div class="line"><a name="l03442"></a><span class="lineno"> 3442</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad261194a1dded675599dfdc7212b63b1">DataProcessing::SMOOTHING</a>) == 1)</div>
<div class="line"><a name="l03443"></a><span class="lineno"> 3443</span>&#160;        {</div>
<div class="line"><a name="l03444"></a><span class="lineno"> 3444</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000592\&quot; name=\&quot;smoothing\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03445"></a><span class="lineno"> 3445</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03446"></a><span class="lineno"> 3446</span>&#160;        }</div>
<div class="line"><a name="l03447"></a><span class="lineno"> 3447</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9af083c14a6a074a19ac7a75066eb83866">DataProcessing::CHARGE_CALCULATION</a>) == 1)</div>
<div class="line"><a name="l03448"></a><span class="lineno"> 3448</span>&#160;        {</div>
<div class="line"><a name="l03449"></a><span class="lineno"> 3449</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000778\&quot; name=\&quot;charge state calculation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03450"></a><span class="lineno"> 3450</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03451"></a><span class="lineno"> 3451</span>&#160;        }</div>
<div class="line"><a name="l03452"></a><span class="lineno"> 3452</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a2ca454d58033fd433df401a2406fb173">DataProcessing::PRECURSOR_RECALCULATION</a>) == 1)</div>
<div class="line"><a name="l03453"></a><span class="lineno"> 3453</span>&#160;        {</div>
<div class="line"><a name="l03454"></a><span class="lineno"> 3454</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000780\&quot; name=\&quot;precursor recalculation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03455"></a><span class="lineno"> 3455</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03456"></a><span class="lineno"> 3456</span>&#160;        }</div>
<div class="line"><a name="l03457"></a><span class="lineno"> 3457</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9aec300465e654790d9154eb0d64ca3267">DataProcessing::BASELINE_REDUCTION</a>) == 1)</div>
<div class="line"><a name="l03458"></a><span class="lineno"> 3458</span>&#160;        {</div>
<div class="line"><a name="l03459"></a><span class="lineno"> 3459</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000593\&quot; name=\&quot;baseline reduction\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03460"></a><span class="lineno"> 3460</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03461"></a><span class="lineno"> 3461</span>&#160;        }</div>
<div class="line"><a name="l03462"></a><span class="lineno"> 3462</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">DataProcessing::PEAK_PICKING</a>) == 1)</div>
<div class="line"><a name="l03463"></a><span class="lineno"> 3463</span>&#160;        {</div>
<div class="line"><a name="l03464"></a><span class="lineno"> 3464</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000035\&quot; name=\&quot;peak picking\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03465"></a><span class="lineno"> 3465</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03466"></a><span class="lineno"> 3466</span>&#160;        }</div>
<div class="line"><a name="l03467"></a><span class="lineno"> 3467</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">DataProcessing::ALIGNMENT</a>) == 1)</div>
<div class="line"><a name="l03468"></a><span class="lineno"> 3468</span>&#160;        {</div>
<div class="line"><a name="l03469"></a><span class="lineno"> 3469</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000745\&quot; name=\&quot;retention time alignment\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03470"></a><span class="lineno"> 3470</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03471"></a><span class="lineno"> 3471</span>&#160;        }</div>
<div class="line"><a name="l03472"></a><span class="lineno"> 3472</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a03940d78fb7ee5fc71b49ca87cfdfb1c">DataProcessing::CALIBRATION</a>) == 1)</div>
<div class="line"><a name="l03473"></a><span class="lineno"> 3473</span>&#160;        {</div>
<div class="line"><a name="l03474"></a><span class="lineno"> 3474</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001485\&quot; name=\&quot;m/z calibration\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03475"></a><span class="lineno"> 3475</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03476"></a><span class="lineno"> 3476</span>&#160;        }</div>
<div class="line"><a name="l03477"></a><span class="lineno"> 3477</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a0de981225527baadd805eabc7a029173">DataProcessing::NORMALIZATION</a>) == 1)</div>
<div class="line"><a name="l03478"></a><span class="lineno"> 3478</span>&#160;        {</div>
<div class="line"><a name="l03479"></a><span class="lineno"> 3479</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001484\&quot; name=\&quot;intensity normalization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03480"></a><span class="lineno"> 3480</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03481"></a><span class="lineno"> 3481</span>&#160;        }</div>
<div class="line"><a name="l03482"></a><span class="lineno"> 3482</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a9159f47bf89a34ad71b71f283ff09cd9">DataProcessing::FILTERING</a>) == 1)</div>
<div class="line"><a name="l03483"></a><span class="lineno"> 3483</span>&#160;        {</div>
<div class="line"><a name="l03484"></a><span class="lineno"> 3484</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001486\&quot; name=\&quot;data filtering\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03485"></a><span class="lineno"> 3485</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03486"></a><span class="lineno"> 3486</span>&#160;        }</div>
<div class="line"><a name="l03487"></a><span class="lineno"> 3487</span>&#160;        <span class="comment">//file format conversion</span></div>
<div class="line"><a name="l03488"></a><span class="lineno"> 3488</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ab269e4bf446e6556e4f49a5737931643">DataProcessing::FORMAT_CONVERSION</a>) == 1)</div>
<div class="line"><a name="l03489"></a><span class="lineno"> 3489</span>&#160;        {</div>
<div class="line"><a name="l03490"></a><span class="lineno"> 3490</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000530\&quot; name=\&quot;file format conversion\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03491"></a><span class="lineno"> 3491</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03492"></a><span class="lineno"> 3492</span>&#160;        }</div>
<div class="line"><a name="l03493"></a><span class="lineno"> 3493</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ac7b870e1adfeb8747214d4ef5144376c">DataProcessing::CONVERSION_MZDATA</a>) == 1)</div>
<div class="line"><a name="l03494"></a><span class="lineno"> 3494</span>&#160;        {</div>
<div class="line"><a name="l03495"></a><span class="lineno"> 3495</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000546\&quot; name=\&quot;Conversion to mzData\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03496"></a><span class="lineno"> 3496</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03497"></a><span class="lineno"> 3497</span>&#160;        }</div>
<div class="line"><a name="l03498"></a><span class="lineno"> 3498</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9abb654c12968c8c4c658d61af4a6e0765">DataProcessing::CONVERSION_MZML</a>) == 1)</div>
<div class="line"><a name="l03499"></a><span class="lineno"> 3499</span>&#160;        {</div>
<div class="line"><a name="l03500"></a><span class="lineno"> 3500</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000544\&quot; name=\&quot;Conversion to mzML\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03501"></a><span class="lineno"> 3501</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03502"></a><span class="lineno"> 3502</span>&#160;        }</div>
<div class="line"><a name="l03503"></a><span class="lineno"> 3503</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ac6602550db94324f2d4b712d8962c4cd">DataProcessing::CONVERSION_MZXML</a>) == 1)</div>
<div class="line"><a name="l03504"></a><span class="lineno"> 3504</span>&#160;        {</div>
<div class="line"><a name="l03505"></a><span class="lineno"> 3505</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000545\&quot; name=\&quot;Conversion to mzXML\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03506"></a><span class="lineno"> 3506</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03507"></a><span class="lineno"> 3507</span>&#160;        }</div>
<div class="line"><a name="l03508"></a><span class="lineno"> 3508</span>&#160;        <span class="keywordflow">if</span> (dps[i].getProcessingActions().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9aa20c95ae75ff9c98d471a6e0c30b1f88">DataProcessing::CONVERSION_DTA</a>) == 1)</div>
<div class="line"><a name="l03509"></a><span class="lineno"> 3509</span>&#160;        {</div>
<div class="line"><a name="l03510"></a><span class="lineno"> 3510</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000741\&quot; name=\&quot;Conversion to dta\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03511"></a><span class="lineno"> 3511</span>&#160;          written = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03512"></a><span class="lineno"> 3512</span>&#160;        }</div>
<div class="line"><a name="l03513"></a><span class="lineno"> 3513</span>&#160;        <span class="keywordflow">if</span> (!written)</div>
<div class="line"><a name="l03514"></a><span class="lineno"> 3514</span>&#160;        {</div>
<div class="line"><a name="l03515"></a><span class="lineno"> 3515</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000543\&quot; name=\&quot;data processing action\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03516"></a><span class="lineno"> 3516</span>&#160;        }</div>
<div class="line"><a name="l03517"></a><span class="lineno"> 3517</span>&#160;</div>
<div class="line"><a name="l03518"></a><span class="lineno"> 3518</span>&#160;        <span class="comment">//data processing attribute</span></div>
<div class="line"><a name="l03519"></a><span class="lineno"> 3519</span>&#160;        <span class="keywordflow">if</span> (dps[i].getCompletionTime().isValid())</div>
<div class="line"><a name="l03520"></a><span class="lineno"> 3520</span>&#160;        {</div>
<div class="line"><a name="l03521"></a><span class="lineno"> 3521</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000747\&quot; name=\&quot;completion time\&quot; value=\&quot;&quot;</span> &lt;&lt; dps[i].getCompletionTime().toString(<span class="stringliteral">&quot;yyyy-MM-dd+hh:mm&quot;</span>).toStdString() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03522"></a><span class="lineno"> 3522</span>&#160;        }</div>
<div class="line"><a name="l03523"></a><span class="lineno"> 3523</span>&#160;</div>
<div class="line"><a name="l03524"></a><span class="lineno"> 3524</span>&#160;        writeUserParam_(os, dps[i], 4, <span class="stringliteral">&quot;/mzML/dataProcessingList/dataProcessing/processingMethod/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03525"></a><span class="lineno"> 3525</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/processingMethod&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03526"></a><span class="lineno"> 3526</span>&#160;      }</div>
<div class="line"><a name="l03527"></a><span class="lineno"> 3527</span>&#160;</div>
<div class="line"><a name="l03528"></a><span class="lineno"> 3528</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/dataProcessing&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03529"></a><span class="lineno"> 3529</span>&#160;    }</div>
<div class="line"><a name="l03530"></a><span class="lineno"> 3530</span>&#160;</div>
<div class="line"><a name="l03531"></a><span class="lineno"> 3531</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03532"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a77eccf58c9f605c9535709430c66a5be"> 3532</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a77eccf58c9f605c9535709430c66a5be">MzMLHandler&lt;MapType&gt;::writePrecursor_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>&amp; precursor, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l03533"></a><span class="lineno"> 3533</span>&#160;    {</div>
<div class="line"><a name="l03534"></a><span class="lineno"> 3534</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;precursor&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03535"></a><span class="lineno"> 3535</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03536"></a><span class="lineno"> 3536</span>&#160;      <span class="comment">//isolation window</span></div>
<div class="line"><a name="l03537"></a><span class="lineno"> 3537</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03538"></a><span class="lineno"> 3538</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;isolationWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03539"></a><span class="lineno"> 3539</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000827\&quot; name=\&quot;isolation window target m/z\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03540"></a><span class="lineno"> 3540</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000828\&quot; name=\&quot;isolation window lower offset\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ac6f71e641c709dfabecce317d07ac4f7">getIsolationWindowLowerOffset</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03541"></a><span class="lineno"> 3541</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000829\&quot; name=\&quot;isolation window upper offset\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a0d3c115101baf89ff0d81602ad6cc635">getIsolationWindowUpperOffset</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03542"></a><span class="lineno"> 3542</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;/isolationWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03543"></a><span class="lineno"> 3543</span>&#160;      <span class="comment">//userParam: no extra object for it =&gt; no user parameters</span></div>
<div class="line"><a name="l03544"></a><span class="lineno"> 3544</span>&#160;</div>
<div class="line"><a name="l03545"></a><span class="lineno"> 3545</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03546"></a><span class="lineno"> 3546</span>&#160;      <span class="comment">//selected ion list</span></div>
<div class="line"><a name="l03547"></a><span class="lineno"> 3547</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03548"></a><span class="lineno"> 3548</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;selectedIonList count=\&quot;1\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03549"></a><span class="lineno"> 3549</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;selectedIon&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03550"></a><span class="lineno"> 3550</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000744\&quot; name=\&quot;selected ion m/z\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03551"></a><span class="lineno"> 3551</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000041\&quot; name=\&quot;charge state\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03552"></a><span class="lineno"> 3552</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000042\&quot; name=\&quot;peak intensity\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000132\&quot; unitName=\&quot;percent of base peak\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03553"></a><span class="lineno"> 3553</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a2dbe025c03208c3d01e5ce0794350970">getPossibleChargeStates</a>().size(); ++j)</div>
<div class="line"><a name="l03554"></a><span class="lineno"> 3554</span>&#160;      {</div>
<div class="line"><a name="l03555"></a><span class="lineno"> 3555</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000633\&quot; name=\&quot;possible charge state\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a2dbe025c03208c3d01e5ce0794350970">getPossibleChargeStates</a>()[j] &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03556"></a><span class="lineno"> 3556</span>&#160;      }</div>
<div class="line"><a name="l03557"></a><span class="lineno"> 3557</span>&#160;      <span class="comment">//userParam: no extra object for it =&gt; no user parameters</span></div>
<div class="line"><a name="l03558"></a><span class="lineno"> 3558</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;/selectedIon&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03559"></a><span class="lineno"> 3559</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;/selectedIonList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03560"></a><span class="lineno"> 3560</span>&#160;</div>
<div class="line"><a name="l03561"></a><span class="lineno"> 3561</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03562"></a><span class="lineno"> 3562</span>&#160;      <span class="comment">//activation</span></div>
<div class="line"><a name="l03563"></a><span class="lineno"> 3563</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03564"></a><span class="lineno"> 3564</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;activation&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03565"></a><span class="lineno"> 3565</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ad34cda135f7788348ea8866353407d38">getActivationEnergy</a>() != 0)</div>
<div class="line"><a name="l03566"></a><span class="lineno"> 3566</span>&#160;      {</div>
<div class="line"><a name="l03567"></a><span class="lineno"> 3567</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000509\&quot; name=\&quot;activation energy\&quot; value=\&quot;&quot;</span> &lt;&lt; precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ad34cda135f7788348ea8866353407d38">getActivationEnergy</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000266\&quot; unitName=\&quot;electronvolt\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03568"></a><span class="lineno"> 3568</span>&#160;      }</div>
<div class="line"><a name="l03569"></a><span class="lineno"> 3569</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab20b009dfccc7838ba06622a9d53daff">Precursor::CID</a>) != 0)</div>
<div class="line"><a name="l03570"></a><span class="lineno"> 3570</span>&#160;      {</div>
<div class="line"><a name="l03571"></a><span class="lineno"> 3571</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000133\&quot; name=\&quot;collision-induced dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03572"></a><span class="lineno"> 3572</span>&#160;      }</div>
<div class="line"><a name="l03573"></a><span class="lineno"> 3573</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1aefbc069e0ac4cd293f3ba527bec2befe">Precursor::PD</a>) != 0)</div>
<div class="line"><a name="l03574"></a><span class="lineno"> 3574</span>&#160;      {</div>
<div class="line"><a name="l03575"></a><span class="lineno"> 3575</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000134\&quot; name=\&quot;plasma desorption\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03576"></a><span class="lineno"> 3576</span>&#160;      }</div>
<div class="line"><a name="l03577"></a><span class="lineno"> 3577</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a7d2afca1f43e915528abd513b30b7a55">Precursor::PSD</a>) != 0)</div>
<div class="line"><a name="l03578"></a><span class="lineno"> 3578</span>&#160;      {</div>
<div class="line"><a name="l03579"></a><span class="lineno"> 3579</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000135\&quot; name=\&quot;post-source decay\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03580"></a><span class="lineno"> 3580</span>&#160;      }</div>
<div class="line"><a name="l03581"></a><span class="lineno"> 3581</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab2fca50c5baefb10e5ecdc553e372586">Precursor::SID</a>) != 0)</div>
<div class="line"><a name="l03582"></a><span class="lineno"> 3582</span>&#160;      {</div>
<div class="line"><a name="l03583"></a><span class="lineno"> 3583</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000136\&quot; name=\&quot;surface-induced dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03584"></a><span class="lineno"> 3584</span>&#160;      }</div>
<div class="line"><a name="l03585"></a><span class="lineno"> 3585</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a3901fa9d6f534ab0c36a34a0850dffa0">Precursor::BIRD</a>) != 0)</div>
<div class="line"><a name="l03586"></a><span class="lineno"> 3586</span>&#160;      {</div>
<div class="line"><a name="l03587"></a><span class="lineno"> 3587</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000242\&quot; name=\&quot;blackbody infrared radiative dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03588"></a><span class="lineno"> 3588</span>&#160;      }</div>
<div class="line"><a name="l03589"></a><span class="lineno"> 3589</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a2634661cb45dc1d0f135daebb5fa118b">Precursor::ECD</a>) != 0)</div>
<div class="line"><a name="l03590"></a><span class="lineno"> 3590</span>&#160;      {</div>
<div class="line"><a name="l03591"></a><span class="lineno"> 3591</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000250\&quot; name=\&quot;electron capture dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03592"></a><span class="lineno"> 3592</span>&#160;      }</div>
<div class="line"><a name="l03593"></a><span class="lineno"> 3593</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a8c41c05a63a15c5d188d02f6f4db4303">Precursor::IMD</a>) != 0)</div>
<div class="line"><a name="l03594"></a><span class="lineno"> 3594</span>&#160;      {</div>
<div class="line"><a name="l03595"></a><span class="lineno"> 3595</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000262\&quot; name=\&quot;infrared multiphoton dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03596"></a><span class="lineno"> 3596</span>&#160;      }</div>
<div class="line"><a name="l03597"></a><span class="lineno"> 3597</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a0ce1e0457af4bc9ab4bd841128c6ea84">Precursor::SORI</a>) != 0)</div>
<div class="line"><a name="l03598"></a><span class="lineno"> 3598</span>&#160;      {</div>
<div class="line"><a name="l03599"></a><span class="lineno"> 3599</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000282\&quot; name=\&quot;sustained off-resonance irradiation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03600"></a><span class="lineno"> 3600</span>&#160;      }</div>
<div class="line"><a name="l03601"></a><span class="lineno"> 3601</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a1bf627bed7951e975a31ba7033786d05">Precursor::HCID</a>) != 0)</div>
<div class="line"><a name="l03602"></a><span class="lineno"> 3602</span>&#160;      {</div>
<div class="line"><a name="l03603"></a><span class="lineno"> 3603</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000422\&quot; name=\&quot;high-energy collision-induced dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03604"></a><span class="lineno"> 3604</span>&#160;      }</div>
<div class="line"><a name="l03605"></a><span class="lineno"> 3605</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4437a3dbac928dd5e3ee699f931bd355">Precursor::LCID</a>) != 0)</div>
<div class="line"><a name="l03606"></a><span class="lineno"> 3606</span>&#160;      {</div>
<div class="line"><a name="l03607"></a><span class="lineno"> 3607</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000433\&quot; name=\&quot;low-energy collision-induced dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03608"></a><span class="lineno"> 3608</span>&#160;      }</div>
<div class="line"><a name="l03609"></a><span class="lineno"> 3609</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4187f6dae406f24b70e3c34a7448b15f">Precursor::PHD</a>) != 0)</div>
<div class="line"><a name="l03610"></a><span class="lineno"> 3610</span>&#160;      {</div>
<div class="line"><a name="l03611"></a><span class="lineno"> 3611</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000435\&quot; name=\&quot;photodissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03612"></a><span class="lineno"> 3612</span>&#160;      }</div>
<div class="line"><a name="l03613"></a><span class="lineno"> 3613</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a56a28ad07746c6bae402cc7d7ec0839a">Precursor::ETD</a>) != 0)</div>
<div class="line"><a name="l03614"></a><span class="lineno"> 3614</span>&#160;      {</div>
<div class="line"><a name="l03615"></a><span class="lineno"> 3615</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000598\&quot; name=\&quot;electron transfer dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03616"></a><span class="lineno"> 3616</span>&#160;      }</div>
<div class="line"><a name="l03617"></a><span class="lineno"> 3617</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().count(<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a22a843b242764a6b3b320c1b26274433">Precursor::PQD</a>) != 0)</div>
<div class="line"><a name="l03618"></a><span class="lineno"> 3618</span>&#160;      {</div>
<div class="line"><a name="l03619"></a><span class="lineno"> 3619</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000599\&quot; name=\&quot;pulsed q dissociation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03620"></a><span class="lineno"> 3620</span>&#160;      }</div>
<div class="line"><a name="l03621"></a><span class="lineno"> 3621</span>&#160;      <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().empty())</div>
<div class="line"><a name="l03622"></a><span class="lineno"> 3622</span>&#160;      {</div>
<div class="line"><a name="l03623"></a><span class="lineno"> 3623</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000044\&quot; name=\&quot;dissociation method\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03624"></a><span class="lineno"> 3624</span>&#160;      }</div>
<div class="line"><a name="l03625"></a><span class="lineno"> 3625</span>&#160;      <span class="comment">//as &quot;precursor&quot; has no own user param its userParam is stored here</span></div>
<div class="line"><a name="l03626"></a><span class="lineno"> 3626</span>&#160;      writeUserParam_(os, precursor, 6, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/precursorList/precursor/activation/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03627"></a><span class="lineno"> 3627</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;/activation&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03628"></a><span class="lineno"> 3628</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/precursor&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03629"></a><span class="lineno"> 3629</span>&#160;</div>
<div class="line"><a name="l03630"></a><span class="lineno"> 3630</span>&#160;    }</div>
<div class="line"><a name="l03631"></a><span class="lineno"> 3631</span>&#160;</div>
<div class="line"><a name="l03632"></a><span class="lineno"> 3632</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03633"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7a5d9d8d742f5950d5a3c0fa22805b2a"> 3633</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7a5d9d8d742f5950d5a3c0fa22805b2a">MzMLHandler&lt;MapType&gt;::writeProduct_</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Product.html">Product</a>&amp; product, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l03634"></a><span class="lineno"> 3634</span>&#160;    {</div>
<div class="line"><a name="l03635"></a><span class="lineno"> 3635</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;product&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03636"></a><span class="lineno"> 3636</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;isolationWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03637"></a><span class="lineno"> 3637</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000827\&quot; name=\&quot;isolation window target m/z\&quot; value=\&quot;&quot;</span> &lt;&lt; product.<a class="code" href="classOpenMS_1_1Product.html#adf13f6e49cf05563669b4481aaced5f2">getMZ</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03638"></a><span class="lineno"> 3638</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000828\&quot; name=\&quot;isolation window lower offset\&quot; value=\&quot;&quot;</span> &lt;&lt; product.<a class="code" href="classOpenMS_1_1Product.html#ac6f71e641c709dfabecce317d07ac4f7">getIsolationWindowLowerOffset</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03639"></a><span class="lineno"> 3639</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000829\&quot; name=\&quot;isolation window upper offset\&quot; value=\&quot;&quot;</span> &lt;&lt; product.<a class="code" href="classOpenMS_1_1Product.html#a0d3c115101baf89ff0d81602ad6cc635">getIsolationWindowUpperOffset</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03640"></a><span class="lineno"> 3640</span>&#160;      writeUserParam_(os, product, 7, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/productList/product/isolationWindow/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03641"></a><span class="lineno"> 3641</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;/isolationWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03642"></a><span class="lineno"> 3642</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/product&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03643"></a><span class="lineno"> 3643</span>&#160;    }</div>
<div class="line"><a name="l03644"></a><span class="lineno"> 3644</span>&#160;</div>
<div class="line"><a name="l03645"></a><span class="lineno"> 3645</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03646"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf"> 3646</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf">MzMLHandler&lt;MapType&gt;::writeTo</a>(std::ostream&amp; os)</div>
<div class="line"><a name="l03647"></a><span class="lineno"> 3647</span>&#160;    {</div>
<div class="line"><a name="l03648"></a><span class="lineno"> 3648</span>&#160;      <span class="keyword">const</span> MapType&amp; exp = *(cexp_);</div>
<div class="line"><a name="l03649"></a><span class="lineno"> 3649</span>&#160;      logger_.startProgress(0, exp.size() + exp.getChromatograms().size(), <span class="stringliteral">&quot;storing mzML file&quot;</span>);</div>
<div class="line"><a name="l03650"></a><span class="lineno"> 3650</span>&#160;      <span class="keywordtype">int</span> progress = 0;</div>
<div class="line"><a name="l03651"></a><span class="lineno"> 3651</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a> validator(mapping_, cv_);</div>
<div class="line"><a name="l03652"></a><span class="lineno"> 3652</span>&#160;</div>
<div class="line"><a name="l03653"></a><span class="lineno"> 3653</span>&#160;      std::vector&lt;std::vector&lt;DataProcessing&gt; &gt; dps;</div>
<div class="line"><a name="l03654"></a><span class="lineno"> 3654</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03655"></a><span class="lineno"> 3655</span>&#160;      <span class="comment">//header</span></div>
<div class="line"><a name="l03656"></a><span class="lineno"> 3656</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03657"></a><span class="lineno"> 3657</span>&#160;      writeHeader_(os, exp, dps, validator);</div>
<div class="line"><a name="l03658"></a><span class="lineno"> 3658</span>&#160;</div>
<div class="line"><a name="l03659"></a><span class="lineno"> 3659</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03660"></a><span class="lineno"> 3660</span>&#160;      <span class="comment">//spectrum</span></div>
<div class="line"><a name="l03661"></a><span class="lineno"> 3661</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03662"></a><span class="lineno"> 3662</span>&#160;      <span class="keywordflow">if</span> (exp.size() != 0)</div>
<div class="line"><a name="l03663"></a><span class="lineno"> 3663</span>&#160;      {</div>
<div class="line"><a name="l03664"></a><span class="lineno"> 3664</span>&#160;        <span class="comment">// INFO : do not try to be smart and skip empty spectra or</span></div>
<div class="line"><a name="l03665"></a><span class="lineno"> 3665</span>&#160;        <span class="comment">// chromatograms. There can be very good reasons for this (e.g. if the</span></div>
<div class="line"><a name="l03666"></a><span class="lineno"> 3666</span>&#160;        <span class="comment">// meta information needs to be stored here but the actual data is</span></div>
<div class="line"><a name="l03667"></a><span class="lineno"> 3667</span>&#160;        <span class="comment">// stored somewhere else).</span></div>
<div class="line"><a name="l03668"></a><span class="lineno"> 3668</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;spectrumList count=\&quot;&quot;</span> &lt;&lt; exp.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; defaultDataProcessingRef=\&quot;dp_sp_0\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03669"></a><span class="lineno"> 3669</span>&#160;</div>
<div class="line"><a name="l03670"></a><span class="lineno"> 3670</span>&#160;        <span class="comment">//check native ids</span></div>
<div class="line"><a name="l03671"></a><span class="lineno"> 3671</span>&#160;        <span class="keywordtype">bool</span> renew_native_ids = <span class="keyword">false</span>;</div>
<div class="line"><a name="l03672"></a><span class="lineno"> 3672</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l03673"></a><span class="lineno"> 3673</span>&#160;        {</div>
<div class="line"><a name="l03674"></a><span class="lineno"> 3674</span>&#160;          <span class="keywordflow">if</span> (!exp[s].getNativeID().has(<span class="charliteral">&#39;=&#39;</span>))</div>
<div class="line"><a name="l03675"></a><span class="lineno"> 3675</span>&#160;          {</div>
<div class="line"><a name="l03676"></a><span class="lineno"> 3676</span>&#160;            renew_native_ids = <span class="keyword">true</span>;</div>
<div class="line"><a name="l03677"></a><span class="lineno"> 3677</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l03678"></a><span class="lineno"> 3678</span>&#160;          }</div>
<div class="line"><a name="l03679"></a><span class="lineno"> 3679</span>&#160;        }</div>
<div class="line"><a name="l03680"></a><span class="lineno"> 3680</span>&#160;        <span class="comment">//issue warning if something is wrong</span></div>
<div class="line"><a name="l03681"></a><span class="lineno"> 3681</span>&#160;        <span class="keywordflow">if</span> (renew_native_ids)</div>
<div class="line"><a name="l03682"></a><span class="lineno"> 3682</span>&#160;        {</div>
<div class="line"><a name="l03683"></a><span class="lineno"> 3683</span>&#160;          warning(STORE, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Invalid native IDs detected. Using spectrum identifier nativeID format (spectrum=xsd:nonNegativeInteger) for all spectra.&quot;</span>));</div>
<div class="line"><a name="l03684"></a><span class="lineno"> 3684</span>&#160;        }</div>
<div class="line"><a name="l03685"></a><span class="lineno"> 3685</span>&#160;</div>
<div class="line"><a name="l03686"></a><span class="lineno"> 3686</span>&#160;        <span class="comment">//write actual data</span></div>
<div class="line"><a name="l03687"></a><span class="lineno"> 3687</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l03688"></a><span class="lineno"> 3688</span>&#160;        {</div>
<div class="line"><a name="l03689"></a><span class="lineno"> 3689</span>&#160;          logger_.setProgress(progress++);</div>
<div class="line"><a name="l03690"></a><span class="lineno"> 3690</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spec = exp[s];</div>
<div class="line"><a name="l03691"></a><span class="lineno"> 3691</span>&#160;          writeSpectrum_(os, spec, s, validator, renew_native_ids, dps);</div>
<div class="line"><a name="l03692"></a><span class="lineno"> 3692</span>&#160;        }</div>
<div class="line"><a name="l03693"></a><span class="lineno"> 3693</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/spectrumList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03694"></a><span class="lineno"> 3694</span>&#160;      }</div>
<div class="line"><a name="l03695"></a><span class="lineno"> 3695</span>&#160;</div>
<div class="line"><a name="l03696"></a><span class="lineno"> 3696</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03697"></a><span class="lineno"> 3697</span>&#160;      <span class="comment">//chromatograms</span></div>
<div class="line"><a name="l03698"></a><span class="lineno"> 3698</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03699"></a><span class="lineno"> 3699</span>&#160;      <span class="keywordflow">if</span> (!exp.getChromatograms().empty())</div>
<div class="line"><a name="l03700"></a><span class="lineno"> 3700</span>&#160;      {</div>
<div class="line"><a name="l03701"></a><span class="lineno"> 3701</span>&#160;        <span class="comment">// INFO : do not try to be smart and skip empty spectra or</span></div>
<div class="line"><a name="l03702"></a><span class="lineno"> 3702</span>&#160;        <span class="comment">// chromatograms. There can be very good reasons for this (e.g. if the</span></div>
<div class="line"><a name="l03703"></a><span class="lineno"> 3703</span>&#160;        <span class="comment">// meta information needs to be stored here but the actual data is</span></div>
<div class="line"><a name="l03704"></a><span class="lineno"> 3704</span>&#160;        <span class="comment">// stored somewhere else).</span></div>
<div class="line"><a name="l03705"></a><span class="lineno"> 3705</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;chromatogramList count=\&quot;&quot;</span> &lt;&lt; exp.getChromatograms().size() &lt;&lt; <span class="stringliteral">&quot;\&quot; defaultDataProcessingRef=\&quot;dp_sp_0\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03706"></a><span class="lineno"> 3706</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> != exp.getChromatograms().size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>)</div>
<div class="line"><a name="l03707"></a><span class="lineno"> 3707</span>&#160;        {</div>
<div class="line"><a name="l03708"></a><span class="lineno"> 3708</span>&#160;          logger_.setProgress(progress++);</div>
<div class="line"><a name="l03709"></a><span class="lineno"> 3709</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a>&amp; chromatogram = exp.getChromatograms()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>];</div>
<div class="line"><a name="l03710"></a><span class="lineno"> 3710</span>&#160;          writeChromatogram_(os, chromatogram, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, validator);</div>
<div class="line"><a name="l03711"></a><span class="lineno"> 3711</span>&#160;        }</div>
<div class="line"><a name="l03712"></a><span class="lineno"> 3712</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/chromatogramList&gt;&quot;</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l03713"></a><span class="lineno"> 3713</span>&#160;      }</div>
<div class="line"><a name="l03714"></a><span class="lineno"> 3714</span>&#160;</div>
<div class="line"><a name="l03715"></a><span class="lineno"> 3715</span>&#160;      writeFooter_(os);</div>
<div class="line"><a name="l03716"></a><span class="lineno"> 3716</span>&#160;      logger_.endProgress();</div>
<div class="line"><a name="l03717"></a><span class="lineno"> 3717</span>&#160;    }</div>
<div class="line"><a name="l03718"></a><span class="lineno"> 3718</span>&#160;</div>
<div class="line"><a name="l03719"></a><span class="lineno"> 3719</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l03720"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aeee3146ed1c95bbbc3e69b4d5dca3041"> 3720</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aeee3146ed1c95bbbc3e69b4d5dca3041">MzMLHandler&lt;MapType&gt;::writeHeader_</a>(std::ostream&amp; os, <span class="keyword">const</span> MapType&amp; exp, </div>
<div class="line"><a name="l03721"></a><span class="lineno"> 3721</span>&#160;            std::vector&lt;std::vector&lt;DataProcessing&gt; &gt; &amp; dps, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l03722"></a><span class="lineno"> 3722</span>&#160;    {</div>
<div class="line"><a name="l03723"></a><span class="lineno"> 3723</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;&lt;?xml version=\&quot;1.0\&quot; encoding=\&quot;ISO-8859-1\&quot;?&gt;\n&quot;</span></div>
<div class="line"><a name="l03724"></a><span class="lineno"> 3724</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;&lt;mzML xmlns=\&quot;http://psi.hupo.org/ms/mzml\&quot; xmlns:xsi=\&quot;http://www.w3.org/2001/XMLSchema-instance\&quot; xsi:schemaLocation=\&quot;http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd\&quot; accession=\&quot;&quot;</span> &lt;&lt; exp.getIdentifier() &lt;&lt; <span class="stringliteral">&quot;\&quot; version=\&quot;&quot;</span> &lt;&lt; version_ &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03725"></a><span class="lineno"> 3725</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03726"></a><span class="lineno"> 3726</span>&#160;      <span class="comment">// CV list</span></div>
<div class="line"><a name="l03727"></a><span class="lineno"> 3727</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03728"></a><span class="lineno"> 3728</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;cvList count=\&quot;5\&quot;&gt;\n&quot;</span></div>
<div class="line"><a name="l03729"></a><span class="lineno"> 3729</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;cv id=\&quot;MS\&quot; fullName=\&quot;Proteomics Standards Initiative Mass Spectrometry Ontology\&quot; URI=\&quot;http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\&quot;/&gt;\n&quot;</span></div>
<div class="line"><a name="l03730"></a><span class="lineno"> 3730</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;cv id=\&quot;UO\&quot; fullName=\&quot;Unit Ontology\&quot; URI=\&quot;http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo\&quot;/&gt;\n&quot;</span></div>
<div class="line"><a name="l03731"></a><span class="lineno"> 3731</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;cv id=\&quot;BTO\&quot; fullName=\&quot;BrendaTissue545\&quot; version=\&quot;unknown\&quot; URI=\&quot;http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO\&quot;/&gt;\n&quot;</span></div>
<div class="line"><a name="l03732"></a><span class="lineno"> 3732</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;cv id=\&quot;GO\&quot; fullName=\&quot;Gene Ontology - Slim Versions\&quot; version=\&quot;unknown\&quot; URI=\&quot;http://www.geneontology.org/GO_slims/goslim_goa.obo\&quot;/&gt;\n&quot;</span></div>
<div class="line"><a name="l03733"></a><span class="lineno"> 3733</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;cv id=\&quot;PATO\&quot; fullName=\&quot;Quality ontology\&quot; version=\&quot;unknown\&quot; URI=\&quot;http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo\&quot;/&gt;\n&quot;</span></div>
<div class="line"><a name="l03734"></a><span class="lineno"> 3734</span>&#160;         &lt;&lt; <span class="stringliteral">&quot;\t&lt;/cvList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03735"></a><span class="lineno"> 3735</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03736"></a><span class="lineno"> 3736</span>&#160;      <span class="comment">// file content</span></div>
<div class="line"><a name="l03737"></a><span class="lineno"> 3737</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03738"></a><span class="lineno"> 3738</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;fileDescription&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03739"></a><span class="lineno"> 3739</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;fileContent&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03740"></a><span class="lineno"> 3740</span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;InstrumentSettings::ScanMode, UInt&gt;</a> file_content;</div>
<div class="line"><a name="l03741"></a><span class="lineno"> 3741</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; exp.size(); ++i)</div>
<div class="line"><a name="l03742"></a><span class="lineno"> 3742</span>&#160;      {</div>
<div class="line"><a name="l03743"></a><span class="lineno"> 3743</span>&#160;        ++file_content[exp[i].getInstrumentSettings().getScanMode()];</div>
<div class="line"><a name="l03744"></a><span class="lineno"> 3744</span>&#160;      }</div>
<div class="line"><a name="l03745"></a><span class="lineno"> 3745</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>))</div>
<div class="line"><a name="l03746"></a><span class="lineno"> 3746</span>&#160;      {</div>
<div class="line"><a name="l03747"></a><span class="lineno"> 3747</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000294\&quot; name=\&quot;mass spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03748"></a><span class="lineno"> 3748</span>&#160;      }</div>
<div class="line"><a name="l03749"></a><span class="lineno"> 3749</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">InstrumentSettings::MS1SPECTRUM</a>))</div>
<div class="line"><a name="l03750"></a><span class="lineno"> 3750</span>&#160;      {</div>
<div class="line"><a name="l03751"></a><span class="lineno"> 3751</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000579\&quot; name=\&quot;MS1 spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03752"></a><span class="lineno"> 3752</span>&#160;      }</div>
<div class="line"><a name="l03753"></a><span class="lineno"> 3753</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>))</div>
<div class="line"><a name="l03754"></a><span class="lineno"> 3754</span>&#160;      {</div>
<div class="line"><a name="l03755"></a><span class="lineno"> 3755</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000580\&quot; name=\&quot;MSn spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03756"></a><span class="lineno"> 3756</span>&#160;      }</div>
<div class="line"><a name="l03757"></a><span class="lineno"> 3757</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>))</div>
<div class="line"><a name="l03758"></a><span class="lineno"> 3758</span>&#160;      {</div>
<div class="line"><a name="l03759"></a><span class="lineno"> 3759</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000582\&quot; name=\&quot;SIM spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03760"></a><span class="lineno"> 3760</span>&#160;      }</div>
<div class="line"><a name="l03761"></a><span class="lineno"> 3761</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>))</div>
<div class="line"><a name="l03762"></a><span class="lineno"> 3762</span>&#160;      {</div>
<div class="line"><a name="l03763"></a><span class="lineno"> 3763</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000583\&quot; name=\&quot;SRM spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03764"></a><span class="lineno"> 3764</span>&#160;      }</div>
<div class="line"><a name="l03765"></a><span class="lineno"> 3765</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>))</div>
<div class="line"><a name="l03766"></a><span class="lineno"> 3766</span>&#160;      {</div>
<div class="line"><a name="l03767"></a><span class="lineno"> 3767</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000581\&quot; name=\&quot;CRM spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03768"></a><span class="lineno"> 3768</span>&#160;      }</div>
<div class="line"><a name="l03769"></a><span class="lineno"> 3769</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f">InstrumentSettings::PRECURSOR</a>))</div>
<div class="line"><a name="l03770"></a><span class="lineno"> 3770</span>&#160;      {</div>
<div class="line"><a name="l03771"></a><span class="lineno"> 3771</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000341\&quot; name=\&quot;precursor ion spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03772"></a><span class="lineno"> 3772</span>&#160;      }</div>
<div class="line"><a name="l03773"></a><span class="lineno"> 3773</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f">InstrumentSettings::CNG</a>))</div>
<div class="line"><a name="l03774"></a><span class="lineno"> 3774</span>&#160;      {</div>
<div class="line"><a name="l03775"></a><span class="lineno"> 3775</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000325\&quot; name=\&quot;constant neutral gain spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03776"></a><span class="lineno"> 3776</span>&#160;      }</div>
<div class="line"><a name="l03777"></a><span class="lineno"> 3777</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca">InstrumentSettings::CNL</a>))</div>
