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<a href="MascotXMLHandler_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;<span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;<span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Nico Pfeifer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Nico Pfeifer, Chris Bielow $</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_MASCOTXMLHANDLER_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_MASCOTXMLHANDLER_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="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.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="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.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="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.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="Map_8h.html">OpenMS/DATASTRUCTURES/Map.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;boost/regex.hpp&gt;</span></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">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;{</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;  {</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html">   54</a></span>&#160;    <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html">MascotXMLHandler</a> :</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</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="l00056"></a><span class="lineno">   56</span>&#160;    {</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6a5b7dd69471128e9cb680649b058f4f">   59</a></span>&#160;      <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Map.html">Map&lt;Size, Real&gt;</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6a5b7dd69471128e9cb680649b058f4f">RTMapping</a>;</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;      <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html">MascotXMLHandler</a>(<a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>&amp; protein_identification,</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;                       std::vector&lt;PeptideIdentification&gt;&amp; identifications,</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;                       <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; filename,</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</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="l00066"></a><span class="lineno">   66</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="l00067"></a><span class="lineno">   67</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="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;      <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html">MascotXMLHandler</a>();</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</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="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</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="l00077"></a><span class="lineno">   77</span>&#160;</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</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 <span class="comment">/*length*/</span>);</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <span class="comment">// Primary regex used to extract a scan number (for use by PepXMLFile)</span></div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ae69cc55a2b148fffca769bfda6772e0d">   82</a></span>&#160;      <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ae69cc55a2b148fffca769bfda6772e0d">primary_scan_regex</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;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ad7e41c17634f004ae1088633302eb41d">   86</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &amp; <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ad7e41c17634f004ae1088633302eb41d">protein_identification_</a>; </div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a7c6965c3b3bbf3b4160bea79ac0ebd8f">   87</a></span>&#160;      std::vector&lt;PeptideIdentification&gt; &amp; <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a7c6965c3b3bbf3b4160bea79ac0ebd8f">id_data_</a>; </div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a93a77811f5326cca0fb9d8bffc8067de">   88</a></span>&#160;      <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a93a77811f5326cca0fb9d8bffc8067de">actual_protein_hit_</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a43cc7d5ee6248c0217e00a0144679937">   89</a></span>&#160;      <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a43cc7d5ee6248c0217e00a0144679937">actual_peptide_hit_</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ab7e20aceddd0561a9d5b3b7b1b34f4c2">   90</a></span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ab7e20aceddd0561a9d5b3b7b1b34f4c2">peptide_identification_index_</a>;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">   91</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">tag_</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">   92</a></span>&#160;      <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">date_</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6ce7ed578bfc533680cf08026b59a80e">   93</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6ce7ed578bfc533680cf08026b59a80e">date_time_string_</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a0d2018e966345d3ec6940b163bd7004c">   94</a></span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a0d2018e966345d3ec6940b163bd7004c">actual_query_</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a46a83aed02e7b1fef97b803b788120c2">   95</a></span>&#160;      <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">ProteinIdentification::SearchParameters</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a46a83aed02e7b1fef97b803b788120c2">search_parameters_</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#afa114f78621074f8411ee9c53b327ee0">   