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<a href="MzDataHandler_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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <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> <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> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <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> <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> <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> <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> <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> <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> <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> <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> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <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> <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> <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> <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> <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> <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> <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> <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> <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> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_HANDLERS_MZDATAHANDLER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_HANDLERS_MZDATAHANDLER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="PeakFileOptions_8h.html">OpenMS/FORMAT/OPTIONS/PeakFileOptions.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="Base64_8h.html">OpenMS/FORMAT/Base64.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <sstream></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  {</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html"> 60</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html">MzDataHandler</a> :</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  {</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21c6981f49bad30b573e09ece24bccc4">MzDataHandler</a>(MapType & exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & version, <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> & logger) :</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2f223274d440404ba700768cd15ef661">XMLHandler</a>(filename, version),</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21e306967405afb217201901a2d75351">exp_</a>(&exp),</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>(0),</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">peak_count_</a>(0),</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac19bbe5ccf16799cdf273dbc3cc28ea5">meta_id_descs_</a>(),</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>(),</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>(<span class="keyword">false</span>),</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>(logger)</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  {</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a009a30591b3297275a4db1359fcd82ed">init_</a>();</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  }</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4b8fc915bd9da6b6acf96bdcd67f0163"> 81</a></span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4b8fc915bd9da6b6acf96bdcd67f0163">MzDataHandler</a>(<span class="keyword">const</span> MapType & exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> & logger) :</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a>(filename, version),</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21e306967405afb217201901a2d75351">exp_</a>(0),</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>(&exp),</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">peak_count_</a>(0),</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac19bbe5ccf16799cdf273dbc3cc28ea5">meta_id_descs_</a>(),</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>(),</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>(false),</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>(logger)</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  {</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a009a30591b3297275a4db1359fcd82ed">init_</a>();</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  }</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a75dfe025bbcb3cf65fd7c515476f178e"> 95</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a75dfe025bbcb3cf65fd7c515476f178e">~MzDataHandler</a>()</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  {</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  }</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.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="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.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 & attributes);</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.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="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0038ff865ac073e00ca829d977f2ccdf">writeTo</a>(std::ostream & os);</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a2d6d13f6b8cb30e7943d4996e9ef2af7"> 115</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a2d6d13f6b8cb30e7943d4996e9ef2af7">setOptions</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> & options)</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  {</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a> = options;</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  }</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a009a30591b3297275a4db1359fcd82ed"> 121</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a009a30591b3297275a4db1359fcd82ed">init_</a>()</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  {</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>.resize(19);</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="comment">// SampleState</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Solid;Liquid;Gas;Solution;Emulsion;Suspension"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[0]);</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">// IonizationMode</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";PositiveIonMode;NegativeIonMode"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[1]);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">// ResolutionMethod</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";FWHM;TenPercentValley;Baseline"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[2]);</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="comment">// ResolutionType</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Constant;Proportional"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[3]);</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="comment">// ScanFunction</span></div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="comment">// is no longer used cv_terms_[4] is empty now</span></div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="comment">// ScanDirection</span></div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Up;Down"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[5]);</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="comment">// ScanLaw</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Exponential;Linear;Quadratic"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[6]);</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="comment">// PeakProcessing</span></div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";CentroidMassSpectrum;ContinuumMassSpectrum"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[7]);</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="comment">// ReflectronState</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";On;Off;None"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[8]);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="comment">// AcquisitionMode</span></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";PulseCounting;ADC;TDC;TransientRecorder"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[9]);</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="comment">// IonizationType</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";ESI;EI;CI;FAB;TSP;LD;FD;FI;PD;SI;TI;API;ISI;CID;CAD;HN;APCI;APPI;ICP"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[10]);</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">// InletType</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Direct;Batch;Chromatography;ParticleBeam;MembraneSeparator;OpenSplit;JetSeparator;Septum;Reservoir;MovingBelt;MovingWire;FlowInjectionAnalysis;ElectrosprayInlet;ThermosprayInlet;Infusion;ContinuousFlowFastAtomBombardment;InductivelyCoupledPlasma"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[11]);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  <span class="comment">// TandemScanningMethod</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="comment">// is no longer used cv_terms_[12] is empty now</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <span class="comment">// DetectorType</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";EM;Photomultiplier;FocalPlaneArray;FaradayCup;ConversionDynodeElectronMultiplier;ConversionDynodePhotomultiplier;Multi-Collector;ChannelElectronMultiplier"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[13]);</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// AnalyzerType</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Quadrupole;PaulIonTrap;RadialEjectionLinearIonTrap;AxialEjectionLinearIonTrap;TOF;Sector;FourierTransform;IonStorage"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[14]);</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="comment">// EnergyUnits</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// is no longer used cv_terms_[15] is empty now</span></div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="comment">// ScanMode</span></div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="comment">// is no longer used cv_terms_[16] is empty now</span></div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="comment">// Polarity</span></div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="comment">// is no longer used cv_terms_[17] is empty now</span></div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="comment">// ActivationMethod</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"CID;PSD;PD;SID"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[18]);</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  }</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a name="l00167"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884"> 167</a></span>  <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_1MzDataHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a>;</div>
<div class="line"><a name="l00169"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a066042ae14211da37d4fa66d466bfa3e"> 169</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a066042ae14211da37d4fa66d466bfa3e">SpectrumType</a>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span> </div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21e306967405afb217201901a2d75351"> 172</a></span>  MapType * <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21e306967405afb217201901a2d75351">exp_</a>;</div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ae19606cee74ec0ac3662fcfba274cbd0"> 174</a></span>  <span class="keyword">const</span> MapType * <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>;</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a654a0b5941d937e303c64bc9e732baec"> 177</a></span>  <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">peak_count_</a>;</div>
<div class="line"><a name="l00184"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a56bc42e12243f36ea7d533b03609e30d"> 184</a></span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a56bc42e12243f36ea7d533b03609e30d">spec_</a>;</div>
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac19bbe5ccf16799cdf273dbc3cc28ea5"> 186</a></span>  std::vector<std::pair<String, MetaInfoDescription> > <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac19bbe5ccf16799cdf273dbc3cc28ea5">meta_id_descs_</a>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0a00a4c4321f0e123b8ab6e68882865e"> 188</a></span>  std::vector<String> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0a00a4c4321f0e123b8ab6e68882865e">data_to_decode_</a>;</div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a536eb31a991f01c5047f1fe1d6b5db70"> 190</a></span>  std::vector<Real> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a536eb31a991f01c5047f1fe1d6b5db70">data_to_encode_</a>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9606cd5b118bdb7ec690a362e127690e"> 191</a></span>  std::vector<std::vector<Real> > <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9606cd5b118bdb7ec690a362e127690e">decoded_list_</a>;</div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a53098f01ff2026b860b917fa4df0ea31"> 192</a></span>  std::vector<std::vector<DoubleReal> > <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a53098f01ff2026b860b917fa4df0ea31">decoded_double_list_</a>;</div>
<div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac983ab0d4acb0c9fe2b4d80346588625"> 193</a></span>  std::vector<String> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac983ab0d4acb0c9fe2b4d80346588625">precisions_</a>;</div>
<div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a19e786a978c9050cdb613a02a7f38676"> 194</a></span>  std::vector<String> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a19e786a978c9050cdb613a02a7f38676">endians_</a>;</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
<div class="line"><a name="l00198"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3"> 198</a></span>  <a class="code" href="classOpenMS_1_1Base64.html">Base64</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>;</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a name="l00201"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a81dc4d91ca22493e81272673e507a8c4"> 201</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>;</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e"> 204</a></span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> & <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>;</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#add1bc02b038fe1abde05c0352577f1df">fillData_</a>();</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> </div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> </div>
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a02142528005396ed2f37e387a59882b0"> 222</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a02142528005396ed2f37e387a59882b0">writeCVS_</a>(std::ostream & os, <a class="code" href="classdouble.html">DoubleReal</a> value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & acc, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & name, <a class="code" href="classunsigned_01int.html">UInt</a> indent = 4)<span class="keyword"> const</span></div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">if</span> (value != 0.0)</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  {</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(indent, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<cvParam cvLabel=\"psi\" accession=\"PSI:"</span> << acc << <span class="stringliteral">"\" name=\""</span> << name << <span class="stringliteral">"\" value=\""</span> << value << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  }</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  }</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a1401bdd07b2039bdf39ae4af22b2a23d"> 241</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a1401bdd07b2039bdf39ae4af22b2a23d">writeCVS_</a>(std::ostream & os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & value, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & acc, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & name, <a class="code" href="classunsigned_01int.html">UInt</a> indent = 4)<span class="keyword"> const</span></div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">if</span> (value != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  {</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(indent, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<cvParam cvLabel=\"psi\" accession=\"PSI:"</span> << acc << <span class="stringliteral">"\" name=\""</span> << name << <span class="stringliteral">"\" value=\""</span> << value << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  }</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  }</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
<div class="line"><a name="l00262"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9923434c5650af9e3f1f76d1b3236bf9"> 262</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9923434c5650af9e3f1f76d1b3236bf9">writeCVS_</a>(std::ostream & os, <a class="code" href="classunsigned_01int.html">UInt</a> value, <a class="code" href="classunsigned_01int.html">UInt</a> map, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & acc, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & name, <a class="code" href="classunsigned_01int.html">UInt</a> indent = 4)</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  {</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="comment">//abort when receiving a wrong map index</span></div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keywordflow">if</span> (map >= <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>.size())</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  {</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#af86a807dd4b1ed6f4ba006b9bcd24763">warning</a>(<a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6cc566e3bbfdcb8a5a9d85941238cef5afeb01cb4572ba190cd7932e49446c480">STORE</a>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Cannot find map '"</span>) + map + <span class="stringliteral">"' needed to write CV term '"</span> + name + <span class="stringliteral">"' with accession '"</span> + acc + <span class="stringliteral">"'."</span>);</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  }</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="comment">//abort when receiving a wrong term index</span></div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keywordflow">if</span> (value >= <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[map].size())</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  {</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#af86a807dd4b1ed6f4ba006b9bcd24763">warning</a>(<a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6cc566e3bbfdcb8a5a9d85941238cef5afeb01cb4572ba190cd7932e49446c480">STORE</a>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Cannot find value '"</span>) + value + <span class="stringliteral">"' needed to write CV term '"</span> + name + <span class="stringliteral">"' with accession '"</span> + acc + <span class="stringliteral">"'."</span>);</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  }</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a02142528005396ed2f37e387a59882b0">writeCVS_</a>(os, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[map][value], acc, name, indent);</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  }</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span> </div>
<div class="line"><a name="l00280"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ad95ce47c6061b79f9457062c35318164"> 280</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ad95ce47c6061b79f9457062c35318164">writeUserParam_</a>(std::ostream & os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> & meta, <a class="code" href="classunsigned_01int.html">UInt</a> indent = 4)</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  {</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  std::vector<String> keys;</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aaefa2a4a5d50f899cdd82d686104d164">getKeys</a>(keys);</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordflow">for</span> (std::vector<String>::const_iterator it = keys.begin(); it != keys.end(); ++it)</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  {</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="keywordflow">if</span> ((*it)[0] != <span class="charliteral">'#'</span>) <span class="comment">// internally used meta info start with '#'</span></div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  {</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(indent, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<userParam name=\""</span> << *it << <span class="stringliteral">"\" value=\""</span> << meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(*it) << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  }</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  }</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  }</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span> </div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a246d2ed7a27643da899d40062055882a">cvParam_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & value);</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span> </div>
<div class="line"><a name="l00308"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#aa276c2358b6e8e0fa3e336d410d85802"> 308</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#aa276c2358b6e8e0fa3e336d410d85802">writeBinary_</a>(std::ostream & os, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> size, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & name = <span class="stringliteral">""</span>, <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> <span class="keywordtype">id</span> = -1)</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  {</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  os << <span class="stringliteral">"\t\t\t<"</span> << tag;</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">if</span> (tag == <span class="stringliteral">"supDataArrayBinary"</span> || tag == <span class="stringliteral">"supDataArray"</span>)</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  {</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  os << <span class="stringliteral">" id=\""</span> << <span class="keywordtype">id</span> << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  }</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  os << <span class="stringliteral">">\n"</span>;</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="keywordflow">if</span> (tag == <span class="stringliteral">"supDataArrayBinary"</span> || tag == <span class="stringliteral">"supDataArray"</span>)</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  {</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  os << <span class="stringliteral">"\t\t\t\t<arrayName>"</span> << name << <span class="stringliteral">"</arrayName>\n"</span>;</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  }</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span> </div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> str;</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>.<a class="code" href="classOpenMS_1_1Base64.html#ac70a32569b52ad3f7f462ca6c03d723a">encode</a>(<a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a536eb31a991f01c5047f1fe1d6b5db70">data_to_encode_</a>, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, str);</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a536eb31a991f01c5047f1fe1d6b5db70">data_to_encode_</a>.clear();</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  os << <span class="stringliteral">"\t\t\t\t<data precision=\"32\" endian=\"little\" length=\""</span></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  << size << <span class="stringliteral">"\">"</span></div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  << str</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  << <span class="stringliteral">"</data>\n\t\t\t</"</span> << tag << <span class="stringliteral">">\n"</span>;</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span> </div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="comment">//Data processing auxilary variable</span></div>