<div class="line"><a name="l03778"></a><span class="lineno"> 3778</span>&#160;      {</div>
<div class="line"><a name="l03779"></a><span class="lineno"> 3779</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000326\&quot; name=\&quot;constant neutral loss spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03780"></a><span class="lineno"> 3780</span>&#160;      }</div>
<div class="line"><a name="l03781"></a><span class="lineno"> 3781</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a45cd2a1ea065b4909b86190b372ed7da">InstrumentSettings::EMR</a>))</div>
<div class="line"><a name="l03782"></a><span class="lineno"> 3782</span>&#160;      {</div>
<div class="line"><a name="l03783"></a><span class="lineno"> 3783</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000804\&quot; name=\&quot;electromagnetic radiation spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03784"></a><span class="lineno"> 3784</span>&#160;      }</div>
<div class="line"><a name="l03785"></a><span class="lineno"> 3785</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6b66c706c4bc43ff1a3b5a0044fdfa18">InstrumentSettings::EMISSION</a>))</div>
<div class="line"><a name="l03786"></a><span class="lineno"> 3786</span>&#160;      {</div>
<div class="line"><a name="l03787"></a><span class="lineno"> 3787</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000805\&quot; name=\&quot;emission spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03788"></a><span class="lineno"> 3788</span>&#160;      }</div>
<div class="line"><a name="l03789"></a><span class="lineno"> 3789</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac1923f59816bf846e2a62d41cfb91b2f">InstrumentSettings::ABSORBTION</a>))</div>
<div class="line"><a name="l03790"></a><span class="lineno"> 3790</span>&#160;      {</div>
<div class="line"><a name="l03791"></a><span class="lineno"> 3791</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000806\&quot; name=\&quot;absorption spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03792"></a><span class="lineno"> 3792</span>&#160;      }</div>
<div class="line"><a name="l03793"></a><span class="lineno"> 3793</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac21206f76146b8913723119f609be907">InstrumentSettings::EMC</a>))</div>
<div class="line"><a name="l03794"></a><span class="lineno"> 3794</span>&#160;      {</div>
<div class="line"><a name="l03795"></a><span class="lineno"> 3795</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000789\&quot; name=\&quot;enhanced multiply charged spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03796"></a><span class="lineno"> 3796</span>&#160;      }</div>
<div class="line"><a name="l03797"></a><span class="lineno"> 3797</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a5980df92dcce7a0e1e8bc482e4f07aa6">InstrumentSettings::TDF</a>))</div>
<div class="line"><a name="l03798"></a><span class="lineno"> 3798</span>&#160;      {</div>
<div class="line"><a name="l03799"></a><span class="lineno"> 3799</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000789\&quot; name=\&quot;time-delayed fragmentation spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03800"></a><span class="lineno"> 3800</span>&#160;      }</div>
<div class="line"><a name="l03801"></a><span class="lineno"> 3801</span>&#160;      <span class="keywordflow">if</span> (file_content.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c">InstrumentSettings::UNKNOWN</a>) || file_content.empty())</div>
<div class="line"><a name="l03802"></a><span class="lineno"> 3802</span>&#160;      {</div>
<div class="line"><a name="l03803"></a><span class="lineno"> 3803</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000294\&quot; name=\&quot;mass spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03804"></a><span class="lineno"> 3804</span>&#160;      }</div>
<div class="line"><a name="l03805"></a><span class="lineno"> 3805</span>&#160;      <span class="comment">// writeUserParam_(os, exp, 3, &quot;/mzML/fileDescription/fileContent/cvParam/@accession&quot;, validator);</span></div>
<div class="line"><a name="l03806"></a><span class="lineno"> 3806</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/fileContent&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03807"></a><span class="lineno"> 3807</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03808"></a><span class="lineno"> 3808</span>&#160;      <span class="comment">// source file list</span></div>
<div class="line"><a name="l03809"></a><span class="lineno"> 3809</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03810"></a><span class="lineno"> 3810</span>&#160;      <span class="comment">//find out how many spectra source files need to be written</span></div>
<div class="line"><a name="l03811"></a><span class="lineno"> 3811</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> sf_sp_count = 0;</div>
<div class="line"><a name="l03812"></a><span class="lineno"> 3812</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; exp.size(); ++i)</div>
<div class="line"><a name="l03813"></a><span class="lineno"> 3813</span>&#160;      {</div>
<div class="line"><a name="l03814"></a><span class="lineno"> 3814</span>&#160;        <span class="keywordflow">if</span> (exp[i].getSourceFile() != <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a>())</div>
<div class="line"><a name="l03815"></a><span class="lineno"> 3815</span>&#160;          ++sf_sp_count;</div>
<div class="line"><a name="l03816"></a><span class="lineno"> 3816</span>&#160;      }</div>
<div class="line"><a name="l03817"></a><span class="lineno"> 3817</span>&#160;      <span class="keywordflow">if</span> (exp.getSourceFiles().size() &gt; 0 || sf_sp_count &gt; 0)</div>
<div class="line"><a name="l03818"></a><span class="lineno"> 3818</span>&#160;      {</div>
<div class="line"><a name="l03819"></a><span class="lineno"> 3819</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;sourceFileList count=\&quot;&quot;</span> &lt;&lt; exp.getSourceFiles().size() + sf_sp_count &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03820"></a><span class="lineno"> 3820</span>&#160;        <span class="comment">//write source file of run</span></div>
<div class="line"><a name="l03821"></a><span class="lineno"> 3821</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i=0; i&lt;exp.getSourceFiles().size(); ++i)</div>
<div class="line"><a name="l03822"></a><span class="lineno"> 3822</span>&#160;        {</div>
<div class="line"><a name="l03823"></a><span class="lineno"> 3823</span>&#160;          writeSourceFile_(os, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;sf_ru_&quot;</span>) + <a class="code" href="classOpenMS_1_1String.html">String</a>(i), exp.getSourceFiles()[i], validator);</div>
<div class="line"><a name="l03824"></a><span class="lineno"> 3824</span>&#160;        }</div>
<div class="line"><a name="l03825"></a><span class="lineno"> 3825</span>&#160;        <span class="comment">// write source files of spectra</span></div>
<div class="line"><a name="l03826"></a><span class="lineno"> 3826</span>&#160;        <span class="keywordflow">if</span> (sf_sp_count &gt; 0 )</div>
<div class="line"><a name="l03827"></a><span class="lineno"> 3827</span>&#160;        {</div>
<div class="line"><a name="l03828"></a><span class="lineno"> 3828</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a> sf_default;</div>
<div class="line"><a name="l03829"></a><span class="lineno"> 3829</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; exp.size(); ++i)</div>
<div class="line"><a name="l03830"></a><span class="lineno"> 3830</span>&#160;          {</div>
<div class="line"><a name="l03831"></a><span class="lineno"> 3831</span>&#160;            <span class="keywordflow">if</span> (exp[i].getSourceFile() != sf_default)</div>
<div class="line"><a name="l03832"></a><span class="lineno"> 3832</span>&#160;            {</div>
<div class="line"><a name="l03833"></a><span class="lineno"> 3833</span>&#160;              writeSourceFile_(os, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;sf_sp_&quot;</span>) + i, exp[i].getSourceFile(), validator);</div>
<div class="line"><a name="l03834"></a><span class="lineno"> 3834</span>&#160;            }</div>
<div class="line"><a name="l03835"></a><span class="lineno"> 3835</span>&#160;          }</div>
<div class="line"><a name="l03836"></a><span class="lineno"> 3836</span>&#160;        }</div>
<div class="line"><a name="l03837"></a><span class="lineno"> 3837</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/sourceFileList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03838"></a><span class="lineno"> 3838</span>&#160;      }</div>
<div class="line"><a name="l03839"></a><span class="lineno"> 3839</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03840"></a><span class="lineno"> 3840</span>&#160;      <span class="comment">// contacts</span></div>
<div class="line"><a name="l03841"></a><span class="lineno"> 3841</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03842"></a><span class="lineno"> 3842</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; exp.getContacts().size(); ++i)</div>
<div class="line"><a name="l03843"></a><span class="lineno"> 3843</span>&#160;      {</div>
<div class="line"><a name="l03844"></a><span class="lineno"> 3844</span>&#160;        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ContactPerson.html">ContactPerson</a>&amp; cp = exp.getContacts()[i];</div>
<div class="line"><a name="l03845"></a><span class="lineno"> 3845</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;contact&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03846"></a><span class="lineno"> 3846</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000586\&quot; name=\&quot;contact name\&quot; value=\&quot;&quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#a36df0ae8f5b0e98a1e0009ccbf8e1972">getLastName</a>() &lt;&lt; <span class="stringliteral">&quot;, &quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#ac02fa25060dabd021d726903e7d0d2ea">getFirstName</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03847"></a><span class="lineno"> 3847</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000590\&quot; name=\&quot;contact organization\&quot; value=\&quot;&quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#a29888f3b4cd1692005e9b0625ceb4608">getInstitution</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03848"></a><span class="lineno"> 3848</span>&#160;</div>
<div class="line"><a name="l03849"></a><span class="lineno"> 3849</span>&#160;        <span class="keywordflow">if</span> (cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#aea861f8342ba549d72dda0674103e2cd">getAddress</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03850"></a><span class="lineno"> 3850</span>&#160;        {</div>
<div class="line"><a name="l03851"></a><span class="lineno"> 3851</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000587\&quot; name=\&quot;contact address\&quot; value=\&quot;&quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#aea861f8342ba549d72dda0674103e2cd">getAddress</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03852"></a><span class="lineno"> 3852</span>&#160;        }</div>
<div class="line"><a name="l03853"></a><span class="lineno"> 3853</span>&#160;        <span class="keywordflow">if</span> (cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#a9d7de80efbcfc8f49025772de7806a23">getURL</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03854"></a><span class="lineno"> 3854</span>&#160;        {</div>
<div class="line"><a name="l03855"></a><span class="lineno"> 3855</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000588\&quot; name=\&quot;contact URL\&quot; value=\&quot;&quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#a9d7de80efbcfc8f49025772de7806a23">getURL</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03856"></a><span class="lineno"> 3856</span>&#160;        }</div>
<div class="line"><a name="l03857"></a><span class="lineno"> 3857</span>&#160;        <span class="keywordflow">if</span> (cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#aa40d949517afa236a88a9eb41ea4f35c">getEmail</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03858"></a><span class="lineno"> 3858</span>&#160;        {</div>
<div class="line"><a name="l03859"></a><span class="lineno"> 3859</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000589\&quot; name=\&quot;contact email\&quot; value=\&quot;&quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#aa40d949517afa236a88a9eb41ea4f35c">getEmail</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03860"></a><span class="lineno"> 3860</span>&#160;        }</div>
<div class="line"><a name="l03861"></a><span class="lineno"> 3861</span>&#160;        <span class="keywordflow">if</span> (cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#a15b36efd7557a43d6096476d19122e91">getContactInfo</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03862"></a><span class="lineno"> 3862</span>&#160;        {</div>
<div class="line"><a name="l03863"></a><span class="lineno"> 3863</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;userParam name=\&quot;contact_info\&quot; type=\&quot;xsd:string\&quot; value=\&quot;&quot;</span> &lt;&lt; cp.<a class="code" href="classOpenMS_1_1ContactPerson.html#a15b36efd7557a43d6096476d19122e91">getContactInfo</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03864"></a><span class="lineno"> 3864</span>&#160;        }</div>
<div class="line"><a name="l03865"></a><span class="lineno"> 3865</span>&#160;        writeUserParam_(os, cp, 3, <span class="stringliteral">&quot;/mzML/fileDescription/contact/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03866"></a><span class="lineno"> 3866</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/contact&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03867"></a><span class="lineno"> 3867</span>&#160;      }</div>
<div class="line"><a name="l03868"></a><span class="lineno"> 3868</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;/fileDescription&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03869"></a><span class="lineno"> 3869</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03870"></a><span class="lineno"> 3870</span>&#160;      <span class="comment">// sample</span></div>
<div class="line"><a name="l03871"></a><span class="lineno"> 3871</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03872"></a><span class="lineno"> 3872</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Sample.html">Sample</a>&amp; sa = exp.getSample();</div>
<div class="line"><a name="l03873"></a><span class="lineno"> 3873</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;sampleList count=\&quot;1\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03874"></a><span class="lineno"> 3874</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;sample id=\&quot;sa_0\&quot; name=\&quot;&quot;</span> &lt;&lt; sa.<a class="code" href="classOpenMS_1_1Sample.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03875"></a><span class="lineno"> 3875</span>&#160;      <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#ac06ffdb7464bbdb7304aa4f741e67a75">getNumber</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03876"></a><span class="lineno"> 3876</span>&#160;      {</div>
<div class="line"><a name="l03877"></a><span class="lineno"> 3877</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000001\&quot; name=\&quot;sample number\&quot; value=\&quot;&quot;</span> &lt;&lt; sa.<a class="code" href="classOpenMS_1_1Sample.html#ac06ffdb7464bbdb7304aa4f741e67a75">getNumber</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03878"></a><span class="lineno"> 3878</span>&#160;      }</div>
<div class="line"><a name="l03879"></a><span class="lineno"> 3879</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000004\&quot; name=\&quot;sample mass\&quot; value=\&quot;&quot;</span> &lt;&lt; sa.<a class="code" href="classOpenMS_1_1Sample.html#a51e7ec6e73028e6e0f073b01382bcaea">getMass</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000021\&quot; unitName=\&quot;gram\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03880"></a><span class="lineno"> 3880</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000005\&quot; name=\&quot;sample volume\&quot; value=\&quot;&quot;</span> &lt;&lt; sa.<a class="code" href="classOpenMS_1_1Sample.html#a2b26ecbcd8002a286574139ad8b2fdbc">getVolume</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000098\&quot; unitName=\&quot;milliliter\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03881"></a><span class="lineno"> 3881</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000006\&quot; name=\&quot;sample concentration\&quot; value=\&quot;&quot;</span> &lt;&lt; sa.<a class="code" href="classOpenMS_1_1Sample.html#afd1e30564c0909e1ada9ca9b6c978352">getConcentration</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000175\&quot; unitName=\&quot;gram per liter\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03882"></a><span class="lineno"> 3882</span>&#160;      <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() == <a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a6c36859458a3b2652671a36349914666">Sample::EMULSION</a>)</div>
<div class="line"><a name="l03883"></a><span class="lineno"> 3883</span>&#160;      {</div>
<div class="line"><a name="l03884"></a><span class="lineno"> 3884</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000047\&quot; name=\&quot;emulsion\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03885"></a><span class="lineno"> 3885</span>&#160;      }</div>
<div class="line"><a name="l03886"></a><span class="lineno"> 3886</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() == <a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a9584dc4fcb96c51dda36a881a6dbb212">Sample::GAS</a>)</div>
<div class="line"><a name="l03887"></a><span class="lineno"> 3887</span>&#160;      {</div>
<div class="line"><a name="l03888"></a><span class="lineno"> 3888</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000048\&quot; name=\&quot;gas\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03889"></a><span class="lineno"> 3889</span>&#160;      }</div>
<div class="line"><a name="l03890"></a><span class="lineno"> 3890</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() == <a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71aa87f9501ff2b390be1ea7d261b0d7cce">Sample::LIQUID</a>)</div>
<div class="line"><a name="l03891"></a><span class="lineno"> 3891</span>&#160;      {</div>
<div class="line"><a name="l03892"></a><span class="lineno"> 3892</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000049\&quot; name=\&quot;liquid\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03893"></a><span class="lineno"> 3893</span>&#160;      }</div>
<div class="line"><a name="l03894"></a><span class="lineno"> 3894</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() == <a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a1b45f84e1f6603b52e5ef442836df9af">Sample::SOLID</a>)</div>
<div class="line"><a name="l03895"></a><span class="lineno"> 3895</span>&#160;      {</div>
<div class="line"><a name="l03896"></a><span class="lineno"> 3896</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000050\&quot; name=\&quot;solid\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03897"></a><span class="lineno"> 3897</span>&#160;      }</div>
<div class="line"><a name="l03898"></a><span class="lineno"> 3898</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() == <a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a0a57d2bc6d4da43c5fdb8c9293764d8d">Sample::SOLUTION</a>)</div>
<div class="line"><a name="l03899"></a><span class="lineno"> 3899</span>&#160;      {</div>
<div class="line"><a name="l03900"></a><span class="lineno"> 3900</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000051\&quot; name=\&quot;solution\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03901"></a><span class="lineno"> 3901</span>&#160;      }</div>
<div class="line"><a name="l03902"></a><span class="lineno"> 3902</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() == <a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a67a73d64984460ab1251bea87b873aab">Sample::SUSPENSION</a>)</div>
<div class="line"><a name="l03903"></a><span class="lineno"> 3903</span>&#160;      {</div>
<div class="line"><a name="l03904"></a><span class="lineno"> 3904</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000052\&quot; name=\&quot;suspension\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03905"></a><span class="lineno"> 3905</span>&#160;      }</div>
<div class="line"><a name="l03906"></a><span class="lineno"> 3906</span>&#160;      <span class="keywordflow">if</span> (sa.<a class="code" href="classOpenMS_1_1Sample.html#af974151b7df6fcfeb6509e26431dcaa0">getComment</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03907"></a><span class="lineno"> 3907</span>&#160;      {</div>
<div class="line"><a name="l03908"></a><span class="lineno"> 3908</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;userParam name=\&quot;comment\&quot; type=\&quot;xsd:string\&quot; value=\&quot;&quot;</span> &lt;&lt; sa.<a class="code" href="classOpenMS_1_1Sample.html#af974151b7df6fcfeb6509e26431dcaa0">getComment</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03909"></a><span class="lineno"> 3909</span>&#160;      }</div>
<div class="line"><a name="l03910"></a><span class="lineno"> 3910</span>&#160;      writeUserParam_(os, sa, 3, <span class="stringliteral">&quot;/mzML/sampleList/sample/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l03911"></a><span class="lineno"> 3911</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/sample&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03912"></a><span class="lineno"> 3912</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;/sampleList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03913"></a><span class="lineno"> 3913</span>&#160;</div>
<div class="line"><a name="l03914"></a><span class="lineno"> 3914</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03915"></a><span class="lineno"> 3915</span>&#160;      <span class="comment">// software</span></div>
<div class="line"><a name="l03916"></a><span class="lineno"> 3916</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03917"></a><span class="lineno"> 3917</span>&#160;</div>
<div class="line"><a name="l03918"></a><span class="lineno"> 3918</span>&#160;      <span class="comment">// create a list of all different data processings</span></div>
<div class="line"><a name="l03919"></a><span class="lineno"> 3919</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_software(2); <span class="comment">// instrument software is always written</span></div>
<div class="line"><a name="l03920"></a><span class="lineno"> 3920</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l03921"></a><span class="lineno"> 3921</span>&#160;      {</div>
<div class="line"><a name="l03922"></a><span class="lineno"> 3922</span>&#160;        <span class="keywordflow">if</span> (find(dps.begin(), dps.end(), exp[s].getDataProcessing()) == dps.end())</div>
<div class="line"><a name="l03923"></a><span class="lineno"> 3923</span>&#160;        {</div>
<div class="line"><a name="l03924"></a><span class="lineno"> 3924</span>&#160;          dps.push_back(exp[s].getDataProcessing());</div>
<div class="line"><a name="l03925"></a><span class="lineno"> 3925</span>&#160;          num_software += exp[s].getDataProcessing().size();</div>
<div class="line"><a name="l03926"></a><span class="lineno"> 3926</span>&#160;        }</div>
<div class="line"><a name="l03927"></a><span class="lineno"> 3927</span>&#160;      }</div>
<div class="line"><a name="l03928"></a><span class="lineno"> 3928</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.getChromatograms().size(); ++s)</div>
<div class="line"><a name="l03929"></a><span class="lineno"> 3929</span>&#160;      {</div>
<div class="line"><a name="l03930"></a><span class="lineno"> 3930</span>&#160;        <span class="keywordflow">if</span> (find(dps.begin(), dps.end(), exp.getChromatograms()[s].getDataProcessing()) == dps.end())</div>
<div class="line"><a name="l03931"></a><span class="lineno"> 3931</span>&#160;        {</div>
<div class="line"><a name="l03932"></a><span class="lineno"> 3932</span>&#160;          dps.push_back(exp.getChromatograms()[s].getDataProcessing());</div>
<div class="line"><a name="l03933"></a><span class="lineno"> 3933</span>&#160;          num_software += exp.getChromatograms()[s].getDataProcessing().size();</div>
<div class="line"><a name="l03934"></a><span class="lineno"> 3934</span>&#160;        }</div>
<div class="line"><a name="l03935"></a><span class="lineno"> 3935</span>&#160;      }</div>
<div class="line"><a name="l03936"></a><span class="lineno"> 3936</span>&#160;</div>
<div class="line"><a name="l03937"></a><span class="lineno"> 3937</span>&#160;      <span class="comment">// count binary data array software</span></div>
<div class="line"><a name="l03938"></a><span class="lineno"> 3938</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_bi_software(0);</div>
<div class="line"><a name="l03939"></a><span class="lineno"> 3939</span>&#160;</div>
<div class="line"><a name="l03940"></a><span class="lineno"> 3940</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l03941"></a><span class="lineno"> 3941</span>&#160;      {</div>
<div class="line"><a name="l03942"></a><span class="lineno"> 3942</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; exp[s].getFloatDataArrays().size(); ++m)</div>
<div class="line"><a name="l03943"></a><span class="lineno"> 3943</span>&#160;        {</div>
<div class="line"><a name="l03944"></a><span class="lineno"> 3944</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; exp[s].getFloatDataArrays()[m].getDataProcessing().size(); ++i)</div>
<div class="line"><a name="l03945"></a><span class="lineno"> 3945</span>&#160;          {</div>
<div class="line"><a name="l03946"></a><span class="lineno"> 3946</span>&#160;            ++num_bi_software;</div>
<div class="line"><a name="l03947"></a><span class="lineno"> 3947</span>&#160;          }</div>
<div class="line"><a name="l03948"></a><span class="lineno"> 3948</span>&#160;        }</div>
<div class="line"><a name="l03949"></a><span class="lineno"> 3949</span>&#160;      }</div>
<div class="line"><a name="l03950"></a><span class="lineno"> 3950</span>&#160;</div>
<div class="line"><a name="l03951"></a><span class="lineno"> 3951</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;softwareList count=\&quot;&quot;</span> &lt;&lt; num_software + num_bi_software &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03952"></a><span class="lineno"> 3952</span>&#160;      <span class="comment">//write instrument software</span></div>
<div class="line"><a name="l03953"></a><span class="lineno"> 3953</span>&#160;      writeSoftware_(os, <span class="stringliteral">&quot;so_in_0&quot;</span>, exp.getInstrument().getSoftware(), validator);</div>
<div class="line"><a name="l03954"></a><span class="lineno"> 3954</span>&#160;</div>
<div class="line"><a name="l03955"></a><span class="lineno"> 3955</span>&#160;      <span class="comment">//write fallback software</span></div>
<div class="line"><a name="l03956"></a><span class="lineno"> 3956</span>&#160;      writeSoftware_(os, <span class="stringliteral">&quot;so_default&quot;</span>, <a class="code" href="classOpenMS_1_1Software.html">Software</a>(), validator);</div>
<div class="line"><a name="l03957"></a><span class="lineno"> 3957</span>&#160;</div>
<div class="line"><a name="l03958"></a><span class="lineno"> 3958</span>&#160;      <span class="comment">// write the software of the dps</span></div>
<div class="line"><a name="l03959"></a><span class="lineno"> 3959</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s1 = 0; s1 != dps.size(); ++s1)</div>
<div class="line"><a name="l03960"></a><span class="lineno"> 3960</span>&#160;      {</div>
<div class="line"><a name="l03961"></a><span class="lineno"> 3961</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s2 = 0; s2 != dps[s1].size(); ++s2)</div>
<div class="line"><a name="l03962"></a><span class="lineno"> 3962</span>&#160;        {</div>
<div class="line"><a name="l03963"></a><span class="lineno"> 3963</span>&#160;          writeSoftware_(os, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;so_dp_sp_&quot;</span>) + s1 + <span class="stringliteral">&quot;_pm_&quot;</span> + s2, dps[s1][s2].getSoftware(), validator);</div>
<div class="line"><a name="l03964"></a><span class="lineno"> 3964</span>&#160;        }</div>
<div class="line"><a name="l03965"></a><span class="lineno"> 3965</span>&#160;      }</div>
<div class="line"><a name="l03966"></a><span class="lineno"> 3966</span>&#160;</div>
<div class="line"><a name="l03967"></a><span class="lineno"> 3967</span>&#160;      <span class="comment">//write data processing (for each binary data array)</span></div>
<div class="line"><a name="l03968"></a><span class="lineno"> 3968</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l03969"></a><span class="lineno"> 3969</span>&#160;      {</div>
<div class="line"><a name="l03970"></a><span class="lineno"> 3970</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; exp[s].getFloatDataArrays().size(); ++m)</div>
<div class="line"><a name="l03971"></a><span class="lineno"> 3971</span>&#160;        {</div>
<div class="line"><a name="l03972"></a><span class="lineno"> 3972</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; exp[s].getFloatDataArrays()[m].getDataProcessing().size(); ++i)</div>
<div class="line"><a name="l03973"></a><span class="lineno"> 3973</span>&#160;          {</div>
<div class="line"><a name="l03974"></a><span class="lineno"> 3974</span>&#160;            writeSoftware_(os, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;so_dp_sp_&quot;</span>) + s + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;_pm_&quot;</span> + i, exp[s].getFloatDataArrays()[m].getDataProcessing()[i].getSoftware(), validator);</div>
<div class="line"><a name="l03975"></a><span class="lineno"> 3975</span>&#160;          }</div>
<div class="line"><a name="l03976"></a><span class="lineno"> 3976</span>&#160;        }</div>
<div class="line"><a name="l03977"></a><span class="lineno"> 3977</span>&#160;      }</div>
<div class="line"><a name="l03978"></a><span class="lineno"> 3978</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;/softwareList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03979"></a><span class="lineno"> 3979</span>&#160;</div>
<div class="line"><a name="l03980"></a><span class="lineno"> 3980</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03981"></a><span class="lineno"> 3981</span>&#160;      <span class="comment">// instrument configuration (enclosing ion source, mass analyzer and detector)</span></div>
<div class="line"><a name="l03982"></a><span class="lineno"> 3982</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l03983"></a><span class="lineno"> 3983</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Instrument.html">Instrument</a>&amp; in = exp.getInstrument();</div>
<div class="line"><a name="l03984"></a><span class="lineno"> 3984</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;instrumentConfigurationList count=\&quot;1\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03985"></a><span class="lineno"> 3985</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;instrumentConfiguration id=\&quot;ic_0\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03986"></a><span class="lineno"> 3986</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> in_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000031&quot;</span>, in.<a class="code" href="classOpenMS_1_1Instrument.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>());</div>
<div class="line"><a name="l03987"></a><span class="lineno"> 3987</span>&#160;      <span class="keywordflow">if</span> (in_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03988"></a><span class="lineno"> 3988</span>&#160;      {</div>
<div class="line"><a name="l03989"></a><span class="lineno"> 3989</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; in_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; in_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03990"></a><span class="lineno"> 3990</span>&#160;      }</div>
<div class="line"><a name="l03991"></a><span class="lineno"> 3991</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l03992"></a><span class="lineno"> 3992</span>&#160;      {</div>
<div class="line"><a name="l03993"></a><span class="lineno"> 3993</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000031\&quot; name=\&quot;instrument model\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03994"></a><span class="lineno"> 3994</span>&#160;      }</div>
<div class="line"><a name="l03995"></a><span class="lineno"> 3995</span>&#160;</div>
<div class="line"><a name="l03996"></a><span class="lineno"> 3996</span>&#160;      <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a935d3c82c309ed3c0ed94d5edb12ce08">getCustomizations</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l03997"></a><span class="lineno"> 3997</span>&#160;      {</div>
<div class="line"><a name="l03998"></a><span class="lineno"> 3998</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000032\&quot; name=\&quot;customization\&quot; value=\&quot;&quot;</span> &lt;&lt; in.<a class="code" href="classOpenMS_1_1Instrument.html#a935d3c82c309ed3c0ed94d5edb12ce08">getCustomizations</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l03999"></a><span class="lineno"> 3999</span>&#160;      }</div>
<div class="line"><a name="l04000"></a><span class="lineno"> 4000</span>&#160;</div>
<div class="line"><a name="l04001"></a><span class="lineno"> 4001</span>&#160;      <span class="comment">//ion optics</span></div>
<div class="line"><a name="l04002"></a><span class="lineno"> 4002</span>&#160;      <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea78e072856cb37e4c51c595d8236347d7">Instrument::MAGNETIC_DEFLECTION</a>)</div>
<div class="line"><a name="l04003"></a><span class="lineno"> 4003</span>&#160;      {</div>
<div class="line"><a name="l04004"></a><span class="lineno"> 4004</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000221\&quot; name=\&quot;magnetic deflection\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04005"></a><span class="lineno"> 4005</span>&#160;      }</div>
<div class="line"><a name="l04006"></a><span class="lineno"> 4006</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea9f31dbfcc7e3828fea80213c74fa76e2">Instrument::DELAYED_EXTRACTION</a>)</div>
<div class="line"><a name="l04007"></a><span class="lineno"> 4007</span>&#160;      {</div>
<div class="line"><a name="l04008"></a><span class="lineno"> 4008</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000246\&quot; name=\&quot;delayed extraction\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04009"></a><span class="lineno"> 4009</span>&#160;      }</div>
<div class="line"><a name="l04010"></a><span class="lineno"> 4010</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea2573b581168afac70eeffa4a02e4ac66">Instrument::COLLISION_QUADRUPOLE</a>)</div>
<div class="line"><a name="l04011"></a><span class="lineno"> 4011</span>&#160;      {</div>
<div class="line"><a name="l04012"></a><span class="lineno"> 4012</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000275\&quot; name=\&quot;collision quadrupole\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04013"></a><span class="lineno"> 4013</span>&#160;      }</div>
<div class="line"><a name="l04014"></a><span class="lineno"> 4014</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825eaad34ce194cef545b3decfad97565ea17">Instrument::SELECTED_ION_FLOW_TUBE</a>)</div>
<div class="line"><a name="l04015"></a><span class="lineno"> 4015</span>&#160;      {</div>
<div class="line"><a name="l04016"></a><span class="lineno"> 4016</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000281\&quot; name=\&quot;selected ion flow tube\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04017"></a><span class="lineno"> 4017</span>&#160;      }</div>
<div class="line"><a name="l04018"></a><span class="lineno"> 4018</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea1a077c77350bebae4e5a37f5ef2d4d98">Instrument::TIME_LAG_FOCUSING</a>)</div>
<div class="line"><a name="l04019"></a><span class="lineno"> 4019</span>&#160;      {</div>
<div class="line"><a name="l04020"></a><span class="lineno"> 4020</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000286\&quot; name=\&quot;time lag focusing\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04021"></a><span class="lineno"> 4021</span>&#160;      }</div>
<div class="line"><a name="l04022"></a><span class="lineno"> 4022</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea00c6731b4cbe1c7f48610afb10686c9c">Instrument::REFLECTRON</a>)</div>
<div class="line"><a name="l04023"></a><span class="lineno"> 4023</span>&#160;      {</div>
<div class="line"><a name="l04024"></a><span class="lineno"> 4024</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000300\&quot; name=\&quot;reflectron\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04025"></a><span class="lineno"> 4025</span>&#160;      }</div>
<div class="line"><a name="l04026"></a><span class="lineno"> 4026</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825eabac1358aab1b37a968f2dc90facf110e">Instrument::EINZEL_LENS</a>)</div>
<div class="line"><a name="l04027"></a><span class="lineno"> 4027</span>&#160;      {</div>
<div class="line"><a name="l04028"></a><span class="lineno"> 4028</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000307\&quot; name=\&quot;einzel lens\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04029"></a><span class="lineno"> 4029</span>&#160;      }</div>
<div class="line"><a name="l04030"></a><span class="lineno"> 4030</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea02fb42fb91d78f40b3280cec43ff67a9">Instrument::FIRST_STABILITY_REGION</a>)</div>
<div class="line"><a name="l04031"></a><span class="lineno"> 4031</span>&#160;      {</div>
<div class="line"><a name="l04032"></a><span class="lineno"> 4032</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000309\&quot; name=\&quot;first stability region\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04033"></a><span class="lineno"> 4033</span>&#160;      }</div>
<div class="line"><a name="l04034"></a><span class="lineno"> 4034</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea9503ab7efe8e81ba7b6ec9e11a4aec86">Instrument::FRINGING_FIELD</a>)</div>
<div class="line"><a name="l04035"></a><span class="lineno"> 4035</span>&#160;      {</div>
<div class="line"><a name="l04036"></a><span class="lineno"> 4036</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000310\&quot; name=\&quot;fringing field\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04037"></a><span class="lineno"> 4037</span>&#160;      }</div>
<div class="line"><a name="l04038"></a><span class="lineno"> 4038</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea17e86bcc9b8f78ff8c458d7b9253699d">Instrument::KINETIC_ENERGY_ANALYZER</a>)</div>
<div class="line"><a name="l04039"></a><span class="lineno"> 4039</span>&#160;      {</div>
<div class="line"><a name="l04040"></a><span class="lineno"> 4040</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000311\&quot; name=\&quot;kinetic energy analyzer\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04041"></a><span class="lineno"> 4041</span>&#160;      }</div>
<div class="line"><a name="l04042"></a><span class="lineno"> 4042</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (in.<a class="code" href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">getIonOptics</a>() == <a class="code" href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea15567a4ebc7d975ae3be35e3efd7daae">Instrument::STATIC_FIELD</a>)</div>
<div class="line"><a name="l04043"></a><span class="lineno"> 4043</span>&#160;      {</div>
<div class="line"><a name="l04044"></a><span class="lineno"> 4044</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000320\&quot; name=\&quot;static field\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04045"></a><span class="lineno"> 4045</span>&#160;      }</div>
<div class="line"><a name="l04046"></a><span class="lineno"> 4046</span>&#160;</div>
<div class="line"><a name="l04047"></a><span class="lineno"> 4047</span>&#160;      writeUserParam_(os, in, 3, <span class="stringliteral">&quot;/mzML/instrumentConfigurationList/instrumentConfiguration/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04048"></a><span class="lineno"> 4048</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> component_count = in.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>().size() + in.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>().size() + in.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>().size();</div>
<div class="line"><a name="l04049"></a><span class="lineno"> 4049</span>&#160;      <span class="keywordflow">if</span> (component_count != 0)</div>
<div class="line"><a name="l04050"></a><span class="lineno"> 4050</span>&#160;      {</div>
<div class="line"><a name="l04051"></a><span class="lineno"> 4051</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;componentList count=\&quot;&quot;</span> &lt;&lt; (std::max)((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)3, component_count) &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04052"></a><span class="lineno"> 4052</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04053"></a><span class="lineno"> 4053</span>&#160;        <span class="comment">// ion source</span></div>
<div class="line"><a name="l04054"></a><span class="lineno"> 4054</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04055"></a><span class="lineno"> 4055</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; in.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>().size(); ++i)</div>
<div class="line"><a name="l04056"></a><span class="lineno"> 4056</span>&#160;        {</div>
<div class="line"><a name="l04057"></a><span class="lineno"> 4057</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IonSource.html">IonSource</a>&amp; so = in.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[i];</div>
<div class="line"><a name="l04058"></a><span class="lineno"> 4058</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;source order=\&quot;&quot;</span> &lt;&lt; so.<a class="code" href="classOpenMS_1_1IonSource.html#ad4e0ad3506a3256ecfbc50e925b40f99">getOrder</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04059"></a><span class="lineno"> 4059</span>&#160;</div>
<div class="line"><a name="l04060"></a><span class="lineno"> 4060</span>&#160;          <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fab6d52778aef5ed31ac17025f4bffd8f4">IonSource::CONTINUOUSFLOWFASTATOMBOMBARDMENT</a>)</div>
<div class="line"><a name="l04061"></a><span class="lineno"> 4061</span>&#160;          {</div>
<div class="line"><a name="l04062"></a><span class="lineno"> 4062</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000055\&quot; name=\&quot;continuous flow fast atom bombardment\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04063"></a><span class="lineno"> 4063</span>&#160;          }</div>
<div class="line"><a name="l04064"></a><span class="lineno"> 4064</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa1ea328a644e627283a35716a54108248">IonSource::DIRECT</a>)</div>
<div class="line"><a name="l04065"></a><span class="lineno"> 4065</span>&#160;          {</div>
<div class="line"><a name="l04066"></a><span class="lineno"> 4066</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000056\&quot; name=\&quot;direct inlet\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04067"></a><span class="lineno"> 4067</span>&#160;          }</div>
<div class="line"><a name="l04068"></a><span class="lineno"> 4068</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa9c897c6cdabbcc5b84159ac533e72f32">IonSource::ELECTROSPRAYINLET</a>)</div>
<div class="line"><a name="l04069"></a><span class="lineno"> 4069</span>&#160;          {</div>
<div class="line"><a name="l04070"></a><span class="lineno"> 4070</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000057\&quot; name=\&quot;electrospray inlet\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04071"></a><span class="lineno"> 4071</span>&#160;          }</div>
<div class="line"><a name="l04072"></a><span class="lineno"> 4072</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa6c48ed9c4442494fd5f122c94860447d">IonSource::FLOWINJECTIONANALYSIS</a>)</div>
<div class="line"><a name="l04073"></a><span class="lineno"> 4073</span>&#160;          {</div>
<div class="line"><a name="l04074"></a><span class="lineno"> 4074</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000058\&quot; name=\&quot;flow injection analysis\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04075"></a><span class="lineno"> 4075</span>&#160;          }</div>
<div class="line"><a name="l04076"></a><span class="lineno"> 4076</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa8f610db6e93fa153152a1c46b49539b2">IonSource::INDUCTIVELYCOUPLEDPLASMA</a>)</div>
<div class="line"><a name="l04077"></a><span class="lineno"> 4077</span>&#160;          {</div>
<div class="line"><a name="l04078"></a><span class="lineno"> 4078</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000059\&quot; name=\&quot;inductively coupled plasma\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04079"></a><span class="lineno"> 4079</span>&#160;          }</div>
<div class="line"><a name="l04080"></a><span class="lineno"> 4080</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa27dcc04b8d9859dfe2ea21b888c26189">IonSource::INFUSION</a>)</div>
<div class="line"><a name="l04081"></a><span class="lineno"> 4081</span>&#160;          {</div>
<div class="line"><a name="l04082"></a><span class="lineno"> 4082</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000060\&quot; name=\&quot;infusion\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04083"></a><span class="lineno"> 4083</span>&#160;          }</div>
<div class="line"><a name="l04084"></a><span class="lineno"> 4084</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa0598d1c2cd7107bff01eb8de6ff74f94">IonSource::JETSEPARATOR</a>)</div>
<div class="line"><a name="l04085"></a><span class="lineno"> 4085</span>&#160;          {</div>
<div class="line"><a name="l04086"></a><span class="lineno"> 4086</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000061\&quot; name=\&quot;jet separator\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04087"></a><span class="lineno"> 4087</span>&#160;          }</div>
<div class="line"><a name="l04088"></a><span class="lineno"> 4088</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa19ff98c123f82fd251780c91d5d52f13">IonSource::MEMBRANESEPARATOR</a>)</div>
<div class="line"><a name="l04089"></a><span class="lineno"> 4089</span>&#160;          {</div>
<div class="line"><a name="l04090"></a><span class="lineno"> 4090</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000062\&quot; name=\&quot;membrane separator\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04091"></a><span class="lineno"> 4091</span>&#160;          }</div>
<div class="line"><a name="l04092"></a><span class="lineno"> 4092</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fafc825adbdcb19797aad0ed340db940c3">IonSource::MOVINGBELT</a>)</div>
<div class="line"><a name="l04093"></a><span class="lineno"> 4093</span>&#160;          {</div>
<div class="line"><a name="l04094"></a><span class="lineno"> 4094</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000063\&quot; name=\&quot;moving belt\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04095"></a><span class="lineno"> 4095</span>&#160;          }</div>
<div class="line"><a name="l04096"></a><span class="lineno"> 4096</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa3c5780d8602eb19c5c2d688498c29de8">IonSource::MOVINGWIRE</a>)</div>
<div class="line"><a name="l04097"></a><span class="lineno"> 4097</span>&#160;          {</div>
<div class="line"><a name="l04098"></a><span class="lineno"> 4098</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000064\&quot; name=\&quot;moving wire\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04099"></a><span class="lineno"> 4099</span>&#160;          }</div>
<div class="line"><a name="l04100"></a><span class="lineno"> 4100</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa884aab0e62a0e1db261a95022a6ef25d">IonSource::OPENSPLIT</a>)</div>
<div class="line"><a name="l04101"></a><span class="lineno"> 4101</span>&#160;          {</div>
<div class="line"><a name="l04102"></a><span class="lineno"> 4102</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000065\&quot; name=\&quot;open split\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04103"></a><span class="lineno"> 4103</span>&#160;          }</div>
