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<a href="MzIdentMLHandler_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
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<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Mathias Walzer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Mathias Walzer, Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_HANDLERS_MZIDENTMLHANDLER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ControlledVocabulary_8h.html">OpenMS/FORMAT/ControlledVocabulary.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="IdentificationHit_8h.html">OpenMS/METADATA/IdentificationHit.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Identification_8h.html">OpenMS/METADATA/Identification.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProteinHit_8h.html">OpenMS/METADATA/ProteinHit.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="AASequence_8h.html">OpenMS/CHEMISTRY/AASequence.h</a>&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="UniqueIdGenerator_8h.html">OpenMS/CONCEPT/UniqueIdGenerator.h</a>&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.h</a>&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>&gt;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;{</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;  <span class="keyword">class </span>ProgressLogger;</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;  {</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">   64</a></span>&#160;    <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a> :</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;      <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    {</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Identification.html">Identification</a> &amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; logger);</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>(<span class="keyword">const</span> std::vector&lt;ProteinIdentification&gt; &amp; pro_id, <span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; pep_id, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; logger);</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>(<a class="code" href="classOpenMS_1_1Identification.html">Identification</a> &amp; <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; logger);</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>(std::vector&lt;ProteinIdentification&gt; &amp; pro_id, std::vector&lt;PeptideIdentification&gt; &amp; pep_id, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; logger);</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>();</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> endElement(<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="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> startElement(<span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh * <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes &amp; attributes);</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> characters(<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="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      <span class="comment">//Docu in base class</span></div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;      <span class="keyword">virtual</span> <span class="keywordtype">void</span> writeTo(std::ostream &amp; os);</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">  100</a></span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a> &amp; <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">  103</a></span>&#160;      <a class="code" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">cv_</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a8b6d5ceb18b45ae4fadedb7558427708">  105</a></span>&#160;      <a class="code" href="classOpenMS_1_1ControlledVocabulary.html">ControlledVocabulary</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a8b6d5ceb18b45ae4fadedb7558427708">unimod_</a>;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;      <span class="comment">//~ MSExperiment&lt;&gt;* ms_exp_;</span></div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">  110</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">tag_</a>;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a7eb64eb4790a0860181ff29dbe9a0960">  113</a></span>&#160;      <a class="code" href="classOpenMS_1_1Identification.html">Identification</a> * <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a7eb64eb4790a0860181ff29dbe9a0960">id_</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a76323913576f0692264bd3a3ae0d5156">  115</a></span>&#160;      std::vector&lt;ProteinIdentification&gt; * <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a76323913576f0692264bd3a3ae0d5156">pro_id_</a>;</div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a85ffcc3e0ab0440589f81115a8fcc945">  117</a></span>&#160;      std::vector&lt;PeptideIdentification&gt; * <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a85ffcc3e0ab0440589f81115a8fcc945">pep_id_</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a08877c4558f2218a27cfa395c1acd183">  119</a></span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Identification.html">Identification</a> * <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a08877c4558f2218a27cfa395c1acd183">cid_</a>;</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4b9a58fa9dceaf97c8fd41c991df15bd">  120</a></span>&#160;      <span class="keyword">const</span> std::vector&lt;ProteinIdentification&gt; * <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4b9a58fa9dceaf97c8fd41c991df15bd">cpro_id_</a>;</div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#acb8701b19084ad0aa3a5921a0e4805c6">  121</a></span>&#160;      <span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; * <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#acb8701b19084ad0aa3a5921a0e4805c6">cpep_id_</a>;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a6d7ea1807458e70398f7afe8df74b61e">  124</a></span>&#160;      <a class="code" href="classOpenMS_1_1SpectrumIdentification.html">SpectrumIdentification</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a6d7ea1807458e70398f7afe8df74b61e">current_spectrum_id_</a>;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a48dfe8d6bfeda7349a686c8a8ca8af08">  