<div class="line"><a name="l00331"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a318165d3ac3b2191496c625d455f2293"> 331</a></span>  <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a318165d3ac3b2191496c625d455f2293">data_processing_</a>;</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span> </div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  };</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="comment">//--------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span> </div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00338"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a742bdba7e6348fe6c549aada2a116944"> 338</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a742bdba7e6348fe6c549aada2a116944">MzDataHandler<MapType>::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="l00339"></a><span class="lineno"> 339</span>  {</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="comment">// skip current spectrum</span></div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keywordflow">if</span> (skip_spectrum_)</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="keywordtype">char</span> * transcoded_chars = sm_.convert(chars);</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="comment">//current tag</span></div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & current_tag = open_tags_.back();</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="comment">//determine the parent tag</span></div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> parent_tag;</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keywordflow">if</span> (open_tags_.size() > 1)</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span> </div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> </div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"sampleName"</span>)</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  {</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  exp_->getSample().setName(sm_.convert(chars));</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  }</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"instrumentName"</span>)</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  {</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  exp_->getInstrument().setName(sm_.convert(chars));</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  }</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"version"</span>)</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  {</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  data_processing_.getSoftware().setVersion(sm_.convert(chars));</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  }</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"institution"</span>)</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  {</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  exp_->getContacts().back().setInstitution(sm_.convert(chars));</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  }</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"contactInfo"</span>)</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  {</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  exp_->getContacts().back().setContactInfo(sm_.convert(chars));</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  }</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"name"</span> && parent_tag == <span class="stringliteral">"contact"</span>)</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  {</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  exp_->getContacts().back().setName(sm_.convert(chars));</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  }</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"name"</span> && parent_tag == <span class="stringliteral">"software"</span>)</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  {</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  data_processing_.getSoftware().setName(sm_.convert(chars));</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  }</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"comments"</span> && parent_tag == <span class="stringliteral">"software"</span>)</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  {</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  data_processing_.getSoftware().setMetaValue(<span class="stringliteral">"comment"</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(sm_.convert(chars)));</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  }</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"comments"</span> && parent_tag == <span class="stringliteral">"spectrumDesc"</span>)</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  {</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  spec_.setComment(transcoded_chars);</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  }</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"data"</span>)</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  {</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="comment">//chars may be split to several chunks => concatenate them</span></div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  data_to_decode_.back() += transcoded_chars;</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  }</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"arrayName"</span> && parent_tag == <span class="stringliteral">"supDataArrayBinary"</span>)</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  {</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  spec_.getFloatDataArrays().back().setName(transcoded_chars);</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  }</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"nameOfFile"</span> && parent_tag == <span class="stringliteral">"sourceFile"</span>)</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  {</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  exp_->getSourceFiles().back().setNameOfFile(sm_.convert(chars));</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  }</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"nameOfFile"</span> && parent_tag == <span class="stringliteral">"supSourceFile"</span>)</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  {</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="comment">//ignored</span></div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  }</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"pathToFile"</span> && parent_tag == <span class="stringliteral">"sourceFile"</span>)</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  {</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  exp_->getSourceFiles().back().setPathToFile(sm_.convert(chars));</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  }</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"pathToFile"</span> && parent_tag == <span class="stringliteral">"supSourceFile"</span>)</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  {</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <span class="comment">//ignored</span></div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  }</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"fileType"</span> && parent_tag == <span class="stringliteral">"sourceFile"</span>)</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  {</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  exp_->getSourceFiles().back().setFileType(sm_.convert(chars));</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  }</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (current_tag == <span class="stringliteral">"fileType"</span> && parent_tag == <span class="stringliteral">"supSourceFile"</span>)</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  {</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="comment">//ignored</span></div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  }</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  {</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> trimmed_transcoded_chars = transcoded_chars;</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  trimmed_transcoded_chars.<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>();</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordflow">if</span> (trimmed_transcoded_chars != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  {</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Unhandled character content in tag '"</span>) + current_tag + <span class="stringliteral">"': "</span> + trimmed_transcoded_chars);</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  }</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  }</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  }</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span> </div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00436"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a484c33c30ea480bd831a92847f61006e"> 436</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a484c33c30ea480bd831a92847f61006e">MzDataHandler<MapType>::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 & attributes)</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  {</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_name = xercesc::XMLString::transcode(<span class="stringliteral">"name"</span>);</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_accession = xercesc::XMLString::transcode(<span class="stringliteral">"accession"</span>);</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_value = xercesc::XMLString::transcode(<span class="stringliteral">"value"</span>);</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_id = xercesc::XMLString::transcode(<span class="stringliteral">"id"</span>);</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_count = xercesc::XMLString::transcode(<span class="stringliteral">"count"</span>);</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_spectrumtype = xercesc::XMLString::transcode(<span class="stringliteral">"spectrumType"</span>);</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_methodofcombination = xercesc::XMLString::transcode(<span class="stringliteral">"methodOfCombination"</span>);</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_acqnumber = xercesc::XMLString::transcode(<span class="stringliteral">"acqNumber"</span>);</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_mslevel = xercesc::XMLString::transcode(<span class="stringliteral">"msLevel"</span>);</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_mzrangestart = xercesc::XMLString::transcode(<span class="stringliteral">"mzRangeStart"</span>);</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_mzrangestop = xercesc::XMLString::transcode(<span class="stringliteral">"mzRangeStop"</span>);</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_supdataarrayref = xercesc::XMLString::transcode(<span class="stringliteral">"supDataArrayRef"</span>);</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_precision = xercesc::XMLString::transcode(<span class="stringliteral">"precision"</span>);</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_endian = xercesc::XMLString::transcode(<span class="stringliteral">"endian"</span>);</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_length = xercesc::XMLString::transcode(<span class="stringliteral">"length"</span>);</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_comment = xercesc::XMLString::transcode(<span class="stringliteral">"comment"</span>);</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_accessionnumber = xercesc::XMLString::transcode(<span class="stringliteral">"accessionNumber"</span>);</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span> </div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> tag = sm_.convert(qname);</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  open_tags_.push_back(tag);</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  <span class="comment">//std::cout << "Start: '" << tag << "'" << std::endl;</span></div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="comment">//determine the parent tag</span></div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> parent_tag;</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  <span class="keywordflow">if</span> (open_tags_.size() > 1)</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span> </div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="comment">//do nothing until a new spectrum is reached</span></div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordflow">if</span> (tag != <span class="stringliteral">"spectrum"</span> && skip_spectrum_)</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span> </div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> </div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="comment">// Do something depending on the tag</span></div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  <span class="keywordflow">if</span> (tag == <span class="stringliteral">"sourceFile"</span>)</div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  {</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  exp_->getSourceFiles().push_back(<a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a>());</div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  }</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordflow">if</span> (tag == <span class="stringliteral">"contact"</span>)</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  {</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  exp_->getContacts().resize(exp_->getContacts().size() + 1);</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  }</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"source"</span>)</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  {</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  exp_->getInstrument().getIonSources().resize(1);</div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  }</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"detector"</span>)</div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  {</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  exp_->getInstrument().getIonDetectors().resize(1);</div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  }</div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"analyzer"</span>)</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  {</div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  exp_->getInstrument().getMassAnalyzers().resize(exp_->getInstrument().getMassAnalyzers().size() + 1);</div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  }</div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"software"</span>)</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  {</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  data_processing_ = <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>();</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  <span class="keywordflow">if</span> (attributes.getIndex(sm_.convert(<span class="stringliteral">"completionTime"</span>)) != -1)</div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  {</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  data_processing_.setCompletionTime(asDateTime_(sm_.convert(attributes.getValue(sm_.convert(<span class="stringliteral">"completionTime"</span>)))));</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  }</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  }</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"precursor"</span>)</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  {</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  spec_.getPrecursors().push_back(<a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>());</div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  }</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"cvParam"</span>)</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  {</div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> accession = attributeAsString_(attributes, s_accession);</div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> value = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  optionalAttributeAsString_(value, attributes, s_value);</div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  cvParam_(accession, value);</div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  }</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"supDataDesc"</span>)</div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  {</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> comment;</div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  <span class="keywordflow">if</span> (optionalAttributeAsString_(comment, attributes, s_comment))</div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  {</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  meta_id_descs_.back().second.setMetaValue(<span class="stringliteral">"comment"</span>, comment);</div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  }</div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  }</div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"userParam"</span>)</div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  {</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> name = attributeAsString_(attributes, s_name);</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> value = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  optionalAttributeAsString_(value, attributes, s_value);</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span> </div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"spectrumInstrument"</span>)</div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  {</div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  spec_.getInstrumentSettings().setMetaValue(name, value);</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  }</div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"acquisition"</span>)</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  {</div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  spec_.getAcquisitionInfo().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  }</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"ionSelection"</span>)</div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  {</div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  spec_.getPrecursors().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  }</div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"activation"</span>)</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  {</div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  spec_.getPrecursors().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  }</div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"supDataDesc"</span>)</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  {</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  meta_id_descs_.back().second.setMetaValue(name, value);</div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  }</div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"detector"</span>)</div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  {</div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  exp_->getInstrument().getIonDetectors().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  }</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"source"</span>)</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  {</div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  exp_->getInstrument().getIonSources().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  }</div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"sampleDescription"</span>)</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  {</div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  exp_->getSample().setMetaValue(name, value);</div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  }</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"analyzer"</span>)</div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  {</div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  exp_->getInstrument().getMassAnalyzers().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  }</div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"additional"</span>)</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  {</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  exp_->getInstrument().setMetaValue(name, value);</div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  }</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"processingMethod"</span>)</div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  {</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  data_processing_.setMetaValue(name, value);</div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  }</div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  {</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  warning(LOAD, <span class="stringliteral">"Invalid userParam: name=\""</span> + name + <span class="stringliteral">", value=\""</span> + value + <span class="stringliteral">"\""</span>);</div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  }</div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  }</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"supDataArrayBinary"</span>)</div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  {</div>
<div class="line"><a name="l00575"></a><span class="lineno"> 575</span> </div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="comment">//create FloatDataArray</span></div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  <span class="keyword">typename</span> MapType::SpectrumType::FloatDataArray mda;</div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  <span class="comment">//Assign the right MetaInfoDescription ("supDesc" tag)</span></div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <span class="keywordtype">id</span> = attributeAsString_(attributes, s_id);</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < meta_id_descs_.size(); ++i)</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  {</div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  <span class="keywordflow">if</span> (meta_id_descs_[i].first == <span class="keywordtype">id</span>)</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  {</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  mda.MetaInfoDescription::operator=(meta_id_descs_[i].second);</div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  }</div>
<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  }</div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="comment">//append FloatDataArray</span></div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  spec_.getFloatDataArrays().push_back(mda);</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  }</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"spectrum"</span>)</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  {</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  spec_ = <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>();</div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  spec_.setNativeID(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"spectrum="</span>) + attributeAsString_(attributes, s_id));</div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  spec_.getDataProcessing().push_back(data_processing_);</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  }</div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"spectrumList"</span>)</div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  {</div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  <span class="keywordflow">if</span> (options_.getMetadataOnly())</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  <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="l00601"></a><span class="lineno"> 601</span>  <span class="comment">//std::cout << Date::now() << " Reserving space for spectra" << std::endl;</span></div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  <a class="code" href="classunsigned_01int.html">UInt</a> count = attributeAsInt_(attributes, s_count);</div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  exp_->reserve(count);</div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  logger_.startProgress(0, count, <span class="stringliteral">"loading mzData file"</span>);</div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  <span class="comment">//std::cout << Date::now() << " done" << std::endl;</span></div>
<div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  }</div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"mzData"</span>)</div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  {</div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <span class="comment">//handle file id</span></div>
<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  exp_->setIdentifier(attributeAsString_(attributes, s_accessionnumber));</div>
<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  }</div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"acqSpecification"</span>)</div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  {</div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> tmp_type = attributeAsString_(attributes, s_spectrumtype);</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  <span class="keywordflow">if</span> (tmp_type == <span class="stringliteral">"discrete"</span>)</div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  {</div>
<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  spec_.setType(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>);</div>
<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  }</div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tmp_type == <span class="stringliteral">"continuous"</span>)</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  {</div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  spec_.setType(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9ac4247d1d6a6d7690023932e58b441533">SpectrumSettings::RAWDATA</a>);</div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  }</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  {</div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  spec_.setType(<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a6ce26a62afab55d7606ad4e92428b30c">SpectrumSettings::UNKNOWN</a>);</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid spectrum type '"</span>) + tmp_type + <span class="stringliteral">"'."</span>);</div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  }</div>
<div class="line"><a name="l00628"></a><span class="lineno"> 628</span> </div>
<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  spec_.getAcquisitionInfo().setMethodOfCombination(attributeAsString_(attributes, s_methodofcombination));</div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  }</div>
<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"acquisition"</span>)</div>
<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  {</div>
<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  spec_.getAcquisitionInfo().insert(spec_.getAcquisitionInfo().end(), <a class="code" href="classOpenMS_1_1Acquisition.html">Acquisition</a>());</div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  spec_.getAcquisitionInfo().back().setIdentifier(attributeAsString_(attributes, s_acqnumber));</div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  }</div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"spectrumInstrument"</span> || tag == <span class="stringliteral">"acqInstrument"</span>)</div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  {</div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  spec_.setMSLevel(attributeAsInt_(attributes, s_mslevel));</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  <a class="code" href="structOpenMS_1_1ScanWindow.html">ScanWindow</a> window;</div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  optionalAttributeAsDouble_(window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aea3ca80628c489842c52a61e195dd047">begin</a>, attributes, s_mzrangestart);</div>
<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  optionalAttributeAsDouble_(window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aed18ab075b5c0317ae32335a57f899e8">end</a>, attributes, s_mzrangestop);</div>
<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  <span class="keywordflow">if</span> (window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aea3ca80628c489842c52a61e195dd047">begin</a> != 0.0 || window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aed18ab075b5c0317ae32335a57f899e8">end</a> != 0.0)</div>
<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  {</div>
<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  spec_.getInstrumentSettings().getScanWindows().push_back(window);</div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  }</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span> </div>
<div class="line"><a name="l00647"></a><span class="lineno"> 647</span>  <span class="keywordflow">if</span> (options_.hasMSLevels() && !options_.containsMSLevel(spec_.getMSLevel()))</div>
<div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  {</div>
<div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  skip_spectrum_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00650"></a><span class="lineno"> 650</span>  }</div>
<div class="line"><a name="l00651"></a><span class="lineno"> 651</span>  }</div>
<div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"supDesc"</span>)</div>
<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  {</div>
<div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  meta_id_descs_.push_back(std::make_pair(attributeAsString_(attributes, s_supdataarrayref), <a class="code" href="classOpenMS_1_1MetaInfoDescription.html">MetaInfoDescription</a>()));</div>
<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  }</div>
<div class="line"><a name="l00656"></a><span class="lineno"> 656</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"data"</span>)</div>
<div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  {</div>
<div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  <span class="comment">// store precision for later</span></div>
<div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  precisions_.push_back(attributeAsString_(attributes, s_precision));</div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  endians_.push_back(attributeAsString_(attributes, s_endian));</div>
<div class="line"><a name="l00661"></a><span class="lineno"> 661</span> </div>
<div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  <span class="comment">//reserve enough space in spectrum</span></div>
<div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"mzArrayBinary"</span>)</div>
<div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  {</div>
<div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  peak_count_ = attributeAsInt_(attributes, s_length);</div>
<div class="line"><a name="l00666"></a><span class="lineno"> 666</span>  spec_.reserve(peak_count_);</div>
<div class="line"><a name="l00667"></a><span class="lineno"> 667</span>  }</div>
<div class="line"><a name="l00668"></a><span class="lineno"> 668</span>  }</div>
<div class="line"><a name="l00669"></a><span class="lineno"> 669</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"mzArrayBinary"</span>)</div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  {</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  data_to_decode_.resize(data_to_decode_.size() + 1);</div>
<div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  }</div>
<div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"intenArrayBinary"</span>)</div>
<div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  {</div>
<div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  data_to_decode_.resize(data_to_decode_.size() + 1);</div>