<div class="line"><a name="l04104"></a><span class="lineno"> 4104</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa564313b42cf82a9be19c95050133911b">IonSource::PARTICLEBEAM</a>)</div>
<div class="line"><a name="l04105"></a><span class="lineno"> 4105</span>&#160;          {</div>
<div class="line"><a name="l04106"></a><span class="lineno"> 4106</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000066\&quot; name=\&quot;particle beam\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04107"></a><span class="lineno"> 4107</span>&#160;          }</div>
<div class="line"><a name="l04108"></a><span class="lineno"> 4108</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa73dded3a91104b5de02f9f408023ef18">IonSource::RESERVOIR</a>)</div>
<div class="line"><a name="l04109"></a><span class="lineno"> 4109</span>&#160;          {</div>
<div class="line"><a name="l04110"></a><span class="lineno"> 4110</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000067\&quot; name=\&quot;reservoir\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04111"></a><span class="lineno"> 4111</span>&#160;          }</div>
<div class="line"><a name="l04112"></a><span class="lineno"> 4112</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fad7f5a34d7e508de209ade5decea9e80c">IonSource::SEPTUM</a>)</div>
<div class="line"><a name="l04113"></a><span class="lineno"> 4113</span>&#160;          {</div>
<div class="line"><a name="l04114"></a><span class="lineno"> 4114</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000068\&quot; name=\&quot;septum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04115"></a><span class="lineno"> 4115</span>&#160;          }</div>
<div class="line"><a name="l04116"></a><span class="lineno"> 4116</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675faf72472484541d6de7bfe8151b04b7417">IonSource::THERMOSPRAYINLET</a>)</div>
<div class="line"><a name="l04117"></a><span class="lineno"> 4117</span>&#160;          {</div>
<div class="line"><a name="l04118"></a><span class="lineno"> 4118</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000069\&quot; name=\&quot;thermospray inlet\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04119"></a><span class="lineno"> 4119</span>&#160;          }</div>
<div class="line"><a name="l04120"></a><span class="lineno"> 4120</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fabc04848b2d94351b99f92127e29bb075">IonSource::BATCH</a>)</div>
<div class="line"><a name="l04121"></a><span class="lineno"> 4121</span>&#160;          {</div>
<div class="line"><a name="l04122"></a><span class="lineno"> 4122</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000248\&quot; name=\&quot;direct insertion probe\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04123"></a><span class="lineno"> 4123</span>&#160;          }</div>
<div class="line"><a name="l04124"></a><span class="lineno"> 4124</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa066def527c3472b49e0d152c392ee0d7">IonSource::CHROMATOGRAPHY</a>)</div>
<div class="line"><a name="l04125"></a><span class="lineno"> 4125</span>&#160;          {</div>
<div class="line"><a name="l04126"></a><span class="lineno"> 4126</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000249\&quot; name=\&quot;direct liquid introduction\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04127"></a><span class="lineno"> 4127</span>&#160;          }</div>
<div class="line"><a name="l04128"></a><span class="lineno"> 4128</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa14dec9ac85c4c53db9e1fa17d0bffeea">IonSource::MEMBRANE</a>)</div>
<div class="line"><a name="l04129"></a><span class="lineno"> 4129</span>&#160;          {</div>
<div class="line"><a name="l04130"></a><span class="lineno"> 4130</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000396\&quot; name=\&quot;membrane inlet\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04131"></a><span class="lineno"> 4131</span>&#160;          }</div>
<div class="line"><a name="l04132"></a><span class="lineno"> 4132</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">getInletType</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa2328ee396a2ca9e44bd7a8459bcfef28">IonSource::NANOSPRAY</a>)</div>
<div class="line"><a name="l04133"></a><span class="lineno"> 4133</span>&#160;          {</div>
<div class="line"><a name="l04134"></a><span class="lineno"> 4134</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000485\&quot; name=\&quot;nanospray inlet\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04135"></a><span class="lineno"> 4135</span>&#160;          }</div>
<div class="line"><a name="l04136"></a><span class="lineno"> 4136</span>&#160;</div>
<div class="line"><a name="l04137"></a><span class="lineno"> 4137</span>&#160;          <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aa45f628d1930ccc096fd37583145fccb">IonSource::APCI</a>)</div>
<div class="line"><a name="l04138"></a><span class="lineno"> 4138</span>&#160;          {</div>
<div class="line"><a name="l04139"></a><span class="lineno"> 4139</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000070\&quot; name=\&quot;atmospheric pressure chemical ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04140"></a><span class="lineno"> 4140</span>&#160;          }</div>
<div class="line"><a name="l04141"></a><span class="lineno"> 4141</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aed87f9b08a003dc2ef4c4920060eae14">IonSource::CI</a>)</div>
<div class="line"><a name="l04142"></a><span class="lineno"> 4142</span>&#160;          {</div>
<div class="line"><a name="l04143"></a><span class="lineno"> 4143</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000071\&quot; name=\&quot;chemical ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04144"></a><span class="lineno"> 4144</span>&#160;          }</div>
<div class="line"><a name="l04145"></a><span class="lineno"> 4145</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a4ce1f413b646020308281e301ce1e4ec">IonSource::ESI</a>)</div>
<div class="line"><a name="l04146"></a><span class="lineno"> 4146</span>&#160;          {</div>
<div class="line"><a name="l04147"></a><span class="lineno"> 4147</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000073\&quot; name=\&quot;electrospray ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04148"></a><span class="lineno"> 4148</span>&#160;          }</div>
<div class="line"><a name="l04149"></a><span class="lineno"> 4149</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4abccdeef60efaa51840b2bda65c374e7e">IonSource::FAB</a>)</div>
<div class="line"><a name="l04150"></a><span class="lineno"> 4150</span>&#160;          {</div>
<div class="line"><a name="l04151"></a><span class="lineno"> 4151</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000074\&quot; name=\&quot;fast atom bombardment ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04152"></a><span class="lineno"> 4152</span>&#160;          }</div>
<div class="line"><a name="l04153"></a><span class="lineno"> 4153</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4af44dbf64796c3c09b804546061c39258">IonSource::MALDI</a>)</div>
<div class="line"><a name="l04154"></a><span class="lineno"> 4154</span>&#160;          {</div>
<div class="line"><a name="l04155"></a><span class="lineno"> 4155</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000075\&quot; name=\&quot;matrix-assisted laser desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04156"></a><span class="lineno"> 4156</span>&#160;          }</div>
<div class="line"><a name="l04157"></a><span class="lineno"> 4157</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aece8c4cb0f2685308261ef5409676a18">IonSource::MPI</a>)</div>
<div class="line"><a name="l04158"></a><span class="lineno"> 4158</span>&#160;          {</div>
<div class="line"><a name="l04159"></a><span class="lineno"> 4159</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000227\&quot; name=\&quot;multiphoton ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04160"></a><span class="lineno"> 4160</span>&#160;          }</div>
<div class="line"><a name="l04161"></a><span class="lineno"> 4161</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4adfcd7e7c05c5dda54aa06c36077abab0">IonSource::AP_MALDI</a>)</div>
<div class="line"><a name="l04162"></a><span class="lineno"> 4162</span>&#160;          {</div>
<div class="line"><a name="l04163"></a><span class="lineno"> 4163</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000239\&quot; name=\&quot;atmospheric pressure matrix-assisted laser desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04164"></a><span class="lineno"> 4164</span>&#160;          }</div>
<div class="line"><a name="l04165"></a><span class="lineno"> 4165</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a7fd5f3a93cf5139877f23acb316f99c0">IonSource::API</a>)</div>
<div class="line"><a name="l04166"></a><span class="lineno"> 4166</span>&#160;          {</div>
<div class="line"><a name="l04167"></a><span class="lineno"> 4167</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000240\&quot; name=\&quot;atmospheric pressure ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04168"></a><span class="lineno"> 4168</span>&#160;          }</div>
<div class="line"><a name="l04169"></a><span class="lineno"> 4169</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a527f7ffe8e4e1d4cd85dd9e61eed9795">IonSource::DI</a>)</div>
<div class="line"><a name="l04170"></a><span class="lineno"> 4170</span>&#160;          {</div>
<div class="line"><a name="l04171"></a><span class="lineno"> 4171</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000247\&quot; name=\&quot;desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04172"></a><span class="lineno"> 4172</span>&#160;          }</div>
<div class="line"><a name="l04173"></a><span class="lineno"> 4173</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a587607b9ab280181a8b20a9fb147bad3">IonSource::FA</a>)</div>
<div class="line"><a name="l04174"></a><span class="lineno"> 4174</span>&#160;          {</div>
<div class="line"><a name="l04175"></a><span class="lineno"> 4175</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000255\&quot; name=\&quot;flowing afterglow\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04176"></a><span class="lineno"> 4176</span>&#160;          }</div>
<div class="line"><a name="l04177"></a><span class="lineno"> 4177</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4af6cb3036978c564d260f5016cac04f85">IonSource::FD</a>)</div>
<div class="line"><a name="l04178"></a><span class="lineno"> 4178</span>&#160;          {</div>
<div class="line"><a name="l04179"></a><span class="lineno"> 4179</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000257\&quot; name=\&quot;field desorption\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04180"></a><span class="lineno"> 4180</span>&#160;          }</div>
<div class="line"><a name="l04181"></a><span class="lineno"> 4181</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aa2ce66107d2f686db9a07584da0d730f">IonSource::FI</a>)</div>
<div class="line"><a name="l04182"></a><span class="lineno"> 4182</span>&#160;          {</div>
<div class="line"><a name="l04183"></a><span class="lineno"> 4183</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000258\&quot; name=\&quot;field ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04184"></a><span class="lineno"> 4184</span>&#160;          }</div>
<div class="line"><a name="l04185"></a><span class="lineno"> 4185</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a535e49bf5eee5561caead0a39995a48b">IonSource::GD_MS</a>)</div>
<div class="line"><a name="l04186"></a><span class="lineno"> 4186</span>&#160;          {</div>
<div class="line"><a name="l04187"></a><span class="lineno"> 4187</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000259\&quot; name=\&quot;glow discharge ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04188"></a><span class="lineno"> 4188</span>&#160;          }</div>
<div class="line"><a name="l04189"></a><span class="lineno"> 4189</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a20d56bc7900e25dc3e84f15078eefdf7">IonSource::NICI</a>)</div>
<div class="line"><a name="l04190"></a><span class="lineno"> 4190</span>&#160;          {</div>
<div class="line"><a name="l04191"></a><span class="lineno"> 4191</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000271\&quot; name=\&quot;Negative ion chemical ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04192"></a><span class="lineno"> 4192</span>&#160;          }</div>
<div class="line"><a name="l04193"></a><span class="lineno"> 4193</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a6c146484587d495e53fe377ca0b855fe">IonSource::NRMS</a>)</div>
<div class="line"><a name="l04194"></a><span class="lineno"> 4194</span>&#160;          {</div>
<div class="line"><a name="l04195"></a><span class="lineno"> 4195</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000272\&quot; name=\&quot;neutralization reionization mass spectrometry\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04196"></a><span class="lineno"> 4196</span>&#160;          }</div>
<div class="line"><a name="l04197"></a><span class="lineno"> 4197</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5b26cd07c89ea86afa2fa793fb7fc729">IonSource::PI</a>)</div>
<div class="line"><a name="l04198"></a><span class="lineno"> 4198</span>&#160;          {</div>
<div class="line"><a name="l04199"></a><span class="lineno"> 4199</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000273\&quot; name=\&quot;photoionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04200"></a><span class="lineno"> 4200</span>&#160;          }</div>
<div class="line"><a name="l04201"></a><span class="lineno"> 4201</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aae20fd962cf613d3911e5f7da51de1df">IonSource::PYMS</a>)</div>
<div class="line"><a name="l04202"></a><span class="lineno"> 4202</span>&#160;          {</div>
<div class="line"><a name="l04203"></a><span class="lineno"> 4203</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000274\&quot; name=\&quot;pyrolysis mass spectrometry\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04204"></a><span class="lineno"> 4204</span>&#160;          }</div>
<div class="line"><a name="l04205"></a><span class="lineno"> 4205</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aae01bfe30f377fbd7d8e5f4e431eaacb">IonSource::REMPI</a>)</div>
<div class="line"><a name="l04206"></a><span class="lineno"> 4206</span>&#160;          {</div>
<div class="line"><a name="l04207"></a><span class="lineno"> 4207</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000276\&quot; name=\&quot;resonance enhanced multiphoton ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04208"></a><span class="lineno"> 4208</span>&#160;          }</div>
<div class="line"><a name="l04209"></a><span class="lineno"> 4209</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a259eb726b6a08b2a08164df4e14db708">IonSource::SELDI</a>)</div>
<div class="line"><a name="l04210"></a><span class="lineno"> 4210</span>&#160;          {</div>
<div class="line"><a name="l04211"></a><span class="lineno"> 4211</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000278\&quot; name=\&quot;surface enhanced laser desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04212"></a><span class="lineno"> 4212</span>&#160;          }</div>
<div class="line"><a name="l04213"></a><span class="lineno"> 4213</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a67be7a5f47004345047b32fff72a2230">IonSource::SEND</a>)</div>
<div class="line"><a name="l04214"></a><span class="lineno"> 4214</span>&#160;          {</div>
<div class="line"><a name="l04215"></a><span class="lineno"> 4215</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000279\&quot; name=\&quot;surface enhanced neat desorption\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04216"></a><span class="lineno"> 4216</span>&#160;          }</div>
<div class="line"><a name="l04217"></a><span class="lineno"> 4217</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a9c74caa56a3c05723eb1dbad44bc9bc3">IonSource::AI</a>)</div>
<div class="line"><a name="l04218"></a><span class="lineno"> 4218</span>&#160;          {</div>
<div class="line"><a name="l04219"></a><span class="lineno"> 4219</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000380\&quot; name=\&quot;adiabatic ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04220"></a><span class="lineno"> 4220</span>&#160;          }</div>
<div class="line"><a name="l04221"></a><span class="lineno"> 4221</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ad534995d8fa8bd372ad247e16ff746fa">IonSource::ASI</a>)</div>
<div class="line"><a name="l04222"></a><span class="lineno"> 4222</span>&#160;          {</div>
<div class="line"><a name="l04223"></a><span class="lineno"> 4223</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000381\&quot; name=\&quot;associative ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04224"></a><span class="lineno"> 4224</span>&#160;          }</div>
<div class="line"><a name="l04225"></a><span class="lineno"> 4225</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5c60e3178bb8db38b3970316b0c5aae8">IonSource::APPI</a>)</div>
<div class="line"><a name="l04226"></a><span class="lineno"> 4226</span>&#160;          {</div>
<div class="line"><a name="l04227"></a><span class="lineno"> 4227</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000382\&quot; name=\&quot;atmospheric pressure photoionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04228"></a><span class="lineno"> 4228</span>&#160;          }</div>
<div class="line"><a name="l04229"></a><span class="lineno"> 4229</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ae63d77c61a2a5b9777024af082a36719">IonSource::AD</a>)</div>
<div class="line"><a name="l04230"></a><span class="lineno"> 4230</span>&#160;          {</div>
<div class="line"><a name="l04231"></a><span class="lineno"> 4231</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000383\&quot; name=\&quot;autodetachment\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04232"></a><span class="lineno"> 4232</span>&#160;          }</div>
<div class="line"><a name="l04233"></a><span class="lineno"> 4233</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a3306da16fbcb1fde30d4ec351db99285">IonSource::AUI</a>)</div>
<div class="line"><a name="l04234"></a><span class="lineno"> 4234</span>&#160;          {</div>
<div class="line"><a name="l04235"></a><span class="lineno"> 4235</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000384\&quot; name=\&quot;autoionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04236"></a><span class="lineno"> 4236</span>&#160;          }</div>
<div class="line"><a name="l04237"></a><span class="lineno"> 4237</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a32e4cb82b586a059c77128a1cdcd3282">IonSource::CEI</a>)</div>
<div class="line"><a name="l04238"></a><span class="lineno"> 4238</span>&#160;          {</div>
<div class="line"><a name="l04239"></a><span class="lineno"> 4239</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000385\&quot; name=\&quot;charge exchange ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04240"></a><span class="lineno"> 4240</span>&#160;          }</div>
<div class="line"><a name="l04241"></a><span class="lineno"> 4241</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ae3a31f903a1ebacac4aa4de2409c80ff">IonSource::CHEMI</a>)</div>
<div class="line"><a name="l04242"></a><span class="lineno"> 4242</span>&#160;          {</div>
<div class="line"><a name="l04243"></a><span class="lineno"> 4243</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000386\&quot; name=\&quot;chemi-ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04244"></a><span class="lineno"> 4244</span>&#160;          }</div>
<div class="line"><a name="l04245"></a><span class="lineno"> 4245</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4afda196677d08ccd458e96fe74597d638">IonSource::SILI</a>)</div>
<div class="line"><a name="l04246"></a><span class="lineno"> 4246</span>&#160;          {</div>
<div class="line"><a name="l04247"></a><span class="lineno"> 4247</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000387\&quot; name=\&quot;desorption/ionization on silicon\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04248"></a><span class="lineno"> 4248</span>&#160;          }</div>
<div class="line"><a name="l04249"></a><span class="lineno"> 4249</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4affe4bbe037c9af162387d453f90e129a">IonSource::DISSI</a>)</div>
<div class="line"><a name="l04250"></a><span class="lineno"> 4250</span>&#160;          {</div>
<div class="line"><a name="l04251"></a><span class="lineno"> 4251</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000388\&quot; name=\&quot;dissociative ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04252"></a><span class="lineno"> 4252</span>&#160;          }</div>
<div class="line"><a name="l04253"></a><span class="lineno"> 4253</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a3158578f2cc1fb7fbd261b4094e7f5fd">IonSource::EI</a>)</div>
<div class="line"><a name="l04254"></a><span class="lineno"> 4254</span>&#160;          {</div>
<div class="line"><a name="l04255"></a><span class="lineno"> 4255</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000389\&quot; name=\&quot;electron ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04256"></a><span class="lineno"> 4256</span>&#160;          }</div>
<div class="line"><a name="l04257"></a><span class="lineno"> 4257</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a24a5a956f8abcaacbde751c49c7d5001">IonSource::LD</a>)</div>
<div class="line"><a name="l04258"></a><span class="lineno"> 4258</span>&#160;          {</div>
<div class="line"><a name="l04259"></a><span class="lineno"> 4259</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000393\&quot; name=\&quot;laser desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04260"></a><span class="lineno"> 4260</span>&#160;          }</div>
<div class="line"><a name="l04261"></a><span class="lineno"> 4261</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ac59b221b111954833c988555d5972f88">IonSource::LSI</a>)</div>
<div class="line"><a name="l04262"></a><span class="lineno"> 4262</span>&#160;          {</div>
<div class="line"><a name="l04263"></a><span class="lineno"> 4263</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000395\&quot; name=\&quot;liquid secondary ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04264"></a><span class="lineno"> 4264</span>&#160;          }</div>
<div class="line"><a name="l04265"></a><span class="lineno"> 4265</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a626c8167a1599535349b7288be3895d1">IonSource::MESI</a>)</div>
<div class="line"><a name="l04266"></a><span class="lineno"> 4266</span>&#160;          {</div>
<div class="line"><a name="l04267"></a><span class="lineno"> 4267</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000397\&quot; name=\&quot;microelectrospray\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04268"></a><span class="lineno"> 4268</span>&#160;          }</div>
<div class="line"><a name="l04269"></a><span class="lineno"> 4269</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a07b393b769a687470db848e3eb98f578">IonSource::NESI</a>)</div>
<div class="line"><a name="l04270"></a><span class="lineno"> 4270</span>&#160;          {</div>
<div class="line"><a name="l04271"></a><span class="lineno"> 4271</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000398\&quot; name=\&quot;nanoelectrospray\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04272"></a><span class="lineno"> 4272</span>&#160;          }</div>
<div class="line"><a name="l04273"></a><span class="lineno"> 4273</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a0525c6afa4d96f74d29bbe7511a204db">IonSource::PEI</a>)</div>
<div class="line"><a name="l04274"></a><span class="lineno"> 4274</span>&#160;          {</div>
<div class="line"><a name="l04275"></a><span class="lineno"> 4275</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000399\&quot; name=\&quot;penning ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04276"></a><span class="lineno"> 4276</span>&#160;          }</div>
<div class="line"><a name="l04277"></a><span class="lineno"> 4277</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aefbc069e0ac4cd293f3ba527bec2befe">IonSource::PD</a>)</div>
<div class="line"><a name="l04278"></a><span class="lineno"> 4278</span>&#160;          {</div>
<div class="line"><a name="l04279"></a><span class="lineno"> 4279</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000400\&quot; name=\&quot;plasma desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04280"></a><span class="lineno"> 4280</span>&#160;          }</div>
<div class="line"><a name="l04281"></a><span class="lineno"> 4281</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a6cbe5ff42f143903e1c67abf94613791">IonSource::SI</a>)</div>
<div class="line"><a name="l04282"></a><span class="lineno"> 4282</span>&#160;          {</div>
<div class="line"><a name="l04283"></a><span class="lineno"> 4283</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000402\&quot; name=\&quot;secondary ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04284"></a><span class="lineno"> 4284</span>&#160;          }</div>
<div class="line"><a name="l04285"></a><span class="lineno"> 4285</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a90291956e102c1e1aa6e642164751197">IonSource::SOI</a>)</div>
<div class="line"><a name="l04286"></a><span class="lineno"> 4286</span>&#160;          {</div>
<div class="line"><a name="l04287"></a><span class="lineno"> 4287</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000403\&quot; name=\&quot;soft ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04288"></a><span class="lineno"> 4288</span>&#160;          }</div>
<div class="line"><a name="l04289"></a><span class="lineno"> 4289</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aefea9eb0772378037221a3f1fe759a76">IonSource::SPI</a>)</div>
<div class="line"><a name="l04290"></a><span class="lineno"> 4290</span>&#160;          {</div>
<div class="line"><a name="l04291"></a><span class="lineno"> 4291</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000404\&quot; name=\&quot;spark ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04292"></a><span class="lineno"> 4292</span>&#160;          }</div>
<div class="line"><a name="l04293"></a><span class="lineno"> 4293</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aaade3182d7ec0b4c0ef7a60392ed72b9">IonSource::SALDI</a>)</div>
<div class="line"><a name="l04294"></a><span class="lineno"> 4294</span>&#160;          {</div>
<div class="line"><a name="l04295"></a><span class="lineno"> 4295</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000405\&quot; name=\&quot;surface-assisted laser desorption ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04296"></a><span class="lineno"> 4296</span>&#160;          }</div>
<div class="line"><a name="l04297"></a><span class="lineno"> 4297</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5de3914c3b308664d35967f1a5ffc142">IonSource::SUI</a>)</div>
<div class="line"><a name="l04298"></a><span class="lineno"> 4298</span>&#160;          {</div>
<div class="line"><a name="l04299"></a><span class="lineno"> 4299</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000406\&quot; name=\&quot;surface ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04300"></a><span class="lineno"> 4300</span>&#160;          }</div>
<div class="line"><a name="l04301"></a><span class="lineno"> 4301</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a205ce9325a3a2b1ca71be96bee9d7f89">IonSource::TI</a>)</div>
<div class="line"><a name="l04302"></a><span class="lineno"> 4302</span>&#160;          {</div>
<div class="line"><a name="l04303"></a><span class="lineno"> 4303</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000407\&quot; name=\&quot;thermal ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04304"></a><span class="lineno"> 4304</span>&#160;          }</div>
<div class="line"><a name="l04305"></a><span class="lineno"> 4305</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a97bce951e4585a39601c04d86bb14ffd">IonSource::VI</a>)</div>
<div class="line"><a name="l04306"></a><span class="lineno"> 4306</span>&#160;          {</div>
<div class="line"><a name="l04307"></a><span class="lineno"> 4307</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000408\&quot; name=\&quot;vertical ionization\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04308"></a><span class="lineno"> 4308</span>&#160;          }</div>
<div class="line"><a name="l04309"></a><span class="lineno"> 4309</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aecf7855b0a44ab470fabcb44277200d7">IonSource::FIB</a>)</div>
<div class="line"><a name="l04310"></a><span class="lineno"> 4310</span>&#160;          {</div>
<div class="line"><a name="l04311"></a><span class="lineno"> 4311</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000446\&quot; name=\&quot;fast ion bombardment\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04312"></a><span class="lineno"> 4312</span>&#160;          }</div>
<div class="line"><a name="l04313"></a><span class="lineno"> 4313</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (so.<a class="code" href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">getIonizationMethod</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a4443b16a744c30d496e4b5bcb834b029">IonSource::IONMETHODNULL</a>)</div>
<div class="line"><a name="l04314"></a><span class="lineno"> 4314</span>&#160;          {</div>
<div class="line"><a name="l04315"></a><span class="lineno"> 4315</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000008\&quot; name=\&quot;ionization type\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04316"></a><span class="lineno"> 4316</span>&#160;          }</div>
<div class="line"><a name="l04317"></a><span class="lineno"> 4317</span>&#160;</div>
<div class="line"><a name="l04318"></a><span class="lineno"> 4318</span>&#160;          writeUserParam_(os, so, 5, <span class="stringliteral">&quot;/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/source/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04319"></a><span class="lineno"> 4319</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/source&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04320"></a><span class="lineno"> 4320</span>&#160;        }</div>
<div class="line"><a name="l04321"></a><span class="lineno"> 4321</span>&#160;        <span class="comment">//FORCED</span></div>
<div class="line"><a name="l04322"></a><span class="lineno"> 4322</span>&#160;        <span class="keywordflow">if</span> (component_count &lt; 3 &amp;&amp; in.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>().empty())</div>
<div class="line"><a name="l04323"></a><span class="lineno"> 4323</span>&#160;        {</div>
<div class="line"><a name="l04324"></a><span class="lineno"> 4324</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;source order=\&quot;1234\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04325"></a><span class="lineno"> 4325</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000446\&quot; name=\&quot;fast ion bombardment\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04326"></a><span class="lineno"> 4326</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;userParam name=\&quot;warning\&quot; type=\&quot;xsd:string\&quot; value=\&quot;invented ion source, to fulfill mzML schema\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04327"></a><span class="lineno"> 4327</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/source&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04328"></a><span class="lineno"> 4328</span>&#160;        }</div>
<div class="line"><a name="l04329"></a><span class="lineno"> 4329</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04330"></a><span class="lineno"> 4330</span>&#160;        <span class="comment">// mass analyzer</span></div>
<div class="line"><a name="l04331"></a><span class="lineno"> 4331</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04332"></a><span class="lineno"> 4332</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; in.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>().size(); ++i)</div>
<div class="line"><a name="l04333"></a><span class="lineno"> 4333</span>&#160;        {</div>
<div class="line"><a name="l04334"></a><span class="lineno"> 4334</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MassAnalyzer.html">MassAnalyzer</a>&amp; ma = in.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>()[i];</div>
<div class="line"><a name="l04335"></a><span class="lineno"> 4335</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;analyzer order=\&quot;&quot;</span> &lt;&lt; ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#ad4e0ad3506a3256ecfbc50e925b40f99">getOrder</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04336"></a><span class="lineno"> 4336</span>&#160;</div>
<div class="line"><a name="l04337"></a><span class="lineno"> 4337</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000014\&quot; name=\&quot;accuracy\&quot; value=\&quot;&quot;</span> &lt;&lt; ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#acf76c337ebde51c823ec30c2985afb0d">getAccuracy</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000169\&quot; unitName=\&quot;parts per million\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04338"></a><span class="lineno"> 4338</span>&#160;          <span class="comment">// @todo: the parameters below are instrument specific and should not be written every time</span></div>
<div class="line"><a name="l04339"></a><span class="lineno"> 4339</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000022\&quot; name=\&quot;TOF Total Path Length\&quot; value=\&quot;&quot;</span> &lt;&lt; ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a0f0fb5610d506c55825effbb77450fd5">getTOFTotalPathLength</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000008\&quot; unitName=\&quot;meter\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04340"></a><span class="lineno"> 4340</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000024\&quot; name=\&quot;final MS exponent\&quot; value=\&quot;&quot;</span> &lt;&lt; ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#af7adaa2fa0d50256c073d4bff34b165d">getFinalMSExponent</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04341"></a><span class="lineno"> 4341</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000025\&quot; name=\&quot;magnetic field strength\&quot; value=\&quot;&quot;</span> &lt;&lt; ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#ac5bb0a0896c81277ed75428db51dd8b4">getMagneticFieldStrength</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000228\&quot; unitName=\&quot;tesla\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04342"></a><span class="lineno"> 4342</span>&#160;</div>
<div class="line"><a name="l04343"></a><span class="lineno"> 4343</span>&#160;          <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a171e75c6324f7f4233782be3c4ca1d90">getReflectronState</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52fa977d478dacaae531f95695750d1e9d03">MassAnalyzer::ON</a>)</div>
<div class="line"><a name="l04344"></a><span class="lineno"> 4344</span>&#160;          {</div>
<div class="line"><a name="l04345"></a><span class="lineno"> 4345</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000106\&quot; name=\&quot;reflectron on\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04346"></a><span class="lineno"> 4346</span>&#160;</div>
<div class="line"><a name="l04347"></a><span class="lineno"> 4347</span>&#160;          }</div>
<div class="line"><a name="l04348"></a><span class="lineno"> 4348</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a171e75c6324f7f4233782be3c4ca1d90">getReflectronState</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52faac132f2982b98bcaa3445e535a03ff75">MassAnalyzer::OFF</a>)</div>
<div class="line"><a name="l04349"></a><span class="lineno"> 4349</span>&#160;          {</div>
<div class="line"><a name="l04350"></a><span class="lineno"> 4350</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000105\&quot; name=\&quot;reflectron off\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04351"></a><span class="lineno"> 4351</span>&#160;          }</div>
<div class="line"><a name="l04352"></a><span class="lineno"> 4352</span>&#160;</div>
<div class="line"><a name="l04353"></a><span class="lineno"> 4353</span>&#160;          <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a30b4d649b3cd56fb7e6aa514b67dc75a">MassAnalyzer::FOURIERTRANSFORM</a>)</div>
<div class="line"><a name="l04354"></a><span class="lineno"> 4354</span>&#160;          {</div>
<div class="line"><a name="l04355"></a><span class="lineno"> 4355</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000079\&quot; name=\&quot;fourier transform ion cyclotron resonance mass spectrometer\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04356"></a><span class="lineno"> 4356</span>&#160;          }</div>
<div class="line"><a name="l04357"></a><span class="lineno"> 4357</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a805264162c317eb0e81b8aa508726725">MassAnalyzer::SECTOR</a>)</div>
<div class="line"><a name="l04358"></a><span class="lineno"> 4358</span>&#160;          {</div>
<div class="line"><a name="l04359"></a><span class="lineno"> 4359</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000080\&quot; name=\&quot;magnetic sector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04360"></a><span class="lineno"> 4360</span>&#160;          }</div>
<div class="line"><a name="l04361"></a><span class="lineno"> 4361</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ad9bdaac4d0e7c5cb182ae5da106a75c1">MassAnalyzer::QUADRUPOLE</a>)</div>
<div class="line"><a name="l04362"></a><span class="lineno"> 4362</span>&#160;          {</div>
<div class="line"><a name="l04363"></a><span class="lineno"> 4363</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000081\&quot; name=\&quot;quadrupole\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04364"></a><span class="lineno"> 4364</span>&#160;          }</div>
<div class="line"><a name="l04365"></a><span class="lineno"> 4365</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ac18e0fdb830eeb3a7f657a75000744db">MassAnalyzer::TOF</a>)</div>
<div class="line"><a name="l04366"></a><span class="lineno"> 4366</span>&#160;          {</div>
<div class="line"><a name="l04367"></a><span class="lineno"> 4367</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000084\&quot; name=\&quot;time-of-flight\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04368"></a><span class="lineno"> 4368</span>&#160;          }</div>
<div class="line"><a name="l04369"></a><span class="lineno"> 4369</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ab7a09aace4e7aa91599309ab8b613bb4">MassAnalyzer::ESA</a>)</div>
<div class="line"><a name="l04370"></a><span class="lineno"> 4370</span>&#160;          {</div>
<div class="line"><a name="l04371"></a><span class="lineno"> 4371</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000254\&quot; name=\&quot;electrostatic energy analyzer\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04372"></a><span class="lineno"> 4372</span>&#160;          }</div>
<div class="line"><a name="l04373"></a><span class="lineno"> 4373</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ae9e2537cbd38bd116d7bdb8b634f991a">MassAnalyzer::IT</a>)</div>
<div class="line"><a name="l04374"></a><span class="lineno"> 4374</span>&#160;          {</div>
<div class="line"><a name="l04375"></a><span class="lineno"> 4375</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000264\&quot; name=\&quot;ion trap\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04376"></a><span class="lineno"> 4376</span>&#160;          }</div>
<div class="line"><a name="l04377"></a><span class="lineno"> 4377</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a1cd375d755f36023b93bbd8afd1316f3">MassAnalyzer::SWIFT</a>)</div>
<div class="line"><a name="l04378"></a><span class="lineno"> 4378</span>&#160;          {</div>
<div class="line"><a name="l04379"></a><span class="lineno"> 4379</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000284\&quot; name=\&quot;stored waveform inverse fourier transform\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04380"></a><span class="lineno"> 4380</span>&#160;          }</div>
<div class="line"><a name="l04381"></a><span class="lineno"> 4381</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ac59fe43006f5fee91317753c98fb6fb3">MassAnalyzer::CYCLOTRON</a>)</div>
<div class="line"><a name="l04382"></a><span class="lineno"> 4382</span>&#160;          {</div>
<div class="line"><a name="l04383"></a><span class="lineno"> 4383</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000288\&quot; name=\&quot;cyclotron\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04384"></a><span class="lineno"> 4384</span>&#160;          }</div>
<div class="line"><a name="l04385"></a><span class="lineno"> 4385</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a5d02c7b244115a39bcb42170c21d0a58">MassAnalyzer::ORBITRAP</a>)</div>
<div class="line"><a name="l04386"></a><span class="lineno"> 4386</span>&#160;          {</div>
<div class="line"><a name="l04387"></a><span class="lineno"> 4387</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000484\&quot; name=\&quot;orbitrap\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04388"></a><span class="lineno"> 4388</span>&#160;          }</div>
<div class="line"><a name="l04389"></a><span class="lineno"> 4389</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ace4c2a8d1433baa487103cbcd83bbb01">MassAnalyzer::AXIALEJECTIONLINEARIONTRAP</a>)</div>
<div class="line"><a name="l04390"></a><span class="lineno"> 4390</span>&#160;          {</div>
<div class="line"><a name="l04391"></a><span class="lineno"> 4391</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000078\&quot; name=\&quot;axial ejection linear ion trap\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04392"></a><span class="lineno"> 4392</span>&#160;          }</div>
<div class="line"><a name="l04393"></a><span class="lineno"> 4393</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a1a7f597d623d72306c8adbdbfaaa350d">MassAnalyzer::PAULIONTRAP</a>)</div>
<div class="line"><a name="l04394"></a><span class="lineno"> 4394</span>&#160;          {</div>
<div class="line"><a name="l04395"></a><span class="lineno"> 4395</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000082\&quot; name=\&quot;quadrupole ion trap\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04396"></a><span class="lineno"> 4396</span>&#160;          }</div>
<div class="line"><a name="l04397"></a><span class="lineno"> 4397</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a3da723842841c3ff4194d0d71b0da0fd">MassAnalyzer::RADIALEJECTIONLINEARIONTRAP</a>)</div>
<div class="line"><a name="l04398"></a><span class="lineno"> 4398</span>&#160;          {</div>
<div class="line"><a name="l04399"></a><span class="lineno"> 4399</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000083\&quot; name=\&quot;radial ejection linear ion trap\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04400"></a><span class="lineno"> 4400</span>&#160;          }</div>
<div class="line"><a name="l04401"></a><span class="lineno"> 4401</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a3b759690471ed29ecd243a8f36b93f60">MassAnalyzer::LIT</a>)</div>
<div class="line"><a name="l04402"></a><span class="lineno"> 4402</span>&#160;          {</div>
<div class="line"><a name="l04403"></a><span class="lineno"> 4403</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000291\&quot; name=\&quot;linear ion trap\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04404"></a><span class="lineno"> 4404</span>&#160;          }</div>
<div class="line"><a name="l04405"></a><span class="lineno"> 4405</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (ma.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>() == <a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a39869181b0414af3507c53e260851151">MassAnalyzer::ANALYZERNULL</a>)</div>
<div class="line"><a name="l04406"></a><span class="lineno"> 4406</span>&#160;          {</div>
<div class="line"><a name="l04407"></a><span class="lineno"> 4407</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000443\&quot; name=\&quot;mass analyzer type\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04408"></a><span class="lineno"> 4408</span>&#160;          }</div>
<div class="line"><a name="l04409"></a><span class="lineno"> 4409</span>&#160;</div>
<div class="line"><a name="l04410"></a><span class="lineno"> 4410</span>&#160;          writeUserParam_(os, ma, 5, <span class="stringliteral">&quot;/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/analyzer/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04411"></a><span class="lineno"> 4411</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/analyzer&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04412"></a><span class="lineno"> 4412</span>&#160;        }</div>
<div class="line"><a name="l04413"></a><span class="lineno"> 4413</span>&#160;        <span class="comment">//FORCED</span></div>
<div class="line"><a name="l04414"></a><span class="lineno"> 4414</span>&#160;        <span class="keywordflow">if</span> (component_count &lt; 3 &amp;&amp; in.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>().empty())</div>
<div class="line"><a name="l04415"></a><span class="lineno"> 4415</span>&#160;        {</div>
<div class="line"><a name="l04416"></a><span class="lineno"> 4416</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;analyzer order=\&quot;1234\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04417"></a><span class="lineno"> 4417</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000288\&quot; name=\&quot;cyclotron\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04418"></a><span class="lineno"> 4418</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;userParam name=\&quot;warning\&quot; type=\&quot;xsd:string\&quot; value=\&quot;invented mass analyzer, to fulfill mzML schema\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04419"></a><span class="lineno"> 4419</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/analyzer&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04420"></a><span class="lineno"> 4420</span>&#160;        }</div>
<div class="line"><a name="l04421"></a><span class="lineno"> 4421</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04422"></a><span class="lineno"> 4422</span>&#160;        <span class="comment">// ion detector</span></div>
<div class="line"><a name="l04423"></a><span class="lineno"> 4423</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04424"></a><span class="lineno"> 4424</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; in.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>().size(); ++i)</div>
<div class="line"><a name="l04425"></a><span class="lineno"> 4425</span>&#160;        {</div>
<div class="line"><a name="l04426"></a><span class="lineno"> 4426</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IonDetector.html">IonDetector</a>&amp; <span class="keywordtype">id</span> = in.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[i];</div>
<div class="line"><a name="l04427"></a><span class="lineno"> 4427</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;detector order=\&quot;&quot;</span> &lt;&lt; <span class="keywordtype">id</span>.getOrder() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04428"></a><span class="lineno"> 4428</span>&#160;</div>
<div class="line"><a name="l04429"></a><span class="lineno"> 4429</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000028\&quot; name=\&quot;detector resolution\&quot; value=\&quot;&quot;</span> &lt;&lt; <span class="keywordtype">id</span>.getResolution() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04430"></a><span class="lineno"> 4430</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000029\&quot; name=\&quot;sampling frequency\&quot; value=\&quot;&quot;</span> &lt;&lt; <span class="keywordtype">id</span>.getADCSamplingFrequency() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000106\&quot; unitName=\&quot;hertz\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04431"></a><span class="lineno"> 4431</span>&#160;</div>
<div class="line"><a name="l04432"></a><span class="lineno"> 4432</span>&#160;          <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getAcquisitionMode() == <a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a5ec0e8ce4c96673614190a8852261f4f">IonDetector::ADC</a>)</div>
<div class="line"><a name="l04433"></a><span class="lineno"> 4433</span>&#160;          {</div>