127</a></span>&#160;      <a class="code" href="classOpenMS_1_1IdentificationHit.html">IdentificationHit</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a48dfe8d6bfeda7349a686c8a8ca8af08">current_id_hit_</a>;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;      <span class="keywordtype">void</span> handleCVParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; accession, <span class="comment">/* const String&amp; name, */</span> <span class="comment">/* const String&amp; value, */</span> <span class="keyword">const</span> xercesc::Attributes &amp; attributes, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; cv_ref <span class="comment">/* ,  const String&amp; unit_accession=&quot;&quot; */</span>);</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;      <span class="keywordtype">void</span> handleUserParam_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_tag, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; type, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; value);</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      <span class="keywordtype">void</span> writeUserParam_(std::ostream &amp; os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a> &amp; meta, <a class="code" href="classunsigned_01int.html">UInt</a> indent) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;      <a class="code" href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">ControlledVocabulary::CVTerm</a> getChildWithName_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; parent_accession, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; name) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <span class="comment">//void writeSourceFile_(std::ostream&amp; os, const String&amp; id, const SourceFile&amp; software);</span></div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>();</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a> &amp; rhs);</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">MzIdentMLHandler</a> &amp; rhs);</div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#aff7894089fcb45169b8fbdef2a88074a">  149</a></span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, AASequence&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#aff7894089fcb45169b8fbdef2a88074a">pep_sequences_</a>;</div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#aacf23a3d47e383f29cb9529f3feaf178">  150</a></span>&#160;      <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#aacf23a3d47e383f29cb9529f3feaf178">actual_peptide_</a>;</div>
<div class="line"><a name="l00151"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#ad49790366dea0f94825ad18d6cf69374">  151</a></span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#ad49790366dea0f94825ad18d6cf69374">current_mod_location_</a>;</div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a1890f7dc2cc750bdddfd46ede76847b4">  152</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a1890f7dc2cc750bdddfd46ede76847b4">actual_protein_</a>;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;    };</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;  }   <span class="comment">// namespace Internal</span></div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;<span class="preprocessor">#endif</span></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="ProteinHit_8h_html"><div class="ttname"><a href="ProteinHit_8h.html">ProteinHit.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a6d7ea1807458e70398f7afe8df74b61e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a6d7ea1807458e70398f7afe8df74b61e">OpenMS::Internal::MzIdentMLHandler::current_spectrum_id_</a></div><div class="ttdeci">SpectrumIdentification current_spectrum_id_</div><div class="ttdoc">SpectrumIdentification Item. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:124</div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a85ffcc3e0ab0440589f81115a8fcc945"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a85ffcc3e0ab0440589f81115a8fcc945">OpenMS::Internal::MzIdentMLHandler::pep_id_</a></div><div class="ttdeci">std::vector&lt; PeptideIdentification &gt; * pep_id_</div><div class="ttdoc">Identification Item for peptides. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:117</div></div>
<div class="ttc" id="structOpenMS_1_1ControlledVocabulary_1_1CVTerm_html"><div class="ttname"><a href="structOpenMS_1_1ControlledVocabulary_1_1CVTerm.html">OpenMS::ControlledVocabulary::CVTerm</a></div><div class="ttdoc">Representation of a CV term. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:60</div></div>
<div class="ttc" id="classOpenMS_1_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_1Internal_1_1MzIdentMLHandler_html_aff7894089fcb45169b8fbdef2a88074a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#aff7894089fcb45169b8fbdef2a88074a">OpenMS::Internal::MzIdentMLHandler::pep_sequences_</a></div><div class="ttdeci">Map&lt; String, AASequence &gt; pep_sequences_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:149</div></div>
<div class="ttc" id="ControlledVocabulary_8h_html"><div class="ttname"><a href="ControlledVocabulary_8h.html">ControlledVocabulary.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a48dfe8d6bfeda7349a686c8a8ca8af08"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a48dfe8d6bfeda7349a686c8a8ca8af08">OpenMS::Internal::MzIdentMLHandler::current_id_hit_</a></div><div class="ttdeci">IdentificationHit current_id_hit_</div><div class="ttdoc">IdentificationHit Item. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_ad49790366dea0f94825ad18d6cf69374"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#ad49790366dea0f94825ad18d6cf69374">OpenMS::Internal::MzIdentMLHandler::current_mod_location_</a></div><div class="ttdeci">Int current_mod_location_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:151</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_aacf23a3d47e383f29cb9529f3feaf178"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#aacf23a3d47e383f29cb9529f3feaf178">OpenMS::Internal::MzIdentMLHandler::actual_peptide_</a></div><div class="ttdeci">AASequence actual_peptide_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:150</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="AASequence_8h_html"><div class="ttname"><a href="AASequence_8h.html">AASequence.h</a></div></div>