<div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  }</div>
<div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"arrayName"</span> && parent_tag == <span class="stringliteral">"supDataArrayBinary"</span>)</div>
<div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  {</div>
<div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  <span class="comment">// Note: name is set in closing tag as it is CDATA</span></div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  data_to_decode_.resize(data_to_decode_.size() + 1);</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  }</div>
<div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  <span class="comment">//std::cout << "end startelement" << std::endl;</span></div>
<div class="line"><a name="l00683"></a><span class="lineno"> 683</span>  }</div>
<div class="line"><a name="l00684"></a><span class="lineno"> 684</span> </div>
<div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00686"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9028634d022a74d1fc8db852d99984d6"> 686</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9028634d022a74d1fc8db852d99984d6">MzDataHandler<MapType>::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="l00687"></a><span class="lineno"> 687</span>  {</div>
<div class="line"><a name="l00688"></a><span class="lineno"> 688</span>  <span class="keyword">static</span> <a class="code" href="classunsigned_01int.html">UInt</a> scan_count = 0;</div>
<div class="line"><a name="l00689"></a><span class="lineno"> 689</span> </div>
<div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_spectrum = xercesc::XMLString::transcode(<span class="stringliteral">"spectrum"</span>);</div>
<div class="line"><a name="l00691"></a><span class="lineno"> 691</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh * s_mzdata = xercesc::XMLString::transcode(<span class="stringliteral">"mzData"</span>);</div>
<div class="line"><a name="l00692"></a><span class="lineno"> 692</span> </div>
<div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  open_tags_.pop_back();</div>
<div class="line"><a name="l00694"></a><span class="lineno"> 694</span>  <span class="comment">//std::cout << "End: '" << sm_.convert(qname) << "'" << std::endl;</span></div>
<div class="line"><a name="l00695"></a><span class="lineno"> 695</span> </div>
<div class="line"><a name="l00696"></a><span class="lineno"> 696</span>  <span class="keywordflow">if</span> (equal_(qname, s_spectrum))</div>
<div class="line"><a name="l00697"></a><span class="lineno"> 697</span>  {</div>
<div class="line"><a name="l00698"></a><span class="lineno"> 698</span>  <span class="keywordflow">if</span> (!skip_spectrum_)</div>
<div class="line"><a name="l00699"></a><span class="lineno"> 699</span>  {</div>
<div class="line"><a name="l00700"></a><span class="lineno"> 700</span>  fillData_();</div>
<div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  exp_->addSpectrum(spec_);</div>
<div class="line"><a name="l00702"></a><span class="lineno"> 702</span>  }</div>
<div class="line"><a name="l00703"></a><span class="lineno"> 703</span>  skip_spectrum_ = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00704"></a><span class="lineno"> 704</span>  logger_.setProgress(++scan_count);</div>
<div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  decoded_list_.clear();</div>
<div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  decoded_double_list_.clear();</div>
<div class="line"><a name="l00707"></a><span class="lineno"> 707</span>  data_to_decode_.clear();</div>
<div class="line"><a name="l00708"></a><span class="lineno"> 708</span>  precisions_.clear();</div>
<div class="line"><a name="l00709"></a><span class="lineno"> 709</span>  endians_.clear();</div>
<div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  meta_id_descs_.clear();</div>
<div class="line"><a name="l00711"></a><span class="lineno"> 711</span>  }</div>
<div class="line"><a name="l00712"></a><span class="lineno"> 712</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (equal_(qname, s_mzdata))</div>
<div class="line"><a name="l00713"></a><span class="lineno"> 713</span>  {</div>
<div class="line"><a name="l00714"></a><span class="lineno"> 714</span>  logger_.endProgress();</div>
<div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  scan_count = 0;</div>
<div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  }</div>
<div class="line"><a name="l00717"></a><span class="lineno"> 717</span> </div>
<div class="line"><a name="l00718"></a><span class="lineno"> 718</span>  sm_.clear();</div>
<div class="line"><a name="l00719"></a><span class="lineno"> 719</span>  }</div>
<div class="line"><a name="l00720"></a><span class="lineno"> 720</span> </div>
<div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00722"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#add1bc02b038fe1abde05c0352577f1df"> 722</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#add1bc02b038fe1abde05c0352577f1df">MzDataHandler<MapType>::fillData_</a>()</div>
<div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  {</div>
<div class="line"><a name="l00724"></a><span class="lineno"> 724</span>  std::vector<Real> decoded;</div>
<div class="line"><a name="l00725"></a><span class="lineno"> 725</span>  std::vector<DoubleReal> decoded_double;</div>
<div class="line"><a name="l00726"></a><span class="lineno"> 726</span> </div>
<div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  <span class="comment">// data_to_decode is an encoded spectrum, represented as</span></div>
<div class="line"><a name="l00728"></a><span class="lineno"> 728</span>  <span class="comment">// vector of base64-encoded strings:</span></div>
<div class="line"><a name="l00729"></a><span class="lineno"> 729</span>  <span class="comment">// Each string represents one property (e.g. mzData) and decodes</span></div>
<div class="line"><a name="l00730"></a><span class="lineno"> 730</span>  <span class="comment">// to a vector of property values - one value for every peak in the spectrum.</span></div>
<div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < data_to_decode_.size(); ++i)</div>
<div class="line"><a name="l00732"></a><span class="lineno"> 732</span>  {</div>
<div class="line"><a name="l00733"></a><span class="lineno"> 733</span>  <span class="comment">//remove whitespaces from binary data</span></div>
<div class="line"><a name="l00734"></a><span class="lineno"> 734</span>  <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="l00735"></a><span class="lineno"> 735</span>  data_to_decode_[i].removeWhitespaces();</div>
<div class="line"><a name="l00736"></a><span class="lineno"> 736</span> </div>
<div class="line"><a name="l00737"></a><span class="lineno"> 737</span>  <span class="keywordflow">if</span> (precisions_[i] == <span class="stringliteral">"64"</span>) <span class="comment">// precision 64 Bit</span></div>
<div class="line"><a name="l00738"></a><span class="lineno"> 738</span>  {</div>
<div class="line"><a name="l00739"></a><span class="lineno"> 739</span>  <span class="keywordflow">if</span> (endians_[i] == <span class="stringliteral">"big"</span>)</div>
<div class="line"><a name="l00740"></a><span class="lineno"> 740</span>  {</div>
<div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  <span class="comment">//std::cout << "nr. " << i << ": decoding as high-precision big endian" << std::endl;</span></div>
<div class="line"><a name="l00742"></a><span class="lineno"> 742</span>  decoder_.decode(data_to_decode_[i], <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, decoded_double);</div>
<div class="line"><a name="l00743"></a><span class="lineno"> 743</span>  }</div>
<div class="line"><a name="l00744"></a><span class="lineno"> 744</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00745"></a><span class="lineno"> 745</span>  {</div>
<div class="line"><a name="l00746"></a><span class="lineno"> 746</span>  <span class="comment">//std::cout << "nr. " << i << ": decoding as high-precision little endian" << std::endl;</span></div>
<div class="line"><a name="l00747"></a><span class="lineno"> 747</span>  decoder_.decode(data_to_decode_[i], <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, decoded_double);</div>
<div class="line"><a name="l00748"></a><span class="lineno"> 748</span>  }</div>
<div class="line"><a name="l00749"></a><span class="lineno"> 749</span>  <span class="comment">// push_back the decoded double data - and an empty one into</span></div>
<div class="line"><a name="l00750"></a><span class="lineno"> 750</span>  <span class="comment">// the dingle-precision vector, so that we don't mess up the index</span></div>
<div class="line"><a name="l00751"></a><span class="lineno"> 751</span>  <span class="comment">//std::cout << "list size: " << decoded_double.size() << std::endl;</span></div>
<div class="line"><a name="l00752"></a><span class="lineno"> 752</span>  decoded_double_list_.push_back(decoded_double);</div>
<div class="line"><a name="l00753"></a><span class="lineno"> 753</span>  decoded_list_.push_back(std::vector<float>());</div>
<div class="line"><a name="l00754"></a><span class="lineno"> 754</span>  }</div>
<div class="line"><a name="l00755"></a><span class="lineno"> 755</span>  <span class="keywordflow">else</span> <span class="comment">// precision 32 Bit</span></div>
<div class="line"><a name="l00756"></a><span class="lineno"> 756</span>  {</div>
<div class="line"><a name="l00757"></a><span class="lineno"> 757</span>  <span class="keywordflow">if</span> (endians_[i] == <span class="stringliteral">"big"</span>)</div>
<div class="line"><a name="l00758"></a><span class="lineno"> 758</span>  {</div>
<div class="line"><a name="l00759"></a><span class="lineno"> 759</span>  <span class="comment">//std::cout << "nr. " << i << ": decoding as low-precision big endian" << std::endl;</span></div>
<div class="line"><a name="l00760"></a><span class="lineno"> 760</span>  decoder_.decode(data_to_decode_[i], <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, decoded);</div>
<div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  }</div>
<div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  {</div>
<div class="line"><a name="l00764"></a><span class="lineno"> 764</span>  <span class="comment">//std::cout << "nr. " << i << ": decoding as low-precision little endian" << std::endl;</span></div>
<div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  decoder_.decode(data_to_decode_[i], <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142baa25cd734d923d103214382bbeaee4fbc">Base64::BYTEORDER_LITTLEENDIAN</a>, decoded);</div>
<div class="line"><a name="l00766"></a><span class="lineno"> 766</span>  }</div>
<div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  <span class="comment">//std::cout << "list size: " << decoded.size() << std::endl;</span></div>
<div class="line"><a name="l00768"></a><span class="lineno"> 768</span>  decoded_list_.push_back(decoded);</div>
<div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  decoded_double_list_.push_back(std::vector<double>());</div>
<div class="line"><a name="l00770"></a><span class="lineno"> 770</span>  }</div>
<div class="line"><a name="l00771"></a><span class="lineno"> 771</span>  }</div>
<div class="line"><a name="l00772"></a><span class="lineno"> 772</span> </div>
<div class="line"><a name="l00773"></a><span class="lineno"> 773</span>  <span class="comment">// this works only if MapType::PeakType is a Peak1D or derived from it</span></div>
<div class="line"><a name="l00774"></a><span class="lineno"> 774</span>  {</div>
<div class="line"><a name="l00775"></a><span class="lineno"> 775</span>  <span class="comment">//store what precision is used for intensity and m/z</span></div>
<div class="line"><a name="l00776"></a><span class="lineno"> 776</span>  <span class="keywordtype">bool</span> mz_precision_64 = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00777"></a><span class="lineno"> 777</span>  <span class="keywordflow">if</span> (precisions_[0] == <span class="stringliteral">"32"</span>)</div>
<div class="line"><a name="l00778"></a><span class="lineno"> 778</span>  {</div>
<div class="line"><a name="l00779"></a><span class="lineno"> 779</span>  mz_precision_64 = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00780"></a><span class="lineno"> 780</span>  }</div>
<div class="line"><a name="l00781"></a><span class="lineno"> 781</span>  <span class="keywordtype">bool</span> int_precision_64 = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00782"></a><span class="lineno"> 782</span>  <span class="keywordflow">if</span> (precisions_[1] == <span class="stringliteral">"32"</span>)</div>
<div class="line"><a name="l00783"></a><span class="lineno"> 783</span>  {</div>
<div class="line"><a name="l00784"></a><span class="lineno"> 784</span>  int_precision_64 = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00785"></a><span class="lineno"> 785</span>  }</div>
<div class="line"><a name="l00786"></a><span class="lineno"> 786</span> </div>
<div class="line"><a name="l00787"></a><span class="lineno"> 787</span>  <span class="comment">//reserve space for meta data arrays (peak count)</span></div>
<div class="line"><a name="l00788"></a><span class="lineno"> 788</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec_.getFloatDataArrays().size(); ++i)</div>
<div class="line"><a name="l00789"></a><span class="lineno"> 789</span>  {</div>
<div class="line"><a name="l00790"></a><span class="lineno"> 790</span>  spec_.getFloatDataArrays()[i].reserve(peak_count_);</div>
<div class="line"><a name="l00791"></a><span class="lineno"> 791</span>  }</div>
<div class="line"><a name="l00792"></a><span class="lineno"> 792</span> </div>
<div class="line"><a name="l00793"></a><span class="lineno"> 793</span>  <span class="comment">//push_back the peaks into the container</span></div>
<div class="line"><a name="l00794"></a><span class="lineno"> 794</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n = 0; n < peak_count_; ++n)</div>
<div class="line"><a name="l00795"></a><span class="lineno"> 795</span>  {</div>
<div class="line"><a name="l00796"></a><span class="lineno"> 796</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz = mz_precision_64 ? decoded_double_list_[0][n] : decoded_list_[0][n];</div>
<div class="line"><a name="l00797"></a><span class="lineno"> 797</span>  <a class="code" href="classdouble.html">DoubleReal</a> intensity = int_precision_64 ? decoded_double_list_[1][n] : decoded_list_[1][n];</div>
<div class="line"><a name="l00798"></a><span class="lineno"> 798</span>  <span class="keywordflow">if</span> ((!options_.hasMZRange() || options_.getMZRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(mz)))</div>
<div class="line"><a name="l00799"></a><span class="lineno"> 799</span>  && (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(intensity))))</div>
<div class="line"><a name="l00800"></a><span class="lineno"> 800</span>  {</div>
<div class="line"><a name="l00801"></a><span class="lineno"> 801</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a> tmp;</div>
<div class="line"><a name="l00802"></a><span class="lineno"> 802</span>  tmp.setIntensity(intensity);</div>
<div class="line"><a name="l00803"></a><span class="lineno"> 803</span>  tmp.setMZ(mz);</div>
<div class="line"><a name="l00804"></a><span class="lineno"> 804</span>  spec_.push_back(tmp);</div>
<div class="line"><a name="l00805"></a><span class="lineno"> 805</span>  <span class="comment">//load data from meta data arrays</span></div>
<div class="line"><a name="l00806"></a><span class="lineno"> 806</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec_.getFloatDataArrays().size(); ++i)</div>
<div class="line"><a name="l00807"></a><span class="lineno"> 807</span>  {</div>
<div class="line"><a name="l00808"></a><span class="lineno"> 808</span>  spec_.getFloatDataArrays()[i].push_back(precisions_[2 + i] == <span class="stringliteral">"64"</span> ? decoded_double_list_[2 + i][n] : decoded_list_[2 + i][n]);</div>
<div class="line"><a name="l00809"></a><span class="lineno"> 809</span>  }</div>
<div class="line"><a name="l00810"></a><span class="lineno"> 810</span>  }</div>
<div class="line"><a name="l00811"></a><span class="lineno"> 811</span>  }</div>
<div class="line"><a name="l00812"></a><span class="lineno"> 812</span>  }</div>
<div class="line"><a name="l00813"></a><span class="lineno"> 813</span>  }</div>
<div class="line"><a name="l00814"></a><span class="lineno"> 814</span> </div>
<div class="line"><a name="l00815"></a><span class="lineno"> 815</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00816"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0038ff865ac073e00ca829d977f2ccdf"> 816</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0038ff865ac073e00ca829d977f2ccdf">MzDataHandler<MapType>::writeTo</a>(std::ostream & os)</div>
<div class="line"><a name="l00817"></a><span class="lineno"> 817</span>  {</div>
<div class="line"><a name="l00818"></a><span class="lineno"> 818</span>  logger_.startProgress(0, cexp_->size(), <span class="stringliteral">"storing mzData file"</span>);</div>
<div class="line"><a name="l00819"></a><span class="lineno"> 819</span> </div>
<div class="line"><a name="l00820"></a><span class="lineno"> 820</span>  os << <span class="stringliteral">"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n"</span></div>
<div class="line"><a name="l00821"></a><span class="lineno"> 821</span>  << <span class="stringliteral">"<mzData version=\"1.05\" accessionNumber=\""</span> << cexp_->getIdentifier() << <span class="stringliteral">"\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.xsd\">\n"</span>;</div>
<div class="line"><a name="l00822"></a><span class="lineno"> 822</span> </div>
<div class="line"><a name="l00823"></a><span class="lineno"> 823</span>  <span class="comment">//---------------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00824"></a><span class="lineno"> 824</span>  <span class="comment">//DESCRIPTION</span></div>
<div class="line"><a name="l00825"></a><span class="lineno"> 825</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Sample.html">Sample</a> & sm = cexp_->getSample();</div>
<div class="line"><a name="l00826"></a><span class="lineno"> 826</span>  os << <span class="stringliteral">"\t<description>\n"</span></div>
<div class="line"><a name="l00827"></a><span class="lineno"> 827</span>  << <span class="stringliteral">"\t\t<admin>\n"</span></div>
<div class="line"><a name="l00828"></a><span class="lineno"> 828</span>  << <span class="stringliteral">"\t\t\t<sampleName>"</span></div>
<div class="line"><a name="l00829"></a><span class="lineno"> 829</span>  << sm.<a class="code" href="classOpenMS_1_1Sample.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>()</div>
<div class="line"><a name="l00830"></a><span class="lineno"> 830</span>  << <span class="stringliteral">"</sampleName>\n"</span>;</div>
<div class="line"><a name="l00831"></a><span class="lineno"> 831</span> </div>
<div class="line"><a name="l00832"></a><span class="lineno"> 832</span>  <span class="keywordflow">if</span> (sm.<a class="code" href="classOpenMS_1_1Sample.html#ac06ffdb7464bbdb7304aa4f741e67a75">getNumber</a>() != <span class="stringliteral">""</span> || sm.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>() || sm.<a class="code" href="classOpenMS_1_1Sample.html#a51e7ec6e73028e6e0f073b01382bcaea">getMass</a>() || sm.<a class="code" href="classOpenMS_1_1Sample.html#a2b26ecbcd8002a286574139ad8b2fdbc">getVolume</a>() || sm.<a class="code" href="classOpenMS_1_1Sample.html#afd1e30564c0909e1ada9ca9b6c978352">getConcentration</a>() || !sm.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a001483d1f67f068e585f10d9abcc487d">isMetaEmpty</a>())</div>
<div class="line"><a name="l00833"></a><span class="lineno"> 833</span>  {</div>
<div class="line"><a name="l00834"></a><span class="lineno"> 834</span>  os << <span class="stringliteral">"\t\t\t<sampleDescription>\n"</span>;</div>
<div class="line"><a name="l00835"></a><span class="lineno"> 835</span>  writeCVS_(os, sm.<a class="code" href="classOpenMS_1_1Sample.html#ac06ffdb7464bbdb7304aa4f741e67a75">getNumber</a>(), <span class="stringliteral">"1000001"</span>, <span class="stringliteral">"SampleNumber"</span>);</div>
<div class="line"><a name="l00836"></a><span class="lineno"> 836</span>  writeCVS_(os, sm.<a class="code" href="classOpenMS_1_1Sample.html#a8fee1043a25ea5e1021c04fbd89ca76c">getState</a>(), 0, <span class="stringliteral">"1000003"</span>, <span class="stringliteral">"SampleState"</span>);</div>
<div class="line"><a name="l00837"></a><span class="lineno"> 837</span>  writeCVS_(os, sm.<a class="code" href="classOpenMS_1_1Sample.html#a51e7ec6e73028e6e0f073b01382bcaea">getMass</a>(), <span class="stringliteral">"1000004"</span>, <span class="stringliteral">"SampleMass"</span>);</div>
<div class="line"><a name="l00838"></a><span class="lineno"> 838</span>  writeCVS_(os, sm.<a class="code" href="classOpenMS_1_1Sample.html#a2b26ecbcd8002a286574139ad8b2fdbc">getVolume</a>(), <span class="stringliteral">"1000005"</span>, <span class="stringliteral">"SampleVolume"</span>);</div>
<div class="line"><a name="l00839"></a><span class="lineno"> 839</span>  writeCVS_(os, sm.<a class="code" href="classOpenMS_1_1Sample.html#afd1e30564c0909e1ada9ca9b6c978352">getConcentration</a>(), <span class="stringliteral">"1000006"</span>, <span class="stringliteral">"SampleConcentration"</span>);</div>
<div class="line"><a name="l00840"></a><span class="lineno"> 840</span>  writeUserParam_(os, cexp_->getSample());</div>
<div class="line"><a name="l00841"></a><span class="lineno"> 841</span>  os << <span class="stringliteral">"\t\t\t</sampleDescription>\n"</span>;</div>
<div class="line"><a name="l00842"></a><span class="lineno"> 842</span>  }</div>
<div class="line"><a name="l00843"></a><span class="lineno"> 843</span> </div>
<div class="line"><a name="l00844"></a><span class="lineno"> 844</span>  <span class="keywordflow">if</span> (cexp_->getSourceFiles().size() >= 1)</div>
<div class="line"><a name="l00845"></a><span class="lineno"> 845</span>  {</div>
<div class="line"><a name="l00846"></a><span class="lineno"> 846</span>  os << <span class="stringliteral">"\t\t\t<sourceFile>\n"</span></div>
<div class="line"><a name="l00847"></a><span class="lineno"> 847</span>  << <span class="stringliteral">"\t\t\t\t<nameOfFile>"</span> << cexp_->getSourceFiles()[0].getNameOfFile() << <span class="stringliteral">"</nameOfFile>\n"</span></div>
<div class="line"><a name="l00848"></a><span class="lineno"> 848</span>  << <span class="stringliteral">"\t\t\t\t<pathToFile>"</span> << cexp_->getSourceFiles()[0].getPathToFile() << <span class="stringliteral">"</pathToFile>\n"</span>;</div>
<div class="line"><a name="l00849"></a><span class="lineno"> 849</span>  <span class="keywordflow">if</span> (cexp_->getSourceFiles()[0].getFileType() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00850"></a><span class="lineno"> 850</span>  os << <span class="stringliteral">"\t\t\t\t<fileType>"</span> << cexp_->getSourceFiles()[0].getFileType() << <span class="stringliteral">"</fileType>\n"</span>;</div>
<div class="line"><a name="l00851"></a><span class="lineno"> 851</span>  os << <span class="stringliteral">"\t\t\t</sourceFile>\n"</span>;</div>
<div class="line"><a name="l00852"></a><span class="lineno"> 852</span>  }</div>
<div class="line"><a name="l00853"></a><span class="lineno"> 853</span>  <span class="keywordflow">if</span> (cexp_->getSourceFiles().size() > 1)</div>
<div class="line"><a name="l00854"></a><span class="lineno"> 854</span>  {</div>
<div class="line"><a name="l00855"></a><span class="lineno"> 855</span>  warning(STORE, <span class="stringliteral">"The MzData format can store only one source file. Only the first one is stored!"</span>);</div>
<div class="line"><a name="l00856"></a><span class="lineno"> 856</span>  }</div>
<div class="line"><a name="l00857"></a><span class="lineno"> 857</span> </div>
<div class="line"><a name="l00858"></a><span class="lineno"> 858</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < cexp_->getContacts().size(); ++i)</div>
<div class="line"><a name="l00859"></a><span class="lineno"> 859</span>  {</div>
<div class="line"><a name="l00860"></a><span class="lineno"> 860</span>  os << <span class="stringliteral">"\t\t\t<contact>\n"</span></div>
<div class="line"><a name="l00861"></a><span class="lineno"> 861</span>  << <span class="stringliteral">"\t\t\t\t<name>"</span> << cexp_->getContacts()[i].getFirstName() << <span class="stringliteral">" "</span> << cexp_->getContacts()[i].getLastName() << <span class="stringliteral">"</name>\n"</span></div>
<div class="line"><a name="l00862"></a><span class="lineno"> 862</span>  << <span class="stringliteral">"\t\t\t\t<institution>"</span> << cexp_->getContacts()[i].getInstitution() << <span class="stringliteral">"</institution>\n"</span>;</div>
<div class="line"><a name="l00863"></a><span class="lineno"> 863</span>  <span class="keywordflow">if</span> (cexp_->getContacts()[i].getContactInfo() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00864"></a><span class="lineno"> 864</span>  os << <span class="stringliteral">"\t\t\t\t<contactInfo>"</span> << cexp_->getContacts()[i].getContactInfo() << <span class="stringliteral">"</contactInfo>\n"</span>;</div>
<div class="line"><a name="l00865"></a><span class="lineno"> 865</span>  os << <span class="stringliteral">"\t\t\t</contact>\n"</span>;</div>
<div class="line"><a name="l00866"></a><span class="lineno"> 866</span>  }</div>
<div class="line"><a name="l00867"></a><span class="lineno"> 867</span>  <span class="comment">//no contacts given => add empty entry as there must be a contact entry</span></div>
<div class="line"><a name="l00868"></a><span class="lineno"> 868</span>  <span class="keywordflow">if</span> (cexp_->getContacts().empty())</div>
<div class="line"><a name="l00869"></a><span class="lineno"> 869</span>  {</div>
<div class="line"><a name="l00870"></a><span class="lineno"> 870</span>  os << <span class="stringliteral">"\t\t\t<contact>\n"</span></div>
<div class="line"><a name="l00871"></a><span class="lineno"> 871</span>  << <span class="stringliteral">"\t\t\t\t<name></name>\n"</span></div>
<div class="line"><a name="l00872"></a><span class="lineno"> 872</span>  << <span class="stringliteral">"\t\t\t\t<institution></institution>\n"</span>;</div>
<div class="line"><a name="l00873"></a><span class="lineno"> 873</span>  os << <span class="stringliteral">"\t\t\t</contact>\n"</span>;</div>
<div class="line"><a name="l00874"></a><span class="lineno"> 874</span>  }</div>
<div class="line"><a name="l00875"></a><span class="lineno"> 875</span> </div>
<div class="line"><a name="l00876"></a><span class="lineno"> 876</span>  os << <span class="stringliteral">"\t\t</admin>\n"</span>;</div>
<div class="line"><a name="l00877"></a><span class="lineno"> 877</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Instrument.html">Instrument</a> & inst = cexp_->getInstrument();</div>
<div class="line"><a name="l00878"></a><span class="lineno"> 878</span>  os << <span class="stringliteral">"\t\t<instrument>\n"</span></div>
<div class="line"><a name="l00879"></a><span class="lineno"> 879</span>  << <span class="stringliteral">"\t\t\t<instrumentName>"</span> << inst.<a class="code" href="classOpenMS_1_1Instrument.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() << <span class="stringliteral">"</instrumentName>\n"</span></div>
<div class="line"><a name="l00880"></a><span class="lineno"> 880</span>  << <span class="stringliteral">"\t\t\t<source>\n"</span>;</div>
<div class="line"><a name="l00881"></a><span class="lineno"> 881</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>().size() >= 1)</div>
<div class="line"><a name="l00882"></a><span class="lineno"> 882</span>  {</div>