<div class="line"><a name="l04434"></a><span class="lineno"> 4434</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000117\&quot; name=\&quot;analog-digital converter\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04435"></a><span class="lineno"> 4435</span>&#160;          }</div>
<div class="line"><a name="l04436"></a><span class="lineno"> 4436</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getAcquisitionMode() == <a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a1b9d0cc39dc3d1de4db442674ca8761b">IonDetector::PULSECOUNTING</a>)</div>
<div class="line"><a name="l04437"></a><span class="lineno"> 4437</span>&#160;          {</div>
<div class="line"><a name="l04438"></a><span class="lineno"> 4438</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000118\&quot; name=\&quot;pulse counting\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04439"></a><span class="lineno"> 4439</span>&#160;          }</div>
<div class="line"><a name="l04440"></a><span class="lineno"> 4440</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getAcquisitionMode() == <a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a09970273b87198398bb9192b84b8eea7">IonDetector::TDC</a>)</div>
<div class="line"><a name="l04441"></a><span class="lineno"> 4441</span>&#160;          {</div>
<div class="line"><a name="l04442"></a><span class="lineno"> 4442</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000119\&quot; name=\&quot;time-digital converter\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04443"></a><span class="lineno"> 4443</span>&#160;          }</div>
<div class="line"><a name="l04444"></a><span class="lineno"> 4444</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getAcquisitionMode() == <a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a7caeaaac284597b2a217cbd43f8c7233">IonDetector::TRANSIENTRECORDER</a>)</div>
<div class="line"><a name="l04445"></a><span class="lineno"> 4445</span>&#160;          {</div>
<div class="line"><a name="l04446"></a><span class="lineno"> 4446</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000120\&quot; name=\&quot;transient recorder\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04447"></a><span class="lineno"> 4447</span>&#160;          }</div>
<div class="line"><a name="l04448"></a><span class="lineno"> 4448</span>&#160;</div>
<div class="line"><a name="l04449"></a><span class="lineno"> 4449</span>&#160;          <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7acf7c454254df079071463f080099b4b3">IonDetector::CHANNELTRON</a>)</div>
<div class="line"><a name="l04450"></a><span class="lineno"> 4450</span>&#160;          {</div>
<div class="line"><a name="l04451"></a><span class="lineno"> 4451</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000107\&quot; name=\&quot;channeltron\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04452"></a><span class="lineno"> 4452</span>&#160;          }</div>
<div class="line"><a name="l04453"></a><span class="lineno"> 4453</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ac251cfb1e58eccf7b508c730505ea75e">IonDetector::DALYDETECTOR</a>)</div>
<div class="line"><a name="l04454"></a><span class="lineno"> 4454</span>&#160;          {</div>
<div class="line"><a name="l04455"></a><span class="lineno"> 4455</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000110\&quot; name=\&quot;daly detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04456"></a><span class="lineno"> 4456</span>&#160;          }</div>
<div class="line"><a name="l04457"></a><span class="lineno"> 4457</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a1019d3d05762a5ea12ffec336dd45c35">IonDetector::FARADAYCUP</a>)</div>
<div class="line"><a name="l04458"></a><span class="lineno"> 4458</span>&#160;          {</div>
<div class="line"><a name="l04459"></a><span class="lineno"> 4459</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000112\&quot; name=\&quot;faraday cup\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04460"></a><span class="lineno"> 4460</span>&#160;          }</div>
<div class="line"><a name="l04461"></a><span class="lineno"> 4461</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a8e54f1259bd67fbaa579f32b73b34482">IonDetector::MICROCHANNELPLATEDETECTOR</a>)</div>
<div class="line"><a name="l04462"></a><span class="lineno"> 4462</span>&#160;          {</div>
<div class="line"><a name="l04463"></a><span class="lineno"> 4463</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000114\&quot; name=\&quot;microchannel plate detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04464"></a><span class="lineno"> 4464</span>&#160;          }</div>
<div class="line"><a name="l04465"></a><span class="lineno"> 4465</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7aa6af6570fb6cf6172b241f4230d0bd9f">IonDetector::MULTICOLLECTOR</a>)</div>
<div class="line"><a name="l04466"></a><span class="lineno"> 4466</span>&#160;          {</div>
<div class="line"><a name="l04467"></a><span class="lineno"> 4467</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000115\&quot; name=\&quot;multi-collector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04468"></a><span class="lineno"> 4468</span>&#160;          }</div>
<div class="line"><a name="l04469"></a><span class="lineno"> 4469</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a80abf032317ac0521e7ea0c601e3b387">IonDetector::PHOTOMULTIPLIER</a>)</div>
<div class="line"><a name="l04470"></a><span class="lineno"> 4470</span>&#160;          {</div>
<div class="line"><a name="l04471"></a><span class="lineno"> 4471</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000116\&quot; name=\&quot;photomultiplier\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04472"></a><span class="lineno"> 4472</span>&#160;          }</div>
<div class="line"><a name="l04473"></a><span class="lineno"> 4473</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a5fd9b4a1925c08d12d8d0d3a43b0ab8c">IonDetector::ELECTRONMULTIPLIER</a>)</div>
<div class="line"><a name="l04474"></a><span class="lineno"> 4474</span>&#160;          {</div>
<div class="line"><a name="l04475"></a><span class="lineno"> 4475</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000253\&quot; name=\&quot;electron multiplier\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04476"></a><span class="lineno"> 4476</span>&#160;          }</div>
<div class="line"><a name="l04477"></a><span class="lineno"> 4477</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a04a49f0fe9b8b9be26628d0bd8ee0882">IonDetector::ARRAYDETECTOR</a>)</div>
<div class="line"><a name="l04478"></a><span class="lineno"> 4478</span>&#160;          {</div>
<div class="line"><a name="l04479"></a><span class="lineno"> 4479</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000345\&quot; name=\&quot;array detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04480"></a><span class="lineno"> 4480</span>&#160;          }</div>
<div class="line"><a name="l04481"></a><span class="lineno"> 4481</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a671a0183b391575bccbe91a826e831a2">IonDetector::CONVERSIONDYNODE</a>)</div>
<div class="line"><a name="l04482"></a><span class="lineno"> 4482</span>&#160;          {</div>
<div class="line"><a name="l04483"></a><span class="lineno"> 4483</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000346\&quot; name=\&quot;conversion dynode\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04484"></a><span class="lineno"> 4484</span>&#160;          }</div>
<div class="line"><a name="l04485"></a><span class="lineno"> 4485</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a54d74359f2cede6481a434f8634be324">IonDetector::DYNODE</a>)</div>
<div class="line"><a name="l04486"></a><span class="lineno"> 4486</span>&#160;          {</div>
<div class="line"><a name="l04487"></a><span class="lineno"> 4487</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000347\&quot; name=\&quot;dynode\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04488"></a><span class="lineno"> 4488</span>&#160;          }</div>
<div class="line"><a name="l04489"></a><span class="lineno"> 4489</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a27064596541d23c1b3040817e417d39c">IonDetector::FOCALPLANECOLLECTOR</a>)</div>
<div class="line"><a name="l04490"></a><span class="lineno"> 4490</span>&#160;          {</div>
<div class="line"><a name="l04491"></a><span class="lineno"> 4491</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000348\&quot; name=\&quot;focal plane collector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04492"></a><span class="lineno"> 4492</span>&#160;          }</div>
<div class="line"><a name="l04493"></a><span class="lineno"> 4493</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ac49f262a3810cbb127ca53b2a804b719">IonDetector::IONTOPHOTONDETECTOR</a>)</div>
<div class="line"><a name="l04494"></a><span class="lineno"> 4494</span>&#160;          {</div>
<div class="line"><a name="l04495"></a><span class="lineno"> 4495</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000349\&quot; name=\&quot;ion-to-photon detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04496"></a><span class="lineno"> 4496</span>&#160;          }</div>
<div class="line"><a name="l04497"></a><span class="lineno"> 4497</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a74d32454593ae69307e86dbca912a605">IonDetector::POINTCOLLECTOR</a>)</div>
<div class="line"><a name="l04498"></a><span class="lineno"> 4498</span>&#160;          {</div>
<div class="line"><a name="l04499"></a><span class="lineno"> 4499</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000350\&quot; name=\&quot;point collector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04500"></a><span class="lineno"> 4500</span>&#160;          }</div>
<div class="line"><a name="l04501"></a><span class="lineno"> 4501</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ab853daddf114acf995e3486fe604e849">IonDetector::POSTACCELERATIONDETECTOR</a>)</div>
<div class="line"><a name="l04502"></a><span class="lineno"> 4502</span>&#160;          {</div>
<div class="line"><a name="l04503"></a><span class="lineno"> 4503</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000351\&quot; name=\&quot;postacceleration detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04504"></a><span class="lineno"> 4504</span>&#160;          }</div>
<div class="line"><a name="l04505"></a><span class="lineno"> 4505</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a2b44c2af82a0218d3cb5faa3d163fa1f">IonDetector::PHOTODIODEARRAYDETECTOR</a>)</div>
<div class="line"><a name="l04506"></a><span class="lineno"> 4506</span>&#160;          {</div>
<div class="line"><a name="l04507"></a><span class="lineno"> 4507</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000621\&quot; name=\&quot;photodiode array detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04508"></a><span class="lineno"> 4508</span>&#160;          }</div>
<div class="line"><a name="l04509"></a><span class="lineno"> 4509</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a0f812ecbbe9fffeec4cee4ad92c5a2ce">IonDetector::INDUCTIVEDETECTOR</a>)</div>
<div class="line"><a name="l04510"></a><span class="lineno"> 4510</span>&#160;          {</div>
<div class="line"><a name="l04511"></a><span class="lineno"> 4511</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000624\&quot; name=\&quot;inductive detector\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04512"></a><span class="lineno"> 4512</span>&#160;          }</div>
<div class="line"><a name="l04513"></a><span class="lineno"> 4513</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a7ab83a85e2b66a4d8c4e0a6ccac159c7">IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER</a>)</div>
<div class="line"><a name="l04514"></a><span class="lineno"> 4514</span>&#160;          {</div>
<div class="line"><a name="l04515"></a><span class="lineno"> 4515</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000108\&quot; name=\&quot;conversion dynode electron multiplier\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04516"></a><span class="lineno"> 4516</span>&#160;          }</div>
<div class="line"><a name="l04517"></a><span class="lineno"> 4517</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a2a909086473828f229ef69ee60230fd2">IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER</a>)</div>
<div class="line"><a name="l04518"></a><span class="lineno"> 4518</span>&#160;          {</div>
<div class="line"><a name="l04519"></a><span class="lineno"> 4519</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000109\&quot; name=\&quot;conversion dynode photomultiplier\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04520"></a><span class="lineno"> 4520</span>&#160;          }</div>
<div class="line"><a name="l04521"></a><span class="lineno"> 4521</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7acfbc26fbfdecb47353d1ef9712c4b86d">IonDetector::ELECTRONMULTIPLIERTUBE</a>)</div>
<div class="line"><a name="l04522"></a><span class="lineno"> 4522</span>&#160;          {</div>
<div class="line"><a name="l04523"></a><span class="lineno"> 4523</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000111\&quot; name=\&quot;electron multiplier tube\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04524"></a><span class="lineno"> 4524</span>&#160;          }</div>
<div class="line"><a name="l04525"></a><span class="lineno"> 4525</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7af12c576ac46ce5b814f2613b1aebedc8">IonDetector::FOCALPLANEARRAY</a>)</div>
<div class="line"><a name="l04526"></a><span class="lineno"> 4526</span>&#160;          {</div>
<div class="line"><a name="l04527"></a><span class="lineno"> 4527</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000113\&quot; name=\&quot;focal plane array\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04528"></a><span class="lineno"> 4528</span>&#160;          }</div>
<div class="line"><a name="l04529"></a><span class="lineno"> 4529</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<span class="keywordtype">id</span>.getType() == <a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a7d066f30823d68dafa1f1746027390b5">IonDetector::TYPENULL</a>)</div>
<div class="line"><a name="l04530"></a><span class="lineno"> 4530</span>&#160;          {</div>
<div class="line"><a name="l04531"></a><span class="lineno"> 4531</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000026\&quot; name=\&quot;detector type\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04532"></a><span class="lineno"> 4532</span>&#160;          }</div>
<div class="line"><a name="l04533"></a><span class="lineno"> 4533</span>&#160;</div>
<div class="line"><a name="l04534"></a><span class="lineno"> 4534</span>&#160;          writeUserParam_(os, <span class="keywordtype">id</span>, 5, <span class="stringliteral">&quot;/mzML/instrumentConfigurationList/instrumentConfiguration/componentList/detector/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04535"></a><span class="lineno"> 4535</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/detector&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04536"></a><span class="lineno"> 4536</span>&#160;        }</div>
<div class="line"><a name="l04537"></a><span class="lineno"> 4537</span>&#160;        <span class="comment">//FORCED</span></div>
<div class="line"><a name="l04538"></a><span class="lineno"> 4538</span>&#160;        <span class="keywordflow">if</span> (component_count &lt; 3 &amp;&amp; in.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>().empty())</div>
<div class="line"><a name="l04539"></a><span class="lineno"> 4539</span>&#160;        {</div>
<div class="line"><a name="l04540"></a><span class="lineno"> 4540</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;detector order=\&quot;1234\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04541"></a><span class="lineno"> 4541</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000107\&quot; name=\&quot;channeltron\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04542"></a><span class="lineno"> 4542</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;userParam name=\&quot;warning\&quot; type=\&quot;xsd:string\&quot; value=\&quot;invented ion detector, to fulfill mzML schema\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04543"></a><span class="lineno"> 4543</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/detector&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04544"></a><span class="lineno"> 4544</span>&#160;        }</div>
<div class="line"><a name="l04545"></a><span class="lineno"> 4545</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/componentList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04546"></a><span class="lineno"> 4546</span>&#160;      }</div>
<div class="line"><a name="l04547"></a><span class="lineno"> 4547</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;softwareRef ref=\&quot;so_in_0\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04548"></a><span class="lineno"> 4548</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;/instrumentConfiguration&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04549"></a><span class="lineno"> 4549</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;/instrumentConfigurationList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04550"></a><span class="lineno"> 4550</span>&#160;</div>
<div class="line"><a name="l04551"></a><span class="lineno"> 4551</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04552"></a><span class="lineno"> 4552</span>&#160;      <span class="comment">// data processing</span></div>
<div class="line"><a name="l04553"></a><span class="lineno"> 4553</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04554"></a><span class="lineno"> 4554</span>&#160;</div>
<div class="line"><a name="l04555"></a><span class="lineno"> 4555</span>&#160;      <span class="comment">// count number of float data array dps</span></div>
<div class="line"><a name="l04556"></a><span class="lineno"> 4556</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_bi_dps(0);</div>
<div class="line"><a name="l04557"></a><span class="lineno"> 4557</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l04558"></a><span class="lineno"> 4558</span>&#160;      {</div>
<div class="line"><a name="l04559"></a><span class="lineno"> 4559</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; exp[s].getFloatDataArrays().size(); ++m)</div>
<div class="line"><a name="l04560"></a><span class="lineno"> 4560</span>&#160;        {</div>
<div class="line"><a name="l04561"></a><span class="lineno"> 4561</span>&#160;          ++num_bi_dps;</div>
<div class="line"><a name="l04562"></a><span class="lineno"> 4562</span>&#160;        }</div>
<div class="line"><a name="l04563"></a><span class="lineno"> 4563</span>&#160;      }</div>
<div class="line"><a name="l04564"></a><span class="lineno"> 4564</span>&#160;</div>
<div class="line"><a name="l04565"></a><span class="lineno"> 4565</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;dataProcessingList count=\&quot;&quot;</span> &lt;&lt; (std::max)((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)1, dps.size() + num_bi_dps) &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04566"></a><span class="lineno"> 4566</span>&#160;      <span class="comment">//default (first spectrum data or fictional data)</span></div>
<div class="line"><a name="l04567"></a><span class="lineno"> 4567</span>&#160;      <span class="keywordflow">if</span> (exp.empty())</div>
<div class="line"><a name="l04568"></a><span class="lineno"> 4568</span>&#160;      {</div>
<div class="line"><a name="l04569"></a><span class="lineno"> 4569</span>&#160;        std::vector&lt;DataProcessing&gt; dummy;</div>
<div class="line"><a name="l04570"></a><span class="lineno"> 4570</span>&#160;        writeDataProcessing_(os, <span class="stringliteral">&quot;dp_sp_0&quot;</span>, dummy, validator);</div>
<div class="line"><a name="l04571"></a><span class="lineno"> 4571</span>&#160;      }</div>
<div class="line"><a name="l04572"></a><span class="lineno"> 4572</span>&#160;</div>
<div class="line"><a name="l04573"></a><span class="lineno"> 4573</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; dps.size(); ++s)</div>
<div class="line"><a name="l04574"></a><span class="lineno"> 4574</span>&#160;      {</div>
<div class="line"><a name="l04575"></a><span class="lineno"> 4575</span>&#160;        writeDataProcessing_(os, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dp_sp_&quot;</span>) + s, dps[s], validator);</div>
<div class="line"><a name="l04576"></a><span class="lineno"> 4576</span>&#160;      }</div>
<div class="line"><a name="l04577"></a><span class="lineno"> 4577</span>&#160;</div>
<div class="line"><a name="l04578"></a><span class="lineno"> 4578</span>&#160;      <span class="comment">//for each binary data array</span></div>
<div class="line"><a name="l04579"></a><span class="lineno"> 4579</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; exp.size(); ++s)</div>
<div class="line"><a name="l04580"></a><span class="lineno"> 4580</span>&#160;      {</div>
<div class="line"><a name="l04581"></a><span class="lineno"> 4581</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; exp[s].getFloatDataArrays().size(); ++m)</div>
<div class="line"><a name="l04582"></a><span class="lineno"> 4582</span>&#160;        {</div>
<div class="line"><a name="l04583"></a><span class="lineno"> 4583</span>&#160;          writeDataProcessing_(os, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dp_sp_&quot;</span>) + s + <span class="stringliteral">&quot;_bi_&quot;</span> + m, exp[s].getFloatDataArrays()[m].getDataProcessing(), validator);</div>
<div class="line"><a name="l04584"></a><span class="lineno"> 4584</span>&#160;        }</div>
<div class="line"><a name="l04585"></a><span class="lineno"> 4585</span>&#160;      }</div>
<div class="line"><a name="l04586"></a><span class="lineno"> 4586</span>&#160;</div>
<div class="line"><a name="l04587"></a><span class="lineno"> 4587</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;/dataProcessingList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04588"></a><span class="lineno"> 4588</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04589"></a><span class="lineno"> 4589</span>&#160;      <span class="comment">// acquisitionSettings</span></div>
<div class="line"><a name="l04590"></a><span class="lineno"> 4590</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04591"></a><span class="lineno"> 4591</span>&#160;</div>
<div class="line"><a name="l04592"></a><span class="lineno"> 4592</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04593"></a><span class="lineno"> 4593</span>&#160;      <span class="comment">// run</span></div>
<div class="line"><a name="l04594"></a><span class="lineno"> 4594</span>&#160;      <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04595"></a><span class="lineno"> 4595</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;run id=\&quot;ru_0\&quot; defaultInstrumentConfigurationRef=\&quot;ic_0\&quot; sampleRef=\&quot;sa_0\&quot;&quot;</span>;</div>
<div class="line"><a name="l04596"></a><span class="lineno"> 4596</span>&#160;      <span class="keywordflow">if</span> (exp.getDateTime().isValid())</div>
<div class="line"><a name="l04597"></a><span class="lineno"> 4597</span>&#160;      {</div>
<div class="line"><a name="l04598"></a><span class="lineno"> 4598</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot; startTimeStamp=\&quot;&quot;</span> &lt;&lt; exp.getDateTime().get().substitute(<span class="charliteral">&#39; &#39;</span>, <span class="charliteral">&#39;T&#39;</span>) &lt;&lt; <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04599"></a><span class="lineno"> 4599</span>&#160;      }</div>
<div class="line"><a name="l04600"></a><span class="lineno"> 4600</span>&#160;      <span class="keywordflow">if</span> (exp.getSourceFiles().size() &gt; 0)</div>
<div class="line"><a name="l04601"></a><span class="lineno"> 4601</span>&#160;      {</div>
<div class="line"><a name="l04602"></a><span class="lineno"> 4602</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot; defaultSourceFileRef=\&quot;sf_ru_0\&quot;&quot;</span>;</div>
<div class="line"><a name="l04603"></a><span class="lineno"> 4603</span>&#160;      }</div>
<div class="line"><a name="l04604"></a><span class="lineno"> 4604</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04605"></a><span class="lineno"> 4605</span>&#160;</div>
<div class="line"><a name="l04606"></a><span class="lineno"> 4606</span>&#160;      <span class="comment">//run attributes</span></div>
<div class="line"><a name="l04607"></a><span class="lineno"> 4607</span>&#160;      <span class="keywordflow">if</span> (exp.getFractionIdentifier() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l04608"></a><span class="lineno"> 4608</span>&#160;      {</div>
<div class="line"><a name="l04609"></a><span class="lineno"> 4609</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000858\&quot; name=\&quot;fraction identifier\&quot; value=\&quot;&quot;</span> &lt;&lt; exp.getFractionIdentifier() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04610"></a><span class="lineno"> 4610</span>&#160;      }</div>
<div class="line"><a name="l04611"></a><span class="lineno"> 4611</span>&#160;</div>
<div class="line"><a name="l04612"></a><span class="lineno"> 4612</span>&#160;      writeUserParam_(os, exp, 2, <span class="stringliteral">&quot;/mzML/run/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04613"></a><span class="lineno"> 4613</span>&#160;</div>
<div class="line"><a name="l04614"></a><span class="lineno"> 4614</span>&#160;    }</div>
<div class="line"><a name="l04615"></a><span class="lineno"> 4615</span>&#160;</div>
<div class="line"><a name="l04616"></a><span class="lineno"> 4616</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l04617"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a89efdb9d9ea65cfa7e2065774cd6198c"> 4617</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a89efdb9d9ea65cfa7e2065774cd6198c">MzMLHandler&lt;MapType&gt;::writeSpectrum_</a>(std::ostream&amp; os,</div>
<div class="line"><a name="l04618"></a><span class="lineno"> 4618</span>&#160;            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spec, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s, </div>
<div class="line"><a name="l04619"></a><span class="lineno"> 4619</span>&#160;            <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator, <span class="keywordtype">bool</span> renew_native_ids, </div>
<div class="line"><a name="l04620"></a><span class="lineno"> 4620</span>&#160;            std::vector&lt;std::vector&lt;DataProcessing&gt; &gt; &amp; dps)</div>
<div class="line"><a name="l04621"></a><span class="lineno"> 4621</span>&#160;    {</div>
<div class="line"><a name="l04622"></a><span class="lineno"> 4622</span>&#160;        <span class="comment">//native id</span></div>
<div class="line"><a name="l04623"></a><span class="lineno"> 4623</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> native_id = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>();</div>
<div class="line"><a name="l04624"></a><span class="lineno"> 4624</span>&#160;        <span class="keywordflow">if</span> (renew_native_ids)</div>
<div class="line"><a name="l04625"></a><span class="lineno"> 4625</span>&#160;          native_id = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;spectrum=&quot;</span>) + s;</div>
<div class="line"><a name="l04626"></a><span class="lineno"> 4626</span>&#160;</div>
<div class="line"><a name="l04627"></a><span class="lineno"> 4627</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;spectrum id=\&quot;&quot;</span> &lt;&lt; native_id &lt;&lt; <span class="stringliteral">&quot;\&quot; index=\&quot;&quot;</span> &lt;&lt; s &lt;&lt; <span class="stringliteral">&quot;\&quot; defaultArrayLength=\&quot;&quot;</span> &lt;&lt; spec.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04628"></a><span class="lineno"> 4628</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#af4bd5dc3248bc63b98e8a63d50bcc51a">getSourceFile</a>() != <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a>())</div>
<div class="line"><a name="l04629"></a><span class="lineno"> 4629</span>&#160;        {</div>
<div class="line"><a name="l04630"></a><span class="lineno"> 4630</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot; sourceFileRef=\&quot;sf_sp_&quot;</span> &lt;&lt; s &lt;&lt; <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04631"></a><span class="lineno"> 4631</span>&#160;        }</div>
<div class="line"><a name="l04632"></a><span class="lineno"> 4632</span>&#160;        <span class="comment">//the data processing info of the first spectrum is the default</span></div>
<div class="line"><a name="l04633"></a><span class="lineno"> 4633</span>&#160;        <span class="comment">//if (s==0 || spec.getDataProcessing()!=exp[0].getDataProcessing())</span></div>
<div class="line"><a name="l04634"></a><span class="lineno"> 4634</span>&#160;        <span class="keywordflow">if</span> (s == 0 || spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ae131ea2ec923582f86aa9805e72241ad">getDataProcessing</a>() != dps[0])</div>
<div class="line"><a name="l04635"></a><span class="lineno"> 4635</span>&#160;        {</div>
<div class="line"><a name="l04636"></a><span class="lineno"> 4636</span>&#160;          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> dp_ref_num = s;</div>
<div class="line"><a name="l04637"></a><span class="lineno"> 4637</span>&#160;          <span class="keywordflow">if</span> (s != 0)</div>
<div class="line"><a name="l04638"></a><span class="lineno"> 4638</span>&#160;          {</div>
<div class="line"><a name="l04639"></a><span class="lineno"> 4639</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; dps.size(); ++i)</div>
<div class="line"><a name="l04640"></a><span class="lineno"> 4640</span>&#160;            {</div>
<div class="line"><a name="l04641"></a><span class="lineno"> 4641</span>&#160;              <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ae131ea2ec923582f86aa9805e72241ad">getDataProcessing</a>() == dps[i])</div>
<div class="line"><a name="l04642"></a><span class="lineno"> 4642</span>&#160;              {</div>
<div class="line"><a name="l04643"></a><span class="lineno"> 4643</span>&#160;                dp_ref_num = i;</div>
<div class="line"><a name="l04644"></a><span class="lineno"> 4644</span>&#160;                <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l04645"></a><span class="lineno"> 4645</span>&#160;              }</div>
<div class="line"><a name="l04646"></a><span class="lineno"> 4646</span>&#160;            }</div>
<div class="line"><a name="l04647"></a><span class="lineno"> 4647</span>&#160;          }</div>
<div class="line"><a name="l04648"></a><span class="lineno"> 4648</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot; dataProcessingRef=\&quot;dp_sp_&quot;</span> &lt;&lt; dp_ref_num &lt;&lt; <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04649"></a><span class="lineno"> 4649</span>&#160;        }</div>
<div class="line"><a name="l04650"></a><span class="lineno"> 4650</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04651"></a><span class="lineno"> 4651</span>&#160;</div>
<div class="line"><a name="l04652"></a><span class="lineno"> 4652</span>&#160;        <span class="comment">//spectrum representation</span></div>
<div class="line"><a name="l04653"></a><span class="lineno"> 4653</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ac2b5a9a058d7e84ca3a2beeedb2f2049">getType</a>() == <a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>)</div>
<div class="line"><a name="l04654"></a><span class="lineno"> 4654</span>&#160;        {</div>
<div class="line"><a name="l04655"></a><span class="lineno"> 4655</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000127\&quot; name=\&quot;centroid spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04656"></a><span class="lineno"> 4656</span>&#160;        }</div>
<div class="line"><a name="l04657"></a><span class="lineno"> 4657</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ac2b5a9a058d7e84ca3a2beeedb2f2049">getType</a>() == <a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533">SpectrumSettings::RAWDATA</a>)</div>
<div class="line"><a name="l04658"></a><span class="lineno"> 4658</span>&#160;        {</div>
<div class="line"><a name="l04659"></a><span class="lineno"> 4659</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000128\&quot; name=\&quot;profile spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04660"></a><span class="lineno"> 4660</span>&#160;        }</div>
<div class="line"><a name="l04661"></a><span class="lineno"> 4661</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l04662"></a><span class="lineno"> 4662</span>&#160;        {</div>
<div class="line"><a name="l04663"></a><span class="lineno"> 4663</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000525\&quot; name=\&quot;spectrum representation\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04664"></a><span class="lineno"> 4664</span>&#160;        }</div>
<div class="line"><a name="l04665"></a><span class="lineno"> 4665</span>&#160;</div>
<div class="line"><a name="l04666"></a><span class="lineno"> 4666</span>&#160;        <span class="comment">//spectrum attributes</span></div>
<div class="line"><a name="l04667"></a><span class="lineno"> 4667</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>() != 0)</div>
<div class="line"><a name="l04668"></a><span class="lineno"> 4668</span>&#160;        {</div>
<div class="line"><a name="l04669"></a><span class="lineno"> 4669</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000511\&quot; name=\&quot;ms level\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04670"></a><span class="lineno"> 4670</span>&#160;        }</div>
<div class="line"><a name="l04671"></a><span class="lineno"> 4671</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a3409c914db15bbb4696822e623a69ef1">getZoomScan</a>())</div>
<div class="line"><a name="l04672"></a><span class="lineno"> 4672</span>&#160;        {</div>
<div class="line"><a name="l04673"></a><span class="lineno"> 4673</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000497\&quot; name=\&quot;zoom scan\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04674"></a><span class="lineno"> 4674</span>&#160;        }</div>
<div class="line"><a name="l04675"></a><span class="lineno"> 4675</span>&#160;</div>
<div class="line"><a name="l04676"></a><span class="lineno"> 4676</span>&#160;        <span class="comment">//spectrum type</span></div>
<div class="line"><a name="l04677"></a><span class="lineno"> 4677</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>)</div>
<div class="line"><a name="l04678"></a><span class="lineno"> 4678</span>&#160;        {</div>
<div class="line"><a name="l04679"></a><span class="lineno"> 4679</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000294\&quot; name=\&quot;mass spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04680"></a><span class="lineno"> 4680</span>&#160;        }</div>
<div class="line"><a name="l04681"></a><span class="lineno"> 4681</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">InstrumentSettings::MS1SPECTRUM</a>)</div>
<div class="line"><a name="l04682"></a><span class="lineno"> 4682</span>&#160;        {</div>
<div class="line"><a name="l04683"></a><span class="lineno"> 4683</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000579\&quot; name=\&quot;MS1 spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04684"></a><span class="lineno"> 4684</span>&#160;        }</div>
<div class="line"><a name="l04685"></a><span class="lineno"> 4685</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>)</div>
<div class="line"><a name="l04686"></a><span class="lineno"> 4686</span>&#160;        {</div>
<div class="line"><a name="l04687"></a><span class="lineno"> 4687</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000580\&quot; name=\&quot;MSn spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04688"></a><span class="lineno"> 4688</span>&#160;        }</div>
<div class="line"><a name="l04689"></a><span class="lineno"> 4689</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>)</div>
<div class="line"><a name="l04690"></a><span class="lineno"> 4690</span>&#160;        {</div>
<div class="line"><a name="l04691"></a><span class="lineno"> 4691</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000582\&quot; name=\&quot;SIM spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04692"></a><span class="lineno"> 4692</span>&#160;        }</div>
<div class="line"><a name="l04693"></a><span class="lineno"> 4693</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>)</div>
<div class="line"><a name="l04694"></a><span class="lineno"> 4694</span>&#160;        {</div>
<div class="line"><a name="l04695"></a><span class="lineno"> 4695</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000583\&quot; name=\&quot;SRM spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04696"></a><span class="lineno"> 4696</span>&#160;        }</div>
<div class="line"><a name="l04697"></a><span class="lineno"> 4697</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>)</div>
<div class="line"><a name="l04698"></a><span class="lineno"> 4698</span>&#160;        {</div>
<div class="line"><a name="l04699"></a><span class="lineno"> 4699</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000581\&quot; name=\&quot;CRM spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04700"></a><span class="lineno"> 4700</span>&#160;        }</div>
<div class="line"><a name="l04701"></a><span class="lineno"> 4701</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f">InstrumentSettings::PRECURSOR</a>)</div>
<div class="line"><a name="l04702"></a><span class="lineno"> 4702</span>&#160;        {</div>
<div class="line"><a name="l04703"></a><span class="lineno"> 4703</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000341\&quot; name=\&quot;precursor ion spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04704"></a><span class="lineno"> 4704</span>&#160;        }</div>
<div class="line"><a name="l04705"></a><span class="lineno"> 4705</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f">InstrumentSettings::CNG</a>)</div>
<div class="line"><a name="l04706"></a><span class="lineno"> 4706</span>&#160;        {</div>
<div class="line"><a name="l04707"></a><span class="lineno"> 4707</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000325\&quot; name=\&quot;constant neutral gain spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04708"></a><span class="lineno"> 4708</span>&#160;        }</div>
<div class="line"><a name="l04709"></a><span class="lineno"> 4709</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca">InstrumentSettings::CNL</a>)</div>
<div class="line"><a name="l04710"></a><span class="lineno"> 4710</span>&#160;        {</div>
<div class="line"><a name="l04711"></a><span class="lineno"> 4711</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000326\&quot; name=\&quot;constant neutral loss spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04712"></a><span class="lineno"> 4712</span>&#160;        }</div>
<div class="line"><a name="l04713"></a><span class="lineno"> 4713</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a45cd2a1ea065b4909b86190b372ed7da">InstrumentSettings::EMR</a>)</div>
<div class="line"><a name="l04714"></a><span class="lineno"> 4714</span>&#160;        {</div>
<div class="line"><a name="l04715"></a><span class="lineno"> 4715</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000804\&quot; name=\&quot;electromagnetic radiation spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04716"></a><span class="lineno"> 4716</span>&#160;        }</div>
<div class="line"><a name="l04717"></a><span class="lineno"> 4717</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6b66c706c4bc43ff1a3b5a0044fdfa18">InstrumentSettings::EMISSION</a>)</div>
<div class="line"><a name="l04718"></a><span class="lineno"> 4718</span>&#160;        {</div>
<div class="line"><a name="l04719"></a><span class="lineno"> 4719</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000805\&quot; name=\&quot;emission spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04720"></a><span class="lineno"> 4720</span>&#160;        }</div>
<div class="line"><a name="l04721"></a><span class="lineno"> 4721</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac1923f59816bf846e2a62d41cfb91b2f">InstrumentSettings::ABSORBTION</a>)</div>
<div class="line"><a name="l04722"></a><span class="lineno"> 4722</span>&#160;        {</div>
<div class="line"><a name="l04723"></a><span class="lineno"> 4723</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000806\&quot; name=\&quot;absorption spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04724"></a><span class="lineno"> 4724</span>&#160;        }</div>
<div class="line"><a name="l04725"></a><span class="lineno"> 4725</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac21206f76146b8913723119f609be907">InstrumentSettings::EMC</a>)</div>
<div class="line"><a name="l04726"></a><span class="lineno"> 4726</span>&#160;        {</div>
<div class="line"><a name="l04727"></a><span class="lineno"> 4727</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000789\&quot; name=\&quot;enhanced multiply charged spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04728"></a><span class="lineno"> 4728</span>&#160;        }</div>
<div class="line"><a name="l04729"></a><span class="lineno"> 4729</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a5980df92dcce7a0e1e8bc482e4f07aa6">InstrumentSettings::TDF</a>)</div>
<div class="line"><a name="l04730"></a><span class="lineno"> 4730</span>&#160;        {</div>
<div class="line"><a name="l04731"></a><span class="lineno"> 4731</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000789\&quot; name=\&quot;time-delayed fragmentation spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04732"></a><span class="lineno"> 4732</span>&#160;        }</div>
<div class="line"><a name="l04733"></a><span class="lineno"> 4733</span>&#160;        <span class="keywordflow">else</span> <span class="comment">//FORCED</span></div>
<div class="line"><a name="l04734"></a><span class="lineno"> 4734</span>&#160;        {</div>
<div class="line"><a name="l04735"></a><span class="lineno"> 4735</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000294\&quot; name=\&quot;mass spectrum\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04736"></a><span class="lineno"> 4736</span>&#160;        }</div>
<div class="line"><a name="l04737"></a><span class="lineno"> 4737</span>&#160;</div>
<div class="line"><a name="l04738"></a><span class="lineno"> 4738</span>&#160;        <span class="comment">//scan polarity</span></div>
<div class="line"><a name="l04739"></a><span class="lineno"> 4739</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a8f7be6e80ef1c4599af3aa096c7f7089">getPolarity</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">IonSource::NEGATIVE</a>)</div>
<div class="line"><a name="l04740"></a><span class="lineno"> 4740</span>&#160;        {</div>
<div class="line"><a name="l04741"></a><span class="lineno"> 4741</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000129\&quot; name=\&quot;negative scan\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04742"></a><span class="lineno"> 4742</span>&#160;        }</div>
<div class="line"><a name="l04743"></a><span class="lineno"> 4743</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a8f7be6e80ef1c4599af3aa096c7f7089">getPolarity</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5">IonSource::POSITIVE</a>)</div>
<div class="line"><a name="l04744"></a><span class="lineno"> 4744</span>&#160;        {</div>
<div class="line"><a name="l04745"></a><span class="lineno"> 4745</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000130\&quot; name=\&quot;positive scan\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04746"></a><span class="lineno"> 4746</span>&#160;        }</div>
<div class="line"><a name="l04747"></a><span class="lineno"> 4747</span>&#160;</div>
<div class="line"><a name="l04748"></a><span class="lineno"> 4748</span>&#160;        writeUserParam_(os, spec, 4, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04749"></a><span class="lineno"> 4749</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04750"></a><span class="lineno"> 4750</span>&#160;        <span class="comment">//scan list</span></div>
<div class="line"><a name="l04751"></a><span class="lineno"> 4751</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04752"></a><span class="lineno"> 4752</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;scanList count=\&quot;&quot;</span> &lt;&lt; (std::max)((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)1, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().size()) &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04753"></a><span class="lineno"> 4753</span>&#160;        <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> ai_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000570&quot;</span>, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().<a class="code" href="classOpenMS_1_1AcquisitionInfo.html#a883a8e420b509ac1c9a4b08f4494915d">getMethodOfCombination</a>());</div>
<div class="line"><a name="l04754"></a><span class="lineno"> 4754</span>&#160;        <span class="keywordflow">if</span> (ai_term.id != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l04755"></a><span class="lineno"> 4755</span>&#160;        {</div>
<div class="line"><a name="l04756"></a><span class="lineno"> 4756</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; ai_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; ai_term.name &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04757"></a><span class="lineno"> 4757</span>&#160;        }</div>
<div class="line"><a name="l04758"></a><span class="lineno"> 4758</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l04759"></a><span class="lineno"> 4759</span>&#160;        {</div>
<div class="line"><a name="l04760"></a><span class="lineno"> 4760</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000795\&quot; name=\&quot;no combination\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04761"></a><span class="lineno"> 4761</span>&#160;        }</div>
<div class="line"><a name="l04762"></a><span class="lineno"> 4762</span>&#160;        writeUserParam_(os, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>(), 5, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/scanList/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04763"></a><span class="lineno"> 4763</span>&#160;</div>
<div class="line"><a name="l04764"></a><span class="lineno"> 4764</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04765"></a><span class="lineno"> 4765</span>&#160;        <span class="comment">//scan</span></div>
<div class="line"><a name="l04766"></a><span class="lineno"> 4766</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04767"></a><span class="lineno"> 4767</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().size(); ++j)</div>
<div class="line"><a name="l04768"></a><span class="lineno"> 4768</span>&#160;        {</div>
<div class="line"><a name="l04769"></a><span class="lineno"> 4769</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Acquisition.html">Acquisition</a>&amp; ac = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>()[j];</div>
<div class="line"><a name="l04770"></a><span class="lineno"> 4770</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;scan &quot;</span>;</div>
<div class="line"><a name="l04771"></a><span class="lineno"> 4771</span>&#160;          <span class="keywordflow">if</span> (ac.<a class="code" href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">getIdentifier</a>() != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l04772"></a><span class="lineno"> 4772</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;externalSpectrumID=\&quot;&quot;</span> &lt;&lt; ac.<a class="code" href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">getIdentifier</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04773"></a><span class="lineno"> 4773</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04774"></a><span class="lineno"> 4774</span>&#160;          <span class="keywordflow">if</span> (j == 0)</div>
<div class="line"><a name="l04775"></a><span class="lineno"> 4775</span>&#160;          {</div>
<div class="line"><a name="l04776"></a><span class="lineno"> 4776</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000016\&quot; name=\&quot;scan start time\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000010\&quot; unitName=\&quot;second\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04777"></a><span class="lineno"> 4777</span>&#160;          }</div>
<div class="line"><a name="l04778"></a><span class="lineno"> 4778</span>&#160;          writeUserParam_(os, ac, 6, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/scanList/scan/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04779"></a><span class="lineno"> 4779</span>&#160;          <span class="comment">//scan windows</span></div>
