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<a href="PepXMLFile_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: Chris Bielow, Hendrik Weisser $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Chris Bielow, Hendrik Weisser $</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_PEPXMLFILE_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_PEPXMLFILE_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="AASequence_8h.html">OpenMS/CHEMISTRY/AASequence.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="Element_8h.html">OpenMS/CHEMISTRY/Element.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="XMLFile_8h.html">OpenMS/FORMAT/XMLFile.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.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> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <set></span></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> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> {</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html"> 60</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a> :</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</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="l00062"></a><span class="lineno"> 62</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="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <a class="code" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a>();</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1PepXMLFile.html">PepXMLFile</a>();</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& experiment_name, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a>& experiment, <span class="keywordtype">bool</span> use_precursor_data = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keywordtype">void</span> load(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, std::vector<ProteinIdentification>& proteins, std::vector<PeptideIdentification>& peptides, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& experiment_name = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keywordtype">void</span> store(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <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="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <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& attributes);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> makeScanMap_();</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordtype">void</span> readRTMZCharge_(<span class="keyword">const</span> xercesc::Attributes& attributes);</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">void</span> matchModification_(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> mass, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& origin, <a class="code" href="classOpenMS_1_1String.html">String</a>& modification_description);</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html"> 132</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html">AminoAcidModification</a></div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  {</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a0883863ca7e426c9b5a4e52124d7a86b"> 134</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a0883863ca7e426c9b5a4e52124d7a86b">aminoacid</a>;</div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#ae5ac0e145939c4a27382de2ef68c387d"> 135</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#ae5ac0e145939c4a27382de2ef68c387d">massdiff</a>;</div>
<div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a3b22574bce9d616fec5a607b2391a2f8"> 136</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a3b22574bce9d616fec5a607b2391a2f8">mass</a>;</div>
<div class="line"><a name="l00137"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a9d266d51881fcd2e8ce7fecb8a5ae9ed"> 137</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a9d266d51881fcd2e8ce7fecb8a5ae9ed">variable</a>;</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a76d2b0133d83c43dfd8a19286ac55325"> 138</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a76d2b0133d83c43dfd8a19286ac55325">description</a>;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#aa4ca080975281a5791c1c7ee3ee6f8ab"> 139</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#aa4ca080975281a5791c1c7ee3ee6f8ab">terminus</a>;</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a113b9d8040e40cf4386efc3796fbebfb"> 141</a></span>  <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a113b9d8040e40cf4386efc3796fbebfb">AminoAcidModification</a>() :</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  mass(0),</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  variable(false)</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  {</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"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a539c9d482294ce72ce5d0a60560d8d30"> 147</a></span>  <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a539c9d482294ce72ce5d0a60560d8d30">AminoAcidModification</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html">AminoAcidModification</a>& rhs) :</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  aminoacid(rhs.aminoacid),</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  massdiff(rhs.massdiff),</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  mass(rhs.mass),</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  variable(rhs.variable),</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  description(rhs.description),</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  terminus(rhs.terminus)</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  {</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a7ac19126de2dfc1781ddfc693fb793ba"> 157</a></span>  <span class="keyword">virtual</span> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a7ac19126de2dfc1781ddfc693fb793ba">~AminoAcidModification</a>()</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  {</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  }</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#abed7308e50a9e78e80be417ee1e070cd"> 161</a></span>  <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html">AminoAcidModification</a>& <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#abed7308e50a9e78e80be417ee1e070cd">operator=</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html">AminoAcidModification</a>& rhs)</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  {</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordflow">if</span> (<span class="keyword">this</span> != &rhs)</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  {</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  aminoacid = rhs.