<div class="line"><a name="l00883"></a><span class="lineno"> 883</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[0].getInletType(), 11, <span class="stringliteral">"1000007"</span>, <span class="stringliteral">"InletType"</span>);</div>
<div class="line"><a name="l00884"></a><span class="lineno"> 884</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[0].getIonizationMethod(), 10, <span class="stringliteral">"1000008"</span>, <span class="stringliteral">"IonizationType"</span>);</div>
<div class="line"><a name="l00885"></a><span class="lineno"> 885</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[0].getPolarity(), 1, <span class="stringliteral">"1000009"</span>, <span class="stringliteral">"IonizationMode"</span>);</div>
<div class="line"><a name="l00886"></a><span class="lineno"> 886</span>  writeUserParam_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[0]);</div>
<div class="line"><a name="l00887"></a><span class="lineno"> 887</span>  }</div>
<div class="line"><a name="l00888"></a><span class="lineno"> 888</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>().size() > 1)</div>
<div class="line"><a name="l00889"></a><span class="lineno"> 889</span>  {</div>
<div class="line"><a name="l00890"></a><span class="lineno"> 890</span>  warning(STORE, <span class="stringliteral">"The MzData format can store only one ion source. Only the first one is stored!"</span>);</div>
<div class="line"><a name="l00891"></a><span class="lineno"> 891</span>  }</div>
<div class="line"><a name="l00892"></a><span class="lineno"> 892</span>  os << <span class="stringliteral">"\t\t\t</source>\n"</span>;</div>
<div class="line"><a name="l00893"></a><span class="lineno"> 893</span> </div>
<div class="line"><a name="l00894"></a><span class="lineno"> 894</span>  <span class="comment">//no analyzer given => add empty entry as there must be one entry</span></div>
<div class="line"><a name="l00895"></a><span class="lineno"> 895</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>().empty())</div>
<div class="line"><a name="l00896"></a><span class="lineno"> 896</span>  {</div>
<div class="line"><a name="l00897"></a><span class="lineno"> 897</span>  os << <span class="stringliteral">"\t\t\t<analyzerList count=\"1\">\n"</span></div>
<div class="line"><a name="l00898"></a><span class="lineno"> 898</span>  << <span class="stringliteral">"\t\t\t\t<analyzer>\n"</span></div>
<div class="line"><a name="l00899"></a><span class="lineno"> 899</span>  << <span class="stringliteral">"\t\t\t\t</analyzer>\n"</span>;</div>
<div class="line"><a name="l00900"></a><span class="lineno"> 900</span>  }</div>
<div class="line"><a name="l00901"></a><span class="lineno"> 901</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00902"></a><span class="lineno"> 902</span>  {</div>
<div class="line"><a name="l00903"></a><span class="lineno"> 903</span>  os << <span class="stringliteral">"\t\t\t<analyzerList count=\""</span> << inst.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>().size() << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l00904"></a><span class="lineno"> 904</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < inst.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>().size(); ++i)</div>
<div class="line"><a name="l00905"></a><span class="lineno"> 905</span>  {</div>
<div class="line"><a name="l00906"></a><span class="lineno"> 906</span>  os << <span class="stringliteral">"\t\t\t\t<analyzer>\n"</span>;</div>
<div class="line"><a name="l00907"></a><span class="lineno"> 907</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MassAnalyzer.html">MassAnalyzer</a> & ana = inst.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>()[i];</div>
<div class="line"><a name="l00908"></a><span class="lineno"> 908</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aef9d6cd0e61ef23e650e06389ba4e3f4">getType</a>(), 14, <span class="stringliteral">"1000010"</span>, <span class="stringliteral">"AnalyzerType"</span>, 5);</div>
<div class="line"><a name="l00909"></a><span class="lineno"> 909</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#adff73543752de4ef66823716e9eed3aa">getResolution</a>(), <span class="stringliteral">"1000011"</span>, <span class="stringliteral">"MassResolution"</span>, 5);</div>
<div class="line"><a name="l00910"></a><span class="lineno"> 910</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a790f2511d9b121d15aef56b6a96b45bf">getResolutionMethod</a>(), 2, <span class="stringliteral">"1000012"</span>, <span class="stringliteral">"ResolutionMethod"</span>, 5);</div>
<div class="line"><a name="l00911"></a><span class="lineno"> 911</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a833abbfac1bc606081ab956e723111c1">getResolutionType</a>(), 3, <span class="stringliteral">"1000013"</span>, <span class="stringliteral">"ResolutionType"</span>, 5);</div>
<div class="line"><a name="l00912"></a><span class="lineno"> 912</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#acf76c337ebde51c823ec30c2985afb0d">getAccuracy</a>(), <span class="stringliteral">"1000014"</span>, <span class="stringliteral">"Accuracy"</span>, 5);</div>
<div class="line"><a name="l00913"></a><span class="lineno"> 913</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a4ff959be3f54a8b526a7777f903ebcce">getScanRate</a>(), <span class="stringliteral">"1000015"</span>, <span class="stringliteral">"ScanRate"</span>, 5);</div>
<div class="line"><a name="l00914"></a><span class="lineno"> 914</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a185f5769dc7bacd1054985fbda81dc20">getScanTime</a>(), <span class="stringliteral">"1000016"</span>, <span class="stringliteral">"ScanTime"</span>, 5);</div>
<div class="line"><a name="l00915"></a><span class="lineno"> 915</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a97cb45890678171a2ad985959861b0fc">getScanDirection</a>(), 5, <span class="stringliteral">"1000018"</span>, <span class="stringliteral">"ScanDirection"</span>, 5);</div>
<div class="line"><a name="l00916"></a><span class="lineno"> 916</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#aca0182626ca1b619a5679b02fa4e8a41">getScanLaw</a>(), 6, <span class="stringliteral">"1000019"</span>, <span class="stringliteral">"ScanLaw"</span>, 5);</div>
<div class="line"><a name="l00917"></a><span class="lineno"> 917</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a171e75c6324f7f4233782be3c4ca1d90">getReflectronState</a>(), 8, <span class="stringliteral">"1000021"</span>, <span class="stringliteral">"ReflectronState"</span>, 5);</div>
<div class="line"><a name="l00918"></a><span class="lineno"> 918</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a0f0fb5610d506c55825effbb77450fd5">getTOFTotalPathLength</a>(), <span class="stringliteral">"1000022"</span>, <span class="stringliteral">"TOFTotalPathLength"</span>, 5);</div>
<div class="line"><a name="l00919"></a><span class="lineno"> 919</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#ae40769827bc59bd577d8b81cd1bb8974">getIsolationWidth</a>(), <span class="stringliteral">"1000023"</span>, <span class="stringliteral">"IsolationWidth"</span>, 5);</div>
<div class="line"><a name="l00920"></a><span class="lineno"> 920</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#af7adaa2fa0d50256c073d4bff34b165d">getFinalMSExponent</a>(), <span class="stringliteral">"1000024"</span>, <span class="stringliteral">"FinalMSExponent"</span>, 5);</div>
<div class="line"><a name="l00921"></a><span class="lineno"> 921</span>  writeCVS_(os, ana.<a class="code" href="classOpenMS_1_1MassAnalyzer.html#ac5bb0a0896c81277ed75428db51dd8b4">getMagneticFieldStrength</a>(), <span class="stringliteral">"1000025"</span>, <span class="stringliteral">"MagneticFieldStrength"</span>, 5);</div>
<div class="line"><a name="l00922"></a><span class="lineno"> 922</span>  writeUserParam_(os, ana, 5);</div>
<div class="line"><a name="l00923"></a><span class="lineno"> 923</span>  os << <span class="stringliteral">"\t\t\t\t</analyzer>\n"</span>;</div>
<div class="line"><a name="l00924"></a><span class="lineno"> 924</span>  }</div>
<div class="line"><a name="l00925"></a><span class="lineno"> 925</span>  }</div>
<div class="line"><a name="l00926"></a><span class="lineno"> 926</span>  os << <span class="stringliteral">"\t\t\t</analyzerList>\n"</span>;</div>
<div class="line"><a name="l00927"></a><span class="lineno"> 927</span> </div>
<div class="line"><a name="l00928"></a><span class="lineno"> 928</span>  os << <span class="stringliteral">"\t\t\t<detector>\n"</span>;</div>
<div class="line"><a name="l00929"></a><span class="lineno"> 929</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>().size() >= 1)</div>
<div class="line"><a name="l00930"></a><span class="lineno"> 930</span>  {</div>
<div class="line"><a name="l00931"></a><span class="lineno"> 931</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0].getType(), 13, <span class="stringliteral">"1000026"</span>, <span class="stringliteral">"DetectorType"</span>);</div>
<div class="line"><a name="l00932"></a><span class="lineno"> 932</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0].getAcquisitionMode(), 9, <span class="stringliteral">"1000027"</span>, <span class="stringliteral">"DetectorAcquisitionMode"</span>);</div>
<div class="line"><a name="l00933"></a><span class="lineno"> 933</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0].getResolution(), <span class="stringliteral">"1000028"</span>, <span class="stringliteral">"DetectorResolution"</span>);</div>
<div class="line"><a name="l00934"></a><span class="lineno"> 934</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0].getADCSamplingFrequency(), <span class="stringliteral">"1000029"</span>, <span class="stringliteral">"SamplingFrequency"</span>);</div>
<div class="line"><a name="l00935"></a><span class="lineno"> 935</span>  writeUserParam_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0]);</div>
<div class="line"><a name="l00936"></a><span class="lineno"> 936</span>  }</div>
<div class="line"><a name="l00937"></a><span class="lineno"> 937</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>().size() > 1)</div>
<div class="line"><a name="l00938"></a><span class="lineno"> 938</span>  {</div>
<div class="line"><a name="l00939"></a><span class="lineno"> 939</span>  warning(STORE, <span class="stringliteral">"The MzData format can store only one ion detector. Only the first one is stored!"</span>);</div>
<div class="line"><a name="l00940"></a><span class="lineno"> 940</span>  }</div>
<div class="line"><a name="l00941"></a><span class="lineno"> 941</span>  os << <span class="stringliteral">"\t\t\t</detector>\n"</span>;</div>
<div class="line"><a name="l00942"></a><span class="lineno"> 942</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#adeb3a96bea31dcca5dc2cba4d6e22cb5">getVendor</a>() != <span class="stringliteral">""</span> || inst.<a class="code" href="classOpenMS_1_1Instrument.html#a307ba40c92040f24cb0b496fb5b58b88">getModel</a>() != <span class="stringliteral">""</span> || inst.<a class="code" href="classOpenMS_1_1Instrument.html#a935d3c82c309ed3c0ed94d5edb12ce08">getCustomizations</a>() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00943"></a><span class="lineno"> 943</span>  {</div>
<div class="line"><a name="l00944"></a><span class="lineno"> 944</span>  os << <span class="stringliteral">"\t\t\t<additional>\n"</span>;</div>
<div class="line"><a name="l00945"></a><span class="lineno"> 945</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#adeb3a96bea31dcca5dc2cba4d6e22cb5">getVendor</a>(), <span class="stringliteral">"1000030"</span>, <span class="stringliteral">"Vendor"</span>);</div>
<div class="line"><a name="l00946"></a><span class="lineno"> 946</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a307ba40c92040f24cb0b496fb5b58b88">getModel</a>(), <span class="stringliteral">"1000031"</span>, <span class="stringliteral">"Model"</span>);</div>
<div class="line"><a name="l00947"></a><span class="lineno"> 947</span>  writeCVS_(os, inst.<a class="code" href="classOpenMS_1_1Instrument.html#a935d3c82c309ed3c0ed94d5edb12ce08">getCustomizations</a>(), <span class="stringliteral">"1000032"</span>, <span class="stringliteral">"Customization"</span>);</div>
<div class="line"><a name="l00948"></a><span class="lineno"> 948</span>  writeUserParam_(os, inst);</div>
<div class="line"><a name="l00949"></a><span class="lineno"> 949</span>  os << <span class="stringliteral">"\t\t\t</additional>\n"</span>;</div>
<div class="line"><a name="l00950"></a><span class="lineno"> 950</span>  }</div>
<div class="line"><a name="l00951"></a><span class="lineno"> 951</span>  os << <span class="stringliteral">"\t\t</instrument>\n"</span>;</div>
<div class="line"><a name="l00952"></a><span class="lineno"> 952</span> </div>
<div class="line"><a name="l00953"></a><span class="lineno"> 953</span>  <span class="comment">//the data processing information of the first spectrum is used for the whole file</span></div>
<div class="line"><a name="l00954"></a><span class="lineno"> 954</span>  <span class="keywordflow">if</span> (cexp_->size() == 0 || (*cexp_)[0].getDataProcessing().empty())</div>
<div class="line"><a name="l00955"></a><span class="lineno"> 955</span>  {</div>
<div class="line"><a name="l00956"></a><span class="lineno"> 956</span>  os << <span class="stringliteral">"\t\t<dataProcessing>\n"</span></div>
<div class="line"><a name="l00957"></a><span class="lineno"> 957</span>  << <span class="stringliteral">"\t\t\t<software>\n"</span></div>
<div class="line"><a name="l00958"></a><span class="lineno"> 958</span>  << <span class="stringliteral">"\t\t\t\t<name></name>\n"</span></div>
<div class="line"><a name="l00959"></a><span class="lineno"> 959</span>  << <span class="stringliteral">"\t\t\t\t<version></version>\n"</span></div>
<div class="line"><a name="l00960"></a><span class="lineno"> 960</span>  << <span class="stringliteral">"\t\t\t</software>\n"</span></div>
<div class="line"><a name="l00961"></a><span class="lineno"> 961</span>  << <span class="stringliteral">"\t\t</dataProcessing>\n"</span>;</div>
<div class="line"><a name="l00962"></a><span class="lineno"> 962</span>  }</div>
<div class="line"><a name="l00963"></a><span class="lineno"> 963</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00964"></a><span class="lineno"> 964</span>  {</div>
<div class="line"><a name="l00965"></a><span class="lineno"> 965</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> & data_processing = (*cexp_)[0].getDataProcessing()[0];</div>
<div class="line"><a name="l00966"></a><span class="lineno"> 966</span>  os << <span class="stringliteral">"\t\t<dataProcessing>\n"</span></div>
<div class="line"><a name="l00967"></a><span class="lineno"> 967</span>  << <span class="stringliteral">"\t\t\t<software"</span>;</div>
<div class="line"><a name="l00968"></a><span class="lineno"> 968</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a3bbd5b209e18f9afd4d8b4308787a538">getCompletionTime</a>() != <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a>())</div>
<div class="line"><a name="l00969"></a><span class="lineno"> 969</span>  {</div>
<div class="line"><a name="l00970"></a><span class="lineno"> 970</span>  os << <span class="stringliteral">" completionTime=\""</span> << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a3bbd5b209e18f9afd4d8b4308787a538">getCompletionTime</a>().<a class="code" href="classOpenMS_1_1DateTime.html#ae8d3cac5cd5763984d9ca84d3453ed28">get</a>().substitute(<span class="charliteral">' '</span>, <span class="charliteral">'T'</span>) << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l00971"></a><span class="lineno"> 971</span>  }</div>
<div class="line"><a name="l00972"></a><span class="lineno"> 972</span>  os << <span class="stringliteral">">\n"</span></div>
<div class="line"><a name="l00973"></a><span class="lineno"> 973</span>  << <span class="stringliteral">"\t\t\t\t<name>"</span> << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a219795d06917877c7d946a00f23e2319">getSoftware</a>().<a class="code" href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() << <span class="stringliteral">"</name>\n"</span></div>
<div class="line"><a name="l00974"></a><span class="lineno"> 974</span>  << <span class="stringliteral">"\t\t\t\t<version>"</span> << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a219795d06917877c7d946a00f23e2319">getSoftware</a>().<a class="code" href="classOpenMS_1_1Software.html#ae6b3b4b6857bc1987282e2f29611dd41">getVersion</a>() << <span class="stringliteral">"</version>\n"</span>;</div>
<div class="line"><a name="l00975"></a><span class="lineno"> 975</span>  os << <span class="stringliteral">"\t\t\t</software>\n"</span></div>
<div class="line"><a name="l00976"></a><span class="lineno"> 976</span>  << <span class="stringliteral">"\t\t\t<processingMethod>\n"</span>;</div>
<div class="line"><a name="l00977"></a><span class="lineno"> 977</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">getProcessingActions</a>().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">DataProcessing::DEISOTOPING</a>) == 1)</div>
<div class="line"><a name="l00978"></a><span class="lineno"> 978</span>  {</div>
<div class="line"><a name="l00979"></a><span class="lineno"> 979</span>  os << <span class="stringliteral">"\t\t\t\t<cvParam cvLabel=\"psi\" name=\"Deisotoping\" accession=\"PSI:1000033\" />\n"</span>;</div>
<div class="line"><a name="l00980"></a><span class="lineno"> 980</span>  }</div>
<div class="line"><a name="l00981"></a><span class="lineno"> 981</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">getProcessingActions</a>().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">DataProcessing::CHARGE_DECONVOLUTION</a>) == 1)</div>
<div class="line"><a name="l00982"></a><span class="lineno"> 982</span>  {</div>
<div class="line"><a name="l00983"></a><span class="lineno"> 983</span>  os << <span class="stringliteral">"\t\t\t\t<cvParam cvLabel=\"psi\" name=\"ChargeDeconvolution\" accession=\"PSI:1000034\" />\n"</span>;</div>
<div class="line"><a name="l00984"></a><span class="lineno"> 984</span>  }</div>
<div class="line"><a name="l00985"></a><span class="lineno"> 985</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">getProcessingActions</a>().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">DataProcessing::PEAK_PICKING</a>) == 1)</div>
<div class="line"><a name="l00986"></a><span class="lineno"> 986</span>  {</div>
<div class="line"><a name="l00987"></a><span class="lineno"> 987</span>  os << <span class="stringliteral">"\t\t\t\t<cvParam cvLabel=\"psi\" name=\"Centroid Mass Spectrum\" accession=\"PSI:1000127\"/>\n"</span>;</div>
<div class="line"><a name="l00988"></a><span class="lineno"> 988</span>  }</div>
<div class="line"><a name="l00989"></a><span class="lineno"> 989</span>  writeUserParam_(os, data_processing);</div>
<div class="line"><a name="l00990"></a><span class="lineno"> 990</span>  os << <span class="stringliteral">"\t\t\t</processingMethod>\n"</span></div>
<div class="line"><a name="l00991"></a><span class="lineno"> 991</span>  << <span class="stringliteral">"\t\t</dataProcessing>\n"</span>;</div>
<div class="line"><a name="l00992"></a><span class="lineno"> 992</span>  }</div>
<div class="line"><a name="l00993"></a><span class="lineno"> 993</span>  os << <span class="stringliteral">"\t</description>\n"</span>;</div>
<div class="line"><a name="l00994"></a><span class="lineno"> 994</span> </div>
<div class="line"><a name="l00995"></a><span class="lineno"> 995</span>  <span class="comment">//---------------------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00996"></a><span class="lineno"> 996</span>  <span class="comment">//ACTUAL DATA</span></div>
<div class="line"><a name="l00997"></a><span class="lineno"> 997</span>  <span class="keywordflow">if</span> (cexp_->size() != 0)</div>
<div class="line"><a name="l00998"></a><span class="lineno"> 998</span>  {</div>
<div class="line"><a name="l00999"></a><span class="lineno"> 999</span>  <span class="comment">//check if the nativeID of all spectra are numbers or numbers prefixed with 'spectrum='</span></div>
<div class="line"><a name="l01000"></a><span class="lineno"> 1000</span>  <span class="comment">//If not we need to renumber all spectra.</span></div>
<div class="line"><a name="l01001"></a><span class="lineno"> 1001</span>  <span class="keywordtype">bool</span> all_numbers = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01002"></a><span class="lineno"> 1002</span>  <span class="keywordtype">bool</span> all_empty = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01003"></a><span class="lineno"> 1003</span>  <span class="keywordtype">bool</span> all_prefixed_numbers = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01004"></a><span class="lineno"> 1004</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < cexp_->size(); s++)</div>
<div class="line"><a name="l01005"></a><span class="lineno"> 1005</span>  {</div>
<div class="line"><a name="l01006"></a><span class="lineno"> 1006</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> native_id = (*cexp_)[s].getNativeID();</div>
<div class="line"><a name="l01007"></a><span class="lineno"> 1007</span>  <span class="keywordflow">if</span> (!native_id.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">"spectrum="</span>))</div>
<div class="line"><a name="l01008"></a><span class="lineno"> 1008</span>  {</div>
<div class="line"><a name="l01009"></a><span class="lineno"> 1009</span>  all_prefixed_numbers = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01010"></a><span class="lineno"> 1010</span>  }</div>
<div class="line"><a name="l01011"></a><span class="lineno"> 1011</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01012"></a><span class="lineno"> 1012</span>  {</div>
<div class="line"><a name="l01013"></a><span class="lineno"> 1013</span>  native_id = native_id.<a class="code" href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">substr</a>(9);</div>
<div class="line"><a name="l01014"></a><span class="lineno"> 1014</span>  }</div>
<div class="line"><a name="l01015"></a><span class="lineno"> 1015</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l01016"></a><span class="lineno"> 1016</span>  {</div>
<div class="line"><a name="l01017"></a><span class="lineno"> 1017</span>  native_id.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01018"></a><span class="lineno"> 1018</span>  }</div>
<div class="line"><a name="l01019"></a><span class="lineno"> 1019</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ConversionError.html">Exception::ConversionError</a> &)</div>
<div class="line"><a name="l01020"></a><span class="lineno"> 1020</span>  {</div>
<div class="line"><a name="l01021"></a><span class="lineno"> 1021</span>  all_numbers = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01022"></a><span class="lineno"> 1022</span>  all_prefixed_numbers = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01023"></a><span class="lineno"> 1023</span>  <span class="keywordflow">if</span> (native_id != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l01024"></a><span class="lineno"> 1024</span>  {</div>
<div class="line"><a name="l01025"></a><span class="lineno"> 1025</span>  all_empty = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01026"></a><span class="lineno"> 1026</span>  }</div>
<div class="line"><a name="l01027"></a><span class="lineno"> 1027</span>  }</div>
<div class="line"><a name="l01028"></a><span class="lineno"> 1028</span>  }</div>
<div class="line"><a name="l01029"></a><span class="lineno"> 1029</span>  <span class="comment">//If we need to renumber and the nativeIDs were not empty, warn the user</span></div>
<div class="line"><a name="l01030"></a><span class="lineno"> 1030</span>  <span class="keywordflow">if</span> (!all_numbers && !all_empty)</div>
<div class="line"><a name="l01031"></a><span class="lineno"> 1031</span>  {</div>
<div class="line"><a name="l01032"></a><span class="lineno"> 1032</span>  warning(STORE, <span class="stringliteral">"Not all spectrum native IDs are numbers or correctly prefixed with 'spectrum='. The spectra are renumbered and the native IDs are lost!"</span>);</div>
<div class="line"><a name="l01033"></a><span class="lineno"> 1033</span>  }</div>
<div class="line"><a name="l01034"></a><span class="lineno"> 1034</span>  <span class="comment">//Map to store the last spectrum ID for each MS level (needed to find precursor spectra)</span></div>
<div class="line"><a name="l01035"></a><span class="lineno"> 1035</span>  <a class="code" href="classOpenMS_1_1Map.html">Map<Int, Size></a> level_id;</div>
<div class="line"><a name="l01036"></a><span class="lineno"> 1036</span> </div>
<div class="line"><a name="l01037"></a><span class="lineno"> 1037</span>  os << <span class="stringliteral">"\t<spectrumList count=\""</span> << cexp_->size() << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l01038"></a><span class="lineno"> 1038</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < cexp_->size(); ++s)</div>
<div class="line"><a name="l01039"></a><span class="lineno"> 1039</span>  {</div>
<div class="line"><a name="l01040"></a><span class="lineno"> 1040</span>  logger_.setProgress(s);</div>
<div class="line"><a name="l01041"></a><span class="lineno"> 1041</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a> & spec = (*cexp_)[s];</div>
<div class="line"><a name="l01042"></a><span class="lineno"> 1042</span> </div>
<div class="line"><a name="l01043"></a><span class="lineno"> 1043</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum_id = s + 1;</div>
<div class="line"><a name="l01044"></a><span class="lineno"> 1044</span>  <span class="keywordflow">if</span> (all_prefixed_numbers)</div>
<div class="line"><a name="l01045"></a><span class="lineno"> 1045</span>  {</div>
<div class="line"><a name="l01046"></a><span class="lineno"> 1046</span>  spectrum_id = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>().<a class="code" href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">substr</a>(9).<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01047"></a><span class="lineno"> 1047</span>  }</div>
<div class="line"><a name="l01048"></a><span class="lineno"> 1048</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (all_numbers)</div>
<div class="line"><a name="l01049"></a><span class="lineno"> 1049</span>  {</div>
<div class="line"><a name="l01050"></a><span class="lineno"> 1050</span>  spectrum_id = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>().<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01051"></a><span class="lineno"> 1051</span>  }</div>
<div class="line"><a name="l01052"></a><span class="lineno"> 1052</span>  os << <span class="stringliteral">"\t\t<spectrum id=\""</span> << spectrum_id << <span class="stringliteral">"\">\n"</span></div>
<div class="line"><a name="l01053"></a><span class="lineno"> 1053</span>  << <span class="stringliteral">"\t\t\t<spectrumDesc>\n"</span></div>
<div class="line"><a name="l01054"></a><span class="lineno"> 1054</span>  << <span class="stringliteral">"\t\t\t\t<spectrumSettings>\n"</span>;</div>
<div class="line"><a name="l01055"></a><span class="lineno"> 1055</span> </div>
<div class="line"><a name="l01056"></a><span class="lineno"> 1056</span>  <span class="keywordflow">if</span> (!spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().empty())</div>
<div class="line"><a name="l01057"></a><span class="lineno"> 1057</span>  {</div>
<div class="line"><a name="l01058"></a><span class="lineno"> 1058</span>  os << <span class="stringliteral">"\t\t\t\t\t<acqSpecification spectrumType=\""</span>;</div>
<div class="line"><a name="l01059"></a><span class="lineno"> 1059</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#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>)</div>
<div class="line"><a name="l01060"></a><span class="lineno"> 1060</span>  {</div>
<div class="line"><a name="l01061"></a><span class="lineno"> 1061</span>  os << <span class="stringliteral">"discrete"</span>;</div>
<div class="line"><a name="l01062"></a><span class="lineno"> 1062</span>  }</div>