96</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#afa114f78621074f8411ee9c53b327ee0">identifier_</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6f1ee0b2e58773f8ae22d9dd85deacae">   97</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6f1ee0b2e58773f8ae22d9dd85deacae">actual_title_</a>;</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a3c7f281891996c590998d08dde286924">   98</a></span>&#160;      std::map&lt;String, std::vector&lt;AASequence&gt; &gt; &amp; <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a3c7f281891996c590998d08dde286924">modified_peptides_</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a711619183098a4717cf8f4dfdcd228e7">  100</a></span>&#160;      <a class="code" href="classOpenMS_1_1StringList.html">StringList</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a711619183098a4717cf8f4dfdcd228e7">tags_open_</a>; </div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#acb0786fa857f688d8361de9b00506bd6">  101</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#acb0786fa857f688d8361de9b00506bd6">character_buffer_</a>; </div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a145d5e411e277e0b1055ca2c4dfcfe75">  102</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a145d5e411e277e0b1055ca2c4dfcfe75">major_version_</a>;</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a0a748aa169b06d2444aee364d878fd02">  103</a></span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a0a748aa169b06d2444aee364d878fd02">minor_version_</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a877885217d09009e01a320114fba4961">  105</a></span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Map.html">RTMapping</a> &amp; <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a877885217d09009e01a320114fba4961">rt_mapping_</a>; </div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a458a52289a0b25f6685d0f62111ae2ea">  110</a></span>&#160;      std::vector&lt;boost::regex&gt; <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a458a52289a0b25f6685d0f62111ae2ea">scan_regex_</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_1MascotXMLHandler.html#a46d38f27393b15385794a002e1b49409">  113</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a46d38f27393b15385794a002e1b49409">no_rt_error_</a>;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;    };</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;  }   <span class="comment">// namespace Internal</span></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;} <span class="comment">// namespace OpenMS</span></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">  119</span>&#160;<span class="preprocessor">#endif // OPENMS_FORMAT_HANDLERS_MASCOTXMLHANDLER_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="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></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_1MascotXMLHandler_html_a6ce7ed578bfc533680cf08026b59a80e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6ce7ed578bfc533680cf08026b59a80e">OpenMS::Internal::MascotXMLHandler::date_time_string_</a></div><div class="ttdeci">String date_time_string_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a711619183098a4717cf8f4dfdcd228e7"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a711619183098a4717cf8f4dfdcd228e7">OpenMS::Internal::MascotXMLHandler::tags_open_</a></div><div class="ttdeci">StringList tags_open_</div><div class="ttdoc">tracking the current XML tree </div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a0a748aa169b06d2444aee364d878fd02"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a0a748aa169b06d2444aee364d878fd02">OpenMS::Internal::MascotXMLHandler::minor_version_</a></div><div class="ttdeci">String minor_version_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:103</div></div>
<div class="ttc" id="Map_8h_html"><div class="ttname"><a href="Map_8h.html">Map.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a6f1ee0b2e58773f8ae22d9dd85deacae"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6f1ee0b2e58773f8ae22d9dd85deacae">OpenMS::Internal::MascotXMLHandler::actual_title_</a></div><div class="ttdeci">String actual_title_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:97</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="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_ad7e41c17634f004ae1088633302eb41d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ad7e41c17634f004ae1088633302eb41d">OpenMS::Internal::MascotXMLHandler::protein_identification_</a></div><div class="ttdeci">ProteinIdentification &amp; protein_identification_</div><div class="ttdoc">the protein identifications </div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a93a77811f5326cca0fb9d8bffc8067de"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a93a77811f5326cca0fb9d8bffc8067de">OpenMS::Internal::MascotXMLHandler::actual_protein_hit_</a></div><div class="ttdeci">ProteinHit actual_protein_hit_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html">OpenMS::Internal::MascotXMLHandler</a></div><div class="ttdoc">Handler that is used for parsing MascotXML data. </div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:54</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinIdentification_1_1SearchParameters_html"><div class="ttname"><a href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">OpenMS::ProteinIdentification::SearchParameters</a></div><div class="ttdoc">Search parameters of the DB search. </div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:115</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a46d38f27393b15385794a002e1b49409"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a46d38f27393b15385794a002e1b49409">OpenMS::Internal::MascotXMLHandler::no_rt_error_</a></div><div class="ttdeci">bool no_rt_error_</div><div