<div class="line"><a name="l04780"></a><span class="lineno"> 4780</span>&#160;          <span class="keywordflow">if</span> (j == 0 &amp;&amp; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size() != 0)</div>
<div class="line"><a name="l04781"></a><span class="lineno"> 4781</span>&#160;          {</div>
<div class="line"><a name="l04782"></a><span class="lineno"> 4782</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;scanWindowList count=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04783"></a><span class="lineno"> 4783</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size(); ++j)</div>
<div class="line"><a name="l04784"></a><span class="lineno"> 4784</span>&#160;            {</div>
<div class="line"><a name="l04785"></a><span class="lineno"> 4785</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;scanWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04786"></a><span class="lineno"> 4786</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000501\&quot; name=\&quot;scan window lower limit\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[j].begin &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04787"></a><span class="lineno"> 4787</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000500\&quot; name=\&quot;scan window upper limit\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[j].end &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04788"></a><span class="lineno"> 4788</span>&#160;              writeUserParam_(os, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[j], 8, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/scanList/scan/scanWindowList/scanWindow/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04789"></a><span class="lineno"> 4789</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;/scanWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04790"></a><span class="lineno"> 4790</span>&#160;            }</div>
<div class="line"><a name="l04791"></a><span class="lineno"> 4791</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;/scanWindowList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04792"></a><span class="lineno"> 4792</span>&#160;          }</div>
<div class="line"><a name="l04793"></a><span class="lineno"> 4793</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/scan&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04794"></a><span class="lineno"> 4794</span>&#160;        }</div>
<div class="line"><a name="l04795"></a><span class="lineno"> 4795</span>&#160;        <span class="comment">//fallback if we have no acquisition information (a dummy scan is created for RT and so on)</span></div>
<div class="line"><a name="l04796"></a><span class="lineno"> 4796</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().empty())</div>
<div class="line"><a name="l04797"></a><span class="lineno"> 4797</span>&#160;        {</div>
<div class="line"><a name="l04798"></a><span class="lineno"> 4798</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;scan&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04799"></a><span class="lineno"> 4799</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000016\&quot; name=\&quot;scan start time\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;UO:0000010\&quot; unitName=\&quot;second\&quot; unitCvRef=\&quot;UO\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04800"></a><span class="lineno"> 4800</span>&#160;          <span class="comment">//scan windows</span></div>
<div class="line"><a name="l04801"></a><span class="lineno"> 4801</span>&#160;          <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size() != 0)</div>
<div class="line"><a name="l04802"></a><span class="lineno"> 4802</span>&#160;          {</div>
<div class="line"><a name="l04803"></a><span class="lineno"> 4803</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;scanWindowList count=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04804"></a><span class="lineno"> 4804</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size(); ++j)</div>
<div class="line"><a name="l04805"></a><span class="lineno"> 4805</span>&#160;            {</div>
<div class="line"><a name="l04806"></a><span class="lineno"> 4806</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;scanWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04807"></a><span class="lineno"> 4807</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000501\&quot; name=\&quot;scan window lower limit\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[j].begin &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04808"></a><span class="lineno"> 4808</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000500\&quot; name=\&quot;scan window upper limit\&quot; value=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[j].end &lt;&lt; <span class="stringliteral">&quot;\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04809"></a><span class="lineno"> 4809</span>&#160;              writeUserParam_(os, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[j], 8, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/scanList/scan/scanWindowList/scanWindow/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04810"></a><span class="lineno"> 4810</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t\t&lt;/scanWindow&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04811"></a><span class="lineno"> 4811</span>&#160;            }</div>
<div class="line"><a name="l04812"></a><span class="lineno"> 4812</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;/scanWindowList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04813"></a><span class="lineno"> 4813</span>&#160;          }</div>
<div class="line"><a name="l04814"></a><span class="lineno"> 4814</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/scan&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04815"></a><span class="lineno"> 4815</span>&#160;        }</div>
<div class="line"><a name="l04816"></a><span class="lineno"> 4816</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/scanList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04817"></a><span class="lineno"> 4817</span>&#160;</div>
<div class="line"><a name="l04818"></a><span class="lineno"> 4818</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04819"></a><span class="lineno"> 4819</span>&#160;        <span class="comment">//precursor list</span></div>
<div class="line"><a name="l04820"></a><span class="lineno"> 4820</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04821"></a><span class="lineno"> 4821</span>&#160;        <span class="keywordflow">if</span> (!spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().empty())</div>
<div class="line"><a name="l04822"></a><span class="lineno"> 4822</span>&#160;        {</div>
<div class="line"><a name="l04823"></a><span class="lineno"> 4823</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;precursorList count=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04824"></a><span class="lineno"> 4824</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p != spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().size(); ++p)</div>
<div class="line"><a name="l04825"></a><span class="lineno"> 4825</span>&#160;          {</div>
<div class="line"><a name="l04826"></a><span class="lineno"> 4826</span>&#160;            writePrecursor_(os, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>()[p], validator);</div>
<div class="line"><a name="l04827"></a><span class="lineno"> 4827</span>&#160;          }</div>
<div class="line"><a name="l04828"></a><span class="lineno"> 4828</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/precursorList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04829"></a><span class="lineno"> 4829</span>&#160;        }</div>
<div class="line"><a name="l04830"></a><span class="lineno"> 4830</span>&#160;</div>
<div class="line"><a name="l04831"></a><span class="lineno"> 4831</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04832"></a><span class="lineno"> 4832</span>&#160;        <span class="comment">//product list</span></div>
<div class="line"><a name="l04833"></a><span class="lineno"> 4833</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04834"></a><span class="lineno"> 4834</span>&#160;        <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a7b5920c33d8fb58da6481e66ddd2a572">getProducts</a>().size() != 0)</div>
<div class="line"><a name="l04835"></a><span class="lineno"> 4835</span>&#160;        {</div>
<div class="line"><a name="l04836"></a><span class="lineno"> 4836</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;productList count=\&quot;&quot;</span> &lt;&lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a7b5920c33d8fb58da6481e66ddd2a572">getProducts</a>().size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04837"></a><span class="lineno"> 4837</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a7b5920c33d8fb58da6481e66ddd2a572">getProducts</a>().size(); ++p)</div>
<div class="line"><a name="l04838"></a><span class="lineno"> 4838</span>&#160;          {</div>
<div class="line"><a name="l04839"></a><span class="lineno"> 4839</span>&#160;            writeProduct_(os, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a7b5920c33d8fb58da6481e66ddd2a572">getProducts</a>()[p], validator);</div>
<div class="line"><a name="l04840"></a><span class="lineno"> 4840</span>&#160;          }</div>
<div class="line"><a name="l04841"></a><span class="lineno"> 4841</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/productList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04842"></a><span class="lineno"> 4842</span>&#160;        }</div>
<div class="line"><a name="l04843"></a><span class="lineno"> 4843</span>&#160;</div>
<div class="line"><a name="l04844"></a><span class="lineno"> 4844</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04845"></a><span class="lineno"> 4845</span>&#160;        <span class="comment">//binary data array list</span></div>
<div class="line"><a name="l04846"></a><span class="lineno"> 4846</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l04847"></a><span class="lineno"> 4847</span>&#160;        <span class="keywordflow">if</span> (spec.size() != 0)</div>
<div class="line"><a name="l04848"></a><span class="lineno"> 4848</span>&#160;        {</div>
<div class="line"><a name="l04849"></a><span class="lineno"> 4849</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> compression_term;</div>
<div class="line"><a name="l04850"></a><span class="lineno"> 4850</span>&#160;          <span class="keywordflow">if</span> (options_.getCompression())</div>
<div class="line"><a name="l04851"></a><span class="lineno"> 4851</span>&#160;          {</div>
<div class="line"><a name="l04852"></a><span class="lineno"> 4852</span>&#160;            compression_term = <span class="stringliteral">&quot;&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000574\&quot; name=\&quot;zlib compression\&quot; /&gt;&quot;</span>;</div>
<div class="line"><a name="l04853"></a><span class="lineno"> 4853</span>&#160;          }</div>
<div class="line"><a name="l04854"></a><span class="lineno"> 4854</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l04855"></a><span class="lineno"> 4855</span>&#160;          {</div>
<div class="line"><a name="l04856"></a><span class="lineno"> 4856</span>&#160;            compression_term = <span class="stringliteral">&quot;&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000576\&quot; name=\&quot;no compression\&quot; /&gt;&quot;</span>;</div>
<div class="line"><a name="l04857"></a><span class="lineno"> 4857</span>&#160;          }</div>
<div class="line"><a name="l04858"></a><span class="lineno"> 4858</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> encoded_string;</div>
<div class="line"><a name="l04859"></a><span class="lineno"> 4859</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;binaryDataArrayList count=\&quot;&quot;</span> &lt;&lt; (2 + spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>().size() + spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#ace039d325c112e45c9d37e0e656ba9a2">getStringDataArrays</a>().size() + spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">getIntegerDataArrays</a>().size()) &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04860"></a><span class="lineno"> 4860</span>&#160;          <span class="comment">//write m/z array (default 64 bit precision)</span></div>
<div class="line"><a name="l04861"></a><span class="lineno"> 4861</span>&#160;          {</div>
<div class="line"><a name="l04862"></a><span class="lineno"> 4862</span>&#160;</div>
<div class="line"><a name="l04863"></a><span class="lineno"> 4863</span>&#160;            <span class="keywordflow">if</span> (options_.getMz32Bit())</div>
<div class="line"><a name="l04864"></a><span class="lineno"> 4864</span>&#160;            {</div>
<div class="line"><a name="l04865"></a><span class="lineno"> 4865</span>&#160;              std::vector&lt;Real&gt; data_to_encode(spec.size());</div>
<div class="line"><a name="l04866"></a><span class="lineno"> 4866</span>&#160;              <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spec.size(); ++p)</div>
<div class="line"><a name="l04867"></a><span class="lineno"> 4867</span>&#160;                data_to_encode[p] = spec[p].getMZ();</div>
<div class="line"><a name="l04868"></a><span class="lineno"> 4868</span>&#160;              decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04869"></a><span class="lineno"> 4869</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04870"></a><span class="lineno"> 4870</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000514\&quot; name=\&quot;m/z array\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04871"></a><span class="lineno"> 4871</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000521\&quot; name=\&quot;32-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04872"></a><span class="lineno"> 4872</span>&#160;            }</div>
<div class="line"><a name="l04873"></a><span class="lineno"> 4873</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l04874"></a><span class="lineno"> 4874</span>&#160;            {</div>
<div class="line"><a name="l04875"></a><span class="lineno"> 4875</span>&#160;              std::vector&lt;DoubleReal&gt; data_to_encode(spec.size());</div>
<div class="line"><a name="l04876"></a><span class="lineno"> 4876</span>&#160;              <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spec.size(); ++p)</div>
<div class="line"><a name="l04877"></a><span class="lineno"> 4877</span>&#160;                data_to_encode[p] = spec[p].getMZ();</div>
<div class="line"><a name="l04878"></a><span class="lineno"> 4878</span>&#160;              decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04879"></a><span class="lineno"> 4879</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04880"></a><span class="lineno"> 4880</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000514\&quot; name=\&quot;m/z array\&quot; unitAccession=\&quot;MS:1000040\&quot; unitName=\&quot;m/z\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04881"></a><span class="lineno"> 4881</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000523\&quot; name=\&quot;64-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04882"></a><span class="lineno"> 4882</span>&#160;            }</div>
<div class="line"><a name="l04883"></a><span class="lineno"> 4883</span>&#160;</div>
<div class="line"><a name="l04884"></a><span class="lineno"> 4884</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l04885"></a><span class="lineno"> 4885</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04886"></a><span class="lineno"> 4886</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04887"></a><span class="lineno"> 4887</span>&#160;          }</div>
<div class="line"><a name="l04888"></a><span class="lineno"> 4888</span>&#160;          <span class="comment">//write intensity array (default 32 bit precision)</span></div>
<div class="line"><a name="l04889"></a><span class="lineno"> 4889</span>&#160;          {</div>
<div class="line"><a name="l04890"></a><span class="lineno"> 4890</span>&#160;</div>
<div class="line"><a name="l04891"></a><span class="lineno"> 4891</span>&#160;            <span class="keywordflow">if</span> (options_.getIntensity32Bit())</div>
<div class="line"><a name="l04892"></a><span class="lineno"> 4892</span>&#160;            {</div>
<div class="line"><a name="l04893"></a><span class="lineno"> 4893</span>&#160;              std::vector&lt;Real&gt; data_to_encode(spec.size());</div>
<div class="line"><a name="l04894"></a><span class="lineno"> 4894</span>&#160;              <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spec.size(); ++p)</div>
<div class="line"><a name="l04895"></a><span class="lineno"> 4895</span>&#160;                data_to_encode[p] = spec[p].getIntensity();</div>
<div class="line"><a name="l04896"></a><span class="lineno"> 4896</span>&#160;              decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04897"></a><span class="lineno"> 4897</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04898"></a><span class="lineno"> 4898</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000515\&quot; name=\&quot;intensity array\&quot; unitAccession=\&quot;MS:1000131\&quot; unitName=\&quot;number of counts\&quot; unitCvRef=\&quot;MS\&quot;/&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04899"></a><span class="lineno"> 4899</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000521\&quot; name=\&quot;32-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04900"></a><span class="lineno"> 4900</span>&#160;            }</div>
<div class="line"><a name="l04901"></a><span class="lineno"> 4901</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l04902"></a><span class="lineno"> 4902</span>&#160;            {</div>
<div class="line"><a name="l04903"></a><span class="lineno"> 4903</span>&#160;              std::vector&lt;DoubleReal&gt; data_to_encode(spec.size());</div>
<div class="line"><a name="l04904"></a><span class="lineno"> 4904</span>&#160;              <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spec.size(); ++p)</div>
<div class="line"><a name="l04905"></a><span class="lineno"> 4905</span>&#160;                data_to_encode[p] = spec[p].getIntensity();</div>
<div class="line"><a name="l04906"></a><span class="lineno"> 4906</span>&#160;              decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04907"></a><span class="lineno"> 4907</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04908"></a><span class="lineno"> 4908</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000515\&quot; name=\&quot;intensity array\&quot; unitAccession=\&quot;MS:1000131\&quot; unitName=\&quot;number of counts\&quot; unitCvRef=\&quot;MS\&quot;/&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04909"></a><span class="lineno"> 4909</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000523\&quot; name=\&quot;64-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04910"></a><span class="lineno"> 4910</span>&#160;            }</div>
<div class="line"><a name="l04911"></a><span class="lineno"> 4911</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l04912"></a><span class="lineno"> 4912</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04913"></a><span class="lineno"> 4913</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04914"></a><span class="lineno"> 4914</span>&#160;          }</div>
<div class="line"><a name="l04915"></a><span class="lineno"> 4915</span>&#160;          <span class="comment">//write float data array</span></div>
<div class="line"><a name="l04916"></a><span class="lineno"> 4916</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>().size(); ++m)</div>
<div class="line"><a name="l04917"></a><span class="lineno"> 4917</span>&#160;          {</div>
<div class="line"><a name="l04918"></a><span class="lineno"> 4918</span>&#160;            <span class="keyword">const</span> <span class="keyword">typename</span> SpectrumType::FloatDataArray&amp; array = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[m];</div>
<div class="line"><a name="l04919"></a><span class="lineno"> 4919</span>&#160;            std::vector&lt;DoubleReal&gt; data64_to_encode(array.size());</div>
<div class="line"><a name="l04920"></a><span class="lineno"> 4920</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; array.size(); ++p)</div>
<div class="line"><a name="l04921"></a><span class="lineno"> 4921</span>&#160;              data64_to_encode[p] = array[p];</div>
<div class="line"><a name="l04922"></a><span class="lineno"> 4922</span>&#160;            decoder_.encode(data64_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04923"></a><span class="lineno"> 4923</span>&#160;            <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref_string = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l04924"></a><span class="lineno"> 4924</span>&#160;            <span class="keywordflow">if</span> (array.getDataProcessing().size() != 0)</div>
<div class="line"><a name="l04925"></a><span class="lineno"> 4925</span>&#160;            {</div>
<div class="line"><a name="l04926"></a><span class="lineno"> 4926</span>&#160;              data_processing_ref_string = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dataProcessingRef=\&quot;dp_sp_&quot;</span>) + s + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04927"></a><span class="lineno"> 4927</span>&#160;            }</div>
<div class="line"><a name="l04928"></a><span class="lineno"> 4928</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray arrayLength=\&quot;&quot;</span> &lt;&lt; array.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; &quot;</span> &lt;&lt; data_processing_ref_string &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04929"></a><span class="lineno"> 4929</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000523\&quot; name=\&quot;64-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04930"></a><span class="lineno"> 4930</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l04931"></a><span class="lineno"> 4931</span>&#160;            <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> bi_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000513&quot;</span>, array.getName());</div>
<div class="line"><a name="l04932"></a><span class="lineno"> 4932</span>&#160;            <span class="keywordflow">if</span> (bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l04933"></a><span class="lineno"> 4933</span>&#160;            {</div>
<div class="line"><a name="l04934"></a><span class="lineno"> 4934</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04935"></a><span class="lineno"> 4935</span>&#160;            }</div>
<div class="line"><a name="l04936"></a><span class="lineno"> 4936</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l04937"></a><span class="lineno"> 4937</span>&#160;            {</div>
<div class="line"><a name="l04938"></a><span class="lineno"> 4938</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000786\&quot; name=\&quot;non-standard data array\&quot; value=\&quot;&quot;</span> &lt;&lt; array.getName() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04939"></a><span class="lineno"> 4939</span>&#160;            }</div>
<div class="line"><a name="l04940"></a><span class="lineno"> 4940</span>&#160;            writeUserParam_(os, array, 6, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/binaryDataArrayList/binaryDataArray/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04941"></a><span class="lineno"> 4941</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04942"></a><span class="lineno"> 4942</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04943"></a><span class="lineno"> 4943</span>&#160;          }</div>
<div class="line"><a name="l04944"></a><span class="lineno"> 4944</span>&#160;          <span class="comment">//write integer data array</span></div>
<div class="line"><a name="l04945"></a><span class="lineno"> 4945</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">getIntegerDataArrays</a>().size(); ++m)</div>
<div class="line"><a name="l04946"></a><span class="lineno"> 4946</span>&#160;          {</div>
<div class="line"><a name="l04947"></a><span class="lineno"> 4947</span>&#160;            <span class="keyword">const</span> <span class="keyword">typename</span> SpectrumType::IntegerDataArray&amp; array = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">getIntegerDataArrays</a>()[m];</div>
<div class="line"><a name="l04948"></a><span class="lineno"> 4948</span>&#160;            std::vector&lt;Int64&gt; data64_to_encode(array.size());</div>
<div class="line"><a name="l04949"></a><span class="lineno"> 4949</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; array.size(); ++p)</div>
<div class="line"><a name="l04950"></a><span class="lineno"> 4950</span>&#160;              data64_to_encode[p] = array[p];</div>
<div class="line"><a name="l04951"></a><span class="lineno"> 4951</span>&#160;            decoder_.encodeIntegers(data64_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04952"></a><span class="lineno"> 4952</span>&#160;            <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref_string = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l04953"></a><span class="lineno"> 4953</span>&#160;            <span class="keywordflow">if</span> (array.getDataProcessing().size() != 0)</div>
<div class="line"><a name="l04954"></a><span class="lineno"> 4954</span>&#160;            {</div>
<div class="line"><a name="l04955"></a><span class="lineno"> 4955</span>&#160;              data_processing_ref_string = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dataProcessingRef=\&quot;dp_sp_&quot;</span>) + s + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04956"></a><span class="lineno"> 4956</span>&#160;            }</div>
<div class="line"><a name="l04957"></a><span class="lineno"> 4957</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray arrayLength=\&quot;&quot;</span> &lt;&lt; array.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; &quot;</span> &lt;&lt; data_processing_ref_string &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04958"></a><span class="lineno"> 4958</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000522\&quot; name=\&quot;64-bit integer\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04959"></a><span class="lineno"> 4959</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l04960"></a><span class="lineno"> 4960</span>&#160;            <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> bi_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000513&quot;</span>, array.getName());</div>
<div class="line"><a name="l04961"></a><span class="lineno"> 4961</span>&#160;            <span class="keywordflow">if</span> (bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l04962"></a><span class="lineno"> 4962</span>&#160;            {</div>
<div class="line"><a name="l04963"></a><span class="lineno"> 4963</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04964"></a><span class="lineno"> 4964</span>&#160;            }</div>
<div class="line"><a name="l04965"></a><span class="lineno"> 4965</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l04966"></a><span class="lineno"> 4966</span>&#160;            {</div>
<div class="line"><a name="l04967"></a><span class="lineno"> 4967</span>&#160;              os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000786\&quot; name=\&quot;non-standard data array\&quot; value=\&quot;&quot;</span> &lt;&lt; array.getName() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04968"></a><span class="lineno"> 4968</span>&#160;            }</div>
<div class="line"><a name="l04969"></a><span class="lineno"> 4969</span>&#160;            writeUserParam_(os, array, 6, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/binaryDataArrayList/binaryDataArray/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04970"></a><span class="lineno"> 4970</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04971"></a><span class="lineno"> 4971</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04972"></a><span class="lineno"> 4972</span>&#160;          }</div>
<div class="line"><a name="l04973"></a><span class="lineno"> 4973</span>&#160;          <span class="comment">//write string data arrays</span></div>
<div class="line"><a name="l04974"></a><span class="lineno"> 4974</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#ace039d325c112e45c9d37e0e656ba9a2">getStringDataArrays</a>().size(); ++m)</div>
<div class="line"><a name="l04975"></a><span class="lineno"> 4975</span>&#160;          {</div>
<div class="line"><a name="l04976"></a><span class="lineno"> 4976</span>&#160;            <span class="keyword">const</span> <span class="keyword">typename</span> SpectrumType::StringDataArray&amp; array = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#ace039d325c112e45c9d37e0e656ba9a2">getStringDataArrays</a>()[m];</div>
<div class="line"><a name="l04977"></a><span class="lineno"> 4977</span>&#160;            std::vector&lt;String&gt; data_to_encode;</div>
<div class="line"><a name="l04978"></a><span class="lineno"> 4978</span>&#160;            data_to_encode.resize(array.size());</div>
<div class="line"><a name="l04979"></a><span class="lineno"> 4979</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; array.size(); ++p)</div>
<div class="line"><a name="l04980"></a><span class="lineno"> 4980</span>&#160;              data_to_encode[p] = array[p];</div>
<div class="line"><a name="l04981"></a><span class="lineno"> 4981</span>&#160;            decoder_.encodeStrings(data_to_encode, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l04982"></a><span class="lineno"> 4982</span>&#160;            <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref_string = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l04983"></a><span class="lineno"> 4983</span>&#160;            <span class="keywordflow">if</span> (array.getDataProcessing().size() != 0)</div>
<div class="line"><a name="l04984"></a><span class="lineno"> 4984</span>&#160;            {</div>
<div class="line"><a name="l04985"></a><span class="lineno"> 4985</span>&#160;              data_processing_ref_string = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dataProcessingRef=\&quot;dp_sp_&quot;</span>) + s + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l04986"></a><span class="lineno"> 4986</span>&#160;            }</div>
<div class="line"><a name="l04987"></a><span class="lineno"> 4987</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray arrayLength=\&quot;&quot;</span> &lt;&lt; array.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; &quot;</span> &lt;&lt; data_processing_ref_string &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04988"></a><span class="lineno"> 4988</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001479\&quot; name=\&quot;null-terminated ASCII string\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04989"></a><span class="lineno"> 4989</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l04990"></a><span class="lineno"> 4990</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000786\&quot; name=\&quot;non-standard data array\&quot; value=\&quot;&quot;</span> &lt;&lt; array.getName() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04991"></a><span class="lineno"> 4991</span>&#160;            writeUserParam_(os, array, 6, <span class="stringliteral">&quot;/mzML/run/spectrumList/spectrum/binaryDataArrayList/binaryDataArray/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l04992"></a><span class="lineno"> 4992</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04993"></a><span class="lineno"> 4993</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04994"></a><span class="lineno"> 4994</span>&#160;          }</div>
<div class="line"><a name="l04995"></a><span class="lineno"> 4995</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/binaryDataArrayList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04996"></a><span class="lineno"> 4996</span>&#160;        }</div>
<div class="line"><a name="l04997"></a><span class="lineno"> 4997</span>&#160;</div>
<div class="line"><a name="l04998"></a><span class="lineno"> 4998</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/spectrum&gt;\n&quot;</span>;</div>
<div class="line"><a name="l04999"></a><span class="lineno"> 4999</span>&#160;</div>
<div class="line"><a name="l05000"></a><span class="lineno"> 5000</span>&#160;</div>
<div class="line"><a name="l05001"></a><span class="lineno"> 5001</span>&#160;</div>
<div class="line"><a name="l05002"></a><span class="lineno"> 5002</span>&#160;    }</div>
<div class="line"><a name="l05003"></a><span class="lineno"> 5003</span>&#160;</div>
<div class="line"><a name="l05004"></a><span class="lineno"> 5004</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l05005"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9da388304c18a628979434640b7bb9c8"> 5005</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9da388304c18a628979434640b7bb9c8">MzMLHandler&lt;MapType&gt;::writeChromatogram_</a>(std::ostream&amp; os,</div>
<div class="line"><a name="l05006"></a><span class="lineno"> 5006</span>&#160;            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSChromatogram.html">ChromatogramType</a>&amp; chromatogram, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <a class="code" href="classOpenMS_1_1Internal_1_1MzMLValidator.html">Internal::MzMLValidator</a>&amp; validator)</div>
<div class="line"><a name="l05007"></a><span class="lineno"> 5007</span>&#160;    {</div>
<div class="line"><a name="l05008"></a><span class="lineno"> 5008</span>&#160;        <span class="comment">// TODO native id with chromatogram=?? prefix?</span></div>
<div class="line"><a name="l05009"></a><span class="lineno"> 5009</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;      &lt;chromatogram id=\&quot;&quot;</span> &lt;&lt; chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>() &lt;&lt; <span class="stringliteral">&quot;\&quot; index=\&quot;&quot;</span> &lt;&lt; c &lt;&lt; <span class="stringliteral">&quot;\&quot; defaultArrayLength=\&quot;&quot;</span> &lt;&lt; chromatogram.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;&quot;</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05010"></a><span class="lineno"> 5010</span>&#160;</div>
<div class="line"><a name="l05011"></a><span class="lineno"> 5011</span>&#160;        <span class="comment">// write cvParams (chromatogram type)</span></div>
<div class="line"><a name="l05012"></a><span class="lineno"> 5012</span>&#160;        <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdad97236e33b7a22bd5b44ca5404d069cb">ChromatogramSettings::MASS_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05013"></a><span class="lineno"> 5013</span>&#160;        {</div>
<div class="line"><a name="l05014"></a><span class="lineno"> 5014</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000810\&quot; name=\&quot;mass chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05015"></a><span class="lineno"> 5015</span>&#160;        }</div>
<div class="line"><a name="l05016"></a><span class="lineno"> 5016</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda9761ce23aa0bea120a7d581477316953">ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05017"></a><span class="lineno"> 5017</span>&#160;        {</div>
<div class="line"><a name="l05018"></a><span class="lineno"> 5018</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000235\&quot; name=\&quot;total ion current chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05019"></a><span class="lineno"> 5019</span>&#160;        }</div>
<div class="line"><a name="l05020"></a><span class="lineno"> 5020</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda5e1f2677edbc482d260e873a4a9660c6">ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05021"></a><span class="lineno"> 5021</span>&#160;        {</div>
<div class="line"><a name="l05022"></a><span class="lineno"> 5022</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000627\&quot; name=\&quot;selected ion current chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05023"></a><span class="lineno"> 5023</span>&#160;        }</div>
<div class="line"><a name="l05024"></a><span class="lineno"> 5024</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda6becb3aa48a0fbb4401e98e6b99a9428">ChromatogramSettings::BASEPEAK_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05025"></a><span class="lineno"> 5025</span>&#160;        {</div>
<div class="line"><a name="l05026"></a><span class="lineno"> 5026</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000628\&quot; name=\&quot;basepeak chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05027"></a><span class="lineno"> 5027</span>&#160;        }</div>
<div class="line"><a name="l05028"></a><span class="lineno"> 5028</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa">ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05029"></a><span class="lineno"> 5029</span>&#160;        {</div>
<div class="line"><a name="l05030"></a><span class="lineno"> 5030</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001472\&quot; name=\&quot;selected ion monitoring chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05031"></a><span class="lineno"> 5031</span>&#160;        }</div>
<div class="line"><a name="l05032"></a><span class="lineno"> 5032</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05033"></a><span class="lineno"> 5033</span>&#160;        {</div>
<div class="line"><a name="l05034"></a><span class="lineno"> 5034</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001473\&quot; name=\&quot;selected reaction monitoring chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05035"></a><span class="lineno"> 5035</span>&#160;        }</div>
<div class="line"><a name="l05036"></a><span class="lineno"> 5036</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdaa227021fdc2a25d98a5113afc918b75b">ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05037"></a><span class="lineno"> 5037</span>&#160;        {</div>
<div class="line"><a name="l05038"></a><span class="lineno"> 5038</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000811\&quot; name=\&quot;electromagnetic radiation chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05039"></a><span class="lineno"> 5039</span>&#160;        }</div>
<div class="line"><a name="l05040"></a><span class="lineno"> 5040</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda1a3d139c1d36a9c7462f3e1e8bbba110">ChromatogramSettings::ABSORPTION_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05041"></a><span class="lineno"> 5041</span>&#160;        {</div>
<div class="line"><a name="l05042"></a><span class="lineno"> 5042</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000812\&quot; name=\&quot;absorption chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05043"></a><span class="lineno"> 5043</span>&#160;        }</div>
<div class="line"><a name="l05044"></a><span class="lineno"> 5044</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">getChromatogramType</a>() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda37ef0f7f2bed3939a8c3e135067b8705">ChromatogramSettings::EMISSION_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l05045"></a><span class="lineno"> 5045</span>&#160;        {</div>
<div class="line"><a name="l05046"></a><span class="lineno"> 5046</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000813\&quot; name=\&quot;emission chromatogram\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05047"></a><span class="lineno"> 5047</span>&#160;        }</div>
<div class="line"><a name="l05048"></a><span class="lineno"> 5048</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l05049"></a><span class="lineno"> 5049</span>&#160;        {</div>
<div class="line"><a name="l05050"></a><span class="lineno"> 5050</span>&#160;          <span class="comment">// TODO</span></div>
<div class="line"><a name="l05051"></a><span class="lineno"> 5051</span>&#160;        }</div>
<div class="line"><a name="l05052"></a><span class="lineno"> 5052</span>&#160;        writePrecursor_(os, chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#ab714caa4d58fc603439a5a0109860704">getPrecursor</a>(), validator);</div>
<div class="line"><a name="l05053"></a><span class="lineno"> 5053</span>&#160;        writeProduct_(os, chromatogram.<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#ad315e04a79cddc41e8e12d92086e46d6">getProduct</a>(), validator);</div>
<div class="line"><a name="l05054"></a><span class="lineno"> 5054</span>&#160;</div>
<div class="line"><a name="l05055"></a><span class="lineno"> 5055</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l05056"></a><span class="lineno"> 5056</span>&#160;        <span class="comment">//binary data array list</span></div>
<div class="line"><a name="l05057"></a><span class="lineno"> 5057</span>&#160;        <span class="comment">//--------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l05058"></a><span class="lineno"> 5058</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> compression_term;</div>
<div class="line"><a name="l05059"></a><span class="lineno"> 5059</span>&#160;        <span class="keywordflow">if</span> (options_.getCompression())</div>
<div class="line"><a name="l05060"></a><span class="lineno"> 5060</span>&#160;        {</div>
<div class="line"><a name="l05061"></a><span class="lineno"> 5061</span>&#160;          compression_term = <span class="stringliteral">&quot;&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000574\&quot; name=\&quot;zlib compression\&quot; /&gt;&quot;</span>;</div>
<div class="line"><a name="l05062"></a><span class="lineno"> 5062</span>&#160;        }</div>
<div class="line"><a name="l05063"></a><span class="lineno"> 5063</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l05064"></a><span class="lineno"> 5064</span>&#160;        {</div>
<div class="line"><a name="l05065"></a><span class="lineno"> 5065</span>&#160;          compression_term = <span class="stringliteral">&quot;&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000576\&quot; name=\&quot;no compression\&quot; /&gt;&quot;</span>;</div>
<div class="line"><a name="l05066"></a><span class="lineno"> 5066</span>&#160;        }</div>
<div class="line"><a name="l05067"></a><span class="lineno"> 5067</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> encoded_string;</div>
<div class="line"><a name="l05068"></a><span class="lineno"> 5068</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;binaryDataArrayList count=\&quot;&quot;</span> &lt;&lt; (2 + chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>().size() + chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#ace039d325c112e45c9d37e0e656ba9a2">getStringDataArrays</a>().size() + chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">getIntegerDataArrays</a>().size()) &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05069"></a><span class="lineno"> 5069</span>&#160;        <span class="comment">//write m/z array (default 64 bit precision)</span></div>
<div class="line"><a name="l05070"></a><span class="lineno"> 5070</span>&#160;        {</div>
<div class="line"><a name="l05071"></a><span class="lineno"> 5071</span>&#160;</div>
<div class="line"><a name="l05072"></a><span class="lineno"> 5072</span>&#160;          <span class="keywordflow">if</span> (options_.getMz32Bit())</div>
<div class="line"><a name="l05073"></a><span class="lineno"> 5073</span>&#160;          {</div>
<div class="line"><a name="l05074"></a><span class="lineno"> 5074</span>&#160;            std::vector&lt;Real&gt; data_to_encode(chromatogram.size());</div>
<div class="line"><a name="l05075"></a><span class="lineno"> 5075</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; chromatogram.size(); ++p)</div>
<div class="line"><a name="l05076"></a><span class="lineno"> 5076</span>&#160;              data_to_encode[p] = chromatogram[p].getRT();</div>
<div class="line"><a name="l05077"></a><span class="lineno"> 5077</span>&#160;            decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05078"></a><span class="lineno"> 5078</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05079"></a><span class="lineno"> 5079</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000595\&quot; name=\&quot;time array\&quot; unitAccession=\&quot;UO:0000010\&quot; unitName=\&quot;second\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05080"></a><span class="lineno"> 5080</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000521\&quot; name=\&quot;32-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05081"></a><span class="lineno"> 5081</span>&#160;          }</div>
<div class="line"><a name="l05082"></a><span class="lineno"> 5082</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l05083"></a><span class="lineno"> 5083</span>&#160;          {</div>
<div class="line"><a name="l05084"></a><span class="lineno"> 5084</span>&#160;            std::vector&lt;DoubleReal&gt; data_to_encode(chromatogram.size());</div>
<div class="line"><a name="l05085"></a><span class="lineno"> 5085</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; chromatogram.size(); ++p)</div>
<div class="line"><a name="l05086"></a><span class="lineno"> 5086</span>&#160;              data_to_encode[p] = chromatogram[p].getRT();</div>
<div class="line"><a name="l05087"></a><span class="lineno"> 5087</span>&#160;            decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05088"></a><span class="lineno"> 5088</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05089"></a><span class="lineno"> 5089</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000595\&quot; name=\&quot;time array\&quot; unitAccession=\&quot;UO:0000010\&quot; unitName=\&quot;second\&quot; unitCvRef=\&quot;MS\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05090"></a><span class="lineno"> 5090</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000523\&quot; name=\&quot;64-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05091"></a><span class="lineno"> 5091</span>&#160;          }</div>
<div class="line"><a name="l05092"></a><span class="lineno"> 5092</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05093"></a><span class="lineno"> 5093</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05094"></a><span class="lineno"> 5094</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05095"></a><span class="lineno"> 5095</span>&#160;</div>
<div class="line"><a name="l05096"></a><span class="lineno"> 5096</span>&#160;        }</div>
<div class="line"><a name="l05097"></a><span class="lineno"> 5097</span>&#160;        <span class="comment">//write intensity array (default 32 bit precision)</span></div>
<div class="line"><a name="l05098"></a><span class="lineno"> 5098</span>&#160;        {</div>
<div class="line"><a name="l05099"></a><span class="lineno"> 5099</span>&#160;          <span class="keywordflow">if</span> (options_.getIntensity32Bit())</div>
<div class="line"><a name="l05100"></a><span class="lineno"> 5100</span>&#160;          {</div>
<div class="line"><a name="l05101"></a><span class="lineno"> 5101</span>&#160;            std::vector&lt;Real&gt; data_to_encode(chromatogram.size());</div>
<div class="line"><a name="l05102"></a><span class="lineno"> 5102</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; chromatogram.size(); ++p)</div>
<div class="line"><a name="l05103"></a><span class="lineno"> 5103</span>&#160;              data_to_encode[p] = chromatogram[p].getIntensity();</div>
<div class="line"><a name="l05104"></a><span class="lineno"> 5104</span>&#160;            decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05105"></a><span class="lineno"> 5105</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05106"></a><span class="lineno"> 5106</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000515\&quot; name=\&quot;intensity array\&quot; unitAccession=\&quot;MS:1000131\&quot; unitName=\&quot;number of counts\&quot; unitCvRef=\&quot;MS\&quot;/&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05107"></a><span class="lineno"> 5107</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000521\&quot; name=\&quot;32-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05108"></a><span class="lineno"> 5108</span>&#160;          }</div>
<div class="line"><a name="l05109"></a><span class="lineno"> 5109</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l05110"></a><span class="lineno"> 5110</span>&#160;          {</div>
<div class="line"><a name="l05111"></a><span class="lineno"> 5111</span>&#160;            std::vector&lt;DoubleReal&gt; data_to_encode(chromatogram.size());</div>
<div class="line"><a name="l05112"></a><span class="lineno"> 5112</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; chromatogram.size(); ++p)</div>
<div class="line"><a name="l05113"></a><span class="lineno"> 5113</span>&#160;              data_to_encode[p] = chromatogram[p].getIntensity();</div>