<div class="line"><a name="l01063"></a><span class="lineno"> 1063</span>  <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="l01064"></a><span class="lineno"> 1064</span>  {</div>
<div class="line"><a name="l01065"></a><span class="lineno"> 1065</span>  os << <span class="stringliteral">"continuous"</span>;</div>
<div class="line"><a name="l01066"></a><span class="lineno"> 1066</span>  }</div>
<div class="line"><a name="l01067"></a><span class="lineno"> 1067</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01068"></a><span class="lineno"> 1068</span>  {</div>
<div class="line"><a name="l01069"></a><span class="lineno"> 1069</span>  warning(STORE, <span class="stringliteral">"Spectrum type is unknown, assuming 'discrete'"</span>);</div>
<div class="line"><a name="l01070"></a><span class="lineno"> 1070</span>  os << <span class="stringliteral">"discrete"</span>;</div>
<div class="line"><a name="l01071"></a><span class="lineno"> 1071</span>  }</div>
<div class="line"><a name="l01072"></a><span class="lineno"> 1072</span> </div>
<div class="line"><a name="l01073"></a><span class="lineno"> 1073</span>  os << <span class="stringliteral">"\" methodOfCombination=\""</span> << spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().<a class="code" href="classOpenMS_1_1AcquisitionInfo.html#a883a8e420b509ac1c9a4b08f4494915d">getMethodOfCombination</a>() << <span class="stringliteral">"\""</span></div>
<div class="line"><a name="l01074"></a><span class="lineno"> 1074</span>  << <span class="stringliteral">" count=\""</span> << spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().size() << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l01075"></a><span class="lineno"> 1075</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>().size(); ++i)</div>
<div class="line"><a name="l01076"></a><span class="lineno"> 1076</span>  {</div>
<div class="line"><a name="l01077"></a><span class="lineno"> 1077</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Acquisition.html">Acquisition</a> & ac = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#acd72014f8324c633851b7b4f169f3749">getAcquisitionInfo</a>()[i];</div>
<div class="line"><a name="l01078"></a><span class="lineno"> 1078</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> acq_number = 0;</div>
<div class="line"><a name="l01079"></a><span class="lineno"> 1079</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l01080"></a><span class="lineno"> 1080</span>  {</div>
<div class="line"><a name="l01081"></a><span class="lineno"> 1081</span>  <span class="keywordflow">if</span> (ac.<a class="code" href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">getIdentifier</a>() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l01082"></a><span class="lineno"> 1082</span>  {</div>
<div class="line"><a name="l01083"></a><span class="lineno"> 1083</span>  acq_number = ac.<a class="code" href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">getIdentifier</a>().<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01084"></a><span class="lineno"> 1084</span>  }</div>
<div class="line"><a name="l01085"></a><span class="lineno"> 1085</span>  }</div>
<div class="line"><a name="l01086"></a><span class="lineno"> 1086</span>  <span class="keywordflow">catch</span> (...)</div>
<div class="line"><a name="l01087"></a><span class="lineno"> 1087</span>  {</div>
<div class="line"><a name="l01088"></a><span class="lineno"> 1088</span>  warning(STORE, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Could not convert acquisition identifier '"</span>) + ac.<a class="code" href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">getIdentifier</a>() + <span class="stringliteral">"' to an integer. Using '0' instead!"</span>);</div>
<div class="line"><a name="l01089"></a><span class="lineno"> 1089</span>  acq_number = 0;</div>
<div class="line"><a name="l01090"></a><span class="lineno"> 1090</span>  }</div>
<div class="line"><a name="l01091"></a><span class="lineno"> 1091</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<acquisition acqNumber=\""</span> << acq_number << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l01092"></a><span class="lineno"> 1092</span>  writeUserParam_(os, ac, 7);</div>
<div class="line"><a name="l01093"></a><span class="lineno"> 1093</span>  os << <span class="stringliteral">"\t\t\t\t\t\t</acquisition>\n"</span>;</div>
<div class="line"><a name="l01094"></a><span class="lineno"> 1094</span>  }</div>
<div class="line"><a name="l01095"></a><span class="lineno"> 1095</span>  os << <span class="stringliteral">"\t\t\t\t\t</acqSpecification>\n"</span>;</div>
<div class="line"><a name="l01096"></a><span class="lineno"> 1096</span>  }</div>
<div class="line"><a name="l01097"></a><span class="lineno"> 1097</span> </div>
<div class="line"><a name="l01098"></a><span class="lineno"> 1098</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html">InstrumentSettings</a> & iset = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>();</div>
<div class="line"><a name="l01099"></a><span class="lineno"> 1099</span>  os << <span class="stringliteral">"\t\t\t\t\t<spectrumInstrument msLevel=\""</span> << spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>() << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01100"></a><span class="lineno"> 1100</span>  level_id[spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>()] = spectrum_id;</div>
<div class="line"><a name="l01101"></a><span class="lineno"> 1101</span> </div>
<div class="line"><a name="l01102"></a><span class="lineno"> 1102</span>  <span class="keywordflow">if</span> (!iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().empty())</div>
<div class="line"><a name="l01103"></a><span class="lineno"> 1103</span>  {</div>
<div class="line"><a name="l01104"></a><span class="lineno"> 1104</span>  os << <span class="stringliteral">" mzRangeStart=\""</span> << iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[0].begin << <span class="stringliteral">"\" mzRangeStop=\""</span> << iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[0].end << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01105"></a><span class="lineno"> 1105</span>  }</div>
<div class="line"><a name="l01106"></a><span class="lineno"> 1106</span>  <span class="keywordflow">if</span> (iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size() > 1)</div>
<div class="line"><a name="l01107"></a><span class="lineno"> 1107</span>  {</div>
<div class="line"><a name="l01108"></a><span class="lineno"> 1108</span>  warning(STORE, <span class="stringliteral">"The MzData format can store only one scan window for each scan. Only the first one is stored!"</span>);</div>
<div class="line"><a name="l01109"></a><span class="lineno"> 1109</span>  }</div>
<div class="line"><a name="l01110"></a><span class="lineno"> 1110</span>  os << <span class="stringliteral">">\n"</span>;</div>
<div class="line"><a name="l01111"></a><span class="lineno"> 1111</span> </div>
<div class="line"><a name="l01112"></a><span class="lineno"> 1112</span>  <span class="comment">//scan mode</span></div>
<div class="line"><a name="l01113"></a><span class="lineno"> 1113</span>  <span class="keywordflow">switch</span> (iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>())</div>
<div class="line"><a name="l01114"></a><span class="lineno"> 1114</span>  {</div>
<div class="line"><a name="l01115"></a><span class="lineno"> 1115</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c">InstrumentSettings::UNKNOWN</a>:</div>
<div class="line"><a name="l01116"></a><span class="lineno"> 1116</span>  <span class="comment">//do nothing here</span></div>
<div class="line"><a name="l01117"></a><span class="lineno"> 1117</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01118"></a><span class="lineno"> 1118</span> </div>
<div class="line"><a name="l01119"></a><span class="lineno"> 1119</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>:</div>
<div class="line"><a name="l01120"></a><span class="lineno"> 1120</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">InstrumentSettings::MS1SPECTRUM</a>:</div>
<div class="line"><a name="l01121"></a><span class="lineno"> 1121</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>:</div>
<div class="line"><a name="l01122"></a><span class="lineno"> 1122</span>  <span class="keywordflow">if</span> (iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a3409c914db15bbb4696822e623a69ef1">getZoomScan</a>())</div>
<div class="line"><a name="l01123"></a><span class="lineno"> 1123</span>  {</div>
<div class="line"><a name="l01124"></a><span class="lineno"> 1124</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"Zoom\"/>\n"</span>;</div>
<div class="line"><a name="l01125"></a><span class="lineno"> 1125</span>  }</div>
<div class="line"><a name="l01126"></a><span class="lineno"> 1126</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01127"></a><span class="lineno"> 1127</span>  {</div>
<div class="line"><a name="l01128"></a><span class="lineno"> 1128</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"MassScan\"/>\n"</span>;</div>
<div class="line"><a name="l01129"></a><span class="lineno"> 1129</span>  }</div>
<div class="line"><a name="l01130"></a><span class="lineno"> 1130</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01131"></a><span class="lineno"> 1131</span> </div>
<div class="line"><a name="l01132"></a><span class="lineno"> 1132</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>:</div>
<div class="line"><a name="l01133"></a><span class="lineno"> 1133</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"SelectedIonDetection\"/>\n"</span>;</div>
<div class="line"><a name="l01134"></a><span class="lineno"> 1134</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01135"></a><span class="lineno"> 1135</span> </div>
<div class="line"><a name="l01136"></a><span class="lineno"> 1136</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>:</div>
<div class="line"><a name="l01137"></a><span class="lineno"> 1137</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"SelectedReactionMonitoring\"/>\n"</span>;</div>
<div class="line"><a name="l01138"></a><span class="lineno"> 1138</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01139"></a><span class="lineno"> 1139</span> </div>
<div class="line"><a name="l01140"></a><span class="lineno"> 1140</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>:</div>
<div class="line"><a name="l01141"></a><span class="lineno"> 1141</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"ConsecutiveReactionMonitoring\"/>\n"</span>;</div>
<div class="line"><a name="l01142"></a><span class="lineno"> 1142</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01143"></a><span class="lineno"> 1143</span> </div>
<div class="line"><a name="l01144"></a><span class="lineno"> 1144</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f">InstrumentSettings::CNG</a>:</div>
<div class="line"><a name="l01145"></a><span class="lineno"> 1145</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"ConstantNeutralGainScan\"/>\n"</span>;</div>
<div class="line"><a name="l01146"></a><span class="lineno"> 1146</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01147"></a><span class="lineno"> 1147</span> </div>
<div class="line"><a name="l01148"></a><span class="lineno"> 1148</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca">InstrumentSettings::CNL</a>:</div>
<div class="line"><a name="l01149"></a><span class="lineno"> 1149</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"ConstantNeutralLossScan\"/>\n"</span>;</div>
<div class="line"><a name="l01150"></a><span class="lineno"> 1150</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01151"></a><span class="lineno"> 1151</span> </div>
<div class="line"><a name="l01152"></a><span class="lineno"> 1152</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f">InstrumentSettings::PRECURSOR</a>:</div>
<div class="line"><a name="l01153"></a><span class="lineno"> 1153</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"PrecursorIonScan\"/>\n"</span>;</div>
<div class="line"><a name="l01154"></a><span class="lineno"> 1154</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01155"></a><span class="lineno"> 1155</span> </div>
<div class="line"><a name="l01156"></a><span class="lineno"> 1156</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac1923f59816bf846e2a62d41cfb91b2f">InstrumentSettings::ABSORBTION</a>:</div>
<div class="line"><a name="l01157"></a><span class="lineno"> 1157</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"PhotodiodeArrayDetector\"/>\n"</span>;</div>
<div class="line"><a name="l01158"></a><span class="lineno"> 1158</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01159"></a><span class="lineno"> 1159</span> </div>
<div class="line"><a name="l01160"></a><span class="lineno"> 1160</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ac21206f76146b8913723119f609be907">InstrumentSettings::EMC</a>:</div>
<div class="line"><a name="l01161"></a><span class="lineno"> 1161</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"EnhancedMultiplyChargedScan\"/>\n"</span>;</div>
<div class="line"><a name="l01162"></a><span class="lineno"> 1162</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01163"></a><span class="lineno"> 1163</span> </div>
<div class="line"><a name="l01164"></a><span class="lineno"> 1164</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a5980df92dcce7a0e1e8bc482e4f07aa6">InstrumentSettings::TDF</a>:</div>
<div class="line"><a name="l01165"></a><span class="lineno"> 1165</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"TimeDelayedFragmentationScan\"/>\n"</span>;</div>
<div class="line"><a name="l01166"></a><span class="lineno"> 1166</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01167"></a><span class="lineno"> 1167</span> </div>
<div class="line"><a name="l01168"></a><span class="lineno"> 1168</span>  <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l01169"></a><span class="lineno"> 1169</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000036\" name=\"ScanMode\" value=\"MassScan\"/>\n"</span>;</div>
<div class="line"><a name="l01170"></a><span class="lineno"> 1170</span>  warning(STORE, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Scan mode '"</span>) + <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9ecf94ffd05a020cce7a2d10794a192">InstrumentSettings::NamesOfScanMode</a>[iset.<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>()] + <span class="stringliteral">"' not supported by mzData. Using 'MassScan' scan mode!"</span>);</div>
<div class="line"><a name="l01171"></a><span class="lineno"> 1171</span>  }</div>
<div class="line"><a name="l01172"></a><span class="lineno"> 1172</span> </div>
<div class="line"><a name="l01173"></a><span class="lineno"> 1173</span>  <span class="comment">//scan polarity</span></div>
<div class="line"><a name="l01174"></a><span class="lineno"> 1174</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="l01175"></a><span class="lineno"> 1175</span>  {</div>
<div class="line"><a name="l01176"></a><span class="lineno"> 1176</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(6, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<cvParam cvLabel=\"psi\" accession=\"PSI:1000037\" name=\"Polarity\" value=\"Positive\"/>\n"</span>;</div>
<div class="line"><a name="l01177"></a><span class="lineno"> 1177</span>  }</div>
<div class="line"><a name="l01178"></a><span class="lineno"> 1178</span>  <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#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">IonSource::NEGATIVE</a>)</div>
<div class="line"><a name="l01179"></a><span class="lineno"> 1179</span>  {</div>
<div class="line"><a name="l01180"></a><span class="lineno"> 1180</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(6, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<cvParam cvLabel=\"psi\" accession=\"PSI:1000037\" name=\"Polarity\" value=\"Negative\"/>\n"</span>;</div>
<div class="line"><a name="l01181"></a><span class="lineno"> 1181</span>  }</div>
<div class="line"><a name="l01182"></a><span class="lineno"> 1182</span> </div>
<div class="line"><a name="l01183"></a><span class="lineno"> 1183</span>  <span class="comment">//Retiontion time already in TimeInSeconds</span></div>
<div class="line"><a name="l01184"></a><span class="lineno"> 1184</span>  writeCVS_(os, spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>(), <span class="stringliteral">"1000039"</span>, <span class="stringliteral">"TimeInSeconds"</span>, 6);</div>
<div class="line"><a name="l01185"></a><span class="lineno"> 1185</span>  writeUserParam_(os, spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>(), 6);</div>
<div class="line"><a name="l01186"></a><span class="lineno"> 1186</span>  os << <span class="stringliteral">"\t\t\t\t\t</spectrumInstrument>\n\t\t\t\t</spectrumSettings>\n"</span>;</div>
<div class="line"><a name="l01187"></a><span class="lineno"> 1187</span> </div>
<div class="line"><a name="l01188"></a><span class="lineno"> 1188</span>  <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().size() != 0)</div>
<div class="line"><a name="l01189"></a><span class="lineno"> 1189</span>  {</div>
<div class="line"><a name="l01190"></a><span class="lineno"> 1190</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> precursor_ms_level = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>() - 1;</div>
<div class="line"><a name="l01191"></a><span class="lineno"> 1191</span>  <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> precursor_id = -1;</div>
<div class="line"><a name="l01192"></a><span class="lineno"> 1192</span>  <span class="keywordflow">if</span> (level_id.<a class="code" href="classOpenMS_1_1Map.html#a9eabefcb1631e53589789d97d0a72f9d">has</a>(precursor_ms_level))</div>
<div class="line"><a name="l01193"></a><span class="lineno"> 1193</span>  {</div>
<div class="line"><a name="l01194"></a><span class="lineno"> 1194</span>  precursor_id = level_id[precursor_ms_level];</div>
<div class="line"><a name="l01195"></a><span class="lineno"> 1195</span>  }</div>
<div class="line"><a name="l01196"></a><span class="lineno"> 1196</span>  os << <span class="stringliteral">"\t\t\t\t<precursorList count=\""</span> << spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().size() << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l01197"></a><span class="lineno"> 1197</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().size(); ++i)</div>
<div class="line"><a name="l01198"></a><span class="lineno"> 1198</span>  {</div>
<div class="line"><a name="l01199"></a><span class="lineno"> 1199</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a> & precursor = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>()[i];</div>
<div class="line"><a name="l01200"></a><span class="lineno"> 1200</span>  os << <span class="stringliteral">"\t\t\t\t\t<precursor msLevel=\""</span> << precursor_ms_level << <span class="stringliteral">"\" spectrumRef=\""</span> << precursor_id << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l01201"></a><span class="lineno"> 1201</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<ionSelection>\n"</span>;</div>
<div class="line"><a name="l01202"></a><span class="lineno"> 1202</span>  <span class="keywordflow">if</span> (precursor != <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>())</div>
<div class="line"><a name="l01203"></a><span class="lineno"> 1203</span>  {</div>
<div class="line"><a name="l01204"></a><span class="lineno"> 1204</span>  writeCVS_(os, precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>(), <span class="stringliteral">"1000040"</span>, <span class="stringliteral">"MassToChargeRatio"</span>, 7);</div>
<div class="line"><a name="l01205"></a><span class="lineno"> 1205</span>  writeCVS_(os, precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>(), <span class="stringliteral">"1000041"</span>, <span class="stringliteral">"ChargeState"</span>, 7);</div>
<div class="line"><a name="l01206"></a><span class="lineno"> 1206</span>  writeCVS_(os, precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>(), <span class="stringliteral">"1000042"</span>, <span class="stringliteral">"Intensity"</span>, 7);</div>
<div class="line"><a name="l01207"></a><span class="lineno"> 1207</span>  os << <span class="stringliteral">"\t\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000043\" name=\"IntensityUnit\" value=\"NumberOfCounts\"/>\n"</span>;</div>
<div class="line"><a name="l01208"></a><span class="lineno"> 1208</span>  writeUserParam_(os, precursor, 7);</div>
<div class="line"><a name="l01209"></a><span class="lineno"> 1209</span>  }</div>
<div class="line"><a name="l01210"></a><span class="lineno"> 1210</span>  os << <span class="stringliteral">"\t\t\t\t\t\t</ionSelection>\n"</span>;</div>
<div class="line"><a name="l01211"></a><span class="lineno"> 1211</span>  os << <span class="stringliteral">"\t\t\t\t\t\t<activation>\n"</span>;</div>
<div class="line"><a name="l01212"></a><span class="lineno"> 1212</span>  <span class="keywordflow">if</span> (precursor != <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>())</div>
<div class="line"><a name="l01213"></a><span class="lineno"> 1213</span>  {</div>
<div class="line"><a name="l01214"></a><span class="lineno"> 1214</span>  <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().size() > 0)</div>
<div class="line"><a name="l01215"></a><span class="lineno"> 1215</span>  {</div>
<div class="line"><a name="l01216"></a><span class="lineno"> 1216</span>  writeCVS_(os, *(precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a9933807a51860e1320ce47c3b83bcbd2">getActivationMethods</a>().begin()), 18, <span class="stringliteral">"1000044"</span>, <span class="stringliteral">"ActivationMethod"</span>, 7);</div>
<div class="line"><a name="l01217"></a><span class="lineno"> 1217</span>  }</div>
<div class="line"><a name="l01218"></a><span class="lineno"> 1218</span>  writeCVS_(os, precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ad34cda135f7788348ea8866353407d38">getActivationEnergy</a>(), <span class="stringliteral">"1000045"</span>, <span class="stringliteral">"CollisionEnergy"</span>, 7);</div>
<div class="line"><a name="l01219"></a><span class="lineno"> 1219</span>  os << <span class="stringliteral">"\t\t\t\t\t\t\t<cvParam cvLabel=\"psi\" accession=\"PSI:1000046\" name=\"EnergyUnit\" value=\"eV\"/>\n"</span>;</div>
<div class="line"><a name="l01220"></a><span class="lineno"> 1220</span>  }</div>
<div class="line"><a name="l01221"></a><span class="lineno"> 1221</span>  os << <span class="stringliteral">"\t\t\t\t\t\t</activation>\n"</span>;</div>
<div class="line"><a name="l01222"></a><span class="lineno"> 1222</span>  os << <span class="stringliteral">"\t\t\t\t\t</precursor>\n"</span>;</div>
<div class="line"><a name="l01223"></a><span class="lineno"> 1223</span>  }</div>
<div class="line"><a name="l01224"></a><span class="lineno"> 1224</span>  os << <span class="stringliteral">"\t\t\t\t</precursorList>\n"</span>;</div>
<div class="line"><a name="l01225"></a><span class="lineno"> 1225</span>  }</div>
<div class="line"><a name="l01226"></a><span class="lineno"> 1226</span>  os << <span class="stringliteral">"\t\t\t</spectrumDesc>\n"</span>;</div>
<div class="line"><a name="l01227"></a><span class="lineno"> 1227</span> </div>
<div class="line"><a name="l01228"></a><span class="lineno"> 1228</span>  <span class="comment">// write the supplementary data?</span></div>
<div class="line"><a name="l01229"></a><span class="lineno"> 1229</span>  <span class="keywordflow">if</span> (options_.getWriteSupplementalData())</div>
<div class="line"><a name="l01230"></a><span class="lineno"> 1230</span>  {</div>
<div class="line"><a name="l01231"></a><span class="lineno"> 1231</span>  <span class="comment">//write meta data array descriptions</span></div>
<div class="line"><a name="l01232"></a><span class="lineno"> 1232</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>().size(); ++i)</div>
<div class="line"><a name="l01233"></a><span class="lineno"> 1233</span>  {</div>
<div class="line"><a name="l01234"></a><span class="lineno"> 1234</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoDescription.html">MetaInfoDescription</a> & desc = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[i];</div>
<div class="line"><a name="l01235"></a><span class="lineno"> 1235</span>  os << <span class="stringliteral">"\t\t\t<supDesc supDataArrayRef=\""</span> << (i + 1) << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l01236"></a><span class="lineno"> 1236</span>  <span class="keywordflow">if</span> (!desc.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a001483d1f67f068e585f10d9abcc487d">isMetaEmpty</a>())</div>
<div class="line"><a name="l01237"></a><span class="lineno"> 1237</span>  {</div>
<div class="line"><a name="l01238"></a><span class="lineno"> 1238</span>  os << <span class="stringliteral">"\t\t\t\t<supDataDesc>\n"</span>;</div>
<div class="line"><a name="l01239"></a><span class="lineno"> 1239</span>  writeUserParam_(os, desc, 5);</div>
<div class="line"><a name="l01240"></a><span class="lineno"> 1240</span>  os << <span class="stringliteral">"\t\t\t\t</supDataDesc>\n"</span>;</div>
<div class="line"><a name="l01241"></a><span class="lineno"> 1241</span>  }</div>
<div class="line"><a name="l01242"></a><span class="lineno"> 1242</span>  os << <span class="stringliteral">"\t\t\t</supDesc>\n"</span>;</div>
<div class="line"><a name="l01243"></a><span class="lineno"> 1243</span>  }</div>
<div class="line"><a name="l01244"></a><span class="lineno"> 1244</span>  }</div>
<div class="line"><a name="l01245"></a><span class="lineno"> 1245</span> </div>
<div class="line"><a name="l01246"></a><span class="lineno"> 1246</span>  <span class="comment">//write m/z and intensity arrays</span></div>
<div class="line"><a name="l01247"></a><span class="lineno"> 1247</span>  data_to_encode_.clear();</div>
<div class="line"><a name="l01248"></a><span class="lineno"> 1248</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.size(); i++)</div>
<div class="line"><a name="l01249"></a><span class="lineno"> 1249</span>  {</div>
<div class="line"><a name="l01250"></a><span class="lineno"> 1250</span>  data_to_encode_.push_back(spec[i].getPosition()[0]);</div>
<div class="line"><a name="l01251"></a><span class="lineno"> 1251</span>  }</div>
<div class="line"><a name="l01252"></a><span class="lineno"> 1252</span> </div>
<div class="line"><a name="l01253"></a><span class="lineno"> 1253</span>  writeBinary_(os, spec.size(), <span class="stringliteral">"mzArrayBinary"</span>);</div>
<div class="line"><a name="l01254"></a><span class="lineno"> 1254</span> </div>
<div class="line"><a name="l01255"></a><span class="lineno"> 1255</span>  <span class="comment">// intensity</span></div>
<div class="line"><a name="l01256"></a><span class="lineno"> 1256</span>  data_to_encode_.clear();</div>
<div class="line"><a name="l01257"></a><span class="lineno"> 1257</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.size(); i++)</div>
<div class="line"><a name="l01258"></a><span class="lineno"> 1258</span>  {</div>
<div class="line"><a name="l01259"></a><span class="lineno"> 1259</span>  data_to_encode_.push_back(spec[i].getIntensity());</div>
<div class="line"><a name="l01260"></a><span class="lineno"> 1260</span>  }</div>
<div class="line"><a name="l01261"></a><span class="lineno"> 1261</span> </div>
<div class="line"><a name="l01262"></a><span class="lineno"> 1262</span>  writeBinary_(os, spec.size(), <span class="stringliteral">"intenArrayBinary"</span>);</div>
<div class="line"><a name="l01263"></a><span class="lineno"> 1263</span> </div>
<div class="line"><a name="l01264"></a><span class="lineno"> 1264</span>  <span class="comment">// write the supplementary data?</span></div>
<div class="line"><a name="l01265"></a><span class="lineno"> 1265</span>  <span class="keywordflow">if</span> (options_.getWriteSupplementalData())</div>