class="ttdoc">Error for missing RT information already reported? </div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a4efa4aca7642864fed4e7e4cca9e2a79"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a4efa4aca7642864fed4e7e4cca9e2a79">OpenMS::Internal::MascotXMLHandler::tag_</a></div><div class="ttdeci">String tag_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a145d5e411e277e0b1055ca2c4dfcfe75"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a145d5e411e277e0b1055ca2c4dfcfe75">OpenMS::Internal::MascotXMLHandler::major_version_</a></div><div class="ttdeci">String major_version_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:102</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_1MascotXMLHandler_html_ab11b7dd5f2f6ffc800af0152f5c2e69a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">OpenMS::Internal::MascotXMLHandler::date_</a></div><div class="ttdeci">DateTime date_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideHit_html"><div class="ttname"><a href="classOpenMS_1_1PeptideHit.html">OpenMS::PeptideHit</a></div><div class="ttdoc">Representation of a peptide hit. </div><div class="ttdef"><b>Definition:</b> PeptideHit.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a0d2018e966345d3ec6940b163bd7004c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a0d2018e966345d3ec6940b163bd7004c">OpenMS::Internal::MascotXMLHandler::actual_query_</a></div><div class="ttdeci">UInt actual_query_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a7c6965c3b3bbf3b4160bea79ac0ebd8f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a7c6965c3b3bbf3b4160bea79ac0ebd8f">OpenMS::Internal::MascotXMLHandler::id_data_</a></div><div class="ttdeci">std::vector&lt; PeptideIdentification &gt; &amp; id_data_</div><div class="ttdoc">the identifications (storing the peptide hits) </div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:87</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_1MascotXMLHandler_html_ab7e20aceddd0561a9d5b3b7b1b34f4c2"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ab7e20aceddd0561a9d5b3b7b1b34f4c2">OpenMS::Internal::MascotXMLHandler::peptide_identification_index_</a></div><div class="ttdeci">UInt peptide_identification_index_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html"><div class="ttname"><a href="classOpenMS_1_1StringList.html">OpenMS::StringList</a></div><div class="ttdoc">String list. </div><div class="ttdef"><b>Definition:</b> StringList.h:56</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_1Internal_1_1MascotXMLHandler_html_a458a52289a0b25f6685d0f62111ae2ea"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a458a52289a0b25f6685d0f62111ae2ea">OpenMS::Internal::MascotXMLHandler::scan_regex_</a></div><div class="ttdeci">std::vector&lt; boost::regex &gt; scan_regex_</div><div class="ttdoc">List of possible Perl-style regular expressions used to extract the scan number (named group &amp;quot;SCAN&amp;quot;) ...</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:110</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_1Internal_1_1MascotXMLHandler_html_afa114f78621074f8411ee9c53b327ee0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#afa114f78621074f8411ee9c53b327ee0">OpenMS::Internal::MascotXMLHandler::identifier_</a></div><div class="ttdeci">String identifier_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:96</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a877885217d09009e01a320114fba4961"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a877885217d09009e01a320114fba4961">OpenMS::Internal::MascotXMLHandler::rt_mapping_</a></div><div class="ttdeci">const RTMapping &amp; rt_mapping_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a43cc7d5ee6248c0217e00a0144679937"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a43cc7d5ee6248c0217e00a0144679937">OpenMS::Internal::MascotXMLHandler::actual_peptide_hit_</a></div><div class="ttdeci">PeptideHit actual_peptide_hit_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a46a83aed02e7b1fef97b803b788120c2"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a46a83aed02e7b1fef97b803b788120c2">OpenMS::Internal::MascotXMLHandler::search_parameters_</a></div><div class="ttdeci">ProteinIdentification::SearchParameters search_parameters_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a6a5b7dd69471128e9cb680649b058f4f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a6a5b7dd69471128e9cb680649b058f4f">OpenMS::Internal::MascotXMLHandler::RTMapping</a></div><div class="ttdeci">Map&lt; Size, Real &gt; RTMapping</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_acb0786fa857f688d8361de9b00506bd6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#acb0786fa857f688d8361de9b00506bd6">OpenMS::Internal::MascotXMLHandler::character_buffer_</a></div><div class="ttdeci">String character_buffer_</div><div class="ttdoc">filled by MascotXMLHandler::characters </div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:101</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>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_ae69cc55a2b148fffca769bfda6772e0d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#ae69cc55a2b148fffca769bfda6772e0d">OpenMS::Internal::MascotXMLHandler::primary_scan_regex</a></div><div class="ttdeci">static const String primary_scan_regex</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:82</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MascotXMLHandler_html_a3c7f281891996c590998d08dde286924"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MascotXMLHandler.html#a3c7f281891996c590998d08dde286924">OpenMS::Internal::MascotXMLHandler::modified_peptides_</a></div><div class="ttdeci">std::map&lt; String, std::vector&lt; AASequence &gt; &gt; &amp; modified_peptides_</div><div class="ttdef"><b>Definition:</b> MascotXMLHandler.h:98</div></div>
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