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<a href="OMSSAXMLFile_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: Andreas Bertsch $</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_OMSSAXMLFILE_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_OMSSAXMLFILE_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="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="XMLFile_8h.html">OpenMS/FORMAT/XMLFile.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="Map_8h.html">OpenMS/DATASTRUCTURES/Map.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="ResidueModification_8h.html">OpenMS/CHEMISTRY/ResidueModification.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="ModificationDefinitionsSet_8h.html">OpenMS/CHEMISTRY/ModificationDefinitionsSet.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> {</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keyword">class </span>String;</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">class </span>ModificationsDB;</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html"> 61</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">protected</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">Internal::XMLHandler</a>,</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLFile.html">Internal::XMLFile</a></div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  {</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a>();</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename, <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> & protein_identification, std::vector<PeptideIdentification> & id_data, <span class="keywordtype">bool</span> load_proteins = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">void</span> setModificationDefinitionsSet(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a> & rhs);</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> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</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="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</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 & attributes);</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</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="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="keyword">private</span>:</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>  <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a> & rhs);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html">OMSSAXMLFile</a> & rhs);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keywordtype">void</span> readMappingFile_();</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a4495a14668db286a3a306cb0d41b3b82"> 113</a></span>  std::vector<PeptideIdentification> * <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a4495a14668db286a3a306cb0d41b3b82">peptide_identifications_</a>;</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a93a77811f5326cca0fb9d8bffc8067de"> 115</a></span>  <a class="code" href="classOpenMS_1_1ProteinHit.html">ProteinHit</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a93a77811f5326cca0fb9d8bffc8067de">actual_protein_hit_</a>;</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a43cc7d5ee6248c0217e00a0144679937"> 117</a></span>  <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a43cc7d5ee6248c0217e00a0144679937">actual_peptide_hit_</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a31fe0c91f986f6ee0f80c8ec6800d429"> 119</a></span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a31fe0c91f986f6ee0f80c8ec6800d429">actual_peptide_id_</a>;</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a2309dbcbc3196dd9c0b71e16c374db22"> 121</a></span>  <a class="code" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a2309dbcbc3196dd9c0b71e16c374db22">actual_protein_id_</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"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a4efa4aca7642864fed4e7e4cca9e2a79"> 123</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a4efa4aca7642864fed4e7e4cca9e2a79">tag_</a>;</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
<div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#ae3b91376f11377b07f7cb15eae1eb4ca"> 126</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#ae3b91376f11377b07f7cb15eae1eb4ca">actual_mod_site_</a>;</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#aba6aefe8110d89d821425146602b3cf5"> 129</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#aba6aefe8110d89d821425146602b3cf5">actual_mod_type_</a>;</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#acfb1af20ce79c331812bd0c4cec8aa63"> 132</a></span>  std::vector<std::pair<UInt, String> > <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#acfb1af20ce79c331812bd0c4cec8aa63">modifications_</a>;</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#ac1faf727757c5be8efb68780de8c97dd"> 135</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#ac1faf727757c5be8efb68780de8c97dd">load_proteins_</a>;</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#add24b2274dc5b9eadd9cbda4e0d3e7d1"> 138</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<UInt, std::vector<ResidueModification></a> > <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#add24b2274dc5b9eadd9cbda4e0d3e7d1">mods_map_</a>;</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#ac0e9f1caf3d4803de16048afeea2ae0b"> 141</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<String, UInt></a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#ac0e9f1caf3d4803de16048afeea2ae0b">mods_to_num_</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> </div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OMSSAXMLFile.html#a5bd43fa850d01d775ede410cfd336610"> 144</a></span>  <a class="code" href="classOpenMS_1_1ModificationDefinitionsSet.html">ModificationDefinitionsSet</a> <a class="code" href="classOpenMS_1_1OMSSAXMLFile.html#a5bd43fa850d01d775ede410cfd336610">mod_def_set_</a>;</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  };</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> </div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="preprocessor">#endif // OPENMS_FORMAT_OMSSAXMLFILE_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_1OMSSAXMLFile_html_add24b2274dc5b9eadd9cbda4e0d3e7d1"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#add24b2274dc5b9eadd9cbda4e0d3e7d1">OpenMS::OMSSAXMLFile::mods_map_</a></div><div class="ttdeci">Map< UInt, std::vector< ResidueModification > > mods_map_</div><div class="ttdoc">modifications mapping file from OMSSA mod num to UniMod accession </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:138</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_1OMSSAXMLFile_html_a31fe0c91f986f6ee0f80c8ec6800d429"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a31fe0c91f986f6ee0f80c8ec6800d429">OpenMS::OMSSAXMLFile::actual_peptide_id_</a></div><div class="ttdeci">PeptideIdentification actual_peptide_id_</div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:119</div></div>