<div class="line"><a name="l01266"></a><span class="lineno"> 1266</span>  {</div>
<div class="line"><a name="l01267"></a><span class="lineno"> 1267</span>  <span class="comment">//write supplemental data arrays</span></div>
<div class="line"><a name="l01268"></a><span class="lineno"> 1268</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>().size(); ++i)</div>
<div class="line"><a name="l01269"></a><span class="lineno"> 1269</span>  {</div>
<div class="line"><a name="l01270"></a><span class="lineno"> 1270</span>  <span class="keyword">const</span> <span class="keyword">typename</span> MapType::SpectrumType::FloatDataArray & mda = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[i];</div>
<div class="line"><a name="l01271"></a><span class="lineno"> 1271</span>  <span class="comment">//check if spectrum and meta data array have the same length</span></div>
<div class="line"><a name="l01272"></a><span class="lineno"> 1272</span>  <span class="keywordflow">if</span> (mda.size() != spec.size())</div>
<div class="line"><a name="l01273"></a><span class="lineno"> 1273</span>  {</div>
<div class="line"><a name="l01274"></a><span class="lineno"> 1274</span>  error(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Length of meta data array (index:'"</span>) + i + <span class="stringliteral">"' name:'"</span> + mda.getName() + <span class="stringliteral">"') differs from spectrum length. meta data array: "</span> + mda.size() + <span class="stringliteral">" / spectrum: "</span> + spec.size() + <span class="stringliteral">" ."</span>);</div>
<div class="line"><a name="l01275"></a><span class="lineno"> 1275</span>  }</div>
<div class="line"><a name="l01276"></a><span class="lineno"> 1276</span>  <span class="comment">//encode meta data array</span></div>
<div class="line"><a name="l01277"></a><span class="lineno"> 1277</span>  data_to_encode_.clear();</div>
<div class="line"><a name="l01278"></a><span class="lineno"> 1278</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < mda.size(); j++)</div>
<div class="line"><a name="l01279"></a><span class="lineno"> 1279</span>  {</div>
<div class="line"><a name="l01280"></a><span class="lineno"> 1280</span>  data_to_encode_.push_back(mda[j]);</div>
<div class="line"><a name="l01281"></a><span class="lineno"> 1281</span>  }</div>
<div class="line"><a name="l01282"></a><span class="lineno"> 1282</span>  <span class="comment">//write meta data array</span></div>
<div class="line"><a name="l01283"></a><span class="lineno"> 1283</span>  writeBinary_(os, mda.size(), <span class="stringliteral">"supDataArrayBinary"</span>, mda.getName(), i + 1);</div>
<div class="line"><a name="l01284"></a><span class="lineno"> 1284</span>  }</div>
<div class="line"><a name="l01285"></a><span class="lineno"> 1285</span>  }</div>
<div class="line"><a name="l01286"></a><span class="lineno"> 1286</span> </div>
<div class="line"><a name="l01287"></a><span class="lineno"> 1287</span>  os << <span class="stringliteral">"\t\t</spectrum>\n"</span>;</div>
<div class="line"><a name="l01288"></a><span class="lineno"> 1288</span>  }</div>
<div class="line"><a name="l01289"></a><span class="lineno"> 1289</span>  }</div>
<div class="line"><a name="l01290"></a><span class="lineno"> 1290</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01291"></a><span class="lineno"> 1291</span>  {</div>
<div class="line"><a name="l01292"></a><span class="lineno"> 1292</span>  os << <span class="stringliteral">"\t<spectrumList count=\"1\">\n"</span>;</div>
<div class="line"><a name="l01293"></a><span class="lineno"> 1293</span>  os << <span class="stringliteral">"\t\t<spectrum id=\"1\">\n"</span>;</div>
<div class="line"><a name="l01294"></a><span class="lineno"> 1294</span>  os << <span class="stringliteral">"\t\t\t<spectrumDesc>\n"</span>;</div>
<div class="line"><a name="l01295"></a><span class="lineno"> 1295</span>  os << <span class="stringliteral">"\t\t\t\t<spectrumSettings>\n"</span>;</div>
<div class="line"><a name="l01296"></a><span class="lineno"> 1296</span>  os << <span class="stringliteral">"\t\t\t\t\t<spectrumInstrument msLevel=\"1\"/>\n"</span>;</div>
<div class="line"><a name="l01297"></a><span class="lineno"> 1297</span>  os << <span class="stringliteral">"\t\t\t\t</spectrumSettings>\n"</span>;</div>
<div class="line"><a name="l01298"></a><span class="lineno"> 1298</span>  os << <span class="stringliteral">"\t\t\t</spectrumDesc>\n"</span>;</div>
<div class="line"><a name="l01299"></a><span class="lineno"> 1299</span>  os << <span class="stringliteral">"\t\t\t<mzArrayBinary>\n"</span>;</div>
<div class="line"><a name="l01300"></a><span class="lineno"> 1300</span>  os << <span class="stringliteral">"\t\t\t\t<data length=\"0\" endian=\"little\" precision=\"32\"></data>\n"</span>;</div>
<div class="line"><a name="l01301"></a><span class="lineno"> 1301</span>  os << <span class="stringliteral">"\t\t\t</mzArrayBinary>\n"</span>;</div>
<div class="line"><a name="l01302"></a><span class="lineno"> 1302</span>  os << <span class="stringliteral">"\t\t\t<intenArrayBinary>\n"</span>;</div>
<div class="line"><a name="l01303"></a><span class="lineno"> 1303</span>  os << <span class="stringliteral">"\t\t\t\t<data length=\"0\" endian=\"little\" precision=\"32\"></data>\n"</span>;</div>
<div class="line"><a name="l01304"></a><span class="lineno"> 1304</span>  os << <span class="stringliteral">"\t\t\t</intenArrayBinary>\n"</span>;</div>
<div class="line"><a name="l01305"></a><span class="lineno"> 1305</span>  os << <span class="stringliteral">"\t\t</spectrum>\n"</span>;</div>
<div class="line"><a name="l01306"></a><span class="lineno"> 1306</span>  }</div>
<div class="line"><a name="l01307"></a><span class="lineno"> 1307</span>  os << <span class="stringliteral">"\t</spectrumList>\n</mzData>\n"</span>;</div>
<div class="line"><a name="l01308"></a><span class="lineno"> 1308</span> </div>
<div class="line"><a name="l01309"></a><span class="lineno"> 1309</span>  logger_.endProgress();</div>
<div class="line"><a name="l01310"></a><span class="lineno"> 1310</span>  }</div>
<div class="line"><a name="l01311"></a><span class="lineno"> 1311</span> </div>
<div class="line"><a name="l01312"></a><span class="lineno"> 1312</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l01313"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a246d2ed7a27643da899d40062055882a"> 1313</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a246d2ed7a27643da899d40062055882a">MzDataHandler<MapType>::cvParam_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & value)</div>
<div class="line"><a name="l01314"></a><span class="lineno"> 1314</span>  {</div>
<div class="line"><a name="l01315"></a><span class="lineno"> 1315</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> error = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l01316"></a><span class="lineno"> 1316</span> </div>
<div class="line"><a name="l01317"></a><span class="lineno"> 1317</span>  <span class="comment">//determine the parent tag</span></div>
<div class="line"><a name="l01318"></a><span class="lineno"> 1318</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> parent_tag;</div>
<div class="line"><a name="l01319"></a><span class="lineno"> 1319</span>  <span class="keywordflow">if</span> (open_tags_.size() > 1)</div>
<div class="line"><a name="l01320"></a><span class="lineno"> 1320</span>  parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l01321"></a><span class="lineno"> 1321</span> </div>
<div class="line"><a name="l01322"></a><span class="lineno"> 1322</span>  <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"spectrumInstrument"</span>)</div>
<div class="line"><a name="l01323"></a><span class="lineno"> 1323</span>  {</div>
<div class="line"><a name="l01324"></a><span class="lineno"> 1324</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000036"</span>) <span class="comment">//Scan Mode</span></div>
<div class="line"><a name="l01325"></a><span class="lineno"> 1325</span>  {</div>
<div class="line"><a name="l01326"></a><span class="lineno"> 1326</span>  <span class="keywordflow">if</span> (value == <span class="stringliteral">"Zoom"</span>)</div>
<div class="line"><a name="l01327"></a><span class="lineno"> 1327</span>  {</div>
<div class="line"><a name="l01328"></a><span class="lineno"> 1328</span>  spec_.getInstrumentSettings().setZoomScan(<span class="keyword">true</span>);</div>
<div class="line"><a name="l01329"></a><span class="lineno"> 1329</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l01330"></a><span class="lineno"> 1330</span>  }</div>
<div class="line"><a name="l01331"></a><span class="lineno"> 1331</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"MassScan"</span>)</div>
<div class="line"><a name="l01332"></a><span class="lineno"> 1332</span>  {</div>
<div class="line"><a name="l01333"></a><span class="lineno"> 1333</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l01334"></a><span class="lineno"> 1334</span>  }</div>
<div class="line"><a name="l01335"></a><span class="lineno"> 1335</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"SelectedIonDetection"</span>)</div>
<div class="line"><a name="l01336"></a><span class="lineno"> 1336</span>  {</div>
<div class="line"><a name="l01337"></a><span class="lineno"> 1337</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>);</div>
<div class="line"><a name="l01338"></a><span class="lineno"> 1338</span>  }</div>
<div class="line"><a name="l01339"></a><span class="lineno"> 1339</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"SelectedReactionMonitoring"</span>)</div>
<div class="line"><a name="l01340"></a><span class="lineno"> 1340</span>  {</div>
<div class="line"><a name="l01341"></a><span class="lineno"> 1341</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>);</div>
<div class="line"><a name="l01342"></a><span class="lineno"> 1342</span>  }</div>
<div class="line"><a name="l01343"></a><span class="lineno"> 1343</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"ConsecutiveReactionMonitoring"</span>)</div>
<div class="line"><a name="l01344"></a><span class="lineno"> 1344</span>  {</div>
<div class="line"><a name="l01345"></a><span class="lineno"> 1345</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>);</div>
<div class="line"><a name="l01346"></a><span class="lineno"> 1346</span>  }</div>
<div class="line"><a name="l01347"></a><span class="lineno"> 1347</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"ConstantNeutralGainScan"</span>)</div>
<div class="line"><a name="l01348"></a><span class="lineno"> 1348</span>  {</div>
<div class="line"><a name="l01349"></a><span class="lineno"> 1349</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ab5247ec213d542e5520176f6ae032f5f">InstrumentSettings::CNG</a>);</div>
<div class="line"><a name="l01350"></a><span class="lineno"> 1350</span>  }</div>
<div class="line"><a name="l01351"></a><span class="lineno"> 1351</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"ConstantNeutralLossScan"</span>)</div>
<div class="line"><a name="l01352"></a><span class="lineno"> 1352</span>  {</div>
<div class="line"><a name="l01353"></a><span class="lineno"> 1353</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0afd0b89ab5c7b08831a232ab0b0b66cca">InstrumentSettings::CNL</a>);</div>
<div class="line"><a name="l01354"></a><span class="lineno"> 1354</span>  }</div>
<div class="line"><a name="l01355"></a><span class="lineno"> 1355</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"ProductIonScan"</span>)</div>
<div class="line"><a name="l01356"></a><span class="lineno"> 1356</span>  {</div>
<div class="line"><a name="l01357"></a><span class="lineno"> 1357</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>);</div>
<div class="line"><a name="l01358"></a><span class="lineno"> 1358</span>  spec_.setMSLevel(2);</div>
<div class="line"><a name="l01359"></a><span class="lineno"> 1359</span>  }</div>
<div class="line"><a name="l01360"></a><span class="lineno"> 1360</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"PrecursorIonScan"</span>)</div>
<div class="line"><a name="l01361"></a><span class="lineno"> 1361</span>  {</div>
<div class="line"><a name="l01362"></a><span class="lineno"> 1362</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a8664157176347ebc7a0bfd5196498a8f">InstrumentSettings::PRECURSOR</a>);</div>
<div class="line"><a name="l01363"></a><span class="lineno"> 1363</span>  }</div>
<div class="line"><a name="l01364"></a><span class="lineno"> 1364</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"EnhancedResolutionScan"</span>)</div>
<div class="line"><a name="l01365"></a><span class="lineno"> 1365</span>  {</div>
<div class="line"><a name="l01366"></a><span class="lineno"> 1366</span>  spec_.getInstrumentSettings().setZoomScan(<span class="keyword">true</span>);</div>
<div class="line"><a name="l01367"></a><span class="lineno"> 1367</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l01368"></a><span class="lineno"> 1368</span>  }</div>
<div class="line"><a name="l01369"></a><span class="lineno"> 1369</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01370"></a><span class="lineno"> 1370</span>  {</div>
<div class="line"><a name="l01371"></a><span class="lineno"> 1371</span>  <span class="keywordflow">if</span> (spec_.getMSLevel() >= 2)</div>
<div class="line"><a name="l01372"></a><span class="lineno"> 1372</span>  {</div>
<div class="line"><a name="l01373"></a><span class="lineno"> 1373</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>);</div>
<div class="line"><a name="l01374"></a><span class="lineno"> 1374</span>  }</div>
<div class="line"><a name="l01375"></a><span class="lineno"> 1375</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01376"></a><span class="lineno"> 1376</span>  {</div>
<div class="line"><a name="l01377"></a><span class="lineno"> 1377</span>  spec_.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l01378"></a><span class="lineno"> 1378</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Unknown scan mode '"</span>) + value + <span class="stringliteral">"'. Assuming full scan"</span>);</div>
<div class="line"><a name="l01379"></a><span class="lineno"> 1379</span>  }</div>
<div class="line"><a name="l01380"></a><span class="lineno"> 1380</span>  }</div>
<div class="line"><a name="l01381"></a><span class="lineno"> 1381</span>  }</div>
<div class="line"><a name="l01382"></a><span class="lineno"> 1382</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000038"</span>) <span class="comment">//Time in minutes</span></div>
<div class="line"><a name="l01383"></a><span class="lineno"> 1383</span>  {</div>
<div class="line"><a name="l01384"></a><span class="lineno"> 1384</span>  spec_.setRT(asDouble_(value) * 60); <span class="comment">//Minutes to seconds</span></div>
<div class="line"><a name="l01385"></a><span class="lineno"> 1385</span>  <span class="keywordflow">if</span> (options_.hasRTRange() && !options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(spec_.getRT())))</div>
<div class="line"><a name="l01386"></a><span class="lineno"> 1386</span>  {</div>
<div class="line"><a name="l01387"></a><span class="lineno"> 1387</span>  skip_spectrum_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01388"></a><span class="lineno"> 1388</span>  }</div>
<div class="line"><a name="l01389"></a><span class="lineno"> 1389</span>  }</div>
<div class="line"><a name="l01390"></a><span class="lineno"> 1390</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000039"</span>) <span class="comment">//Time in seconds</span></div>
<div class="line"><a name="l01391"></a><span class="lineno"> 1391</span>  {</div>
<div class="line"><a name="l01392"></a><span class="lineno"> 1392</span>  spec_.setRT(asDouble_(value));</div>
<div class="line"><a name="l01393"></a><span class="lineno"> 1393</span>  <span class="keywordflow">if</span> (options_.hasRTRange() && !options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(spec_.getRT())))</div>
<div class="line"><a name="l01394"></a><span class="lineno"> 1394</span>  {</div>
<div class="line"><a name="l01395"></a><span class="lineno"> 1395</span>  skip_spectrum_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01396"></a><span class="lineno"> 1396</span>  }</div>
<div class="line"><a name="l01397"></a><span class="lineno"> 1397</span>  }</div>
<div class="line"><a name="l01398"></a><span class="lineno"> 1398</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000037"</span>) <span class="comment">//Polarity</span></div>
<div class="line"><a name="l01399"></a><span class="lineno"> 1399</span>  {</div>
<div class="line"><a name="l01400"></a><span class="lineno"> 1400</span>  <span class="keywordflow">if</span> (value == <span class="stringliteral">"Positive"</span> || value == <span class="stringliteral">"positive"</span> || value == <span class="stringliteral">"+"</span>) <span class="comment">//be flexible here, actually only the first one is correct</span></div>
<div class="line"><a name="l01401"></a><span class="lineno"> 1401</span>  {</div>
<div class="line"><a name="l01402"></a><span class="lineno"> 1402</span>  spec_.getInstrumentSettings().setPolarity(<a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5">IonSource::POSITIVE</a>);</div>
<div class="line"><a name="l01403"></a><span class="lineno"> 1403</span>  }</div>
<div class="line"><a name="l01404"></a><span class="lineno"> 1404</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value == <span class="stringliteral">"Negative"</span> || value == <span class="stringliteral">"negative"</span> || value == <span class="stringliteral">"-"</span>) <span class="comment">//be flexible here, actually only the first one is correct</span></div>
<div class="line"><a name="l01405"></a><span class="lineno"> 1405</span>  {</div>
<div class="line"><a name="l01406"></a><span class="lineno"> 1406</span>  spec_.getInstrumentSettings().setPolarity(<a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">IonSource::NEGATIVE</a>);</div>
<div class="line"><a name="l01407"></a><span class="lineno"> 1407</span>  }</div>
<div class="line"><a name="l01408"></a><span class="lineno"> 1408</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01409"></a><span class="lineno"> 1409</span>  {</div>
<div class="line"><a name="l01410"></a><span class="lineno"> 1410</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid scan polarity (PSI:1000037) detected: \""</span>) + value + <span class="stringliteral">"\". Valid are 'Positive' or 'Negative'."</span>);</div>
<div class="line"><a name="l01411"></a><span class="lineno"> 1411</span>  }</div>
<div class="line"><a name="l01412"></a><span class="lineno"> 1412</span>  }</div>
<div class="line"><a name="l01413"></a><span class="lineno"> 1413</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01414"></a><span class="lineno"> 1414</span>  {</div>
<div class="line"><a name="l01415"></a><span class="lineno"> 1415</span>  error = <span class="stringliteral">"SpectrumDescription.SpectrumSettings.SpectrumInstrument"</span>;</div>
<div class="line"><a name="l01416"></a><span class="lineno"> 1416</span>  }</div>
<div class="line"><a name="l01417"></a><span class="lineno"> 1417</span>  }</div>
<div class="line"><a name="l01418"></a><span class="lineno"> 1418</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"ionSelection"</span>)</div>
<div class="line"><a name="l01419"></a><span class="lineno"> 1419</span>  {</div>
<div class="line"><a name="l01420"></a><span class="lineno"> 1420</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000040"</span>) <span class="comment">//m/z</span></div>
<div class="line"><a name="l01421"></a><span class="lineno"> 1421</span>  {</div>
<div class="line"><a name="l01422"></a><span class="lineno"> 1422</span>  spec_.getPrecursors().back().setMZ(asDouble_(value));</div>
<div class="line"><a name="l01423"></a><span class="lineno"> 1423</span>  }</div>
<div class="line"><a name="l01424"></a><span class="lineno"> 1424</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000041"</span>) <span class="comment">//Charge</span></div>
<div class="line"><a name="l01425"></a><span class="lineno"> 1425</span>  {</div>
<div class="line"><a name="l01426"></a><span class="lineno"> 1426</span>  <span class="keywordflow">if</span> (spec_.getPrecursors().back().getCharge() != 0)</div>
<div class="line"><a name="l01427"></a><span class="lineno"> 1427</span>  {</div>
<div class="line"><a name="l01428"></a><span class="lineno"> 1428</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Multiple precursor charges detected, expected only one! Ignoring this charge settings! accession=\""</span>) + accession + <span class="stringliteral">"\", value=\""</span> + value + <span class="stringliteral">"\""</span>);</div>
<div class="line"><a name="l01429"></a><span class="lineno"> 1429</span>  spec_.getPrecursors().back().setCharge(0);</div>
<div class="line"><a name="l01430"></a><span class="lineno"> 1430</span>  }</div>
<div class="line"><a name="l01431"></a><span class="lineno"> 1431</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01432"></a><span class="lineno"> 1432</span>  {</div>
<div class="line"><a name="l01433"></a><span class="lineno"> 1433</span>  spec_.getPrecursors().back().setCharge(asInt_(value));</div>
<div class="line"><a name="l01434"></a><span class="lineno"> 1434</span>  }</div>
<div class="line"><a name="l01435"></a><span class="lineno"> 1435</span>  }</div>
<div class="line"><a name="l01436"></a><span class="lineno"> 1436</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000042"</span>) <span class="comment">//Intensity</span></div>
<div class="line"><a name="l01437"></a><span class="lineno"> 1437</span>  {</div>
<div class="line"><a name="l01438"></a><span class="lineno"> 1438</span>  spec_.getPrecursors().back().setIntensity(asDouble_(value));</div>
<div class="line"><a name="l01439"></a><span class="lineno"> 1439</span>  }</div>
<div class="line"><a name="l01440"></a><span class="lineno"> 1440</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000043"</span>) <span class="comment">//Intensity unit</span></div>
<div class="line"><a name="l01441"></a><span class="lineno"> 1441</span>  {</div>
<div class="line"><a name="l01442"></a><span class="lineno"> 1442</span>  <span class="comment">//ignored</span></div>
<div class="line"><a name="l01443"></a><span class="lineno"> 1443</span>  }</div>
<div class="line"><a name="l01444"></a><span class="lineno"> 1444</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01445"></a><span class="lineno"> 1445</span>  {</div>
<div class="line"><a name="l01446"></a><span class="lineno"> 1446</span>  error = <span class="stringliteral">"PrecursorList.Precursor.IonSelection.UserParam"</span>;</div>
<div class="line"><a name="l01447"></a><span class="lineno"> 1447</span>  }</div>
<div class="line"><a name="l01448"></a><span class="lineno"> 1448</span>  }</div>
<div class="line"><a name="l01449"></a><span class="lineno"> 1449</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"activation"</span>)</div>
<div class="line"><a name="l01450"></a><span class="lineno"> 1450</span>  {</div>
<div class="line"><a name="l01451"></a><span class="lineno"> 1451</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000044"</span>) <span class="comment">//activationmethod</span></div>
<div class="line"><a name="l01452"></a><span class="lineno"> 1452</span>  {</div>
<div class="line"><a name="l01453"></a><span class="lineno"> 1453</span>  spec_.getPrecursors().back().getActivationMethods().insert((<a class="code" href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1">Precursor::ActivationMethod</a>)cvStringToEnum_(18, value, <span class="stringliteral">"activation method"</span>));</div>
<div class="line"><a name="l01454"></a><span class="lineno"> 1454</span>  }</div>
<div class="line"><a name="l01455"></a><span class="lineno"> 1455</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000045"</span>) <span class="comment">//Energy</span></div>
<div class="line"><a name="l01456"></a><span class="lineno"> 1456</span>  {</div>
<div class="line"><a name="l01457"></a><span class="lineno"> 1457</span>  spec_.getPrecursors().back().setActivationEnergy(asDouble_(value));</div>
<div class="line"><a name="l01458"></a><span class="lineno"> 1458</span>  }</div>
<div class="line"><a name="l01459"></a><span class="lineno"> 1459</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000046"</span>) <span class="comment">//Energy unit</span></div>
<div class="line"><a name="l01460"></a><span class="lineno"> 1460</span>  {</div>
<div class="line"><a name="l01461"></a><span class="lineno"> 1461</span>  <span class="comment">//ignored - we assume electronvolt</span></div>
<div class="line"><a name="l01462"></a><span class="lineno"> 1462</span>  }</div>
<div class="line"><a name="l01463"></a><span class="lineno"> 1463</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01464"></a><span class="lineno"> 1464</span>  {</div>
<div class="line"><a name="l01465"></a><span class="lineno"> 1465</span>  error = <span class="stringliteral">"PrecursorList.Precursor.Activation.UserParam"</span>;</div>
<div class="line"><a name="l01466"></a><span class="lineno"> 1466</span>  }</div>
<div class="line"><a name="l01467"></a><span class="lineno"> 1467</span>  }</div>
<div class="line"><a name="l01468"></a><span class="lineno"> 1468</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"supDataDesc"</span>)</div>
<div class="line"><a name="l01469"></a><span class="lineno"> 1469</span>  {</div>
<div class="line"><a name="l01470"></a><span class="lineno"> 1470</span>  <span class="comment">//no terms defined in ontology</span></div>
<div class="line"><a name="l01471"></a><span class="lineno"> 1471</span>  error = <span class="stringliteral">"supDataDesc.UserParam"</span>;</div>
<div class="line"><a name="l01472"></a><span class="lineno"> 1472</span>  }</div>
<div class="line"><a name="l01473"></a><span class="lineno"> 1473</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"acquisition"</span>)</div>
<div class="line"><a name="l01474"></a><span class="lineno"> 1474</span>  {</div>
<div class="line"><a name="l01475"></a><span class="lineno"> 1475</span>  <span class="comment">//no terms defined in ontology</span></div>
<div class="line"><a name="l01476"></a><span class="lineno"> 1476</span>  error = <span class="stringliteral">"spectrumDesc.spectrumSettings.acquisitionSpecification.acquisition.UserParam"</span>;</div>
<div class="line"><a name="l01477"></a><span class="lineno"> 1477</span>  }</div>
<div class="line"><a name="l01478"></a><span class="lineno"> 1478</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"detector"</span>)</div>
<div class="line"><a name="l01479"></a><span class="lineno"> 1479</span>  {</div>
<div class="line"><a name="l01480"></a><span class="lineno"> 1480</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000026"</span>)</div>
<div class="line"><a name="l01481"></a><span class="lineno"> 1481</span>  {</div>
<div class="line"><a name="l01482"></a><span class="lineno"> 1482</span>  exp_->getInstrument().getIonDetectors().back().setType((<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7">IonDetector::Type</a>)cvStringToEnum_(13, value, <span class="stringliteral">"detector type"</span>));</div>
<div class="line"><a name="l01483"></a><span class="lineno"> 1483</span>  }</div>
<div class="line"><a name="l01484"></a><span class="lineno"> 1484</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000028"</span>)</div>
<div class="line"><a name="l01485"></a><span class="lineno"> 1485</span>  {</div>
<div class="line"><a name="l01486"></a><span class="lineno"> 1486</span>  exp_->getInstrument().getIonDetectors().back().setResolution(asDouble_(value));</div>
<div class="line"><a name="l01487"></a><span class="lineno"> 1487</span>  }</div>
<div class="line"><a name="l01488"></a><span class="lineno"> 1488</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000029"</span>)</div>
<div class="line"><a name="l01489"></a><span class="lineno"> 1489</span>  {</div>