<div class="line"><a name="l05114"></a><span class="lineno"> 5114</span>&#160;            decoder_.encode(data_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05115"></a><span class="lineno"> 5115</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05116"></a><span class="lineno"> 5116</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000515\&quot; name=\&quot;intensity array\&quot; unitAccession=\&quot;MS:1000131\&quot; unitName=\&quot;number of counts\&quot; unitCvRef=\&quot;MS\&quot;/&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05117"></a><span class="lineno"> 5117</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000523\&quot; name=\&quot;64-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05118"></a><span class="lineno"> 5118</span>&#160;          }</div>
<div class="line"><a name="l05119"></a><span class="lineno"> 5119</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05120"></a><span class="lineno"> 5120</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05121"></a><span class="lineno"> 5121</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05122"></a><span class="lineno"> 5122</span>&#160;        }</div>
<div class="line"><a name="l05123"></a><span class="lineno"> 5123</span>&#160;        <span class="comment">//write float data array</span></div>
<div class="line"><a name="l05124"></a><span class="lineno"> 5124</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>().size(); ++m)</div>
<div class="line"><a name="l05125"></a><span class="lineno"> 5125</span>&#160;        {</div>
<div class="line"><a name="l05126"></a><span class="lineno"> 5126</span>&#160;          <span class="keyword">const</span> <span class="keyword">typename</span> ChromatogramType::FloatDataArray&amp; array = chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[m];</div>
<div class="line"><a name="l05127"></a><span class="lineno"> 5127</span>&#160;          std::vector&lt;DoubleReal&gt; data64_to_encode(array.size());</div>
<div class="line"><a name="l05128"></a><span class="lineno"> 5128</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; array.size(); ++p)</div>
<div class="line"><a name="l05129"></a><span class="lineno"> 5129</span>&#160;            data64_to_encode[p] = array[p];</div>
<div class="line"><a name="l05130"></a><span class="lineno"> 5130</span>&#160;          decoder_.encode(data64_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05131"></a><span class="lineno"> 5131</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref_string = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l05132"></a><span class="lineno"> 5132</span>&#160;          <span class="keywordflow">if</span> (array.getDataProcessing().size() != 0)</div>
<div class="line"><a name="l05133"></a><span class="lineno"> 5133</span>&#160;          {</div>
<div class="line"><a name="l05134"></a><span class="lineno"> 5134</span>&#160;            data_processing_ref_string = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dataProcessingRef=\&quot;dp_sp_&quot;</span>) + c + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l05135"></a><span class="lineno"> 5135</span>&#160;          }</div>
<div class="line"><a name="l05136"></a><span class="lineno"> 5136</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray arrayLength=\&quot;&quot;</span> &lt;&lt; array.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; &quot;</span> &lt;&lt; data_processing_ref_string &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05137"></a><span class="lineno"> 5137</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000523\&quot; name=\&quot;64-bit float\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05138"></a><span class="lineno"> 5138</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05139"></a><span class="lineno"> 5139</span>&#160;          <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> bi_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000513&quot;</span>, array.getName());</div>
<div class="line"><a name="l05140"></a><span class="lineno"> 5140</span>&#160;          <span class="keywordflow">if</span> (bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l05141"></a><span class="lineno"> 5141</span>&#160;          {</div>
<div class="line"><a name="l05142"></a><span class="lineno"> 5142</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05143"></a><span class="lineno"> 5143</span>&#160;          }</div>
<div class="line"><a name="l05144"></a><span class="lineno"> 5144</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l05145"></a><span class="lineno"> 5145</span>&#160;          {</div>
<div class="line"><a name="l05146"></a><span class="lineno"> 5146</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000786\&quot; name=\&quot;non-standard data array\&quot; value=\&quot;&quot;</span> &lt;&lt; array.getName() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05147"></a><span class="lineno"> 5147</span>&#160;          }</div>
<div class="line"><a name="l05148"></a><span class="lineno"> 5148</span>&#160;          writeUserParam_(os, array, 6, <span class="stringliteral">&quot;/mzML/run/chromatogramList/chromatogram/binaryDataArrayList/binaryDataArray/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l05149"></a><span class="lineno"> 5149</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05150"></a><span class="lineno"> 5150</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05151"></a><span class="lineno"> 5151</span>&#160;        }</div>
<div class="line"><a name="l05152"></a><span class="lineno"> 5152</span>&#160;        <span class="comment">//write integer data array</span></div>
<div class="line"><a name="l05153"></a><span class="lineno"> 5153</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">getIntegerDataArrays</a>().size(); ++m)</div>
<div class="line"><a name="l05154"></a><span class="lineno"> 5154</span>&#160;        {</div>
<div class="line"><a name="l05155"></a><span class="lineno"> 5155</span>&#160;          <span class="keyword">const</span> <span class="keyword">typename</span> ChromatogramType::IntegerDataArray&amp; array = chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">getIntegerDataArrays</a>()[m];</div>
<div class="line"><a name="l05156"></a><span class="lineno"> 5156</span>&#160;          std::vector&lt;Int64&gt; data64_to_encode(array.size());</div>
<div class="line"><a name="l05157"></a><span class="lineno"> 5157</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; array.size(); ++p)</div>
<div class="line"><a name="l05158"></a><span class="lineno"> 5158</span>&#160;            data64_to_encode[p] = array[p];</div>
<div class="line"><a name="l05159"></a><span class="lineno"> 5159</span>&#160;          decoder_.encodeIntegers(data64_to_encode, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05160"></a><span class="lineno"> 5160</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref_string = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l05161"></a><span class="lineno"> 5161</span>&#160;          <span class="keywordflow">if</span> (array.getDataProcessing().size() != 0)</div>
<div class="line"><a name="l05162"></a><span class="lineno"> 5162</span>&#160;          {</div>
<div class="line"><a name="l05163"></a><span class="lineno"> 5163</span>&#160;            data_processing_ref_string = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dataProcessingRef=\&quot;dp_sp_&quot;</span>) + c + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l05164"></a><span class="lineno"> 5164</span>&#160;          }</div>
<div class="line"><a name="l05165"></a><span class="lineno"> 5165</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray arrayLength=\&quot;&quot;</span> &lt;&lt; array.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; &quot;</span> &lt;&lt; data_processing_ref_string &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05166"></a><span class="lineno"> 5166</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000522\&quot; name=\&quot;64-bit integer\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05167"></a><span class="lineno"> 5167</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05168"></a><span class="lineno"> 5168</span>&#160;          <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> bi_term = getChildWithName_(<span class="stringliteral">&quot;MS:1000513&quot;</span>, array.getName());</div>
<div class="line"><a name="l05169"></a><span class="lineno"> 5169</span>&#160;          <span class="keywordflow">if</span> (bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> != <span class="stringliteral">&quot;&quot;</span>)</div>
<div class="line"><a name="l05170"></a><span class="lineno"> 5170</span>&#160;          {</div>
<div class="line"><a name="l05171"></a><span class="lineno"> 5171</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">id</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; name=\&quot;&quot;</span> &lt;&lt; bi_term.<a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">name</a> &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05172"></a><span class="lineno"> 5172</span>&#160;          }</div>
<div class="line"><a name="l05173"></a><span class="lineno"> 5173</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l05174"></a><span class="lineno"> 5174</span>&#160;          {</div>
<div class="line"><a name="l05175"></a><span class="lineno"> 5175</span>&#160;            os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000786\&quot; name=\&quot;non-standard data array\&quot; value=\&quot;&quot;</span> &lt;&lt; array.getName() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05176"></a><span class="lineno"> 5176</span>&#160;          }</div>
<div class="line"><a name="l05177"></a><span class="lineno"> 5177</span>&#160;          writeUserParam_(os, array, 6, <span class="stringliteral">&quot;/mzML/run/chromatogramList/chromatogram/binaryDataArrayList/binaryDataArray/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l05178"></a><span class="lineno"> 5178</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05179"></a><span class="lineno"> 5179</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05180"></a><span class="lineno"> 5180</span>&#160;        }</div>
<div class="line"><a name="l05181"></a><span class="lineno"> 5181</span>&#160;        <span class="comment">//write string data arrays</span></div>
<div class="line"><a name="l05182"></a><span class="lineno"> 5182</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m = 0; m &lt; chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#ace039d325c112e45c9d37e0e656ba9a2">getStringDataArrays</a>().size(); ++m)</div>
<div class="line"><a name="l05183"></a><span class="lineno"> 5183</span>&#160;        {</div>
<div class="line"><a name="l05184"></a><span class="lineno"> 5184</span>&#160;          <span class="keyword">const</span> <span class="keyword">typename</span> ChromatogramType::StringDataArray&amp; array = chromatogram.<a class="code" href="classOpenMS_1_1MSChromatogram.html#ace039d325c112e45c9d37e0e656ba9a2">getStringDataArrays</a>()[m];</div>
<div class="line"><a name="l05185"></a><span class="lineno"> 5185</span>&#160;          std::vector&lt;String&gt; data_to_encode;</div>
<div class="line"><a name="l05186"></a><span class="lineno"> 5186</span>&#160;          data_to_encode.resize(array.size());</div>
<div class="line"><a name="l05187"></a><span class="lineno"> 5187</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; array.size(); ++p)</div>
<div class="line"><a name="l05188"></a><span class="lineno"> 5188</span>&#160;            data_to_encode[p] = array[p];</div>
<div class="line"><a name="l05189"></a><span class="lineno"> 5189</span>&#160;          decoder_.encodeStrings(data_to_encode, encoded_string, options_.getCompression());</div>
<div class="line"><a name="l05190"></a><span class="lineno"> 5190</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> data_processing_ref_string = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l05191"></a><span class="lineno"> 5191</span>&#160;          <span class="keywordflow">if</span> (array.getDataProcessing().size() != 0)</div>
<div class="line"><a name="l05192"></a><span class="lineno"> 5192</span>&#160;          {</div>
<div class="line"><a name="l05193"></a><span class="lineno"> 5193</span>&#160;            data_processing_ref_string = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;dataProcessingRef=\&quot;dp_sp_&quot;</span>) + c + <span class="stringliteral">&quot;_bi_&quot;</span> + m + <span class="stringliteral">&quot;\&quot;&quot;</span>;</div>
<div class="line"><a name="l05194"></a><span class="lineno"> 5194</span>&#160;          }</div>
<div class="line"><a name="l05195"></a><span class="lineno"> 5195</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;binaryDataArray arrayLength=\&quot;&quot;</span> &lt;&lt; array.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; encodedLength=\&quot;&quot;</span> &lt;&lt; encoded_string.size() &lt;&lt; <span class="stringliteral">&quot;\&quot; &quot;</span> &lt;&lt; data_processing_ref_string &lt;&lt; <span class="stringliteral">&quot;&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05196"></a><span class="lineno"> 5196</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1001479\&quot; name=\&quot;null-terminated ASCII string\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05197"></a><span class="lineno"> 5197</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&quot;</span> &lt;&lt; compression_term &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05198"></a><span class="lineno"> 5198</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;cvParam cvRef=\&quot;MS\&quot; accession=\&quot;MS:1000786\&quot; name=\&quot;non-standard data array\&quot; value=\&quot;&quot;</span> &lt;&lt; array.getName() &lt;&lt; <span class="stringliteral">&quot;\&quot; /&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05199"></a><span class="lineno"> 5199</span>&#160;          writeUserParam_(os, array, 6, <span class="stringliteral">&quot;/mzML/run/chromatogramList/chromatogram/binaryDataArrayList/binaryDataArray/cvParam/@accession&quot;</span>, validator);</div>
<div class="line"><a name="l05200"></a><span class="lineno"> 5200</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t\t&lt;binary&gt;&quot;</span> &lt;&lt; encoded_string &lt;&lt; <span class="stringliteral">&quot;&lt;/binary&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05201"></a><span class="lineno"> 5201</span>&#160;          os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t\t&lt;/binaryDataArray&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05202"></a><span class="lineno"> 5202</span>&#160;        }</div>
<div class="line"><a name="l05203"></a><span class="lineno"> 5203</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t\t&lt;/binaryDataArrayList&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05204"></a><span class="lineno"> 5204</span>&#160;        os &lt;&lt; <span class="stringliteral">&quot;\t\t\t&lt;/chromatogram&gt;&quot;</span> &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span>;</div>
<div class="line"><a name="l05205"></a><span class="lineno"> 5205</span>&#160;</div>
<div class="line"><a name="l05206"></a><span class="lineno"> 5206</span>&#160;</div>
<div class="line"><a name="l05207"></a><span class="lineno"> 5207</span>&#160;    }</div>
<div class="line"><a name="l05208"></a><span class="lineno"> 5208</span>&#160;</div>
<div class="line"><a name="l05209"></a><span class="lineno"> 5209</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> MapType&gt;</div>
<div class="line"><a name="l05210"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a115d84a31a4be5741fe2eddb197c0d6f"> 5210</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a115d84a31a4be5741fe2eddb197c0d6f">MzMLHandler&lt;MapType&gt;::writeFooter_</a>(std::ostream&amp; os)</div>
<div class="line"><a name="l05211"></a><span class="lineno"> 5211</span>&#160;    {</div>
<div class="line"><a name="l05212"></a><span class="lineno"> 5212</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;\t&lt;/run&gt;\n&quot;</span>;</div>
<div class="line"><a name="l05213"></a><span class="lineno"> 5213</span>&#160;</div>
<div class="line"><a name="l05214"></a><span class="lineno"> 5214</span>&#160;      os &lt;&lt; <span class="stringliteral">&quot;&lt;/mzML&gt;&quot;</span>;</div>
<div class="line"><a name="l05215"></a><span class="lineno"> 5215</span>&#160;    }</div>
<div class="line"><a name="l05216"></a><span class="lineno"> 5216</span>&#160;</div>
<div class="line"><a name="l05217"></a><span class="lineno"> 5217</span>&#160;  } <span class="comment">// namespace Internal</span></div>
<div class="line"><a name="l05218"></a><span class="lineno"> 5218</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l05219"></a><span class="lineno"> 5219</span>&#160;</div>
<div class="line"><a name="l05220"></a><span class="lineno"> 5220</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a43aa2dacc04339d6b2cf5eb317f6bb2e"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a43aa2dacc04339d6b2cf5eb317f6bb2e">OpenMS::SourceFile::getPathToFile</a></div><div class="ttdeci">const String &amp; getPathToFile() const </div><div class="ttdoc">returns the file path </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">OpenMS::DataProcessing::DEISOTOPING</a></div><div class="ttdoc">Deisotoping. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_aea861f8342ba549d72dda0674103e2cd"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#aea861f8342ba549d72dda0674103e2cd">OpenMS::ContactPerson::getAddress</a></div><div class="ttdeci">const String &amp; getAddress() const </div><div class="ttdoc">returns the address </div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a93a8dc068053ec44ee7e45864ef969f7"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a></div><div class="ttdeci">const double k</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_aae35ae2dfad88d673b03c787aafca83d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">OpenMS::MetaInfoInterface::getMetaValue</a></div><div class="ttdeci">const DataValue &amp; getMetaValue(const String &amp;name) const </div><div class="ttdoc">returns the value corresponding to a string </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fab6d52778aef5ed31ac17025f4bffd8f4"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fab6d52778aef5ed31ac17025f4bffd8f4">OpenMS::IonSource::CONTINUOUSFLOWFASTATOMBOMBARDMENT</a></div><div class="ttdoc">Continuous flow fast atom bombardment. </div><div class="ttdef"><b>Definition:</b> IonSource.h:70</div></div>
<div class="ttc" id="PeakFileOptions_8h_html"><div class="ttname"><a href="PeakFileOptions_8h.html">PeakFileOptions.h</a></div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_ad368341c22d3447e324134c47adff081"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#ad368341c22d3447e324134c47adff081">OpenMS::ChromatogramSettings::getNativeID</a></div><div class="ttdeci">const String &amp; getNativeID() const </div><div class="ttdoc">returns the native identifier for the spectrum, used by the acquisition software. ...</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html">OpenMS::DataProcessing</a></div><div class="ttdoc">Descripton of the applied preprocessing steps. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a935d3c82c309ed3c0ed94d5edb12ce08"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a935d3c82c309ed3c0ed94d5edb12ce08">OpenMS::Instrument::getCustomizations</a></div><div class="ttdeci">const String &amp; getCustomizations() const </div><div class="ttdoc">returns a description of customizations </div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a2bf1ca8186169631f23edd67ddbd45e1"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a2bf1ca8186169631f23edd67ddbd45e1">OpenMS::SourceFile::getChecksumType</a></div><div class="ttdeci">ChecksumType getChecksumType() const </div><div class="ttdoc">returns the checksum type </div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1aefbc069e0ac4cd293f3ba527bec2befe"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1aefbc069e0ac4cd293f3ba527bec2befe">OpenMS::Precursor::PD</a></div><div class="ttdoc">Plasma desorption. </div><div class="ttdef"><b>Definition:</b> Precursor.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a135a7e818125b31198a8a65d9ac7a3d1"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">OpenMS::MetaInfoInterface::setMetaValue</a></div><div class="ttdeci">void setMetaValue(const String &amp;name, const DataValue &amp;value)</div><div class="ttdoc">sets the DataValue corresponding to a name </div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09a9936481d5130ac6611cf2eff629207f3"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a9936481d5130ac6611cf2eff629207f3">OpenMS::ControlledVocabulary::CVTerm::XSD_DECIMAL</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a5c60e3178bb8db38b3970316b0c5aae8"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5c60e3178bb8db38b3970316b0c5aae8">OpenMS::IonSource::APPI</a></div><div class="ttdoc">atmospheric pressure photo ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea1a077c77350bebae4e5a37f5ef2d4d98"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea1a077c77350bebae4e5a37f5ef2d4d98">OpenMS::Instrument::TIME_LAG_FOCUSING</a></div><div class="ttdoc">time lag focusing </div><div class="ttdef"><b>Definition:</b> Instrument.h:78</div></div>
<div class="ttc" id="structOpenMS_1_1VersionInfo_1_1VersionDetails_html_a8c1650d1d281b01a53b669240c70a4ab"><div class="ttname"><a href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a8c1650d1d281b01a53b669240c70a4ab">OpenMS::VersionInfo::VersionDetails::EMPTY</a></div><div class="ttdeci">static const VersionDetails EMPTY</div><div class="ttdef"><b>Definition:</b> VersionInfo.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a654a0b5941d937e303c64bc9e732baec"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a654a0b5941d937e303c64bc9e732baec">OpenMS::Internal::MzMLHandler::options_</a></div><div class="ttdeci">PeakFileOptions options_</div><div class="ttdoc">Options that can be set for loading/storing. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:232</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html"><div class="ttname"><a href="classOpenMS_1_1Instrument.html">OpenMS::Instrument</a></div><div class="ttdoc">Description of a MS instrument. </div><div class="ttdef"><b>Definition:</b> Instrument.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_aaeec7621a6d5913883828bb69e50c1d9"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#aaeec7621a6d5913883828bb69e50c1d9">OpenMS::DataValue::hasUnit</a></div><div class="ttdeci">bool hasUnit() const </div><div class="ttdoc">Check if the value has a unit. </div><div class="ttdef"><b>Definition:</b> DataValue.h:349</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a30b4d649b3cd56fb7e6aa514b67dc75a"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a30b4d649b3cd56fb7e6aa514b67dc75a">OpenMS::MassAnalyzer::FOURIERTRANSFORM</a></div><div class="ttdoc">Fourier transform ion cyclotron resonance mass spectrometer. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a4f15a2dc6638a7bdbcc97cab181bd52faac132f2982b98bcaa3445e535a03ff75"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52faac132f2982b98bcaa3445e535a03ff75">OpenMS::MassAnalyzer::OFF</a></div><div class="ttdoc">Off. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:130</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_acadddeff186604f0185315e70aab94fb"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#acadddeff186604f0185315e70aab94fb">OpenMS::SourceFile::getNameOfFile</a></div><div class="ttdeci">const String &amp; getNameOfFile() const </div><div class="ttdoc">returns the file name </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a527f7ffe8e4e1d4cd85dd9e61eed9795"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a527f7ffe8e4e1d4cd85dd9e61eed9795">OpenMS::IonSource::DI</a></div><div class="ttdoc">desorption ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:109</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a80abf032317ac0521e7ea0c601e3b387"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a80abf032317ac0521e7ea0c601e3b387">OpenMS::IonDetector::PHOTOMULTIPLIER</a></div><div class="ttdoc">Photo multiplier. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_a8b19d98c71f9926a1a2ff8822c0722c3"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a8b19d98c71f9926a1a2ff8822c0722c3">OpenMS::ControlledVocabulary::CVTerm::getXRefTypeName</a></div><div class="ttdeci">static String getXRefTypeName(XRefType type)</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a3306da16fbcb1fde30d4ec351db99285"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a3306da16fbcb1fde30d4ec351db99285">OpenMS::IonSource::AUI</a></div><div class="ttdoc">autoionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:121</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aecf7855b0a44ab470fabcb44277200d7"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aecf7855b0a44ab470fabcb44277200d7">OpenMS::IonSource::FIB</a></div><div class="ttdoc">Fast ion bombardment. </div><div class="ttdef"><b>Definition:</b> IonSource.h:106</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html_aa4b705e9e4267f64630cacd7fc55fc5d"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#aa4b705e9e4267f64630cacd7fc55fc5d">OpenMS::Internal::SemanticValidator::CVTerm::accession</a></div><div class="ttdeci">String accession</div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:75</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">OpenMS::ControlledVocabulary::CVTerm</a></div><div class="ttdoc">Representation of a CV term. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a2b26ecbcd8002a286574139ad8b2fdbc"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a2b26ecbcd8002a286574139ad8b2fdbc">OpenMS::Sample::getVolume</a></div><div class="ttdeci">DoubleReal getVolume() const </div><div class="ttdoc">returns the volume (in ml) (default: 0.0) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a5f66b708512374f687a8b6598408e9e8"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5f66b708512374f687a8b6598408e9e8">OpenMS::Internal::MzMLHandler::writeCV_</a></div><div class="ttdeci">String writeCV_(const ControlledVocabulary::CVTerm &amp;c, const DataValue &amp;metaValue) const </div><div class="ttdoc">Helper method to write an CV based on a meta value. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3229</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a54d74359f2cede6481a434f8634be324"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a54d74359f2cede6481a434f8634be324">OpenMS::IonDetector::DYNODE</a></div><div class="ttdoc">dynode </div><div class="ttdef"><b>Definition:</b> IonDetector.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa564313b42cf82a9be19c95050133911b"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa564313b42cf82a9be19c95050133911b">OpenMS::IonSource::PARTICLEBEAM</a></div><div class="ttdoc">Particle beam. </div><div class="ttdef"><b>Definition:</b> IonSource.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html"><div class="ttname"><a href="classOpenMS_1_1Precursor.html">OpenMS::Precursor</a></div><div class="ttdoc">Precursor meta information. </div><div class="ttdef"><b>Definition:</b> Precursor.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71a67a73d64984460ab1251bea87b873aab"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a67a73d64984460ab1251bea87b873aab">OpenMS::Sample::SUSPENSION</a></div><div class="ttdef"><b>Definition:</b> Sample.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Base64_html"><div class="ttname"><a href="classOpenMS_1_1Base64.html">OpenMS::Base64</a></div><div class="ttdoc">Class to encode and decode Base64. </div><div class="ttdef"><b>Definition:</b> Base64.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa9c897c6cdabbcc5b84159ac533e72f32"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa9c897c6cdabbcc5b84159ac533e72f32">OpenMS::IonSource::ELECTROSPRAYINLET</a></div><div class="ttdoc">Electro spray. </div><div class="ttdef"><b>Definition:</b> IonSource.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_ac06ffdb7464bbdb7304aa4f741e67a75"><div class="ttname"><a href="classOpenMS_1_1Sample.html#ac06ffdb7464bbdb7304aa4f741e67a75">OpenMS::Sample::getNumber</a></div><div class="ttdeci">const String &amp; getNumber() const </div><div class="ttdoc">returns the sample number (default: &amp;quot;&amp;quot;) </div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a6705637af16394112972298190f7c5b9"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a6705637af16394112972298190f7c5b9">OpenMS::Internal::MzMLHandler::BinaryData::compression</a></div><div class="ttdeci">bool compression</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:206</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a714a1e5663fe78f5dc22d232b1319844"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a714a1e5663fe78f5dc22d232b1319844">OpenMS::Internal::MzMLHandler::BinaryData::decoded_char</a></div><div class="ttdeci">std::vector&lt; String &gt; decoded_char</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:212</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a385c44f6fb256e5716a2302a5b940388a288fa3219db91abed40546c0c9dde29c"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a288fa3219db91abed40546c0c9dde29c">OpenMS::Internal::MzMLHandler::BinaryData::PRE_64</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:204</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly.html">OpenMS::Internal::XMLHandler::EndParsingSoftly</a></div><div class="ttdoc">Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file...</div><div class="ttdef"><b>Definition:</b> XMLHandler.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a80c69c45fa9891b7de1229a3ff53f468"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">OpenMS::Instrument::getIonSources</a></div><div class="ttdeci">const std::vector&lt; IonSource &gt; &amp; getIonSources() const </div><div class="ttdoc">returns a const reference to the ion source list </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a4e6fb8ab8655403a2cb4f07d72559cd7"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">OpenMS::Internal::MzMLHandler::cv_</a></div><div class="ttdeci">ControlledVocabulary cv_</div><div class="ttdoc">Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:274</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a0525c6afa4d96f74d29bbe7511a204db"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a0525c6afa4d96f74d29bbe7511a204db">OpenMS::IonSource::PEI</a></div><div class="ttdoc">penning ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:126</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4adfcd7e7c05c5dda54aa06c36077abab0"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4adfcd7e7c05c5dda54aa06c36077abab0">OpenMS::IonSource::AP_MALDI</a></div><div class="ttdoc">atmospheric pressure matrix-assisted laser desorption ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:131</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a1726d12d7597baa9fca0c1da0492f3da"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">OpenMS::MSSpectrum::getMSLevel</a></div><div class="ttdeci">UInt getMSLevel() const </div><div class="ttdoc">Returns the MS level. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_af1762bc9ec08e10fb80195db59f99432"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#af1762bc9ec08e10fb80195db59f99432">OpenMS::IonSource::getInletType</a></div><div class="ttdeci">InletType getInletType() const </div><div class="ttdoc">returns the inlet type </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aece8c4cb0f2685308261ef5409676a18"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aece8c4cb0f2685308261ef5409676a18">OpenMS::IonSource::MPI</a></div><div class="ttdoc">Multiphoton ionization. </div><div class="ttdef"><b>Definition:</b> IonSource.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ad922a0a88985be1114341e4b83120414"><div class="ttname"><a href="classOpenMS_1_1String.html#ad922a0a88985be1114341e4b83120414">OpenMS::String::toDouble</a></div><div class="ttdeci">DoubleReal toDouble() const </div><div class="ttdoc">Conversion to double. </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_acf76c337ebde51c823ec30c2985afb0d"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#acf76c337ebde51c823ec30c2985afb0d">OpenMS::MassAnalyzer::getAccuracy</a></div><div class="ttdeci">DoubleReal getAccuracy() const </div><div class="ttdoc">returns the mass accuracy i.e. how much the theoretical mass may differ from the measured mass (in pp...</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html_a4e87a8f69bbc06cd56776556dc1680ed"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#a4e87a8f69bbc06cd56776556dc1680ed">OpenMS::Internal::XMLHandler::version_</a></div><div class="ttdeci">String version_</div><div class="ttdoc">Schema version. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:162</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9af083c14a6a074a19ac7a75066eb83866"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9af083c14a6a074a19ac7a75066eb83866">OpenMS::DataProcessing::CHARGE_CALCULATION</a></div><div class="ttdoc">Determination of the peak charge. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fad7f5a34d7e508de209ade5decea9e80c"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fad7f5a34d7e508de209ade5decea9e80c">OpenMS::IonSource::SEPTUM</a></div><div class="ttdoc">Septum. </div><div class="ttdef"><b>Definition:</b> IonSource.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_a09903c7965f8ece31f2c1e07b41ae6dd"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#a09903c7965f8ece31f2c1e07b41ae6dd">OpenMS::Peak1D::getIntensity</a></div><div class="ttdeci">IntensityType getIntensity() const </div><div class="ttdef"><b>Definition:</b> Peak1D.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1Product_html"><div class="ttname"><a href="classOpenMS_1_1Product.html">OpenMS::Product</a></div><div class="ttdoc">Product meta information. </div><div class="ttdef"><b>Definition:</b> Product.h:49</div></div>
<div class="ttc" id="ControlledVocabulary_8h_html"><div class="ttname"><a href="ControlledVocabulary_8h.html">ControlledVocabulary.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DateTime_html_afb2353cf7399e53aa4b59ce122c6fc49"><div class="ttname"><a href="classOpenMS_1_1DateTime.html#afb2353cf7399e53aa4b59ce122c6fc49">OpenMS::DateTime::set</a></div><div class="ttdeci">void set(UInt month, UInt day, UInt year, UInt hour, UInt minute, UInt second)</div><div class="ttdoc">sets data from six integers </div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">OpenMS::SpectrumSettings::PEAKS</a></div><div class="ttdoc">Peak data (also called centroided data or stick data) </div><div class="ttdef"><b>Definition:</b> SpectrumSettings.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3ab7a09aace4e7aa91599309ab8b613bb4"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ab7a09aace4e7aa91599309ab8b613bb4">OpenMS::MassAnalyzer::ESA</a></div><div class="ttdoc">Electrostatic energy analyzer. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a587607b9ab280181a8b20a9fb147bad3"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a587607b9ab280181a8b20a9fb147bad3">OpenMS::IonSource::FA</a></div><div class="ttdoc">flowing afterglow </div><div class="ttdef"><b>Definition:</b> IonSource.h:110</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a626c8167a1599535349b7288be3895d1"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a626c8167a1599535349b7288be3895d1">OpenMS::IonSource::MESI</a></div><div class="ttdoc">Micro electrospray ionization. </div><div class="ttdef"><b>Definition:</b> IonSource.h:103</div></div>
<div class="ttc" id="CVMappingFile_8h_html"><div class="ttname"><a href="CVMappingFile_8h.html">CVMappingFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Map_html_a9eabefcb1631e53589789d97d0a72f9d"><div class="ttname"><a href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">OpenMS::Map::has</a></div><div class="ttdeci">bool has(const Key &amp;key) const </div><div class="ttdoc">Test whether the map contains the given key. </div><div class="ttdef"><b>Definition:</b> Map.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa3c5780d8602eb19c5c2d688498c29de8"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa3c5780d8602eb19c5c2d688498c29de8">OpenMS::IonSource::MOVINGWIRE</a></div><div class="ttdoc">Moving wire. </div><div class="ttdef"><b>Definition:</b> IonSource.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a2ca454d58033fd433df401a2406fb173"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a2ca454d58033fd433df401a2406fb173">OpenMS::DataProcessing::PRECURSOR_RECALCULATION</a></div><div class="ttdoc">Recalculation of precursor m/z. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram&lt; ChromatogramPeakType &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda9761ce23aa0bea120a7d581477316953"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda9761ce23aa0bea120a7d581477316953">OpenMS::ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a7ab83a85e2b66a4d8c4e0a6ccac159c7"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a7ab83a85e2b66a4d8c4e0a6ccac159c7">OpenMS::IonDetector::CONVERSIONDYNODEELECTRONMULTIPLIER</a></div><div class="ttdoc">Conversion dynode electron multiplier. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bdad97236e33b7a22bd5b44ca5404d069cb"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdad97236e33b7a22bd5b44ca5404d069cb">OpenMS::ChromatogramSettings::MASS_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:69</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_a76010eef1edc0406cc2375c25d2a433d"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a76010eef1edc0406cc2375c25d2a433d">OpenMS::ControlledVocabulary::CVTerm::id</a></div><div class="ttdeci">String id</div><div class="ttdoc">Identifier. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:81</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_ab0301b5c82d74538dfffc98406254e11a7caeaaac284597b2a217cbd43f8c7233"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a7caeaaac284597b2a217cbd43f8c7233">OpenMS::IonDetector::TRANSIENTRECORDER</a></div><div class="ttdoc">Transient recorder. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_aebeb2035d3f517fa772979211fa2d514"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aebeb2035d3f517fa772979211fa2d514">OpenMS::Internal::MzMLHandler::writeDataProcessing_</a></div><div class="ttdeci">void writeDataProcessing_(std::ostream &amp;os, const String &amp;id, const std::vector&lt; DataProcessing &gt; &amp;dps, Internal::MzMLValidator &amp;validator)</div><div class="ttdoc">Helper method that writes a data processing list. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3409</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_ab0301b5c82d74538dfffc98406254e11a09970273b87198398bb9192b84b8eea7"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a09970273b87198398bb9192b84b8eea7">OpenMS::IonDetector::TDC</a></div><div class="ttdoc">Time-digital converter. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a1bf627bed7951e975a31ba7033786d05"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a1bf627bed7951e975a31ba7033786d05">OpenMS::Precursor::HCID</a></div><div class="ttdoc">High-energy collision-induced dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html">OpenMS::ContactPerson</a></div><div class="ttdoc">Contact person information. </div><div class="ttdef"><b>Definition:</b> ContactPerson.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a9159f47bf89a34ad71b71f283ff09cd9"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a9159f47bf89a34ad71b71f283ff09cd9">OpenMS::DataProcessing::FILTERING</a></div><div class="ttdoc">Data filtering or extraction. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_af766984226f4f22572e132923218324c"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#af766984226f4f22572e132923218324c">OpenMS::SourceFile::getNativeIDType</a></div><div class="ttdeci">const String &amp; getNativeIDType() const </div><div class="ttdoc">Returns the native ID type of the spectra. </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ae75d9344e9e326323f2b485cd4c1e003"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ae75d9344e9e326323f2b485cd4c1e003">OpenMS::DataProcessing::DATA_PROCESSING</a></div><div class="ttdoc">General data processing (if no other term applies) </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a078588ac6fbb817e4d04ea210c86d323"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a078588ac6fbb817e4d04ea210c86d323">OpenMS::DataValue::EMPTY</a></div><div class="ttdeci">static const DataValue EMPTY</div><div class="ttdoc">Empty data value for comparisons. </div><div class="ttdef"><b>Definition:</b> DataValue.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9aa20c95ae75ff9c98d471a6e0c30b1f88"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9aa20c95ae75ff9c98d471a6e0c30b1f88">OpenMS::DataProcessing::CONVERSION_DTA</a></div><div class="ttdoc">Conversion to DTA format. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLValidator_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLValidator.html">OpenMS::Internal::MzMLValidator</a></div><div class="ttdoc">Semantically validates MzXML files. </div><div class="ttdef"><b>Definition:</b> MzMLValidator.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7acf7c454254df079071463f080099b4b3"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7acf7c454254df079071463f080099b4b3">OpenMS::IonDetector::CHANNELTRON</a></div><div class="ttdoc">channeltron </div><div class="ttdef"><b>Definition:</b> IonDetector.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">OpenMS::IonSource::NEGATIVE</a></div><div class="ttdoc">Negative polarity. </div><div class="ttdef"><b>Definition:</b> IonSource.h:144</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_ad8ed01ff3ff33333d8e19db4d2818bb6acd1ce0b084595a6072a57781dc7738a0"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#ad8ed01ff3ff33333d8e19db4d2818bb6acd1ce0b084595a6072a57781dc7738a0">OpenMS::DataValue::INT_VALUE</a></div><div class="ttdoc">integer value </div><div class="ttdef"><b>Definition:</b> DataValue.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a484c33c30ea480bd831a92847f61006e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a484c33c30ea480bd831a92847f61006e">OpenMS::Internal::MzMLHandler::startElement</a></div><div class="ttdeci">virtual void startElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &amp;attributes)</div><div class="ttdoc">Parsing method for opening tags. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:355</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_af3feca15695c5ad09a91b35d43559e57"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">OpenMS::Instrument::getMassAnalyzers</a></div><div class="ttdeci">const std::vector&lt; MassAnalyzer &gt; &amp; getMassAnalyzers() const </div><div class="ttdoc">returns a const reference to the mass analyer list </div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ad34cda135f7788348ea8866353407d38"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ad34cda135f7788348ea8866353407d38">OpenMS::Precursor::getActivationEnergy</a></div><div class="ttdeci">DoubleReal getActivationEnergy() const </div><div class="ttdoc">returns the activation energy (in electronvolt) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a56bc42e12243f36ea7d533b03609e30d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a56bc42e12243f36ea7d533b03609e30d">OpenMS::Internal::MzMLHandler::spec_</a></div><div class="ttdeci">SpectrumType spec_</div><div class="ttdoc">The current spectrum. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:237</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ac6602550db94324f2d4b712d8962c4cd"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ac6602550db94324f2d4b712d8962c4cd">OpenMS::DataProcessing::CONVERSION_MZXML</a></div><div class="ttdoc">Conversion to mzXML format. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71a1b45f84e1f6603b52e5ef442836df9af"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a1b45f84e1f6603b52e5ef442836df9af">OpenMS::Sample::SOLID</a></div><div class="ttdef"><b>Definition:</b> Sample.h:65</div></div>