<div class="ttc" id="classOpenMS_1_1OMSSAXMLFile_html_a93a77811f5326cca0fb9d8bffc8067de"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a93a77811f5326cca0fb9d8bffc8067de">OpenMS::OMSSAXMLFile::actual_protein_hit_</a></div><div class="ttdeci">ProteinHit actual_protein_hit_</div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:115</div></div>
<div class="ttc" id="ModificationDefinitionsSet_8h_html"><div class="ttname"><a href="ModificationDefinitionsSet_8h.html">ModificationDefinitionsSet.h</a></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_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="classOpenMS_1_1OMSSAXMLFile_html_aba6aefe8110d89d821425146602b3cf5"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#aba6aefe8110d89d821425146602b3cf5">OpenMS::OMSSAXMLFile::actual_mod_type_</a></div><div class="ttdeci">String actual_mod_type_</div><div class="ttdoc">type of the modification </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:129</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_1OMSSAXMLFile_html_a43cc7d5ee6248c0217e00a0144679937"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a43cc7d5ee6248c0217e00a0144679937">OpenMS::OMSSAXMLFile::actual_peptide_hit_</a></div><div class="ttdeci">PeptideHit actual_peptide_hit_</div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:117</div></div>
<div class="ttc" id="ResidueModification_8h_html"><div class="ttname"><a href="ResidueModification_8h.html">ResidueModification.h</a></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_1ModificationDefinitionsSet_html"><div class="ttname"><a href="classOpenMS_1_1ModificationDefinitionsSet.html">OpenMS::ModificationDefinitionsSet</a></div><div class="ttdoc">Representation of a set of modification definitions. </div><div class="ttdef"><b>Definition:</b> ModificationDefinitionsSet.h:57</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="classOpenMS_1_1OMSSAXMLFile_html_ac0e9f1caf3d4803de16048afeea2ae0b"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#ac0e9f1caf3d4803de16048afeea2ae0b">OpenMS::OMSSAXMLFile::mods_to_num_</a></div><div class="ttdeci">Map< String, UInt > mods_to_num_</div><div class="ttdoc">modification mapping reverse, from the modification to the mod_num </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1OMSSAXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html">OpenMS::OMSSAXMLFile</a></div><div class="ttdoc">Used to load OMSSAXML files. </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:61</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_1OMSSAXMLFile_html_a4efa4aca7642864fed4e7e4cca9e2a79"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a4efa4aca7642864fed4e7e4cca9e2a79">OpenMS::OMSSAXMLFile::tag_</a></div><div class="ttdeci">String tag_</div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1OMSSAXMLFile_html_a4495a14668db286a3a306cb0d41b3b82"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a4495a14668db286a3a306cb0d41b3b82">OpenMS::OMSSAXMLFile::peptide_identifications_</a></div><div class="ttdeci">std::vector< PeptideIdentification > * peptide_identifications_</div><div class="ttdoc">the identifications (storing the peptide hits) </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:113</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_1OMSSAXMLFile_html_a2309dbcbc3196dd9c0b71e16c374db22"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a2309dbcbc3196dd9c0b71e16c374db22">OpenMS::OMSSAXMLFile::actual_protein_id_</a></div><div class="ttdeci">ProteinIdentification actual_protein_id_</div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:121</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_1OMSSAXMLFile_html_ae3b91376f11377b07f7cb15eae1eb4ca"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#ae3b91376f11377b07f7cb15eae1eb4ca">OpenMS::OMSSAXMLFile::actual_mod_site_</a></div><div class="ttdeci">UInt actual_mod_site_</div><div class="ttdoc">site of the actual modification (simple position in the peptide) </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:126</div></div>
<div class="ttc" id="classOpenMS_1_1OMSSAXMLFile_html_a5bd43fa850d01d775ede410cfd336610"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#a5bd43fa850d01d775ede410cfd336610">OpenMS::OMSSAXMLFile::mod_def_set_</a></div><div class="ttdeci">ModificationDefinitionsSet mod_def_set_</div><div class="ttdoc">modification definitions set of the search, needed to annotate fixed modifications ...</div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:144</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_1OMSSAXMLFile_html_acfb1af20ce79c331812bd0c4cec8aa63"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#acfb1af20ce79c331812bd0c4cec8aa63">OpenMS::OMSSAXMLFile::modifications_</a></div><div class="ttdeci">std::vector< std::pair< UInt, String > > modifications_</div><div class="ttdoc">modifications of the peptide defined by site and type </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1OMSSAXMLFile_html_ac1faf727757c5be8efb68780de8c97dd"><div class="ttname"><a href="classOpenMS_1_1OMSSAXMLFile.html#ac1faf727757c5be8efb68780de8c97dd">OpenMS::OMSSAXMLFile::load_proteins_</a></div><div class="ttdeci">bool load_proteins_</div><div class="ttdoc">should protein hits be read from the file? </div><div class="ttdef"><b>Definition:</b> OMSSAXMLFile.h:135</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_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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