<div class="line"><a name="l01490"></a><span class="lineno"> 1490</span>  exp_->getInstrument().getIonDetectors().back().setADCSamplingFrequency(asDouble_(value));</div>
<div class="line"><a name="l01491"></a><span class="lineno"> 1491</span>  }</div>
<div class="line"><a name="l01492"></a><span class="lineno"> 1492</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000027"</span>)</div>
<div class="line"><a name="l01493"></a><span class="lineno"> 1493</span>  {</div>
<div class="line"><a name="l01494"></a><span class="lineno"> 1494</span>  exp_->getInstrument().getIonDetectors().back().setAcquisitionMode((<a class="code" href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11">IonDetector::AcquisitionMode</a>)cvStringToEnum_(9, value, <span class="stringliteral">"acquisition mode"</span>));</div>
<div class="line"><a name="l01495"></a><span class="lineno"> 1495</span>  }</div>
<div class="line"><a name="l01496"></a><span class="lineno"> 1496</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01497"></a><span class="lineno"> 1497</span>  {</div>
<div class="line"><a name="l01498"></a><span class="lineno"> 1498</span>  error = <span class="stringliteral">"Description.Instrument.Detector.UserParam"</span>;</div>
<div class="line"><a name="l01499"></a><span class="lineno"> 1499</span>  }</div>
<div class="line"><a name="l01500"></a><span class="lineno"> 1500</span>  }</div>
<div class="line"><a name="l01501"></a><span class="lineno"> 1501</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"source"</span>)</div>
<div class="line"><a name="l01502"></a><span class="lineno"> 1502</span>  {</div>
<div class="line"><a name="l01503"></a><span class="lineno"> 1503</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000008"</span>)</div>
<div class="line"><a name="l01504"></a><span class="lineno"> 1504</span>  {</div>
<div class="line"><a name="l01505"></a><span class="lineno"> 1505</span>  exp_->getInstrument().getIonSources().back().setIonizationMethod((<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4">IonSource::IonizationMethod</a>)cvStringToEnum_(10, value, <span class="stringliteral">"ion source"</span>));</div>
<div class="line"><a name="l01506"></a><span class="lineno"> 1506</span>  }</div>
<div class="line"><a name="l01507"></a><span class="lineno"> 1507</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000007"</span>)</div>
<div class="line"><a name="l01508"></a><span class="lineno"> 1508</span>  {</div>
<div class="line"><a name="l01509"></a><span class="lineno"> 1509</span>  exp_->getInstrument().getIonSources().back().setInletType((<a class="code" href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675f">IonSource::InletType</a>)cvStringToEnum_(11, value, <span class="stringliteral">"inlet type"</span>));</div>
<div class="line"><a name="l01510"></a><span class="lineno"> 1510</span>  }</div>
<div class="line"><a name="l01511"></a><span class="lineno"> 1511</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000009"</span>)</div>
<div class="line"><a name="l01512"></a><span class="lineno"> 1512</span>  {</div>
<div class="line"><a name="l01513"></a><span class="lineno"> 1513</span>  exp_->getInstrument().getIonSources().back().setPolarity((<a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054">IonSource::Polarity</a>)cvStringToEnum_(1, value, <span class="stringliteral">"polarity"</span>));</div>
<div class="line"><a name="l01514"></a><span class="lineno"> 1514</span>  }</div>
<div class="line"><a name="l01515"></a><span class="lineno"> 1515</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01516"></a><span class="lineno"> 1516</span>  {</div>
<div class="line"><a name="l01517"></a><span class="lineno"> 1517</span>  error = <span class="stringliteral">"Description.Instrument.Source.UserParam"</span>;</div>
<div class="line"><a name="l01518"></a><span class="lineno"> 1518</span>  }</div>
<div class="line"><a name="l01519"></a><span class="lineno"> 1519</span>  }</div>
<div class="line"><a name="l01520"></a><span class="lineno"> 1520</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"sampleDescription"</span>)</div>
<div class="line"><a name="l01521"></a><span class="lineno"> 1521</span>  {</div>
<div class="line"><a name="l01522"></a><span class="lineno"> 1522</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000001"</span>)</div>
<div class="line"><a name="l01523"></a><span class="lineno"> 1523</span>  {</div>
<div class="line"><a name="l01524"></a><span class="lineno"> 1524</span>  exp_->getSample().setNumber(value);</div>
<div class="line"><a name="l01525"></a><span class="lineno"> 1525</span>  }</div>
<div class="line"><a name="l01526"></a><span class="lineno"> 1526</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000003"</span>)</div>
<div class="line"><a name="l01527"></a><span class="lineno"> 1527</span>  {</div>
<div class="line"><a name="l01528"></a><span class="lineno"> 1528</span>  exp_->getSample().setState((<a class="code" href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71">Sample::SampleState</a>)cvStringToEnum_(0, value, <span class="stringliteral">"sample state"</span>));</div>
<div class="line"><a name="l01529"></a><span class="lineno"> 1529</span>  }</div>
<div class="line"><a name="l01530"></a><span class="lineno"> 1530</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000004"</span>)</div>
<div class="line"><a name="l01531"></a><span class="lineno"> 1531</span>  {</div>
<div class="line"><a name="l01532"></a><span class="lineno"> 1532</span>  exp_->getSample().setMass(asDouble_(value));</div>
<div class="line"><a name="l01533"></a><span class="lineno"> 1533</span>  }</div>
<div class="line"><a name="l01534"></a><span class="lineno"> 1534</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000005"</span>)</div>
<div class="line"><a name="l01535"></a><span class="lineno"> 1535</span>  {</div>
<div class="line"><a name="l01536"></a><span class="lineno"> 1536</span>  exp_->getSample().setVolume(asDouble_(value));</div>
<div class="line"><a name="l01537"></a><span class="lineno"> 1537</span>  }</div>
<div class="line"><a name="l01538"></a><span class="lineno"> 1538</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000006"</span>)</div>
<div class="line"><a name="l01539"></a><span class="lineno"> 1539</span>  {</div>
<div class="line"><a name="l01540"></a><span class="lineno"> 1540</span>  exp_->getSample().setConcentration(asDouble_(value));</div>
<div class="line"><a name="l01541"></a><span class="lineno"> 1541</span>  }</div>
<div class="line"><a name="l01542"></a><span class="lineno"> 1542</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01543"></a><span class="lineno"> 1543</span>  {</div>
<div class="line"><a name="l01544"></a><span class="lineno"> 1544</span>  error = <span class="stringliteral">"Description.Admin.SampleDescription.UserParam"</span>;</div>
<div class="line"><a name="l01545"></a><span class="lineno"> 1545</span>  }</div>
<div class="line"><a name="l01546"></a><span class="lineno"> 1546</span>  }</div>
<div class="line"><a name="l01547"></a><span class="lineno"> 1547</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"analyzer"</span>)</div>
<div class="line"><a name="l01548"></a><span class="lineno"> 1548</span>  {</div>
<div class="line"><a name="l01549"></a><span class="lineno"> 1549</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000010"</span>)</div>
<div class="line"><a name="l01550"></a><span class="lineno"> 1550</span>  {</div>
<div class="line"><a name="l01551"></a><span class="lineno"> 1551</span>  exp_->getInstrument().getMassAnalyzers().back().setType((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3">MassAnalyzer::AnalyzerType</a>)cvStringToEnum_(14, value, <span class="stringliteral">"analyzer type"</span>));</div>
<div class="line"><a name="l01552"></a><span class="lineno"> 1552</span>  }</div>
<div class="line"><a name="l01553"></a><span class="lineno"> 1553</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000011"</span>)</div>
<div class="line"><a name="l01554"></a><span class="lineno"> 1554</span>  {</div>
<div class="line"><a name="l01555"></a><span class="lineno"> 1555</span>  exp_->getInstrument().getMassAnalyzers().back().setResolution(asDouble_(value));</div>
<div class="line"><a name="l01556"></a><span class="lineno"> 1556</span>  }</div>
<div class="line"><a name="l01557"></a><span class="lineno"> 1557</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000012"</span>)</div>
<div class="line"><a name="l01558"></a><span class="lineno"> 1558</span>  {</div>
<div class="line"><a name="l01559"></a><span class="lineno"> 1559</span>  exp_->getInstrument().getMassAnalyzers().back().setResolutionMethod((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a11053909f1f8edf7b9ccc41c1417ecf6">MassAnalyzer::ResolutionMethod</a>)cvStringToEnum_(2, value, <span class="stringliteral">"resolution method"</span>));</div>
<div class="line"><a name="l01560"></a><span class="lineno"> 1560</span>  }</div>
<div class="line"><a name="l01561"></a><span class="lineno"> 1561</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000013"</span>)</div>
<div class="line"><a name="l01562"></a><span class="lineno"> 1562</span>  {</div>
<div class="line"><a name="l01563"></a><span class="lineno"> 1563</span>  exp_->getInstrument().getMassAnalyzers().back().setResolutionType((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a34bdf8df14c74a4beb0f343aa8141e60">MassAnalyzer::ResolutionType</a>)cvStringToEnum_(3, value, <span class="stringliteral">"resolution type"</span>));</div>
<div class="line"><a name="l01564"></a><span class="lineno"> 1564</span>  }</div>
<div class="line"><a name="l01565"></a><span class="lineno"> 1565</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000014"</span>)</div>
<div class="line"><a name="l01566"></a><span class="lineno"> 1566</span>  {</div>
<div class="line"><a name="l01567"></a><span class="lineno"> 1567</span>  exp_->getInstrument().getMassAnalyzers().back().setAccuracy(asDouble_(value));</div>
<div class="line"><a name="l01568"></a><span class="lineno"> 1568</span>  }</div>
<div class="line"><a name="l01569"></a><span class="lineno"> 1569</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000015"</span>)</div>
<div class="line"><a name="l01570"></a><span class="lineno"> 1570</span>  {</div>
<div class="line"><a name="l01571"></a><span class="lineno"> 1571</span>  exp_->getInstrument().getMassAnalyzers().back().setScanRate(asDouble_(value));</div>
<div class="line"><a name="l01572"></a><span class="lineno"> 1572</span>  }</div>
<div class="line"><a name="l01573"></a><span class="lineno"> 1573</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000016"</span>)</div>
<div class="line"><a name="l01574"></a><span class="lineno"> 1574</span>  {</div>
<div class="line"><a name="l01575"></a><span class="lineno"> 1575</span>  exp_->getInstrument().getMassAnalyzers().back().setScanTime(asDouble_(value));</div>
<div class="line"><a name="l01576"></a><span class="lineno"> 1576</span>  }</div>
<div class="line"><a name="l01577"></a><span class="lineno"> 1577</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000018"</span>)</div>
<div class="line"><a name="l01578"></a><span class="lineno"> 1578</span>  {</div>
<div class="line"><a name="l01579"></a><span class="lineno"> 1579</span>  exp_->getInstrument().getMassAnalyzers().back().setScanDirection((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#af4814792a42869dd07f2a81726b38402">MassAnalyzer::ScanDirection</a>)cvStringToEnum_(5, value, <span class="stringliteral">"scan direction"</span>));</div>
<div class="line"><a name="l01580"></a><span class="lineno"> 1580</span>  }</div>
<div class="line"><a name="l01581"></a><span class="lineno"> 1581</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000019"</span>)</div>
<div class="line"><a name="l01582"></a><span class="lineno"> 1582</span>  {</div>
<div class="line"><a name="l01583"></a><span class="lineno"> 1583</span>  exp_->getInstrument().getMassAnalyzers().back().setScanLaw((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a7652e90863e029a4e3620fdefb4cb854">MassAnalyzer::ScanLaw</a>)cvStringToEnum_(6, value, <span class="stringliteral">"scan law"</span>));</div>
<div class="line"><a name="l01584"></a><span class="lineno"> 1584</span>  }</div>
<div class="line"><a name="l01585"></a><span class="lineno"> 1585</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000020"</span>)</div>
<div class="line"><a name="l01586"></a><span class="lineno"> 1586</span>  {</div>
<div class="line"><a name="l01587"></a><span class="lineno"> 1587</span>  <span class="comment">// ignored</span></div>
<div class="line"><a name="l01588"></a><span class="lineno"> 1588</span>  }</div>
<div class="line"><a name="l01589"></a><span class="lineno"> 1589</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000021"</span>)</div>
<div class="line"><a name="l01590"></a><span class="lineno"> 1590</span>  {</div>
<div class="line"><a name="l01591"></a><span class="lineno"> 1591</span>  exp_->getInstrument().getMassAnalyzers().back().setReflectronState((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52f">MassAnalyzer::ReflectronState</a>)cvStringToEnum_(8, value, <span class="stringliteral">"reflectron state"</span>));</div>
<div class="line"><a name="l01592"></a><span class="lineno"> 1592</span>  }</div>
<div class="line"><a name="l01593"></a><span class="lineno"> 1593</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000022"</span>)</div>
<div class="line"><a name="l01594"></a><span class="lineno"> 1594</span>  {</div>
<div class="line"><a name="l01595"></a><span class="lineno"> 1595</span>  exp_->getInstrument().getMassAnalyzers().back().setTOFTotalPathLength(asDouble_(value));</div>
<div class="line"><a name="l01596"></a><span class="lineno"> 1596</span>  }</div>
<div class="line"><a name="l01597"></a><span class="lineno"> 1597</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000023"</span>)</div>
<div class="line"><a name="l01598"></a><span class="lineno"> 1598</span>  {</div>
<div class="line"><a name="l01599"></a><span class="lineno"> 1599</span>  exp_->getInstrument().getMassAnalyzers().back().setIsolationWidth(asDouble_(value));</div>
<div class="line"><a name="l01600"></a><span class="lineno"> 1600</span>  }</div>
<div class="line"><a name="l01601"></a><span class="lineno"> 1601</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000024"</span>)</div>
<div class="line"><a name="l01602"></a><span class="lineno"> 1602</span>  {</div>
<div class="line"><a name="l01603"></a><span class="lineno"> 1603</span>  exp_->getInstrument().getMassAnalyzers().back().setFinalMSExponent(asInt_(value));</div>
<div class="line"><a name="l01604"></a><span class="lineno"> 1604</span>  }</div>
<div class="line"><a name="l01605"></a><span class="lineno"> 1605</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000025"</span>)</div>
<div class="line"><a name="l01606"></a><span class="lineno"> 1606</span>  {</div>
<div class="line"><a name="l01607"></a><span class="lineno"> 1607</span>  exp_->getInstrument().getMassAnalyzers().back().setMagneticFieldStrength(asDouble_(value));</div>
<div class="line"><a name="l01608"></a><span class="lineno"> 1608</span>  }</div>
<div class="line"><a name="l01609"></a><span class="lineno"> 1609</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000017"</span>)</div>
<div class="line"><a name="l01610"></a><span class="lineno"> 1610</span>  {</div>
<div class="line"><a name="l01611"></a><span class="lineno"> 1611</span>  <span class="comment">//ignored</span></div>
<div class="line"><a name="l01612"></a><span class="lineno"> 1612</span>  }</div>
<div class="line"><a name="l01613"></a><span class="lineno"> 1613</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01614"></a><span class="lineno"> 1614</span>  {</div>
<div class="line"><a name="l01615"></a><span class="lineno"> 1615</span>  error = <span class="stringliteral">"AnalyzerList.Analyzer.UserParam"</span>;</div>
<div class="line"><a name="l01616"></a><span class="lineno"> 1616</span>  }</div>
<div class="line"><a name="l01617"></a><span class="lineno"> 1617</span>  }</div>
<div class="line"><a name="l01618"></a><span class="lineno"> 1618</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"additional"</span>)</div>
<div class="line"><a name="l01619"></a><span class="lineno"> 1619</span>  {</div>
<div class="line"><a name="l01620"></a><span class="lineno"> 1620</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000030"</span>)</div>
<div class="line"><a name="l01621"></a><span class="lineno"> 1621</span>  {</div>
<div class="line"><a name="l01622"></a><span class="lineno"> 1622</span>  exp_->getInstrument().setVendor(value);</div>
<div class="line"><a name="l01623"></a><span class="lineno"> 1623</span>  }</div>
<div class="line"><a name="l01624"></a><span class="lineno"> 1624</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000031"</span>)</div>
<div class="line"><a name="l01625"></a><span class="lineno"> 1625</span>  {</div>
<div class="line"><a name="l01626"></a><span class="lineno"> 1626</span>  exp_->getInstrument().setModel(value);</div>
<div class="line"><a name="l01627"></a><span class="lineno"> 1627</span>  }</div>
<div class="line"><a name="l01628"></a><span class="lineno"> 1628</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000032"</span>)</div>
<div class="line"><a name="l01629"></a><span class="lineno"> 1629</span>  {</div>
<div class="line"><a name="l01630"></a><span class="lineno"> 1630</span>  exp_->getInstrument().setCustomizations(value);</div>
<div class="line"><a name="l01631"></a><span class="lineno"> 1631</span>  }</div>
<div class="line"><a name="l01632"></a><span class="lineno"> 1632</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01633"></a><span class="lineno"> 1633</span>  {</div>
<div class="line"><a name="l01634"></a><span class="lineno"> 1634</span>  error = <span class="stringliteral">"Description.Instrument.Additional"</span>;</div>
<div class="line"><a name="l01635"></a><span class="lineno"> 1635</span>  }</div>
<div class="line"><a name="l01636"></a><span class="lineno"> 1636</span>  }</div>
<div class="line"><a name="l01637"></a><span class="lineno"> 1637</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"processingMethod"</span>)</div>
<div class="line"><a name="l01638"></a><span class="lineno"> 1638</span>  {</div>
<div class="line"><a name="l01639"></a><span class="lineno"> 1639</span>  <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000033"</span>)</div>
<div class="line"><a name="l01640"></a><span class="lineno"> 1640</span>  {</div>
<div class="line"><a name="l01641"></a><span class="lineno"> 1641</span>  data_processing_.getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">DataProcessing::DEISOTOPING</a>);</div>
<div class="line"><a name="l01642"></a><span class="lineno"> 1642</span>  }</div>
<div class="line"><a name="l01643"></a><span class="lineno"> 1643</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000034"</span>)</div>
<div class="line"><a name="l01644"></a><span class="lineno"> 1644</span>  {</div>
<div class="line"><a name="l01645"></a><span class="lineno"> 1645</span>  data_processing_.getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">DataProcessing::CHARGE_DECONVOLUTION</a>);</div>
<div class="line"><a name="l01646"></a><span class="lineno"> 1646</span>  }</div>
<div class="line"><a name="l01647"></a><span class="lineno"> 1647</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000127"</span>)</div>
<div class="line"><a name="l01648"></a><span class="lineno"> 1648</span>  {</div>
<div class="line"><a name="l01649"></a><span class="lineno"> 1649</span>  data_processing_.getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">DataProcessing::PEAK_PICKING</a>);</div>
<div class="line"><a name="l01650"></a><span class="lineno"> 1650</span>  }</div>
<div class="line"><a name="l01651"></a><span class="lineno"> 1651</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (accession == <span class="stringliteral">"PSI:1000035"</span>)</div>
<div class="line"><a name="l01652"></a><span class="lineno"> 1652</span>  {</div>
<div class="line"><a name="l01653"></a><span class="lineno"> 1653</span>  <span class="comment">//ignored</span></div>
<div class="line"><a name="l01654"></a><span class="lineno"> 1654</span>  }</div>
<div class="line"><a name="l01655"></a><span class="lineno"> 1655</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01656"></a><span class="lineno"> 1656</span>  {</div>
<div class="line"><a name="l01657"></a><span class="lineno"> 1657</span>  error = <span class="stringliteral">"DataProcessing.DataProcessing.UserParam"</span>;</div>
<div class="line"><a name="l01658"></a><span class="lineno"> 1658</span>  }</div>
<div class="line"><a name="l01659"></a><span class="lineno"> 1659</span>  }</div>
<div class="line"><a name="l01660"></a><span class="lineno"> 1660</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01661"></a><span class="lineno"> 1661</span>  {</div>
<div class="line"><a name="l01662"></a><span class="lineno"> 1662</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Unexpected cvParam: accession=\""</span>) + accession + <span class="stringliteral">"\" value=\""</span> + value + <span class="stringliteral">"\" in tag "</span> + parent_tag);</div>
<div class="line"><a name="l01663"></a><span class="lineno"> 1663</span>  }</div>
<div class="line"><a name="l01664"></a><span class="lineno"> 1664</span> </div>
<div class="line"><a name="l01665"></a><span class="lineno"> 1665</span>  <span class="keywordflow">if</span> (error != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l01666"></a><span class="lineno"> 1666</span>  {</div>
<div class="line"><a name="l01667"></a><span class="lineno"> 1667</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid cvParam: accession=\""</span>) + accession + <span class="stringliteral">"\" value=\""</span> + value + <span class="stringliteral">"\" in "</span> + error);</div>
<div class="line"><a name="l01668"></a><span class="lineno"> 1668</span>  }</div>
<div class="line"><a name="l01669"></a><span class="lineno"> 1669</span>  <span class="comment">//std::cout << "End of MzDataHander::cvParam_" << std::endl;</span></div>
<div class="line"><a name="l01670"></a><span class="lineno"> 1670</span>  }</div>
<div class="line"><a name="l01671"></a><span class="lineno"> 1671</span> </div>
<div class="line"><a name="l01672"></a><span class="lineno"> 1672</span>  } <span class="comment">// namespace Internal</span></div>
<div class="line"><a name="l01673"></a><span class="lineno"> 1673</span> </div>
<div class="line"><a name="l01674"></a><span class="lineno"> 1674</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l01675"></a><span class="lineno"> 1675</span> </div>
<div class="line"><a name="l01676"></a><span class="lineno"> 1676</span> <span class="preprocessor">#endif</span></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_1MetaInfoInterface_html_aae35ae2dfad88d673b03c787aafca83d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">OpenMS::MetaInfoInterface::getMetaValue</a></div><div class="ttdeci">const DataValue & getMetaValue(const String &name) const </div><div class="ttdoc">returns the value corresponding to a string </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_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 & getCustomizations() const </div><div class="ttdoc">returns a description of customizations </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a9606cd5b118bdb7ec690a362e127690e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9606cd5b118bdb7ec690a362e127690e">OpenMS::Internal::MzDataHandler::decoded_list_</a></div><div class="ttdeci">std::vector< std::vector< Real > > decoded_list_</div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:191</div></div>