<div class="ttc" id="namespaceOpenMS_html_a013338b7bdbb5c3b4c78666656070e23"><div class="ttname"><a href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">OpenMS::PeakType</a></div><div class="ttdeci">Peak2D PeakType</div><div class="ttdef"><b>Definition:</b> MassTrace.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_acd72014f8324c633851b7b4f169f3749"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">OpenMS::SpectrumSettings::getAcquisitionInfo</a></div><div class="ttdeci">const AcquisitionInfo &amp; getAcquisitionInfo() const </div><div class="ttdoc">returns a const reference to the acquisition info </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ac21206f76146b8913723119f609be907"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac21206f76146b8913723119f609be907">OpenMS::InstrumentSettings::EMC</a></div><div class="ttdoc">Enhanced multiply charged scan. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak1D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Non-mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a8e54f1259bd67fbaa579f32b73b34482"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a8e54f1259bd67fbaa579f32b73b34482">OpenMS::IonDetector::MICROCHANNELPLATEDETECTOR</a></div><div class="ttdoc">microchannel plate detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7acfbc26fbfdecb47353d1ef9712c4b86d"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7acfbc26fbfdecb47353d1ef9712c4b86d">OpenMS::IonDetector::ELECTRONMULTIPLIERTUBE</a></div><div class="ttdoc">electron multiplier tube </div><div class="ttdef"><b>Definition:</b> IonDetector.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4abccdeef60efaa51840b2bda65c374e7e"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4abccdeef60efaa51840b2bda65c374e7e">OpenMS::IonSource::FAB</a></div><div class="ttdoc">fast atom bombardment </div><div class="ttdef"><b>Definition:</b> IonSource.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7af12c576ac46ce5b814f2613b1aebedc8"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7af12c576ac46ce5b814f2613b1aebedc8">OpenMS::IonDetector::FOCALPLANEARRAY</a></div><div class="ttdoc">Focal plane array. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_ac59dab55a51bd8862e48cf39be35966e"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#ac59dab55a51bd8862e48cf39be35966e">OpenMS::IonSource::getIonizationMethod</a></div><div class="ttdeci">IonizationMethod getIonizationMethod() const </div><div class="ttdoc">returns the ionization method </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5">OpenMS::IonSource::POSITIVE</a></div><div class="ttdoc">Positive polarity. </div><div class="ttdef"><b>Definition:</b> IonSource.h:143</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aaade3182d7ec0b4c0ef7a60392ed72b9"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aaade3182d7ec0b4c0ef7a60392ed72b9">OpenMS::IonSource::SALDI</a></div><div class="ttdoc">surface-assisted laser desorption ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:133</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a931a07130d981672ac391f7a27a88dfd"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a931a07130d981672ac391f7a27a88dfd">OpenMS::Internal::MzMLHandler::BinaryData::floats_64</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; floats_64</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:209</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_aef9d6cd0e61ef23e650e06389ba4e3f4"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">OpenMS::MassAnalyzer::getType</a></div><div class="ttdeci">AnalyzerType getType() const </div><div class="ttdoc">returns the analyzer type </div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a1a127ee8460671ffdc8de43f82f7de47"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a1a127ee8460671ffdc8de43f82f7de47">OpenMS::Instrument::getIonOptics</a></div><div class="ttdeci">IonOpticsType getIonOptics() const </div><div class="ttdoc">returns the ion optics type </div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html_ace039d325c112e45c9d37e0e656ba9a2"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html#ace039d325c112e45c9d37e0e656ba9a2">OpenMS::MSChromatogram::getStringDataArrays</a></div><div class="ttdeci">const StringDataArrays &amp; getStringDataArrays() const </div><div class="ttdoc">Returns a const reference to the string meta data arrays. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:239</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_abc5c98fcc1211af2b80116dd6e0a035da36f5529746b65d14a498b41e316de090"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da36f5529746b65d14a498b41e316de090">OpenMS::Internal::MzMLHandler::BinaryData::DT_NONE</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:207</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa14dec9ac85c4c53db9e1fa17d0bffeea"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa14dec9ac85c4c53db9e1fa17d0bffeea">OpenMS::IonSource::MEMBRANE</a></div><div class="ttdoc">Membrane inlet. </div><div class="ttdef"><b>Definition:</b> IonSource.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ab91109da6782d902c745c771aa85d03d"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">OpenMS::Precursor::getCharge</a></div><div class="ttdeci">Int getCharge() const </div><div class="ttdoc">Non-mutable access to the charge. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html">OpenMS::Internal::XMLHandler</a></div><div class="ttdoc">Base class for XML handlers. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:89</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="group__Concept_html_gae113cb41304c6692c7bf5d0624dc6f0f"><div class="ttname"><a href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">OpenMS::SignedSize</a></div><div class="ttdeci">ptrdiff_t SignedSize</div><div class="ttdoc">Signed Size type e.g. used as pointer difference. </div><div class="ttdef"><b>Definition:</b> Types.h:151</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa0598d1c2cd7107bff01eb8de6ff74f94"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa0598d1c2cd7107bff01eb8de6ff74f94">OpenMS::IonSource::JETSEPARATOR</a></div><div class="ttdoc">Jet separator. </div><div class="ttdef"><b>Definition:</b> IonSource.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9aec300465e654790d9154eb0d64ca3267"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9aec300465e654790d9154eb0d64ca3267">OpenMS::DataProcessing::BASELINE_REDUCTION</a></div><div class="ttdoc">Baseline reduction. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a796a6cd8072195dfaf282a0827bebb4a"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">OpenMS::Instrument::getIonDetectors</a></div><div class="ttdeci">const std::vector&lt; IonDetector &gt; &amp; getIonDetectors() const </div><div class="ttdoc">returns a const reference to the ion detector list </div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html">OpenMS::SourceFile</a></div><div class="ttdoc">Description of a file location, used to store the origin of (meta) data. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533">OpenMS::SpectrumSettings::RAWDATA</a></div><div class="ttdoc">Raw data (also called profile data) </div><div class="ttdef"><b>Definition:</b> SpectrumSettings.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_ac5bb0a0896c81277ed75428db51dd8b4"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#ac5bb0a0896c81277ed75428db51dd8b4">OpenMS::MassAnalyzer::getMagneticFieldStrength</a></div><div class="ttdeci">DoubleReal getMagneticFieldStrength() const </div><div class="ttdoc">returns the strength of the magnetic field (in T) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html_a2f223274d440404ba700768cd15ef661"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2f223274d440404ba700768cd15ef661">OpenMS::Internal::XMLHandler::XMLHandler</a></div><div class="ttdeci">XMLHandler()</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aa2ce66107d2f686db9a07584da0d730f"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aa2ce66107d2f686db9a07584da0d730f">OpenMS::IonSource::FI</a></div><div class="ttdoc">flame ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a27064596541d23c1b3040817e417d39c"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a27064596541d23c1b3040817e417d39c">OpenMS::IonDetector::FOCALPLANECOLLECTOR</a></div><div class="ttdoc">focal plane collector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Base64_html_aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc"><div class="ttname"><a href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">OpenMS::Base64::BYTEORDER_LITTLEENDIAN</a></div><div class="ttdoc">Little endian type. </div><div class="ttdef"><b>Definition:</b> Base64.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7aa6af6570fb6cf6172b241f4230d0bd9f"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7aa6af6570fb6cf6172b241f4230d0bd9f">OpenMS::IonDetector::MULTICOLLECTOR</a></div><div class="ttdoc">Multi-collector. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a1a7f597d623d72306c8adbdbfaaa350d"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a1a7f597d623d72306c8adbdbfaaa350d">OpenMS::MassAnalyzer::PAULIONTRAP</a></div><div class="ttdoc">Quadrupole ion trap / Paul ion trap. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aae20fd962cf613d3911e5f7da51de1df"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aae20fd962cf613d3911e5f7da51de1df">OpenMS::IonSource::PYMS</a></div><div class="ttdoc">pyrolysis mass spectrometry </div><div class="ttdef"><b>Definition:</b> IonSource.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7ac49f262a3810cbb127ca53b2a804b719"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ac49f262a3810cbb127ca53b2a804b719">OpenMS::IonDetector::IONTOPHOTONDETECTOR</a></div><div class="ttdoc">ion-to-photon detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a5b26cd07c89ea86afa2fa793fb7fc729"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5b26cd07c89ea86afa2fa793fb7fc729">OpenMS::IonSource::PI</a></div><div class="ttdoc">photoionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1Software_html"><div class="ttname"><a href="classOpenMS_1_1Software.html">OpenMS::Software</a></div><div class="ttdoc">Description of the software used for processing. </div><div class="ttdef"><b>Definition:</b> Software.h:49</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a8fc6defe4e499b1b9b9c275689e44352"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">OpenMS::Constants::c</a></div><div class="ttdeci">const double c</div></div>
<div class="ttc" id="classOpenMS_1_1Product_html_ac6f71e641c709dfabecce317d07ac4f7"><div class="ttname"><a href="classOpenMS_1_1Product.html#ac6f71e641c709dfabecce317d07ac4f7">OpenMS::Product::getIsolationWindowLowerOffset</a></div><div class="ttdeci">DoubleReal getIsolationWindowLowerOffset() const </div><div class="ttdoc">returns the lower offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">OpenMS::InstrumentSettings::MSNSPECTRUM</a></div><div class="ttdoc">MS2+ mass spectrum, is a &amp;quot;mass spectrum&amp;quot;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a8b3a6d95f436cb3c0e8f57e526f32ed1"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">OpenMS::MSSpectrum::getIntegerDataArrays</a></div><div class="ttdeci">const IntegerDataArrays &amp; getIntegerDataArrays() const </div><div class="ttdoc">Returns a const reference to the integer meta data arrays. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:294</div></div>
<div class="ttc" id="classOpenMS_1_1File_html_a9c35db3f748619737c43b35b756cc77b"><div class="ttname"><a href="classOpenMS_1_1File.html#a9c35db3f748619737c43b35b756cc77b">OpenMS::File::find</a></div><div class="ttdeci">static String find(const String &amp;filename, StringList directories=StringList())</div><div class="ttdoc">Looks up the location of the file filename. </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a0f0fb5610d506c55825effbb77450fd5"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a0f0fb5610d506c55825effbb77450fd5">OpenMS::MassAnalyzer::getTOFTotalPathLength</a></div><div class="ttdeci">DoubleReal getTOFTotalPathLength() const </div><div class="ttdoc">returns the path length for a TOF mass analyzer (in meter) </div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a1fc42efb4420deedae9f5a59d4c20190"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a1fc42efb4420deedae9f5a59d4c20190">OpenMS::DataValue::getUnit</a></div><div class="ttdeci">const String &amp; getUnit() const </div><div class="ttdoc">Return the unit associated to this DataValue. </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4ae3a31f903a1ebacac4aa4de2409c80ff"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ae3a31f903a1ebacac4aa4de2409c80ff">OpenMS::IonSource::CHEMI</a></div><div class="ttdoc">chemi-ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a0aaf41c383f973bf5a11f3a55022eda5"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0aaf41c383f973bf5a11f3a55022eda5">OpenMS::Internal::MzMLHandler::MzMLHandler</a></div><div class="ttdeci">MzMLHandler(const MapType &amp;exp, const String &amp;filename, const String &amp;version, const ProgressLogger &amp;logger)</div><div class="ttdoc">Constructor for a write-only handler. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:133</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09a38016896f280e9e0f3481f8c96bbf3ff"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a38016896f280e9e0f3481f8c96bbf3ff">OpenMS::ControlledVocabulary::CVTerm::XSD_DATE</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea2573b581168afac70eeffa4a02e4ac66"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea2573b581168afac70eeffa4a02e4ac66">OpenMS::Instrument::COLLISION_QUADRUPOLE</a></div><div class="ttdoc">collision quadrupole </div><div class="ttdef"><b>Definition:</b> Instrument.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoDescription_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoDescription.html">OpenMS::MetaInfoDescription</a></div><div class="ttdoc">Description of the meta data arrays of MSSpectrum. </div><div class="ttdef"><b>Definition:</b> MetaInfoDescription.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a08b65464af573a073ec2e715efdd0150"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a08b65464af573a073ec2e715efdd0150">OpenMS::Internal::MzMLHandler::chromatogram_</a></div><div class="ttdeci">ChromatogramType chromatogram_</div><div class="ttdoc">The current chromatogram. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:239</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ab7b974cef152e339967fce62f49de0d9a6ce26a62afab55d7606ad4e92428b30c"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a6ce26a62afab55d7606ad4e92428b30c">OpenMS::SpectrumSettings::UNKNOWN</a></div><div class="ttdoc">Unknown spectrum type. </div><div class="ttdef"><b>Definition:</b> SpectrumSettings.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda6becb3aa48a0fbb4401e98e6b99a9428"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda6becb3aa48a0fbb4401e98e6b99a9428">OpenMS::ChromatogramSettings::BASEPEAK_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a1019d3d05762a5ea12ffec336dd45c35"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a1019d3d05762a5ea12ffec336dd45c35">OpenMS::IonDetector::FARADAYCUP</a></div><div class="ttdoc">Faraday cup. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">OpenMS::InstrumentSettings::SRM</a></div><div class="ttdoc">Selected reaction monitoring scan   Synonyms: &amp;#39;Multiple reaction monitoring scan&amp;#39;, &amp;#39;SRM scan&amp;#39;, &amp;#39;MRM scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1Product_html_a0d3c115101baf89ff0d81602ad6cc635"><div class="ttname"><a href="classOpenMS_1_1Product.html#a0d3c115101baf89ff0d81602ad6cc635">OpenMS::Product::getIsolationWindowUpperOffset</a></div><div class="ttdeci">DoubleReal getIsolationWindowUpperOffset() const </div><div class="ttdoc">returns the upper offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1ab2fca50c5baefb10e5ecdc553e372586"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab2fca50c5baefb10e5ecdc553e372586">OpenMS::Precursor::SID</a></div><div class="ttdoc">Surface-induced dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:69</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_a89015d9d8ecc70d84c1eeb2d6c983c03"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a89015d9d8ecc70d84c1eeb2d6c983c03">OpenMS::ControlledVocabulary::CVTerm::obsolete</a></div><div class="ttdeci">bool obsolete</div><div class="ttdoc">Flag that indicates of the term is obsolete. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a3901fa9d6f534ab0c36a34a0850dffa0"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a3901fa9d6f534ab0c36a34a0850dffa0">OpenMS::Precursor::BIRD</a></div><div class="ttdoc">Blackbody infrared radiative dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa8f610db6e93fa153152a1c46b49539b2"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa8f610db6e93fa153152a1c46b49539b2">OpenMS::IonSource::INDUCTIVELYCOUPLEDPLASMA</a></div><div class="ttdoc">Inductively coupled plasma. </div><div class="ttdef"><b>Definition:</b> IonSource.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_ad4e0ad3506a3256ecfbc50e925b40f99"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#ad4e0ad3506a3256ecfbc50e925b40f99">OpenMS::MassAnalyzer::getOrder</a></div><div class="ttdeci">Int getOrder() const </div><div class="ttdoc">returns the position of this part in the whole Instrument. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a3dfca77b4f99246a5bf4e9407e27f889"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a3dfca77b4f99246a5bf4e9407e27f889">OpenMS::Internal::MzMLHandler::source_files_</a></div><div class="ttdeci">Map&lt; String, SourceFile &gt; source_files_</div><div class="ttdoc">The source files: id =&amp;gt; SourceFile. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:251</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09a869ef254cbf763367b5f618642d94242"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a869ef254cbf763367b5f618642d94242">OpenMS::ControlledVocabulary::CVTerm::XSD_STRING</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4ae63d77c61a2a5b9777024af082a36719"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ae63d77c61a2a5b9777024af082a36719">OpenMS::IonSource::AD</a></div><div class="ttdoc">autodetachment </div><div class="ttdef"><b>Definition:</b> IonSource.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a4e6e1cb4f8a8a0c70887c3568b86348e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">OpenMS::Internal::MzMLHandler::logger_</a></div><div class="ttdeci">const ProgressLogger &amp; logger_</div><div class="ttdoc">Progress logger. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:268</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_abc5c98fcc1211af2b80116dd6e0a035da4313207b96335e124ddd0664a0794cad"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da4313207b96335e124ddd0664a0794cad">OpenMS::Internal::MzMLHandler::BinaryData::DT_STRING</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:207</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a28d0d143361f7c67c01ef53bd7f3655d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a28d0d143361f7c67c01ef53bd7f3655d">OpenMS::Internal::MzMLHandler::software_</a></div><div class="ttdeci">Map&lt; String, Software &gt; software_</div><div class="ttdoc">The software list: id =&amp;gt; Software. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:255</div></div>
<div class="ttc" id="LogStream_8h_html_aced66975c154ea0e2a8ec3bc818b4e08"><div class="ttname"><a href="LogStream_8h.html#aced66975c154ea0e2a8ec3bc818b4e08">LOG_ERROR</a></div><div class="ttdeci">#define LOG_ERROR</div><div class="ttdoc">Macro to be used if non-fatal error are reported (processing continues) </div><div class="ttdef"><b>Definition:</b> LogStream.h:447</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_aeee3146ed1c95bbbc3e69b4d5dca3041"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aeee3146ed1c95bbbc3e69b4d5dca3041">OpenMS::Internal::MzMLHandler::writeHeader_</a></div><div class="ttdeci">void writeHeader_(std::ostream &amp;os, const MapType &amp;exp, std::vector&lt; std::vector&lt; DataProcessing &gt; &gt; &amp;dps, Internal::MzMLValidator &amp;validator)</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3720</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ac2b5a9a058d7e84ca3a2beeedb2f2049"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ac2b5a9a058d7e84ca3a2beeedb2f2049">OpenMS::SpectrumSettings::getType</a></div><div class="ttdeci">SpectrumType getType() const </div><div class="ttdoc">returns the spectrum type </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a9c74caa56a3c05723eb1dbad44bc9bc3"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a9c74caa56a3c05723eb1dbad44bc9bc3">OpenMS::IonSource::AI</a></div><div class="ttdoc">adiabatic ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ae131ea2ec923582f86aa9805e72241ad"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ae131ea2ec923582f86aa9805e72241ad">OpenMS::SpectrumSettings::getDataProcessing</a></div><div class="ttdeci">const std::vector&lt; DataProcessing &gt; &amp; getDataProcessing() const </div><div class="ttdoc">returns a const reference to the description of the applied processing </div></div>
<div class="ttc" id="classOpenMS_1_1Acquisition_html_a4eb8ec8636a89f575db95a370fd480b6"><div class="ttname"><a href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">OpenMS::Acquisition::getIdentifier</a></div><div class="ttdeci">const String &amp; getIdentifier() const </div><div class="ttdoc">return the identifier/index/number of the acquisition </div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html"><div class="ttname"><a href="classOpenMS_1_1DataValue.html">OpenMS::DataValue</a></div><div class="ttdoc">Class to hold strings, numeric values, lists of strings and lists of numeric values. </div><div class="ttdef"><b>Definition:</b> DataValue.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a6cbe5ff42f143903e1c67abf94613791"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a6cbe5ff42f143903e1c67abf94613791">OpenMS::IonSource::SI</a></div><div class="ttdoc">secondary ion MS </div><div class="ttdef"><b>Definition:</b> IonSource.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aa45f628d1930ccc096fd37583145fccb"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aa45f628d1930ccc096fd37583145fccb">OpenMS::IonSource::APCI</a></div><div class="ttdoc">atmospheric pressure chemical ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:99</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09aab6ed9fc0d339bd90c445e066f13fd67"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09aab6ed9fc0d339bd90c445e066f13fd67">OpenMS::ControlledVocabulary::CVTerm::XSD_NON_NEGATIVE_INTEGER</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3ac18e0fdb830eeb3a7f657a75000744db"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ac18e0fdb830eeb3a7f657a75000744db">OpenMS::MassAnalyzer::TOF</a></div><div class="ttdoc">Time-of-flight. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a3409c914db15bbb4696822e623a69ef1"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a3409c914db15bbb4696822e623a69ef1">OpenMS::InstrumentSettings::getZoomScan</a></div><div class="ttdeci">bool getZoomScan() const </div><div class="ttdoc">return if this scan is a zoom (enhanced resolution) scan </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a541856069e66db2a4cab95d7f1993dc9"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">OpenMS::InstrumentSettings::getScanMode</a></div><div class="ttdeci">ScanMode getScanMode() const </div><div class="ttdoc">returns the scan mode </div></div>
<div class="ttc" id="File_8h_html"><div class="ttname"><a href="File_8h.html">File.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a39869181b0414af3507c53e260851151"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a39869181b0414af3507c53e260851151">OpenMS::MassAnalyzer::ANALYZERNULL</a></div><div class="ttdoc">Unknown. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea78e072856cb37e4c51c595d8236347d7"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea78e072856cb37e4c51c595d8236347d7">OpenMS::Instrument::MAGNETIC_DEFLECTION</a></div><div class="ttdoc">magnetic deflection </div><div class="ttdef"><b>Definition:</b> Instrument.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_a9933807a51860e1320ce47c3b83bcbd2"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">OpenMS::Precursor::getActivationMethods</a></div><div class="ttdeci">const std::set&lt; ActivationMethod &gt; &amp; getActivationMethods() const </div><div class="ttdoc">returns a const reference to the activation methods </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a9028634d022a74d1fc8db852d99984d6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9028634d022a74d1fc8db852d99984d6">OpenMS::Internal::MzMLHandler::endElement</a></div><div class="ttdeci">virtual void endElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname)</div><div class="ttdoc">Parsing method for closing tags. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:771</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a259eb726b6a08b2a08164df4e14db708"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a259eb726b6a08b2a08164df4e14db708">OpenMS::IonSource::SELDI</a></div><div class="ttdoc">Surface enhanced laser desorption ionization. </div><div class="ttdef"><b>Definition:</b> IonSource.h:104</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html_a6d07a35e88f53d1b49ddc99f84163312"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a6d07a35e88f53d1b49ddc99f84163312">OpenMS::Internal::SemanticValidator::CVTerm::unit_accession</a></div><div class="ttdeci">String unit_accession</div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3ac59fe43006f5fee91317753c98fb6fb3"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ac59fe43006f5fee91317753c98fb6fb3">OpenMS::MassAnalyzer::CYCLOTRON</a></div><div class="ttdoc">Cyclotron. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1ControlledVocabulary_html"><div class="ttname"><a href="classOpenMS_1_1ControlledVocabulary.html">OpenMS::ControlledVocabulary</a></div><div class="ttdoc">Representation of a controlled vocabulary. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_afd1e30564c0909e1ada9ca9b6c978352"><div class="ttname"><a href="classOpenMS_1_1Sample.html#afd1e30564c0909e1ada9ca9b6c978352">OpenMS::Sample::getConcentration</a></div><div class="ttdeci">DoubleReal getConcentration() const </div><div class="ttdoc">returns the concentration (in g/l) (default: 0.0) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a06fab32360dcb446ca8d839b4794f15c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a06fab32360dcb446ca8d839b4794f15c">OpenMS::Internal::MzMLHandler::default_array_length_</a></div><div class="ttdeci">Size default_array_length_</div><div class="ttdoc">The default number of peaks in the current spectrum. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:243</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_ab0301b5c82d74538dfffc98406254e11a1b9d0cc39dc3d1de4db442674ca8761b"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a1b9d0cc39dc3d1de4db442674ca8761b">OpenMS::IonDetector::PULSECOUNTING</a></div><div class="ttdoc">Pulse counting. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:85</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09a6606dea51053a6eb746ba4ccaa37a1f3"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a6606dea51053a6eb746ba4ccaa37a1f3">OpenMS::ControlledVocabulary::CVTerm::XSD_NON_POSITIVE_INTEGER</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a74d32454593ae69307e86dbca912a605"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a74d32454593ae69307e86dbca912a605">OpenMS::IonDetector::POINTCOLLECTOR</a></div><div class="ttdoc">point collector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a20d56bc7900e25dc3e84f15078eefdf7"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a20d56bc7900e25dc3e84f15078eefdf7">OpenMS::IonSource::NICI</a></div><div class="ttdoc">negative ion chemical ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda1a3d139c1d36a9c7462f3e1e8bbba110"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda1a3d139c1d36a9c7462f3e1e8bbba110">OpenMS::ChromatogramSettings::ABSORPTION_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:76</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CVMappingFile_html_aef23cbef5854e48a0833a7ab174464ba"><div class="ttname"><a href="classOpenMS_1_1CVMappingFile.html#aef23cbef5854e48a0833a7ab174464ba">OpenMS::CVMappingFile::load</a></div><div class="ttdeci">void load(const String &amp;filename, CVMappings &amp;cv_mappings, bool strip_namespaces=false)</div><div class="ttdoc">loads CvMappings from the given file </div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda5e1f2677edbc482d260e873a4a9660c6"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda5e1f2677edbc482d260e873a4a9660c6">OpenMS::ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html">OpenMS::Internal::MzMLHandler</a></div><div class="ttdoc">XML handler for MzMLFile. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a56a28ad07746c6bae402cc7d7ec0839a"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a56a28ad07746c6bae402cc7d7ec0839a">OpenMS::Precursor::ETD</a></div><div class="ttdoc">Electron transfer dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:77</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a385c44f6fb256e5716a2302a5b940388a45f0d43f4806f81088a4c80516b6a8bc"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a45f0d43f4806f81088a4c80516b6a8bc">OpenMS::Internal::MzMLHandler::BinaryData::PRE_32</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:204</div></div>
<div class="ttc" id="classOpenMS_1_1ControlledVocabulary_html_a3734f5236d43e8e2a3fade2f0d433428"><div class="ttname"><a href="classOpenMS_1_1ControlledVocabulary.html#a3734f5236d43e8e2a3fade2f0d433428">OpenMS::ControlledVocabulary::loadFromOBO</a></div><div class="ttdeci">void loadFromOBO(const String &amp;name, const String &amp;filename)</div><div class="ttdoc">Loads the CV from an OBO file. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_aa7d348ccbf286e2aef8b0fa27453a289"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa7d348ccbf286e2aef8b0fa27453a289">OpenMS::Internal::MzMLHandler::writeSourceFile_</a></div><div class="ttdeci">void writeSourceFile_(std::ostream &amp;os, const String &amp;id, const SourceFile &amp;software, Internal::MzMLValidator &amp;validator)</div><div class="ttdoc">Helper method that writes a source file. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3368</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bdaa227021fdc2a25d98a5113afc918b75b"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdaa227021fdc2a25d98a5113afc918b75b">OpenMS::ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; PeakType &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a28f849a39a6e1a02a891d9e7e7f6eb79"><div class="ttname"><a href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">OpenMS::String::toInt</a></div><div class="ttdeci">Int toInt() const </div><div class="ttdoc">Conversion to int. </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa27dcc04b8d9859dfe2ea21b888c26189"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa27dcc04b8d9859dfe2ea21b888c26189">OpenMS::IonSource::INFUSION</a></div><div class="ttdoc">Infusion. </div><div class="ttdef"><b>Definition:</b> IonSource.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aefea9eb0772378037221a3f1fe759a76"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aefea9eb0772378037221a3f1fe759a76">OpenMS::IonSource::SPI</a></div><div class="ttdoc">spark ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:128</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a67be7a5f47004345047b32fff72a2230"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a67be7a5f47004345047b32fff72a2230">OpenMS::IonSource::SEND</a></div><div class="ttdoc">Surface enhanced neat desorption. </div><div class="ttdef"><b>Definition:</b> IonSource.h:105</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html_ad25f6dba1bbd00a3122302d7bac4beb5"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#ad25f6dba1bbd00a3122302d7bac4beb5">OpenMS::Internal::SemanticValidator::CVTerm::has_unit_accession</a></div><div class="ttdeci">bool has_unit_accession</div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71a0a57d2bc6d4da43c5fdb8c9293764d8d"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a0a57d2bc6d4da43c5fdb8c9293764d8d">OpenMS::Sample::SOLUTION</a></div><div class="ttdef"><b>Definition:</b> Sample.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_ab714caa4d58fc603439a5a0109860704"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#ab714caa4d58fc603439a5a0109860704">OpenMS::ChromatogramSettings::getPrecursor</a></div><div class="ttdeci">const Precursor &amp; getPrecursor() const </div><div class="ttdoc">returns a const reference to the precursors </div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1ab20b009dfccc7838ba06622a9d53daff"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1ab20b009dfccc7838ba06622a9d53daff">OpenMS::Precursor::CID</a></div><div class="ttdoc">Collision-induced dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea9f31dbfcc7e3828fea80213c74fa76e2"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea9f31dbfcc7e3828fea80213c74fa76e2">OpenMS::Instrument::DELAYED_EXTRACTION</a></div><div class="ttdoc">delayed extraction </div><div class="ttdef"><b>Definition:</b> Instrument.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a115d84a31a4be5741fe2eddb197c0d6f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a115d84a31a4be5741fe2eddb197c0d6f">OpenMS::Internal::MzMLHandler::writeFooter_</a></div><div class="ttdeci">void writeFooter_(std::ostream &amp;os)</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:5210</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a021f6acb8bd3a02278cc50f11c489a12"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">OpenMS::InstrumentSettings::getScanWindows</a></div><div class="ttdeci">const std::vector&lt; ScanWindow &gt; &amp; getScanWindows() const </div><div class="ttdoc">returns a const reference to the m/z scan windows </div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_af4bd5dc3248bc63b98e8a63d50bcc51a"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#af4bd5dc3248bc63b98e8a63d50bcc51a">OpenMS::SpectrumSettings::getSourceFile</a></div><div class="ttdeci">const SourceFile &amp; getSourceFile() const </div><div class="ttdoc">returns a const reference to the source file </div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html">OpenMS::Internal::SemanticValidator::CVTerm</a></div><div class="ttdoc">Representation of a parsed CV term. </div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa066def527c3472b49e0d152c392ee0d7"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa066def527c3472b49e0d152c392ee0d7">OpenMS::IonSource::CHROMATOGRAPHY</a></div><div class="ttdoc">Chromatography (liquid) </div><div class="ttdef"><b>Definition:</b> IonSource.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a21e306967405afb217201901a2d75351"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a21e306967405afb217201901a2d75351">OpenMS::Internal::MzMLHandler::exp_</a></div><div class="ttdeci">MapType * exp_</div><div class="ttdoc">map pointer for reading </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:227</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a81dc4d91ca22493e81272673e507a8c4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">OpenMS::Internal::MzMLHandler::skip_spectrum_</a></div><div class="ttdeci">bool skip_spectrum_</div><div class="ttdoc">Flag that indicates whether this spectrum should be skipped (due to options) </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:271</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a22a843b242764a6b3b320c1b26274433"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a22a843b242764a6b3b320c1b26274433">OpenMS::Precursor::PQD</a></div><div class="ttdoc">Pulsed q dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_afea2047eedc730597ab0a7bb9c92c551"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#afea2047eedc730597ab0a7bb9c92c551">OpenMS::Internal::MzMLHandler::processing_</a></div><div class="ttdeci">Map&lt; String, std::vector&lt; DataProcessing &gt; &gt; processing_</div><div class="ttdoc">The data processing list: id =&amp;gt; Instrument. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:259</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_ad03e2dba49bef5ed14e9feb41e161ffe"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#ad03e2dba49bef5ed14e9feb41e161ffe">OpenMS::Internal::MzMLHandler::BinaryData::data_type</a></div><div class="ttdeci">enum OpenMS::Internal::MzMLHandler::BinaryData::@11 data_type</div></div>
<div class="ttc" id="classOpenMS_1_1Product_html_adf13f6e49cf05563669b4481aaced5f2"><div class="ttname"><a href="classOpenMS_1_1Product.html#adf13f6e49cf05563669b4481aaced5f2">OpenMS::Product::getMZ</a></div><div class="ttdeci">DoubleReal getMZ() const </div><div class="ttdoc">returns the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a3158578f2cc1fb7fbd261b4094e7f5fd"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a3158578f2cc1fb7fbd261b4094e7f5fd">OpenMS::IonSource::EI</a></div><div class="ttdoc">electron ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a3b759690471ed29ecd243a8f36b93f60"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a3b759690471ed29ecd243a8f36b93f60">OpenMS::MassAnalyzer::LIT</a></div><div class="ttdoc">Linear ion trap. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a9e8f070ec9479603961d8ad3bf49a9a3"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">OpenMS::Internal::MzMLHandler::decoder_</a></div><div class="ttdeci">Base64 decoder_</div><div class="ttdoc">Decoder/Encoder for Base64-data in MzML. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:265</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a7c587a2ed93cc6d0158daaacb731a840"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a7c587a2ed93cc6d0158daaacb731a840">OpenMS::Internal::MzMLHandler::BinaryData::base64</a></div><div class="ttdeci">String base64</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:203</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa73dded3a91104b5de02f9f408023ef18"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa73dded3a91104b5de02f9f408023ef18">OpenMS::IonSource::RESERVOIR</a></div><div class="ttdoc">Reservoir. </div><div class="ttdef"><b>Definition:</b> IonSource.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_abc5a85a6a61fb96964c186b0bf03e1de"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#abc5a85a6a61fb96964c186b0bf03e1de">OpenMS::DataValue::valueType</a></div><div class="ttdeci">DataType valueType() const </div><div class="ttdoc">returns the type of value stored </div><div class="ttdef"><b>Definition:</b> DataValue.h:330</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_a15b36efd7557a43d6096476d19122e91"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#a15b36efd7557a43d6096476d19122e91">OpenMS::ContactPerson::getContactInfo</a></div><div class="ttdeci">const String &amp; getContactInfo() const </div><div class="ttdoc">returns miscellaneous info about the contact person </div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea02fb42fb91d78f40b3280cec43ff67a9"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea02fb42fb91d78f40b3280cec43ff67a9">OpenMS::Instrument::FIRST_STABILITY_REGION</a></div><div class="ttdoc">first stability region </div><div class="ttdef"><b>Definition:</b> Instrument.h:81</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a2f4d93dd2e2ea2f50e21f943deeb104f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a2f4d93dd2e2ea2f50e21f943deeb104f">OpenMS::Internal::MzMLHandler::samples_</a></div><div class="ttdeci">Map&lt; String, Sample &gt; samples_</div><div class="ttdoc">The sample list: id =&amp;gt; Sample. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_af50693f3924366b3c157bea5dcbe4355"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#af50693f3924366b3c157bea5dcbe4355">OpenMS::Internal::MzMLHandler::ChromatogramPeakType</a></div><div class="ttdeci">MapType::ChromatogramPeakType ChromatogramPeakType</div><div class="ttdoc">Chromatogram peak type. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:194</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a45cd2a1ea065b4909b86190b372ed7da"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a45cd2a1ea065b4909b86190b372ed7da">OpenMS::InstrumentSettings::EMR</a></div><div class="ttdoc">Electromagnetic radiation scan   Synonyms: &amp;#39;EMR spectrum&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition&lt; 1 &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea9503ab7efe8e81ba7b6ec9e11a4aec86"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea9503ab7efe8e81ba7b6ec9e11a4aec86">OpenMS::Instrument::FRINGING_FIELD</a></div><div class="ttdoc">fringing field </div><div class="ttdef"><b>Definition:</b> Instrument.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_ad0643828ff3cbe1273be4760164303e4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ad0643828ff3cbe1273be4760164303e4">OpenMS::Internal::MzMLHandler::default_processing_</a></div><div class="ttdeci">String default_processing_</div><div class="ttdoc">id of the default data processing (used when no processing is defined) </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:261</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a205ce9325a3a2b1ca71be96bee9d7f89"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a205ce9325a3a2b1ca71be96bee9d7f89">OpenMS::IonSource::TI</a></div><div class="ttdoc">thermal ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a5d02c7b244115a39bcb42170c21d0a58"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a5d02c7b244115a39bcb42170c21d0a58">OpenMS::MassAnalyzer::ORBITRAP</a></div><div class="ttdoc">Orbitrap. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7ab853daddf114acf995e3486fe604e849"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ab853daddf114acf995e3486fe604e849">OpenMS::IonDetector::POSTACCELERATIONDETECTOR</a></div><div class="ttdoc">postacceleration detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a1cd375d755f36023b93bbd8afd1316f3"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a1cd375d755f36023b93bbd8afd1316f3">OpenMS::MassAnalyzer::SWIFT</a></div><div class="ttdoc">Stored waveform inverse fourier transform. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a03940d78fb7ee5fc71b49ca87cfdfb1c"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a03940d78fb7ee5fc71b49ca87cfdfb1c">OpenMS::DataProcessing::CALIBRATION</a></div><div class="ttdoc">Calibration of m/z positions. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fafc825adbdcb19797aad0ed340db940c3"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fafc825adbdcb19797aad0ed340db940c3">OpenMS::IonSource::MOVINGBELT</a></div><div class="ttdoc">Moving belt. </div><div class="ttdef"><b>Definition:</b> IonSource.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aae01bfe30f377fbd7d8e5f4e431eaacb"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aae01bfe30f377fbd7d8e5f4e431eaacb">OpenMS::IonSource::REMPI</a></div><div class="ttdoc">resonance enhanced multiphoton ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a86864c88ee12eb322f1645f238c1dbe5"><div class="ttname"><a href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">OpenMS::String::trim</a></div><div class="ttdeci">String &amp; trim()</div><div class="ttdoc">removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a8eca4767d3e8964b5d683c2adbfda0b6"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a8eca4767d3e8964b5d683c2adbfda0b6">OpenMS::Internal::MzMLHandler::BinaryData::meta</a></div><div class="ttdeci">MetaInfoDescription meta</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:213</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea00c6731b4cbe1c7f48610afb10686c9c"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea00c6731b4cbe1c7f48610afb10686c9c">OpenMS::Instrument::REFLECTRON</a></div><div class="ttdoc">reflectron </div><div class="ttdef"><b>Definition:</b> Instrument.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_a8ff34073a7ed3fabe3f5deff96c0282e"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#a8ff34073a7ed3fabe3f5deff96c0282e">OpenMS::DataProcessing::setSoftware</a></div><div class="ttdeci">void setSoftware(const Software &amp;software)</div><div class="ttdoc">sets the software used for processing </div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09a38d413e2b31af5d67c4c71f17f5f63d0"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a38d413e2b31af5d67c4c71f17f5f63d0">OpenMS::ControlledVocabulary::CVTerm::XSD_NEGATIVE_INTEGER</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a671a0183b391575bccbe91a826e831a2"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a671a0183b391575bccbe91a826e831a2">OpenMS::IonDetector::CONVERSIONDYNODE</a></div><div class="ttdoc">conversion dynode </div><div class="ttdef"><b>Definition:</b> IonDetector.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a488014fedfa087421abb7f7c9005869a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a488014fedfa087421abb7f7c9005869a">OpenMS::Internal::MzMLHandler::mapping_</a></div><div class="ttdeci">CVMappings mapping_</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:275</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a90291956e102c1e1aa6e642164751197"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a90291956e102c1e1aa6e642164751197">OpenMS::IonSource::SOI</a></div><div class="ttdoc">soft ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:127</div></div>
<div class="ttc" id="structOpenMS_1_1ScanWindow_html"><div class="ttname"><a href="structOpenMS_1_1ScanWindow.html">OpenMS::ScanWindow</a></div><div class="ttdoc">Scan window description. </div><div class="ttdef"><b>Definition:</b> ScanWindow.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_ad8ed01ff3ff33333d8e19db4d2818bb6a105ee757e9b5050b891a117266e71df0"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#ad8ed01ff3ff33333d8e19db4d2818bb6a105ee757e9b5050b891a117266e71df0">OpenMS::DataValue::DOUBLE_VALUE</a></div><div class="ttdoc">double value </div><div class="ttdef"><b>Definition:</b> DataValue.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aefbc069e0ac4cd293f3ba527bec2befe"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aefbc069e0ac4cd293f3ba527bec2befe">OpenMS::IonSource::PD</a></div><div class="ttdoc">plasma desorption </div><div class="ttdef"><b>Definition:</b> IonSource.h:91</div></div>
<div class="ttc" id="SemanticValidator_8h_html"><div class="ttname"><a href="SemanticValidator_8h.html">SemanticValidator.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a4187f6dae406f24b70e3c34a7448b15f"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4187f6dae406f24b70e3c34a7448b15f">OpenMS::Precursor::PHD</a></div><div class="ttdoc">Photodissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a7d066f30823d68dafa1f1746027390b5"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a7d066f30823d68dafa1f1746027390b5">OpenMS::IonDetector::TYPENULL</a></div><div class="ttdoc">Unknown. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a4f15a2dc6638a7bdbcc97cab181bd52fa977d478dacaae531f95695750d1e9d03"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52fa977d478dacaae531f95695750d1e9d03">OpenMS::MassAnalyzer::ON</a></div><div class="ttdoc">On. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:129</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a171e75c6324f7f4233782be3c4ca1d90"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a171e75c6324f7f4233782be3c4ca1d90">OpenMS::MassAnalyzer::getReflectronState</a></div><div class="ttdeci">ReflectronState getReflectronState() const </div><div class="ttdoc">returns the reflectron state (for TOF) </div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_ab0301b5c82d74538dfffc98406254e11a5ec0e8ce4c96673614190a8852261f4f"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11a5ec0e8ce4c96673614190a8852261f4f">OpenMS::IonDetector::ADC</a></div><div class="ttdoc">Analog-digital converter. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:86</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_affde898a3bfa71810e8e6d3497e3c49b"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#affde898a3bfa71810e8e6d3497e3c49b">OpenMS::Internal::MzMLHandler::BinaryData::floats_32</a></div><div class="ttdeci">std::vector&lt; Real &gt; floats_32</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:208</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_aa730524a83fc19c0ba3a466fb9c62f95"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#aa730524a83fc19c0ba3a466fb9c62f95">OpenMS::ControlledVocabulary::CVTerm::xref_type</a></div><div class="ttdeci">XRefType xref_type</div><div class="ttdoc">xref value-type for the CV-term </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html"><div class="ttname"><a href="classOpenMS_1_1Sample.html">OpenMS::Sample</a></div><div class="ttdoc">Meta information about the sample. </div><div class="ttdef"><b>Definition:</b> Sample.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9abb654c12968c8c4c658d61af4a6e0765"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9abb654c12968c8c4c658d61af4a6e0765">OpenMS::DataProcessing::CONVERSION_MZML</a></div><div class="ttdoc">Conversion to mzML format. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:77</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09ac157bdf0b85a40d2619cbc8bc1ae5fe2"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09ac157bdf0b85a40d2619cbc8bc1ae5fe2">OpenMS::ControlledVocabulary::CVTerm::NONE</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a5bfc152a01835ee1a12f01241b4eda50"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5bfc152a01835ee1a12f01241b4eda50">OpenMS::Internal::MzMLHandler::ChromatogramType</a></div><div class="ttdeci">MSChromatogram&lt; ChromatogramPeakType &gt; ChromatogramType</div><div class="ttdoc">Spectrum type. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:198</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a6c146484587d495e53fe377ca0b855fe"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a6c146484587d495e53fe377ca0b855fe">OpenMS::IonSource::NRMS</a></div><div class="ttdoc">neutralization reionization mass spectrometry </div><div class="ttdef"><b>Definition:</b> IonSource.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">OpenMS::InstrumentSettings::MS1SPECTRUM</a></div><div class="ttdoc">full scan mass spectrum, is a &amp;quot;mass spectrum&amp;quot;   Synonyms: &amp;#39;full spectrum&amp;#39;, &amp;#39;Q1 spectrum&amp;#39;, &amp;#39;Q3 spectrum&amp;#39;, &amp;#39;Single-Stage Mass Spectrometry&amp;#39; </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a0f812ecbbe9fffeec4cee4ad92c5a2ce"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a0f812ecbbe9fffeec4cee4ad92c5a2ce">OpenMS::IonDetector::INDUCTIVEDETECTOR</a></div><div class="ttdoc">inductive detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a066042ae14211da37d4fa66d466bfa3e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a066042ae14211da37d4fa66d466bfa3e">OpenMS::Internal::MzMLHandler::SpectrumType</a></div><div class="ttdeci">MSSpectrum&lt; PeakType &gt; SpectrumType</div><div class="ttdoc">Spectrum type. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:196</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a4ce1f413b646020308281e301ce1e4ec"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a4ce1f413b646020308281e301ce1e4ec">OpenMS::IonSource::ESI</a></div><div class="ttdoc">electrospray ionisation </div><div class="ttdef"><b>Definition:</b> IonSource.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_ab1dc08092ef361e92d6e2cd117c1a63d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1dc08092ef361e92d6e2cd117c1a63d">OpenMS::Internal::MzMLHandler::data_</a></div><div class="ttdeci">std::vector&lt; BinaryData &gt; data_</div><div class="ttdoc">The spectrum data (or chromatogram data) </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:241</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a0de981225527baadd805eabc7a029173"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a0de981225527baadd805eabc7a029173">OpenMS::DataProcessing::NORMALIZATION</a></div><div class="ttdoc">Normalization of intensity values. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html">OpenMS::IonDetector</a></div><div class="ttdoc">Description of a ion detector (part of a MS Instrument) </div><div class="ttdef"><b>Definition:</b> IonDetector.h:47</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html_a9a2326f35466e54c36c070829245c557"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">OpenMS::Internal::SemanticValidator::CVTerm::name</a></div><div class="ttdeci">String name</div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda37ef0f7f2bed3939a8c3e135067b8705"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda37ef0f7f2bed3939a8c3e135067b8705">OpenMS::ChromatogramSettings::EMISSION_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1Acquisition_html"><div class="ttname"><a href="classOpenMS_1_1Acquisition.html">OpenMS::Acquisition</a></div><div class="ttdoc">Information about one raw data spectrum that was combined with several other raw data spectra...</div><div class="ttdef"><b>Definition:</b> Acquisition.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a4437a3dbac928dd5e3ee699f931bd355"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a4437a3dbac928dd5e3ee699f931bd355">OpenMS::Precursor::LCID</a></div><div class="ttdoc">Low-energy collision-induced dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:75</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a6b66c706c4bc43ff1a3b5a0044fdfa18"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6b66c706c4bc43ff1a3b5a0044fdfa18">OpenMS::InstrumentSettings::EMISSION</a></div><div class="ttdoc">Emission scan. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:68</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_a9a2326f35466e54c36c070829245c557"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#a9a2326f35466e54c36c070829245c557">OpenMS::ControlledVocabulary::CVTerm::name</a></div><div class="ttdeci">String name</div><div class="ttdoc">Text name. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a0038ff865ac073e00ca829d977f2ccdf"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf">OpenMS::Internal::MzMLHandler::writeTo</a></div><div class="ttdeci">virtual void writeTo(std::ostream &amp;os)</div><div class="ttdoc">Writes the contents to a stream. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3646</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_aaefa2a4a5d50f899cdd82d686104d164"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aaefa2a4a5d50f899cdd82d686104d164">OpenMS::MetaInfoInterface::getKeys</a></div><div class="ttdeci">void getKeys(std::vector&lt; String &gt; &amp;keys) const </div><div class="ttdoc">fills the given vector with a list of all keys for which a value is set </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a97bce951e4585a39601c04d86bb14ffd"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a97bce951e4585a39601c04d86bb14ffd">OpenMS::IonSource::VI</a></div><div class="ttdoc">vertical ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:130</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_a0d3c115101baf89ff0d81602ad6cc635"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#a0d3c115101baf89ff0d81602ad6cc635">OpenMS::Precursor::getIsolationWindowUpperOffset</a></div><div class="ttdeci">DoubleReal getIsolationWindowUpperOffset() const </div><div class="ttdoc">returns the upper offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a5de3914c3b308664d35967f1a5ffc142"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a5de3914c3b308664d35967f1a5ffc142">OpenMS::IonSource::SUI</a></div><div class="ttdoc">surface ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:129</div></div>