<div class="ttc" id="Identification_8h_html"><div class="ttname"><a href="Identification_8h.html">Identification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a4e6e1cb4f8a8a0c70887c3568b86348e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">OpenMS::Internal::MzIdentMLHandler::logger_</a></div><div class="ttdeci">const ProgressLogger &amp; logger_</div><div class="ttdoc">Progress logger. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a4efa4aca7642864fed4e7e4cca9e2a79"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">OpenMS::Internal::MzIdentMLHandler::tag_</a></div><div class="ttdeci">String tag_</div><div class="ttdoc">XML tag parse element. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:110</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a4b9a58fa9dceaf97c8fd41c991df15bd"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4b9a58fa9dceaf97c8fd41c991df15bd">OpenMS::Internal::MzIdentMLHandler::cpro_id_</a></div><div class="ttdeci">const std::vector&lt; ProteinIdentification &gt; * cpro_id_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:120</div></div>
<div class="ttc" id="IdentificationHit_8h_html"><div class="ttname"><a href="IdentificationHit_8h.html">IdentificationHit.h</a></div></div>
<div class="ttc" id="UniqueIdGenerator_8h_html"><div class="ttname"><a href="UniqueIdGenerator_8h.html">UniqueIdGenerator.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ControlledVocabulary_html"><div class="ttname"><a href="classOpenMS_1_1ControlledVocabulary.html">OpenMS::ControlledVocabulary</a></div><div class="ttdoc">Representation of a controlled vocabulary. </div><div class="ttdef"><b>Definition:</b> ControlledVocabulary.h:54</div></div>
<div class="ttc" id="ProteinIdentification_8h_html"><div class="ttname"><a href="ProteinIdentification_8h.html">ProteinIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a4e6fb8ab8655403a2cb4f07d72559cd7"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a4e6fb8ab8655403a2cb4f07d72559cd7">OpenMS::Internal::MzIdentMLHandler::cv_</a></div><div class="ttdeci">ControlledVocabulary cv_</div><div class="ttdoc">Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html">OpenMS::Internal::MzIdentMLHandler</a></div><div class="ttdoc">XML handler for MzIdentMLFile. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumIdentification_html"><div class="ttname"><a href="classOpenMS_1_1SpectrumIdentification.html">OpenMS::SpectrumIdentification</a></div><div class="ttdoc">Represents a object which can store the information of an analysisXML instance. </div><div class="ttdef"><b>Definition:</b> SpectrumIdentification.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1Identification_html"><div class="ttname"><a href="classOpenMS_1_1Identification.html">OpenMS::Identification</a></div><div class="ttdoc">Represents a object which can store the information of an analysisXML instance. </div><div class="ttdef"><b>Definition:</b> Identification.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a1890f7dc2cc750bdddfd46ede76847b4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a1890f7dc2cc750bdddfd46ede76847b4">OpenMS::Internal::MzIdentMLHandler::actual_protein_</a></div><div class="ttdeci">ProteinHit actual_protein_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:152</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a7eb64eb4790a0860181ff29dbe9a0960"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a7eb64eb4790a0860181ff29dbe9a0960">OpenMS::Internal::MzIdentMLHandler::id_</a></div><div class="ttdeci">Identification * id_</div><div class="ttdoc">Identification Item. </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a8b6d5ceb18b45ae4fadedb7558427708"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a8b6d5ceb18b45ae4fadedb7558427708">OpenMS::Internal::MzIdentMLHandler::unimod_</a></div><div class="ttdeci">ControlledVocabulary unimod_</div><div class="ttdoc">Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo) </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinHit_html"><div class="ttname"><a href="classOpenMS_1_1ProteinHit.html">OpenMS::ProteinHit</a></div><div class="ttdoc">Representation of a protein hit. </div><div class="ttdef"><b>Definition:</b> ProteinHit.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a76323913576f0692264bd3a3ae0d5156"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a76323913576f0692264bd3a3ae0d5156">OpenMS::Internal::MzIdentMLHandler::pro_id_</a></div><div class="ttdeci">std::vector&lt; ProteinIdentification &gt; * pro_id_</div><div class="ttdoc">internal Identification Item for proteins </div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1IdentificationHit_html"><div class="ttname"><a href="classOpenMS_1_1IdentificationHit.html">OpenMS::IdentificationHit</a></div><div class="ttdoc">Represents a object which can store the information of an analysisXML instance. </div><div class="ttdef"><b>Definition:</b> IdentificationHit.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_acb8701b19084ad0aa3a5921a0e4805c6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#acb8701b19084ad0aa3a5921a0e4805c6">OpenMS::Internal::MzIdentMLHandler::cpep_id_</a></div><div class="ttdeci">const std::vector&lt; PeptideIdentification &gt; * cpep_id_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:121</div></div>
<div class="ttc" id="PeptideIdentification_8h_html"><div class="ttname"><a href="PeptideIdentification_8h.html">PeptideIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzIdentMLHandler_html_a08877c4558f2218a27cfa395c1acd183"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzIdentMLHandler.html#a08877c4558f2218a27cfa395c1acd183">OpenMS::Internal::MzIdentMLHandler::cid_</a></div><div class="ttdeci">const Identification * cid_</div><div class="ttdef"><b>Definition:</b> MzIdentMLHandler.h:119</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="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="XMLHandler_8h_html"><div class="ttname"><a href="XMLHandler_8h.html">XMLHandler.h</a></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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