<div class="ttc" id="classOpenMS_1_1Base64_html_aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4"><div class="ttname"><a href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">OpenMS::Base64::BYTEORDER_BIGENDIAN</a></div><div class="ttdoc">Big endian type. </div><div class="ttdef"><b>Definition:</b> Base64.h:78</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_1MassAnalyzer_html_a185f5769dc7bacd1054985fbda81dc20"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a185f5769dc7bacd1054985fbda81dc20">OpenMS::MassAnalyzer::getScanTime</a></div><div class="ttdeci">DoubleReal getScanTime() const </div><div class="ttdoc">returns the scan time for a single scan (in s) </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html">OpenMS::Internal::MzDataHandler</a></div><div class="ttdoc">XML handler for MzDataFile. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html">OpenMS::InstrumentSettings</a></div><div class="ttdoc">Description of the settings a MS Instrument was run with. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:48</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_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_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_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_1Internal_1_1MzDataHandler_html_a4e6e1cb4f8a8a0c70887c3568b86348e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">OpenMS::Internal::MzDataHandler::logger_</a></div><div class="ttdeci">const ProgressLogger & logger_</div><div class="ttdoc">Progress logger. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:204</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 & getNumber() const </div><div class="ttdoc">returns the sample number (default: &quot;&quot;) </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_1Internal_1_1XMLHandler_html_af86a807dd4b1ed6f4ba006b9bcd24763"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#af86a807dd4b1ed6f4ba006b9bcd24763">OpenMS::Internal::XMLHandler::warning</a></div><div class="ttdeci">void warning(const xercesc::SAXParseException &exception)</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< IonSource > & getIonSources() const </div><div class="ttdoc">returns a const reference to the ion source list </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_1Internal_1_1MzDataHandler_html_a2d6d13f6b8cb30e7943d4996e9ef2af7"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a2d6d13f6b8cb30e7943d4996e9ef2af7">OpenMS::Internal::MzDataHandler::setOptions</a></div><div class="ttdeci">void setOptions(const PeakFileOptions &options)</div><div class="ttdoc">Sets the options. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a9923434c5650af9e3f1f76d1b3236bf9"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9923434c5650af9e3f1f76d1b3236bf9">OpenMS::Internal::MzDataHandler::writeCVS_</a></div><div class="ttdeci">void writeCVS_(std::ostream &os, UInt value, UInt map, const String &acc, const String &name, UInt indent=4)</div><div class="ttdoc">write cvParam element to stream </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:262</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_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_1MassAnalyzer_html_a97cb45890678171a2ad985959861b0fc"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a97cb45890678171a2ad985959861b0fc">OpenMS::MassAnalyzer::getScanDirection</a></div><div class="ttdeci">ScanDirection getScanDirection() const </div><div class="ttdoc">returns the direction of scanning </div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_ab0301b5c82d74538dfffc98406254e11"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#ab0301b5c82d74538dfffc98406254e11">OpenMS::IonDetector::AcquisitionMode</a></div><div class="ttdeci">AcquisitionMode</div><div class="ttdoc">Acquisition mode. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:82</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_1Internal_1_1MzDataHandler_html_a81dc4d91ca22493e81272673e507a8c4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a81dc4d91ca22493e81272673e507a8c4">OpenMS::Internal::MzDataHandler::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> MzDataHandler.h:201</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_ac19bbe5ccf16799cdf273dbc3cc28ea5"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac19bbe5ccf16799cdf273dbc3cc28ea5">OpenMS::Internal::MzDataHandler::meta_id_descs_</a></div><div class="ttdeci">std::vector< std::pair< String, MetaInfoDescription > > meta_id_descs_</div><div class="ttdoc">An array of pairs MetaInfodescriptions and their ids. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:186</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 &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_1DataProcessing_html_ad34bb2f8f677e2f6c6c505d11754a765"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">OpenMS::DataProcessing::getProcessingActions</a></div><div class="ttdeci">const std::set< ProcessingAction > & getProcessingActions() const </div><div class="ttdoc">returns a const reference to the applied processing actions </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a0a00a4c4321f0e123b8ab6e68882865e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0a00a4c4321f0e123b8ab6e68882865e">OpenMS::Internal::MzDataHandler::data_to_decode_</a></div><div class="ttdeci">std::vector< String > data_to_decode_</div><div class="ttdoc">encoded data which is read and has to be decoded </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:188</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a742bdba7e6348fe6c549aada2a116944"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a742bdba7e6348fe6c549aada2a116944">OpenMS::Internal::MzDataHandler::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> MzDataHandler.h:338</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_1Internal_1_1MzDataHandler_html_a318165d3ac3b2191496c625d455f2293"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a318165d3ac3b2191496c625d455f2293">OpenMS::Internal::MzDataHandler::data_processing_</a></div><div class="ttdeci">DataProcessing data_processing_</div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:331</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< MassAnalyzer > & 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="structOpenMS_1_1ScanWindow_html_aed18ab075b5c0317ae32335a57f899e8"><div class="ttname"><a href="structOpenMS_1_1ScanWindow.html#aed18ab075b5c0317ae32335a57f899e8">OpenMS::ScanWindow::end</a></div><div class="ttdeci">DoubleReal end</div><div class="ttdoc">End of the window. </div><div class="ttdef"><b>Definition:</b> ScanWindow.h:64</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 & getAcquisitionInfo() const </div><div class="ttdoc">returns a const reference to the acquisition info </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_aa276c2358b6e8e0fa3e336d410d85802"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#aa276c2358b6e8e0fa3e336d410d85802">OpenMS::Internal::MzDataHandler::writeBinary_</a></div><div class="ttdeci">void writeBinary_(std::ostream &os, Size size, const String &tag, const String &name="", SignedSize id=-1)</div><div class="ttdoc">write binary data to stream (first one) </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:308</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_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_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_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="classOpenMS_1_1Internal_1_1MzDataHandler_html_a9e8f070ec9479603961d8ad3bf49a9a3"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">OpenMS::Internal::MzDataHandler::decoder_</a></div><div class="ttdeci">Base64 decoder_</div><div class="ttdoc">Decoder/Encoder for Base64-data in MzData. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:198</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a001483d1f67f068e585f10d9abcc487d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a001483d1f67f068e585f10d9abcc487d">OpenMS::MetaInfoInterface::isMetaEmpty</a></div><div class="ttdeci">bool isMetaEmpty() const </div><div class="ttdoc">returns if the MetaInfo is empty </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_1Instrument_html_a796a6cd8072195dfaf282a0827bebb4a"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">OpenMS::Instrument::getIonDetectors</a></div><div class="ttdeci">const std::vector< IonDetector > & 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_1Internal_1_1MzDataHandler_html_a1401bdd07b2039bdf39ae4af22b2a23d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a1401bdd07b2039bdf39ae4af22b2a23d">OpenMS::Internal::MzDataHandler::writeCVS_</a></div><div class="ttdeci">void writeCVS_(std::ostream &os, const String &value, const String &acc, const String &name, UInt indent=4) const </div><div class="ttdoc">write cvParam containing strings to stream </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:241</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_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="structOpenMS_1_1ScanWindow_html_aea3ca80628c489842c52a61e195dd047"><div class="ttname"><a href="structOpenMS_1_1ScanWindow.html#aea3ca80628c489842c52a61e195dd047">OpenMS::ScanWindow::begin</a></div><div class="ttdeci">DoubleReal begin</div><div class="ttdoc">Begin of the window. </div><div class="ttdef"><b>Definition:</b> ScanWindow.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_af4814792a42869dd07f2a81726b38402"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#af4814792a42869dd07f2a81726b38402">OpenMS::MassAnalyzer::ScanDirection</a></div><div class="ttdeci">ScanDirection</div><div class="ttdoc">direction of scanning </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:103</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 &quot;mass spectrum&quot;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a009a30591b3297275a4db1359fcd82ed"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a009a30591b3297275a4db1359fcd82ed">OpenMS::Internal::MzDataHandler::init_</a></div><div class="ttdeci">void init_()</div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:121</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a654a0b5941d937e303c64bc9e732baec"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a654a0b5941d937e303c64bc9e732baec">OpenMS::Internal::MzDataHandler::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> MzDataHandler.h:177</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_1IonSource_html_a08b8f804d8602840858ce2d533db675f"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a08b8f804d8602840858ce2d533db675f">OpenMS::IonSource::InletType</a></div><div class="ttdeci">InletType</div><div class="ttdoc">inlet type </div><div class="ttdef"><b>Definition:</b> IonSource.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::IonDetector::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Detector type. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:52</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_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_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: &#39;Multiple reaction monitoring scan&#39;, &#39;SRM scan&#39;, &#39;MRM scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a34bdf8df14c74a4beb0f343aa8141e60"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a34bdf8df14c74a4beb0f343aa8141e60">OpenMS::MassAnalyzer::ResolutionType</a></div><div class="ttdeci">ResolutionType</div><div class="ttdoc">Resolution type. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:92</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_1Acquisition_html_a4eb8ec8636a89f575db95a370fd480b6"><div class="ttname"><a href="classOpenMS_1_1Acquisition.html#a4eb8ec8636a89f575db95a370fd480b6">OpenMS::Acquisition::getIdentifier</a></div><div class="ttdeci">const String & getIdentifier() const </div><div class="ttdoc">return the identifier/index/number of the acquisition </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="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< ActivationMethod > & getActivationMethods() const </div><div class="ttdoc">returns a const reference to the activation methods </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_ad95ce47c6061b79f9457062c35318164"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ad95ce47c6061b79f9457062c35318164">OpenMS::Internal::MzDataHandler::writeUserParam_</a></div><div class="ttdeci">void writeUserParam_(std::ostream &os, const MetaInfoInterface &meta, UInt indent=4)</div><div class="ttdoc">Writing the MetaInfo as UserParam to the file. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:280</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_aca0182626ca1b619a5679b02fa4e8a41"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#aca0182626ca1b619a5679b02fa4e8a41">OpenMS::MassAnalyzer::getScanLaw</a></div><div class="ttdeci">ScanLaw getScanLaw() const </div><div class="ttdoc">returns the scan law </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a4ff959be3f54a8b526a7777f903ebcce"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a4ff959be3f54a8b526a7777f903ebcce">OpenMS::MassAnalyzer::getScanRate</a></div><div class="ttdeci">DoubleReal getScanRate() const </div><div class="ttdoc">returns the scan rate (in s) </div></div>
<div class="ttc" id="classOpenMS_1_1DateTime_html_ae8d3cac5cd5763984d9ca84d3453ed28"><div class="ttname"><a href="classOpenMS_1_1DateTime.html#ae8d3cac5cd5763984d9ca84d3453ed28">OpenMS::DateTime::get</a></div><div class="ttdeci">void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const </div><div class="ttdoc">Fills the arguments with the date and the time. </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a11053909f1f8edf7b9ccc41c1417ecf6"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a11053909f1f8edf7b9ccc41c1417ecf6">OpenMS::MassAnalyzer::ResolutionMethod</a></div><div class="ttdeci">ResolutionMethod</div><div class="ttdoc">resolution method </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:80</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="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a484c33c30ea480bd831a92847f61006e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a484c33c30ea480bd831a92847f61006e">OpenMS::Internal::MzDataHandler::startElement</a></div><div class="ttdeci">virtual void startElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes)</div><div class="ttdoc">Parsing method for opening tags. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:436</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></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_1MassAnalyzer_html_ae40769827bc59bd577d8b81cd1bb8974"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#ae40769827bc59bd577d8b81cd1bb8974">OpenMS::MassAnalyzer::getIsolationWidth</a></div><div class="ttdeci">DoubleReal getIsolationWidth() const </div><div class="ttdoc">returns the isolation width i.e. in which m/z range the precursor ion is selected for MS to the n (in...</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< ScanWindow > & getScanWindows() const </div><div class="ttdoc">returns a const reference to the m/z scan windows </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_ac983ab0d4acb0c9fe2b4d80346588625"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ac983ab0d4acb0c9fe2b4d80346588625">OpenMS::Internal::MzDataHandler::precisions_</a></div><div class="ttdeci">std::vector< String > precisions_</div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:193</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a790f2511d9b121d15aef56b6a96b45bf"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a790f2511d9b121d15aef56b6a96b45bf">OpenMS::MassAnalyzer::getResolutionMethod</a></div><div class="ttdeci">ResolutionMethod getResolutionMethod() const </div><div class="ttdoc">returns the method used for determination of the resolution </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_add1bc02b038fe1abde05c0352577f1df"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#add1bc02b038fe1abde05c0352577f1df">OpenMS::Internal::MzDataHandler::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> MzDataHandler.h:722</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 1 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a02142528005396ed2f37e387a59882b0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a02142528005396ed2f37e387a59882b0">OpenMS::Internal::MzDataHandler::writeCVS_</a></div><div class="ttdeci">void writeCVS_(std::ostream &os, DoubleReal value, const String &acc, const String &name, UInt indent=4) const </div><div class="ttdoc">write cvParam containing strings to stream </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:222</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a21e306967405afb217201901a2d75351"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21e306967405afb217201901a2d75351">OpenMS::Internal::MzDataHandler::exp_</a></div><div class="ttdeci">MapType * exp_</div><div class="ttdoc">map pointer for reading </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:172</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html_a6cc566e3bbfdcb8a5a9d85941238cef5afeb01cb4572ba190cd7932e49446c480"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6cc566e3bbfdcb8a5a9d85941238cef5afeb01cb4572ba190cd7932e49446c480">OpenMS::Internal::XMLHandler::STORE</a></div><div class="ttdoc">Storing a file. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:109</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a066042ae14211da37d4fa66d466bfa3e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a066042ae14211da37d4fa66d466bfa3e">OpenMS::Internal::MzDataHandler::SpectrumType</a></div><div class="ttdeci">MSSpectrum< PeakType > SpectrumType</div><div class="ttdoc">Spectrum type. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:169</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a307ba40c92040f24cb0b496fb5b58b88"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a307ba40c92040f24cb0b496fb5b58b88">OpenMS::Instrument::getModel</a></div><div class="ttdeci">const String & getModel() const </div><div class="ttdoc">returns the instrument model </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 & 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_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_1Instrument_html_adeb3a96bea31dcca5dc2cba4d6e22cb5"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#adeb3a96bea31dcca5dc2cba4d6e22cb5">OpenMS::Instrument::getVendor</a></div><div class="ttdeci">const String & getVendor() const </div><div class="ttdoc">returns the instrument vendor </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_1Internal_1_1MzDataHandler_html_a536eb31a991f01c5047f1fe1d6b5db70"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a536eb31a991f01c5047f1fe1d6b5db70">OpenMS::Internal::MzDataHandler::data_to_encode_</a></div><div class="ttdeci">std::vector< Real > data_to_encode_</div><div class="ttdoc">floating point numbers which have to be encoded and written </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a4b8fc915bd9da6b6acf96bdcd67f0163"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a4b8fc915bd9da6b6acf96bdcd67f0163">OpenMS::Internal::MzDataHandler::MzDataHandler</a></div><div class="ttdeci">MzDataHandler(const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)</div><div class="ttdoc">Constructor for a read-only handler. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:81</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a6af0ff50dcb5a916e4cafba2b8f1d884"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">OpenMS::Internal::MzDataHandler::PeakType</a></div><div class="ttdeci">MapType::PeakType PeakType</div><div class="ttdoc">Peak type. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:167</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_1MassAnalyzer_html_a4f15a2dc6638a7bdbcc97cab181bd52f"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a4f15a2dc6638a7bdbcc97cab181bd52f">OpenMS::MassAnalyzer::ReflectronState</a></div><div class="ttdeci">ReflectronState</div><div class="ttdoc">Reflectron state. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:126</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 &quot;mass spectrum&quot; Synonyms: &#39;full spectrum&#39;, &#39;Q1 spectrum&#39;, &#39;Q3 spectrum&#39;, &#39;Single-Stage Mass Spectrometry&#39; </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:57</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_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< String > &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_1Internal_1_1MzDataHandler_html_ae19606cee74ec0ac3662fcfba274cbd0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">OpenMS::Internal::MzDataHandler::cexp_</a></div><div class="ttdeci">const MapType * cexp_</div><div class="ttdoc">map pointer for writing </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:174</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_a219795d06917877c7d946a00f23e2319"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#a219795d06917877c7d946a00f23e2319">OpenMS::DataProcessing::getSoftware</a></div><div class="ttdeci">const Software & getSoftware() const </div><div class="ttdoc">returns a const reference to the software used for processing </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a75dfe025bbcb3cf65fd7c515476f178e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a75dfe025bbcb3cf65fd7c515476f178e">OpenMS::Internal::MzDataHandler::~MzDataHandler</a></div><div class="ttdeci">virtual ~MzDataHandler()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4">OpenMS::IonSource::IonizationMethod</a></div><div class="ttdeci">IonizationMethod</div><div class="ttdoc">ionization method </div><div class="ttdef"><b>Definition:</b> IonSource.h:80</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 & getName() const </div><div class="ttdoc">returns the name of the software </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a53098f01ff2026b860b917fa4df0ea31"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a53098f01ff2026b860b917fa4df0ea31">OpenMS::Internal::MzDataHandler::decoded_double_list_</a></div><div class="ttdeci">std::vector< std::vector< DoubleReal > > decoded_double_list_</div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:192</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: &#39;Multiple ion monitoring scan&#39;, &#39;SIM scan&#39;, &#39;MIM scan&#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: &#39;CNG scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:63</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_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_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="classOpenMS_1_1MassAnalyzer_html_adff73543752de4ef66823716e9eed3aa"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#adff73543752de4ef66823716e9eed3aa">OpenMS::MassAnalyzer::getResolution</a></div><div class="ttdeci">DoubleReal getResolution() const </div><div class="ttdoc">returns the resolution </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a21c6981f49bad30b573e09ece24bccc4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a21c6981f49bad30b573e09ece24bccc4">OpenMS::Internal::MzDataHandler::MzDataHandler</a></div><div class="ttdeci">MzDataHandler(MapType &exp, const String &filename, const String &version, ProgressLogger &logger)</div><div class="ttdoc">Constructor for a write-only handler. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:67</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: &#39;CRM scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a19e786a978c9050cdb613a02a7f38676"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a19e786a978c9050cdb613a02a7f38676">OpenMS::Internal::MzDataHandler::endians_</a></div><div class="ttdeci">std::vector< String > endians_</div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:194</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzDataHandler_html_a189e2aea7a4b8bbfcefbf62176d0966c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">OpenMS::Internal::MzDataHandler::peak_count_</a></div><div class="ttdeci">UInt peak_count_</div><div class="ttdoc">The number of peaks in the current spectrum. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1Sample_html_a44840409b59d07d84f72a6460073ab71"><div class="ttname"><a href="classOpenMS_1_1Sample.html#a44840409b59d07d84f72a6460073ab71">OpenMS::Sample::SampleState</a></div><div class="ttdeci">SampleState</div><div class="ttdoc">state of aggregation of the sample </div><div class="ttdef"><b>Definition:</b> Sample.h:65</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 & getVersion() const </div><div class="ttdoc">returns the software version </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_a3bbd5b209e18f9afd4d8b4308787a538"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#a3bbd5b209e18f9afd4d8b4308787a538">OpenMS::DataProcessing::getCompletionTime</a></div><div class="ttdeci">const DateTime & getCompletionTime() const </div><div class="ttdoc">returns the time of completition of the processing </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="classOpenMS_1_1Internal_1_1MzDataHandler_html_a56bc42e12243f36ea7d533b03609e30d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a56bc42e12243f36ea7d533b03609e30d">OpenMS::Internal::MzDataHandler::spec_</a></div><div class="ttdeci">SpectrumType spec_</div><div class="ttdoc">The current spectrum. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:184</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 & 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_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_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_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_1Instrument_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::Instrument::getName</a></div><div class="ttdeci">const String & 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_1String_html_a226b41d565aa586bd45aa7d046608511"><div class="ttname"><a href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">OpenMS::String::substr</a></div><div class="ttdeci">String substr(size_t pos=0, size_t n=npos) const </div><div class="ttdoc">Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...</div></div>
<div class="ttc" id="classOpenMS_1_1Base64_html_ac70a32569b52ad3f7f462ca6c03d723a"><div class="ttname"><a href="classOpenMS_1_1Base64.html#ac70a32569b52ad3f7f462ca6c03d723a">OpenMS::Base64::encode</a></div><div class="ttdeci">void encode(std::vector< FromType > &in, ByteOrder to_byte_order, String &out, bool zlib_compression=false)</div><div class="ttdoc">Encodes a vector of floating point numbers to a Base64 string. </div><div class="ttdef"><b>Definition:</b> Base64.h:195</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 & 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_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_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_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_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_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_1SpectrumSettings_html_a90b48146f536d2ab932723af63f0cb15"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">OpenMS::SpectrumSettings::getPrecursors</a></div><div class="ttdeci">const std::vector< Precursor > & 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: &#39;CNG scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ade504dd839d796a10e9fc4d840952dc1"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ade504dd839d796a10e9fc4d840952dc1">OpenMS::Precursor::ActivationMethod</a></div><div class="ttdeci">ActivationMethod</div><div class="ttdoc">Method of activation. </div><div class="ttdef"><b>Definition:</b> Precursor.h:64</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_1Internal_1_1XMLHandler_html_a6476bfc5285236c19e7f731e43d05cdd"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">OpenMS::Internal::XMLHandler::cv_terms_</a></div><div class="ttdeci">std::vector< std::vector< String > > cv_terms_</div><div class="ttdoc">Array of CV term lists (one sublist denotes one term and it&#39;s children) </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:192</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3">OpenMS::MassAnalyzer::AnalyzerType</a></div><div class="ttdeci">AnalyzerType</div><div class="ttdoc">analyzer type </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:53</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 & 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_1InstrumentSettings_html_af9ecf94ffd05a020cce7a2d10794a192"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9ecf94ffd05a020cce7a2d10794a192">OpenMS::InstrumentSettings::NamesOfScanMode</a></div><div class="ttdeci">static const std::string NamesOfScanMode[SIZE_OF_SCANMODE]</div><div class="ttdoc">Names of scan modes. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:74</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 & 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_1MassAnalyzer_html_a7652e90863e029a4e3620fdefb4cb854"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a7652e90863e029a4e3620fdefb4cb854">OpenMS::MassAnalyzer::ScanLaw</a></div><div class="ttdeci">ScanLaw</div><div class="ttdoc">Scan law. </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:114</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="classOpenMS_1_1Internal_1_1MzDataHandler_html_a9028634d022a74d1fc8db852d99984d6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a9028634d022a74d1fc8db852d99984d6">OpenMS::Internal::MzDataHandler::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> MzDataHandler.h:686</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_1String_html_ae580d960e12c7f0ebc5c95931cf39ad5"><div class="ttname"><a href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">OpenMS::String::split</a></div><div class="ttdeci">bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const </div><div class="ttdoc">Splits a string into substrings using splitter as delimiter. </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 & getName() const </div><div class="ttdoc">retuns the sample name (default: &quot;&quot;) </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_1Internal_1_1MzDataHandler_html_a246d2ed7a27643da899d40062055882a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a246d2ed7a27643da899d40062055882a">OpenMS::Internal::MzDataHandler::cvParam_</a></div><div class="ttdeci">void cvParam_(const String &name, const String &value)</div><div class="ttdoc">read attributes of MzData&#39;s cvParamType </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:1313</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_1MassAnalyzer_html_a833abbfac1bc606081ab956e723111c1"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a833abbfac1bc606081ab956e723111c1">OpenMS::MassAnalyzer::getResolutionType</a></div><div class="ttdeci">ResolutionType getResolutionType() const </div><div class="ttdoc">returns the resolution type </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a84a045fa4024e050ca8be6d33311a054"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054">OpenMS::IonSource::Polarity</a></div><div class="ttdeci">Polarity</div><div class="ttdoc">Polarity of the ion source. </div><div class="ttdef"><b>Definition:</b> IonSource.h:140</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_1MzDataHandler_html_a0038ff865ac073e00ca829d977f2ccdf"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzDataHandler.html#a0038ff865ac073e00ca829d977f2ccdf">OpenMS::Internal::MzDataHandler::writeTo</a></div><div class="ttdeci">void writeTo(std::ostream &os)</div><div class="ttdoc">Writes the contents to a stream. </div><div class="ttdef"><b>Definition:</b> MzDataHandler.h:816</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 &string) const </div><div class="ttdoc">true if String begins with string, false otherwise </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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