<div class="ttc" id="structOpenMS_1_1VersionInfo_1_1VersionDetails_html"><div class="ttname"><a href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html">OpenMS::VersionInfo::VersionDetails</a></div><div class="ttdef"><b>Definition:</b> VersionInfo.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a07b393b769a687470db848e3eb98f578"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a07b393b769a687470db848e3eb98f578">OpenMS::IonSource::NESI</a></div><div class="ttdoc">Nano electrospray ionization. </div><div class="ttdef"><b>Definition:</b> IonSource.h:102</div></div>
<div class="ttc" id="classOpenMS_1_1Software_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::Software::getName</a></div><div class="ttdeci">const String &amp; getName() const </div><div class="ttdoc">returns the name of the software </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fabc04848b2d94351b99f92127e29bb075"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fabc04848b2d94351b99f92127e29bb075">OpenMS::IonSource::BATCH</a></div><div class="ttdoc">Batch (e.g. in MALDI) </div><div class="ttdef"><b>Definition:</b> IonSource.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4affe4bbe037c9af162387d453f90e129a"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4affe4bbe037c9af162387d453f90e129a">OpenMS::IonSource::DISSI</a></div><div class="ttdoc">dissociative ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">OpenMS::InstrumentSettings::SIM</a></div><div class="ttdoc">Selected ion monitoring scan   Synonyms: &amp;#39;Multiple ion monitoring scan&amp;#39;, &amp;#39;SIM scan&amp;#39;, &amp;#39;MIM scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca">OpenMS::InstrumentSettings::CNL</a></div><div class="ttdoc">Constant neutral loss scan   Synonyms: &amp;#39;CNG scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a1ade56fdfbde5b31702cfbbab985f619"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a1ade56fdfbde5b31702cfbbab985f619">OpenMS::DataValue::setUnit</a></div><div class="ttdeci">void setUnit(const String &amp;unit)</div><div class="ttdoc">Sets the unit to the given String. </div></div>
<div class="ttc" id="MzMLValidator_8h_html"><div class="ttname"><a href="MzMLValidator_8h.html">MzMLValidator.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_aa7116e8293c2e28281202b80eae17994"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#aa7116e8293c2e28281202b80eae17994">OpenMS::ChromatogramSettings::getChromatogramType</a></div><div class="ttdeci">ChromatogramType getChromatogramType() const </div><div class="ttdoc">returns the chromatogram type, e.g. a SRM chromatogram </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a77eccf58c9f605c9535709430c66a5be"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a77eccf58c9f605c9535709430c66a5be">OpenMS::Internal::MzMLHandler::writePrecursor_</a></div><div class="ttdeci">void writePrecursor_(std::ostream &amp;os, const Precursor &amp;precursor, Internal::MzMLValidator &amp;validator)</div><div class="ttdoc">Helper method that write precursor information from spectra and chromatograms. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3532</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_ad315e04a79cddc41e8e12d92086e46d6"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#ad315e04a79cddc41e8e12d92086e46d6">OpenMS::ChromatogramSettings::getProduct</a></div><div class="ttdeci">const Product &amp; getProduct() const </div><div class="ttdoc">returns a const reference to the products </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a5980df92dcce7a0e1e8bc482e4f07aa6"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a5980df92dcce7a0e1e8bc482e4f07aa6">OpenMS::InstrumentSettings::TDF</a></div><div class="ttdoc">Time-delayed fragmentation scan. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4af6cb3036978c564d260f5016cac04f85"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4af6cb3036978c564d260f5016cac04f85">OpenMS::IonSource::FD</a></div><div class="ttdoc">field desorption </div><div class="ttdef"><b>Definition:</b> IonSource.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_add1bc02b038fe1abde05c0352577f1df"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add1bc02b038fe1abde05c0352577f1df">OpenMS::Internal::MzMLHandler::fillData_</a></div><div class="ttdeci">void fillData_()</div><div class="ttdoc">Fills the current spectrum with peaks and meta data. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:847</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1ConversionError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ConversionError.html">OpenMS::Exception::ConversionError</a></div><div class="ttdoc">Invalid conversion exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:363</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a693887ab47dee6ab960fb1ef887c56cf"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a693887ab47dee6ab960fb1ef887c56cf">OpenMS::Internal::MzMLHandler::BinaryData::size</a></div><div class="ttdeci">Size size</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:205</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a8d86de0851abd047aef8c1cbb3c1603b">OpenMS::DataProcessing::ALIGNMENT</a></div><div class="ttdoc">Retention time alignment of different maps. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a479432127ee77145cc19d6a2d1590821"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a479432127ee77145cc19d6a2d1590821">OpenMS::DataValue::isEmpty</a></div><div class="ttdeci">bool isEmpty() const </div><div class="ttdoc">test if the value is empty </div><div class="ttdef"><b>Definition:</b> DataValue.h:339</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_af974151b7df6fcfeb6509e26431dcaa0"><div class="ttname"><a href="classOpenMS_1_1Sample.html#af974151b7df6fcfeb6509e26431dcaa0">OpenMS::Sample::getComment</a></div><div class="ttdeci">const String &amp; getComment() const </div><div class="ttdoc">returns the comment (default: &amp;quot;&amp;quot;) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a65709a774b1201962e142a6be7c17776"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a65709a774b1201962e142a6be7c17776">OpenMS::Internal::MzMLHandler::in_spectrum_list_</a></div><div class="ttdeci">bool in_spectrum_list_</div><div class="ttdoc">Flag that indicates that we&amp;#39;re inside a spectrum (in contrast to a chromatogram) </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_ac82b3cc3ba4c24b0ab9768fede8c3c9c"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#ac82b3cc3ba4c24b0ab9768fede8c3c9c">OpenMS::SourceFile::getFileType</a></div><div class="ttdeci">const String &amp; getFileType() const </div><div class="ttdoc">returns the file type </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa2328ee396a2ca9e44bd7a8459bcfef28"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa2328ee396a2ca9e44bd7a8459bcfef28">OpenMS::IonSource::NANOSPRAY</a></div><div class="ttdoc">Nanospray inlet. </div><div class="ttdef"><b>Definition:</b> IonSource.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7ac251cfb1e58eccf7b508c730505ea75e"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7ac251cfb1e58eccf7b508c730505ea75e">OpenMS::IonDetector::DALYDETECTOR</a></div><div class="ttdoc">daly detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:64</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_abc5c98fcc1211af2b80116dd6e0a035da4959f950b9d109fcf9b4176c28503843"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035da4959f950b9d109fcf9b4176c28503843">OpenMS::Internal::MzMLHandler::BinaryData::DT_FLOAT</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:207</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a535e49bf5eee5561caead0a39995a48b"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a535e49bf5eee5561caead0a39995a48b">OpenMS::IonSource::GD_MS</a></div><div class="ttdoc">glow discharge ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:112</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a2a909086473828f229ef69ee60230fd2"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a2a909086473828f229ef69ee60230fd2">OpenMS::IonDetector::CONVERSIONDYNODEPHOTOMULTIPLIER</a></div><div class="ttdoc">Conversion dynode photo multiplier. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a3da723842841c3ff4194d0d71b0da0fd"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a3da723842841c3ff4194d0d71b0da0fd">OpenMS::MassAnalyzer::RADIALEJECTIONLINEARIONTRAP</a></div><div class="ttdoc">Radial ejection linear ion trap. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825eaad34ce194cef545b3decfad97565ea17"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825eaad34ce194cef545b3decfad97565ea17">OpenMS::Instrument::SELECTED_ION_FLOW_TUBE</a></div><div class="ttdoc">selected ion flow tube </div><div class="ttdef"><b>Definition:</b> Instrument.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">OpenMS::ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">OpenMS::SourceFile::SHA1</a></div><div class="ttdoc">Secure Hash Algorithm-1. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_a9d7de80efbcfc8f49025772de7806a23"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#a9d7de80efbcfc8f49025772de7806a23">OpenMS::ContactPerson::getURL</a></div><div class="ttdeci">const String &amp; getURL() const </div><div class="ttdoc">returns the email address </div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a937618aabd204b43b9974469071419dc"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a937618aabd204b43b9974469071419dc">OpenMS::Internal::MzMLHandler::BinaryData::ints_64</a></div><div class="ttdeci">std::vector&lt; Int64 &gt; ints_64</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:211</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">OpenMS::InstrumentSettings::CRM</a></div><div class="ttdoc">Consecutive reaction monitoring scan   Synonyms: &amp;#39;CRM scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html_a8b3a6d95f436cb3c0e8f57e526f32ed1"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html#a8b3a6d95f436cb3c0e8f57e526f32ed1">OpenMS::MSChromatogram::getIntegerDataArrays</a></div><div class="ttdeci">const IntegerDataArrays &amp; getIntegerDataArrays() const </div><div class="ttdoc">Returns a const reference to the integer meta data arrays. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675faf72472484541d6de7bfe8151b04b7417"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675faf72472484541d6de7bfe8151b04b7417">OpenMS::IonSource::THERMOSPRAYINLET</a></div><div class="ttdoc">Thermo spray. </div><div class="ttdef"><b>Definition:</b> IonSource.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_ace039d325c112e45c9d37e0e656ba9a2"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#ace039d325c112e45c9d37e0e656ba9a2">OpenMS::MSSpectrum::getStringDataArrays</a></div><div class="ttdeci">const StringDataArrays &amp; getStringDataArrays() const </div><div class="ttdoc">Returns a const reference to the string meta data arrays. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:282</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a32e4cb82b586a059c77128a1cdcd3282"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a32e4cb82b586a059c77128a1cdcd3282">OpenMS::IonSource::CEI</a></div><div class="ttdoc">charge exchange ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:122</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_af782cf31c1c251c2abb33b48ab6a8366"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#af782cf31c1c251c2abb33b48ab6a8366">OpenMS::Internal::MzMLHandler::BinaryData::precision</a></div><div class="ttdeci">enum OpenMS::Internal::MzMLHandler::BinaryData::@10 precision</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a385c44f6fb256e5716a2302a5b940388a4e84dda2309e9dfbb3b2300dd44ec145"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a385c44f6fb256e5716a2302a5b940388a4e84dda2309e9dfbb3b2300dd44ec145">OpenMS::Internal::MzMLHandler::BinaryData::PRE_NONE</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:204</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html_a32147dacf0dd0bda3c39144c67347bf3"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a32147dacf0dd0bda3c39144c67347bf3">OpenMS::Internal::SemanticValidator::CVTerm::value</a></div><div class="ttdeci">String value</div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a805264162c317eb0e81b8aa508726725"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a805264162c317eb0e81b8aa508726725">OpenMS::MassAnalyzer::SECTOR</a></div><div class="ttdoc">Magnetic sector. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_ac02fa25060dabd021d726903e7d0d2ea"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#ac02fa25060dabd021d726903e7d0d2ea">OpenMS::ContactPerson::getFirstName</a></div><div class="ttdeci">const String &amp; getFirstName() const </div><div class="ttdoc">returns the first name of the person </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3ae9e2537cbd38bd116d7bdb8b634f991a"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ae9e2537cbd38bd116d7bdb8b634f991a">OpenMS::MassAnalyzer::IT</a></div><div class="ttdoc">Ion trap. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a8c41c05a63a15c5d188d02f6f4db4303"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a8c41c05a63a15c5d188d02f6f4db4303">OpenMS::Precursor::IMD</a></div><div class="ttdoc">Infrared multiphoton dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ad261194a1dded675599dfdc7212b63b1"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad261194a1dded675599dfdc7212b63b1">OpenMS::DataProcessing::SMOOTHING</a></div><div class="ttdoc">Smoothing of the signal to reduce noise. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1Software_html_ae6b3b4b6857bc1987282e2f29611dd41"><div class="ttname"><a href="classOpenMS_1_1Software.html#ae6b3b4b6857bc1987282e2f29611dd41">OpenMS::Software::getVersion</a></div><div class="ttdeci">const String &amp; getVersion() const </div><div class="ttdoc">returns the software version </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a8f7be6e80ef1c4599af3aa096c7f7089"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a8f7be6e80ef1c4599af3aa096c7f7089">OpenMS::InstrumentSettings::getPolarity</a></div><div class="ttdeci">IonSource::Polarity getPolarity() const </div><div class="ttdoc">returns the polarity </div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html">OpenMS::Internal::MzMLHandler::BinaryData</a></div><div class="ttdoc">Spectrum representation. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:201</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ab269e4bf446e6556e4f49a5737931643"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ab269e4bf446e6556e4f49a5737931643">OpenMS::DataProcessing::FORMAT_CONVERSION</a></div><div class="ttdoc">General file format conversion (if no other term applies) </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:75</div></div>
<div class="ttc" id="structOpenMS_1_1VersionInfo_1_1VersionDetails_html_a43f7f28c650b47c685b8b059a716f35c"><div class="ttname"><a href="structOpenMS_1_1VersionInfo_1_1VersionDetails.html#a43f7f28c650b47c685b8b059a716f35c">OpenMS::VersionInfo::VersionDetails::create</a></div><div class="ttdeci">static VersionDetails create(const String &amp;version)</div><div class="ttdoc">parse String and return as proper struct </div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1AcquisitionInfo_html_a883a8e420b509ac1c9a4b08f4494915d"><div class="ttname"><a href="classOpenMS_1_1AcquisitionInfo.html#a883a8e420b509ac1c9a4b08f4494915d">OpenMS::AcquisitionInfo::getMethodOfCombination</a></div><div class="ttdeci">const String &amp; getMethodOfCombination() const </div><div class="ttdoc">returns the method of combination </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c">OpenMS::InstrumentSettings::UNKNOWN</a></div><div class="ttdoc">Unknown scan method. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a3b68228d65702a6a614e8e4226d25b8d"><div class="ttname"><a href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">OpenMS::String::prefix</a></div><div class="ttdeci">String prefix(SizeType length) const </div><div class="ttdoc">returns the prefix of length length </div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a5469cd06bde314b8524d14cd76df2cd1"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">OpenMS::SourceFile::getChecksum</a></div><div class="ttdeci">const String &amp; getChecksum() const </div><div class="ttdoc">returns the file&amp;#39;s checksum </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ac1923f59816bf846e2a62d41cfb91b2f"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac1923f59816bf846e2a62d41cfb91b2f">OpenMS::InstrumentSettings::ABSORBTION</a></div><div class="ttdoc">Absorbtion scan. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a78331edae256b2c5de712ed5eda26bc8"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a78331edae256b2c5de712ed5eda26bc8">OpenMS::Internal::MzMLHandler::writeSoftware_</a></div><div class="ttdeci">void writeSoftware_(std::ostream &amp;os, const String &amp;id, const Software &amp;software, Internal::MzMLValidator &amp;validator)</div><div class="ttdoc">Helper method that writes a software. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3347</div></div>
<div class="ttc" id="classOpenMS_1_1DateTime_html"><div class="ttname"><a href="classOpenMS_1_1DateTime.html">OpenMS::DateTime</a></div><div class="ttdoc">DateTime Class. </div><div class="ttdef"><b>Definition:</b> DateTime.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a8fca08235a25819cf09375f867815f09"><div class="ttname"><a href="classOpenMS_1_1String.html#a8fca08235a25819cf09375f867815f09">OpenMS::String::substitute</a></div><div class="ttdeci">String &amp; substitute(char from, char to)</div><div class="ttdoc">Replaces all occurences of the character from by the character to. </div></div>
<div class="ttc" id="group__Concept_html_ga84f5fc936107ae0a002c345694c41dcd"><div class="ttname"><a href="group__Concept.html#ga84f5fc936107ae0a002c345694c41dcd">OpenMS::Int64</a></div><div class="ttdeci">OPENMS_INT64_TYPE Int64</div><div class="ttdoc">Signed integer type (64bit) </div><div class="ttdef"><b>Definition:</b> Types.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a99395acc13be348e3858856fcc07a933"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a99395acc13be348e3858856fcc07a933">OpenMS::Internal::MzMLHandler::selected_ion_count_</a></div><div class="ttdeci">UInt selected_ion_count_</div><div class="ttdoc">Count of selected ions. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:279</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_a7b5920c33d8fb58da6481e66ddd2a572"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#a7b5920c33d8fb58da6481e66ddd2a572">OpenMS::SpectrumSettings::getProducts</a></div><div class="ttdeci">const std::vector&lt; Product &gt; &amp; getProducts() const </div><div class="ttdoc">returns a const reference to the products </div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::Instrument::getName</a></div><div class="ttdeci">const String &amp; getName() const </div><div class="ttdoc">returns the name of the instrument </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_af7adaa2fa0d50256c073d4bff34b165d"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#af7adaa2fa0d50256c073d4bff34b165d">OpenMS::MassAnalyzer::getFinalMSExponent</a></div><div class="ttdeci">Int getFinalMSExponent() const </div><div class="ttdoc">returns the final MS exponent </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_ab1d4f3e01975ac37c2b0f5b0ed1e1d92"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ab1d4f3e01975ac37c2b0f5b0ed1e1d92">OpenMS::Internal::MzMLHandler::getChildWithName_</a></div><div class="ttdeci">ControlledVocabulary::CVTerm getChildWithName_(const String &amp;parent_accession, const String &amp;name) const </div><div class="ttdoc">Looks up a child CV term of parent_accession with the name name. If no such term is found...</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3332</div></div>
<div class="ttc" id="classOpenMS_1_1Acquisition_html_a3ea2e9a83b6b409b673cac018f5099ab"><div class="ttname"><a href="classOpenMS_1_1Acquisition.html#a3ea2e9a83b6b409b673cac018f5099ab">OpenMS::Acquisition::setIdentifier</a></div><div class="ttdeci">void setIdentifier(const String &amp;identifier)</div><div class="ttdoc">sets the index/number of the scan </div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71a9584dc4fcb96c51dda36a881a6dbb212"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a9584dc4fcb96c51dda36a881a6dbb212">OpenMS::Sample::GAS</a></div><div class="ttdef"><b>Definition:</b> Sample.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a7d2afca1f43e915528abd513b30b7a55"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a7d2afca1f43e915528abd513b30b7a55">OpenMS::Precursor::PSD</a></div><div class="ttdoc">Post-source decay. </div><div class="ttdef"><b>Definition:</b> Precursor.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a6af0ff50dcb5a916e4cafba2b8f1d884"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">OpenMS::Internal::MzMLHandler::PeakType</a></div><div class="ttdeci">MapType::PeakType PeakType</div><div class="ttdoc">Peak type. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:192</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_add88f8d4748f8b7c90f08964ee7938f4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#add88f8d4748f8b7c90f08964ee7938f4">OpenMS::Internal::MzMLHandler::setOptions</a></div><div class="ttdeci">void setOptions(const PeakFileOptions &amp;opt)</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:184</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a83fe4091c0761e944734545d162259a9"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a83fe4091c0761e944734545d162259a9">OpenMS::IonSource::FII</a></div><div class="ttdoc">field ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa19ff98c123f82fd251780c91d5d52f13"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa19ff98c123f82fd251780c91d5d52f13">OpenMS::IonSource::MEMBRANESEPARATOR</a></div><div class="ttdoc">Membrane separator. </div><div class="ttdef"><b>Definition:</b> IonSource.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_afe58ce4b50d9287e52a90ef33e65d9d2"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">OpenMS::SpectrumSettings::getInstrumentSettings</a></div><div class="ttdeci">const InstrumentSettings &amp; getInstrumentSettings() const </div><div class="ttdoc">returns a const reference to the instrument settings of the current spectrum </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_adfdc00e52147d9fba0252e78b76ff477"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adfdc00e52147d9fba0252e78b76ff477">OpenMS::Internal::MzMLHandler::writeUserParam_</a></div><div class="ttdeci">void writeUserParam_(std::ostream &amp;os, const MetaInfoInterface &amp;meta, UInt indent, String path, Internal::MzMLValidator &amp;validator) const </div><div class="ttdoc">Writes user terms. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3250</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_a2dbe025c03208c3d01e5ce0794350970"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#a2dbe025c03208c3d01e5ce0794350970">OpenMS::Precursor::getPossibleChargeStates</a></div><div class="ttdeci">std::vector&lt; Int &gt; &amp; getPossibleChargeStates()</div><div class="ttdoc">Mutable access to possible charge states. </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">OpenMS::DataProcessing::PEAK_PICKING</a></div><div class="ttdoc">Peak picking (conversion from raw to peak data) </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a89efdb9d9ea65cfa7e2065774cd6198c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a89efdb9d9ea65cfa7e2065774cd6198c">OpenMS::Internal::MzMLHandler::writeSpectrum_</a></div><div class="ttdeci">void writeSpectrum_(std::ostream &amp;os, const SpectrumType &amp;spec, Size s, Internal::MzMLValidator &amp;validator, bool renew_native_ids, std::vector&lt; std::vector&lt; DataProcessing &gt; &gt; &amp;dps)</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:4617</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm_html_a6f8965f74e78f28d247f2027d1089d13"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1SemanticValidator_1_1CVTerm.html#a6f8965f74e78f28d247f2027d1089d13">OpenMS::Internal::SemanticValidator::CVTerm::has_unit_name</a></div><div class="ttdeci">bool has_unit_name</div><div class="ttdef"><b>Definition:</b> SemanticValidator.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f">OpenMS::InstrumentSettings::PRECURSOR</a></div><div class="ttdoc">Precursor ion scan. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a96e4bd823df13baa5f500b1776d463ea"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a96e4bd823df13baa5f500b1776d463ea">OpenMS::Internal::MzMLHandler::fillChromatogramData_</a></div><div class="ttdeci">void fillChromatogramData_()</div><div class="ttdoc">Fills the current chromatogram with data points and meta data. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:1086</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a6901ac898ffc10435a46be0b657885b9"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a6901ac898ffc10435a46be0b657885b9">OpenMS::Internal::MzMLHandler::MzMLHandler</a></div><div class="ttdeci">MzMLHandler(MapType &amp;exp, const String &amp;filename, const String &amp;version, ProgressLogger &amp;logger)</div><div class="ttdoc">Constructor for a read-only handler. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a51e7ec6e73028e6e0f073b01382bcaea"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a51e7ec6e73028e6e0f073b01382bcaea">OpenMS::Sample::getMass</a></div><div class="ttdeci">DoubleReal getMass() const </div><div class="ttdoc">returns the mass (in gram) (default: 0.0) </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3ace4c2a8d1433baa487103cbcd83bbb01"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ace4c2a8d1433baa487103cbcd83bbb01">OpenMS::MassAnalyzer::AXIALEJECTIONLINEARIONTRAP</a></div><div class="ttdoc">Axial ejection linear ion trap. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">OpenMS::InstrumentSettings::MASSSPECTRUM</a></div><div class="ttdoc">general spectrum type </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71a6c36859458a3b2652671a36349914666"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71a6c36859458a3b2652671a36349914666">OpenMS::Sample::EMULSION</a></div><div class="ttdef"><b>Definition:</b> Sample.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71aa87f9501ff2b390be1ea7d261b0d7cce"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71aa87f9501ff2b390be1ea7d261b0d7cce">OpenMS::Sample::LIQUID</a></div><div class="ttdef"><b>Definition:</b> Sample.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_adc972b1eb7fa347dda5ee1d46ca8df79"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#adc972b1eb7fa347dda5ee1d46ca8df79">OpenMS::Internal::MzMLHandler::handleUserParam_</a></div><div class="ttdeci">void handleUserParam_(const String &amp;parent_parent_tag, const String &amp;parent_tag, const String &amp;name, const String &amp;type, const String &amp;value)</div><div class="ttdoc">Handles user terms. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3068</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4ad534995d8fa8bd372ad247e16ff746fa"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ad534995d8fa8bd372ad247e16ff746fa">OpenMS::IonSource::ASI</a></div><div class="ttdoc">associative ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:119</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a6440df7f4dbfc4c3370e2b6781bc74e5ad37464787fa5104b0ae6bea524eec264"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5ad37464787fa5104b0ae6bea524eec264">OpenMS::SourceFile::MD5</a></div><div class="ttdoc">Message-Digest algorithm 5. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a7a5d9d8d742f5950d5a3c0fa22805b2a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7a5d9d8d742f5950d5a3c0fa22805b2a">OpenMS::Internal::MzMLHandler::writeProduct_</a></div><div class="ttdeci">void writeProduct_(std::ostream &amp;os, const Product &amp;product, Internal::MzMLValidator &amp;validator)</div><div class="ttdoc">Helper method that write precursor information from spectra and chromatograms. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3633</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_ae921cd780f4f617ca00e45c6c0cd2cf2"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae921cd780f4f617ca00e45c6c0cd2cf2">OpenMS::Internal::MzMLHandler::instruments_</a></div><div class="ttdeci">Map&lt; String, Instrument &gt; instruments_</div><div class="ttdoc">The data processing list: id =&amp;gt; Instrument. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:257</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html_a57213d8c30f9d5d0d6fb3fb472d21f05"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html#a57213d8c30f9d5d0d6fb3fb472d21f05">OpenMS::MSChromatogram::getFloatDataArrays</a></div><div class="ttdeci">const FloatDataArrays &amp; getFloatDataArrays() const </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:227</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a5ca2846674ab26010320d030655cb796"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5ca2846674ab26010320d030655cb796">OpenMS::Internal::MzMLHandler::current_id_</a></div><div class="ttdeci">String current_id_</div><div class="ttdoc">Id of the current list. Used for referencing param group, source file, sample, software, ... </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa">OpenMS::ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_a90b48146f536d2ab932723af63f0cb15"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">OpenMS::SpectrumSettings::getPrecursors</a></div><div class="ttdeci">const std::vector&lt; Precursor &gt; &amp; getPrecursors() const </div><div class="ttdoc">returns a const reference to the precursors </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f">OpenMS::InstrumentSettings::CNG</a></div><div class="ttdoc">Constant neutral gain scan   Synonyms: &amp;#39;CNG scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1CVMappings_html"><div class="ttname"><a href="classOpenMS_1_1CVMappings.html">OpenMS::CVMappings</a></div><div class="ttdoc">Representation of controlled vocabulary mapping rules (for PSI formats) </div><div class="ttdef"><b>Definition:</b> CVMappings.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1PeakFileOptions_html"><div class="ttname"><a href="classOpenMS_1_1PeakFileOptions.html">OpenMS::PeakFileOptions</a></div><div class="ttdoc">Options for loading files containing peak data. </div><div class="ttdef"><b>Definition:</b> PeakFileOptions.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a0ce1e0457af4bc9ab4bd841128c6ea84"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a0ce1e0457af4bc9ab4bd841128c6ea84">OpenMS::Precursor::SORI</a></div><div class="ttdoc">Sustained off-resonance irradiation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a5a4f408867d428d90605cbfdf5b4a507"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a5a4f408867d428d90605cbfdf5b4a507">OpenMS::Internal::MzMLHandler::ref_param_</a></div><div class="ttdeci">Map&lt; String, std::vector&lt; SemanticValidator::CVTerm &gt; &gt; ref_param_</div><div class="ttdoc">The referencing param groups: id =&amp;gt; array (accession, value) </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:249</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a57213d8c30f9d5d0d6fb3fb472d21f05"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">OpenMS::MSSpectrum::getFloatDataArrays</a></div><div class="ttdeci">const FloatDataArrays &amp; getFloatDataArrays() const </div><div class="ttdoc">Returns a const reference to the float meta data arrays. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:270</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_a29888f3b4cd1692005e9b0625ceb4608"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#a29888f3b4cd1692005e9b0625ceb4608">OpenMS::ContactPerson::getInstitution</a></div><div class="ttdeci">const String &amp; getInstitution() const </div><div class="ttdoc">returns the affiliation </div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09ae39436e89ac71af5243d896a4acd6496"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09ae39436e89ac71af5243d896a4acd6496">OpenMS::ControlledVocabulary::CVTerm::XSD_INTEGER</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_ad4e0ad3506a3256ecfbc50e925b40f99"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#ad4e0ad3506a3256ecfbc50e925b40f99">OpenMS::IonSource::getOrder</a></div><div class="ttdeci">Int getOrder() const </div><div class="ttdoc">returns the position of this part in the whole Instrument. </div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ad368341c22d3447e324134c47adff081"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">OpenMS::SpectrumSettings::getNativeID</a></div><div class="ttdeci">const String &amp; getNativeID() const </div><div class="ttdoc">returns the native identifier for the spectrum, used by the acquisition software. ...</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a9da388304c18a628979434640b7bb9c8"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a9da388304c18a628979434640b7bb9c8">OpenMS::Internal::MzMLHandler::writeChromatogram_</a></div><div class="ttdeci">void writeChromatogram_(std::ostream &amp;os, const ChromatogramType &amp;chromatogram, Size c, Internal::MzMLValidator &amp;validator)</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:5005</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a5fd9b4a1925c08d12d8d0d3a43b0ab8c"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a5fd9b4a1925c08d12d8d0d3a43b0ab8c">OpenMS::IonDetector::ELECTRONMULTIPLIER</a></div><div class="ttdoc">Electron multiplier. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4afda196677d08ccd458e96fe74597d638"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4afda196677d08ccd458e96fe74597d638">OpenMS::IonSource::SILI</a></div><div class="ttdoc">desorption/ionization on silicon </div><div class="ttdef"><b>Definition:</b> IonSource.h:132</div></div>
<div class="ttc" id="CVMappings_8h_html"><div class="ttname"><a href="CVMappings_8h.html">CVMappings.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_a36df0ae8f5b0e98a1e0009ccbf8e1972"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#a36df0ae8f5b0e98a1e0009ccbf8e1972">OpenMS::ContactPerson::getLastName</a></div><div class="ttdeci">const String &amp; getLastName() const </div><div class="ttdoc">returns the last name of the person </div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a2b44c2af82a0218d3cb5faa3d163fa1f"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a2b44c2af82a0218d3cb5faa3d163fa1f">OpenMS::IonDetector::PHOTODIODEARRAYDETECTOR</a></div><div class="ttdoc">photodiode array detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:73</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="VersionInfo_8h_html"><div class="ttname"><a href="VersionInfo_8h.html">VersionInfo.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa884aab0e62a0e1db261a95022a6ef25d"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa884aab0e62a0e1db261a95022a6ef25d">OpenMS::IonSource::OPENSPLIT</a></div><div class="ttdoc">Open split. </div><div class="ttdef"><b>Definition:</b> IonSource.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html">OpenMS::MassAnalyzer</a></div><div class="ttdoc">Descripton of a mass analyzer (part of a MS Instrument) </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:48</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html"><div class="ttname"><a href="classOpenMS_1_1IonSource.html">OpenMS::IonSource</a></div><div class="ttdoc">Description of a ion source (part of a MS Instrument) </div><div class="ttdef"><b>Definition:</b> IonSource.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a04a49f0fe9b8b9be26628d0bd8ee0882"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a04a49f0fe9b8b9be26628d0bd8ee0882">OpenMS::IonDetector::ARRAYDETECTOR</a></div><div class="ttdoc">array detector </div><div class="ttdef"><b>Definition:</b> IonDetector.h:66</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_a19ae296603b10b298db255e9d873ab32"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#a19ae296603b10b298db255e9d873ab32">OpenMS::Internal::MzMLHandler::BinaryData::ints_32</a></div><div class="ttdeci">std::vector&lt; Int32 &gt; ints_32</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:210</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_ae19606cee74ec0ac3662fcfba274cbd0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">OpenMS::Internal::MzMLHandler::cexp_</a></div><div class="ttdeci">const MapType * cexp_</div><div class="ttdoc">map pointer for writing </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:229</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1Sample.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::Sample::getName</a></div><div class="ttdeci">const String &amp; getName() const </div><div class="ttdoc">retuns the sample name (default: &amp;quot;&amp;quot;) </div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_aa40d949517afa236a88a9eb41ea4f35c"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#aa40d949517afa236a88a9eb41ea4f35c">OpenMS::ContactPerson::getEmail</a></div><div class="ttdeci">const String &amp; getEmail() const </div><div class="ttdoc">returns the email address </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ac7b870e1adfeb8747214d4ef5144376c"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ac7b870e1adfeb8747214d4ef5144376c">OpenMS::DataProcessing::CONVERSION_MZDATA</a></div><div class="ttdoc">Convertion to mzData format. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:76</div></div>
<div class="ttc" id="XMLHandler_8h_html"><div class="ttname"><a href="XMLHandler_8h.html">XMLHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">OpenMS::DataProcessing::CHARGE_DECONVOLUTION</a></div><div class="ttdoc">Charge deconvolution. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1a2634661cb45dc1d0f135daebb5fa118b"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1a2634661cb45dc1d0f135daebb5fa118b">OpenMS::Precursor::ECD</a></div><div class="ttdoc">Electron capture dissociation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3ad9bdaac4d0e7c5cb182ae5da106a75c1"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3ad9bdaac4d0e7c5cb182ae5da106a75c1">OpenMS::MassAnalyzer::QUADRUPOLE</a></div><div class="ttdoc">Quadrupole. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825eabac1358aab1b37a968f2dc90facf110e"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825eabac1358aab1b37a968f2dc90facf110e">OpenMS::Instrument::EINZEL_LENS</a></div><div class="ttdoc">einzel lens </div><div class="ttdef"><b>Definition:</b> Instrument.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4af44dbf64796c3c09b804546061c39258"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4af44dbf64796c3c09b804546061c39258">OpenMS::IonSource::MALDI</a></div><div class="ttdoc">Matrix-assisted laser desorption ionization. </div><div class="ttdef"><b>Definition:</b> IonSource.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_aaf3831bc627f95286afdf5c6b91c731b"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aaf3831bc627f95286afdf5c6b91c731b">OpenMS::Internal::MzMLHandler::handleCVParam_</a></div><div class="ttdeci">void handleCVParam_(const String &amp;parent_parent_tag, const String &amp;parent_tag, const String &amp;accession, const String &amp;name, const String &amp;value, const String &amp;unit_accession=&quot;&quot;)</div><div class="ttdoc">Handles CV terms. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:1296</div></div>
<div class="ttc" id="Base64_8h_html"><div class="ttname"><a href="Base64_8h.html">Base64.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ac6f71e641c709dfabecce317d07ac4f7"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ac6f71e641c709dfabecce317d07ac4f7">OpenMS::Precursor::getIsolationWindowLowerOffset</a></div><div class="ttdeci">DoubleReal getIsolationWindowLowerOffset() const </div><div class="ttdoc">returns the lower offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4ac59b221b111954833c988555d5972f88"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4ac59b221b111954833c988555d5972f88">OpenMS::IonSource::LSI</a></div><div class="ttdoc">liquid secondary ionization </div><div class="ttdef"><b>Definition:</b> IonSource.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_aa0f96e293e3cf64677e3bd84d26ff6ed"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#aa0f96e293e3cf64677e3bd84d26ff6ed">OpenMS::Internal::MzMLHandler::~MzMLHandler</a></div><div class="ttdeci">virtual ~MzMLHandler()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:165</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a8fee1043a25ea5e1021c04fbd89ca76c"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">OpenMS::Sample::getState</a></div><div class="ttdeci">SampleState getState() const </div><div class="ttdoc">returns the state of aggregation (default: SAMPLENULL) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a7240976da5a0394d00fecce6fd8a7baa"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a7240976da5a0394d00fecce6fd8a7baa">OpenMS::Internal::MzMLHandler::validateCV_</a></div><div class="ttdeci">bool validateCV_(const ControlledVocabulary::CVTerm &amp;c, const String &amp;path, const Internal::MzMLValidator &amp;validator) const </div><div class="ttdoc">Helper method to validate if the given CV is allowed in the current location (path) ...</div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:3216</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a4443b16a744c30d496e4b5bcb834b029"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a4443b16a744c30d496e4b5bcb834b029">OpenMS::IonSource::IONMETHODNULL</a></div><div class="ttdoc">Unknown. </div><div class="ttdef"><b>Definition:</b> IonSource.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa1ea328a644e627283a35716a54108248"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa1ea328a644e627283a35716a54108248">OpenMS::IonSource::DIRECT</a></div><div class="ttdoc">Direct. </div><div class="ttdef"><b>Definition:</b> IonSource.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ae1870a969417d19a33f225046a66a58d"><div class="ttname"><a href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">OpenMS::String::hasPrefix</a></div><div class="ttdeci">bool hasPrefix(const String &amp;string) const </div><div class="ttdoc">true if String begins with string, false otherwise </div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1ParseError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ParseError.html">OpenMS::Exception::ParseError</a></div><div class="ttdoc">Parse Error exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:608</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzMLHandler_html_a742bdba7e6348fe6c549aada2a116944"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzMLHandler.html#a742bdba7e6348fe6c549aada2a116944">OpenMS::Internal::MzMLHandler::characters</a></div><div class="ttdeci">virtual void characters(const XMLCh *const chars, const XMLSize_t length)</div><div class="ttdoc">Parsing method for character data. </div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:324</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData_html_abc5c98fcc1211af2b80116dd6e0a035daf6d3a756d101f02e5aeb13916b1d9eb3"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzMLHandler_1_1BinaryData.html#abc5c98fcc1211af2b80116dd6e0a035daf6d3a756d101f02e5aeb13916b1d9eb3">OpenMS::Internal::MzMLHandler::BinaryData::DT_INT</a></div><div class="ttdef"><b>Definition:</b> MzMLHandler.h:207</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html_ad05efb0dd6b623db53560c4f8f129a09a4452061824c767b63771c808ac8db712"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html#ad05efb0dd6b623db53560c4f8f129a09a4452061824c767b63771c808ac8db712">OpenMS::ControlledVocabulary::CVTerm::XSD_POSITIVE_INTEGER</a></div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea17e86bcc9b8f78ff8c458d7b9253699d"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea17e86bcc9b8f78ff8c458d7b9253699d">OpenMS::Instrument::KINETIC_ENERGY_ANALYZER</a></div><div class="ttdoc">kinetic energy analyzer </div><div class="ttdef"><b>Definition:</b> Instrument.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a24a5a956f8abcaacbde751c49c7d5001"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a24a5a956f8abcaacbde751c49c7d5001">OpenMS::IonSource::LD</a></div><div class="ttdoc">laser desorption </div><div class="ttdef"><b>Definition:</b> IonSource.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4aed87f9b08a003dc2ef4c4920060eae14"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4aed87f9b08a003dc2ef4c4920060eae14">OpenMS::IonSource::CI</a></div><div class="ttdoc">chemical ionisation </div><div class="ttdef"><b>Definition:</b> IonSource.h:85</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_ad37f94415197fe6b7ab39e705877825ea15567a4ebc7d975ae3be35e3efd7daae"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#ad37f94415197fe6b7ab39e705877825ea15567a4ebc7d975ae3be35e3efd7daae">OpenMS::Instrument::STATIC_FIELD</a></div><div class="ttdoc">static field </div><div class="ttdef"><b>Definition:</b> Instrument.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1CVMappingFile_html"><div class="ttname"><a href="classOpenMS_1_1CVMappingFile.html">OpenMS::CVMappingFile</a></div><div class="ttdoc">Used to load CvMapping files. </div><div class="ttdef"><b>Definition:</b> CVMappingFile.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a08b8f804d8602840858ce2d533db675fa6c48ed9c4442494fd5f122c94860447d"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675fa6c48ed9c4442494fd5f122c94860447d">OpenMS::IonSource::FLOWINJECTIONANALYSIS</a></div><div class="ttdoc">Flow injection analysis. </div><div class="ttdef"><b>Definition:</b> IonSource.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4a7fd5f3a93cf5139877f23acb316f99c0"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4a7fd5f3a93cf5139877f23acb316f99c0">OpenMS::IonSource::API</a></div><div class="ttdoc">atmospheric pressure ionisation </div><div class="ttdef"><b>Definition:</b> IonSource.h:94</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:18 using doxygen 1.8.5</font></TD>
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