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<a href="MascotXMLFile_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>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Nico Pfeifer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Nico Pfeifer $</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_MASCOTXMLFILE_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_MASCOTXMLFILE_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="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="AASequence_8h.html">OpenMS/CHEMISTRY/AASequence.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="XMLFile_8h.html">OpenMS/FORMAT/XMLFile.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="MascotXMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/MascotXMLHandler.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="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;{</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;  <span class="keyword">class </span>ProteinIdentification;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotXMLFile.html">   57</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MascotXMLFile.html">MascotXMLFile</a> :</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLFile.html">Internal::XMLFile</a></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;  {</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">   62</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Map.html">Internal::MascotXMLHandler::RTMapping</a> <a class="code" href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">RTMapping</a>;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <a class="code" href="classOpenMS_1_1MascotXMLFile.html">MascotXMLFile</a>();</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename,</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;              <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; protein_identification,</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;              std::vector&lt;PeptideIdentification&gt;&amp; id_data,</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;              <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Map.html">RTMapping</a>&amp; rt_mapping = <a class="code" href="classOpenMS_1_1Map.html">RTMapping</a>(),</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;              <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; scan_regex = <span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename,</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;              <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; protein_identification,</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;              std::vector&lt;PeptideIdentification&gt;&amp; id_data, </div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;              std::map&lt;<a class="code" href="classOpenMS_1_1String.html">String</a>, std::vector&lt;AASequence&gt; &gt;&amp; peptides, </div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;              <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Map.html">RTMapping</a>&amp; rt_mapping = <a class="code" href="classOpenMS_1_1Map.html">RTMapping</a>(),</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;              <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; scan_regex = <span class="stringliteral">&quot;&quot;</span>);</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> generateRTMapping(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MSExperiment&lt;&gt;::ConstIterator</a> begin, </div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;                                  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MSExperiment&lt;&gt;::ConstIterator</a> end, </div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;                                  <a class="code" href="classOpenMS_1_1Map.html">RTMapping</a>&amp; rt_mapping);</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;  };</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;<span class="preprocessor">#endif // OPENMS_FORMAT_MASCOTXMLFILE_H</span></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html">OpenMS::ProteinIdentification</a></div><div class="ttdoc">Representation of a protein identification run. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:61</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="AASequence_8h_html"><div class="ttname"><a href="AASequence_8h.html">AASequence.h</a></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="XMLFile_8h_html"><div class="ttname"><a href="XMLFile_8h.html">XMLFile.h</a></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_1MSExperiment_html_aee0a1a68d0fab63eefa6e14010b4a7f0"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">OpenMS::MSExperiment::ConstIterator</a></div><div class="ttdeci">std::vector&lt; SpectrumType &gt;::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLFile_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLFile.html">OpenMS::Internal::XMLFile</a></div><div class="ttdoc">Base class for loading/storing XML files that have a handler derived from XMLHandler. </div><div class="ttdef"><b>Definition:</b> XMLFile.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1MascotXMLFile_html_a1f47840b5fb63cf1ad9f823ac2e12227"><div class="ttname"><a href="classOpenMS_1_1MascotXMLFile.html#a1f47840b5fb63cf1ad9f823ac2e12227">OpenMS::MascotXMLFile::RTMapping</a></div><div class="ttdeci">Internal::MascotXMLHandler::RTMapping RTMapping</div><div class="ttdef"><b>Definition:</b> MascotXMLFile.h:62</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_1MascotXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1MascotXMLFile.html">OpenMS::MascotXMLFile</a></div><div class="ttdoc">Used to load MascotXML files. </div><div class="ttdef"><b>Definition:</b> MascotXMLFile.h:57</div></div>
<div class="ttc" id="MascotXMLHandler_8h_html"><div class="ttname"><a href="MascotXMLHandler_8h.html">MascotXMLHandler.h</a></div></div>
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