<a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a0883863ca7e426c9b5a4e52124d7a86b">aminoacid</a>;</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  massdiff = rhs.<a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#ae5ac0e145939c4a27382de2ef68c387d">massdiff</a>;</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  mass = rhs.<a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a3b22574bce9d616fec5a607b2391a2f8">mass</a>;</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  variable = rhs.<a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a9d266d51881fcd2e8ce7fecb8a5ae9ed">variable</a>;</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  description = rhs.<a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a76d2b0133d83c43dfd8a19286ac55325">description</a>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  terminus = rhs.<a class="code" href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#aa4ca080975281a5791c1c7ee3ee6f8ab">terminus</a>;</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  }</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  }</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  };</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#aaecddb731d6a7b2f86d458429a6a8529"> 178</a></span>  std::vector<ProteinIdentification>* <a class="code" href="classOpenMS_1_1PepXMLFile.html#aaecddb731d6a7b2f86d458429a6a8529">proteins_</a>;</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a6f28b892172fe0ec098cb6781e58c7f4"> 181</a></span>  std::vector<PeptideIdentification>* <a class="code" href="classOpenMS_1_1PepXMLFile.html#a6f28b892172fe0ec098cb6781e58c7f4">peptides_</a>;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00184"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a911a12c1b01a39d866ca2df63ebe71c2"> 184</a></span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a>* <a class="code" href="classOpenMS_1_1PepXMLFile.html#a911a12c1b01a39d866ca2df63ebe71c2">experiment_</a>;</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div>
<div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a20485bae7a3bd7b2fcd5d491b4cf51c9"> 187</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a20485bae7a3bd7b2fcd5d491b4cf51c9">exp_name_</a>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span> </div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a5025f2dee8f88a7632f01b5cea7043d9"> 190</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a5025f2dee8f88a7632f01b5cea7043d9">search_engine_</a>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span> </div>
<div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#ab727f118bb1450b2204ed4b5bf2d1ab6"> 193</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1PepXMLFile.html#ab727f118bb1450b2204ed4b5bf2d1ab6">use_precursor_data_</a>;</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#add5c0d058e0cee825f46ec0aeeec89da"> 196</a></span>  std::map<Size, Size> <a class="code" href="classOpenMS_1_1PepXMLFile.html#add5c0d058e0cee825f46ec0aeeec89da">scan_map_</a>;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span> </div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a4b56759c1db4a79eb15d182c26752227"> 199</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a4b56759c1db4a79eb15d182c26752227">rt_tol_</a>, mz_tol_;</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div>
<div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#aba244924723289b66a604a9826e8dcd5"> 202</a></span>  <a class="code" href="classOpenMS_1_1Element.html">Element</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#aba244924723289b66a604a9826e8dcd5">hydrogen_</a>;</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> </div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#ae16b642f67c5b8385bb2d967257129ed"> 205</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1PepXMLFile.html#ae16b642f67c5b8385bb2d967257129ed">wrong_experiment_</a>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a27d0704c17599647c1ebd10fe406f69c"> 208</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a27d0704c17599647c1ebd10fe406f69c">seen_experiment_</a>;</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a689c9221bfb5ffea61465aa5018d421c"> 211</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a689c9221bfb5ffea61465aa5018d421c">checked_base_name_</a>;</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a6ecfd3d5770da70f19ca938d6f71d804"> 214</a></span>  std::vector<std::vector<ProteinIdentification>::iterator> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a6ecfd3d5770da70f19ca938d6f71d804">current_proteins_</a>;</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#ac3d586e03dbf806c042823615bb112d7"> 217</a></span>  <a class="code" href="structOpenMS_1_1ProteinIdentification_1_1SearchParameters.html">ProteinIdentification::SearchParameters</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#ac3d586e03dbf806c042823615bb112d7">params_</a>;</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00220"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a59a0e004888af308552b44e57832a5a9"> 220</a></span>  <a class="code" href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">ProteinIdentification::DigestionEnzyme</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a59a0e004888af308552b44e57832a5a9">enzyme_</a>;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a4e96a9037f26680129f5f1b128ec71d0"> 223</a></span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a4e96a9037f26680129f5f1b128ec71d0">current_peptide_</a>;</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span> </div>
<div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a43a54f0e9678737ac75292aad6e394a6"> 226</a></span>  <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a43a54f0e9678737ac75292aad6e394a6">peptide_hit_</a>;</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a3e597f3665d43b306ba043ca6913d706"> 229</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a3e597f3665d43b306ba043ca6913d706">current_sequence_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
<div class="line"><a name="l00232"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a51db91c41ce0919dd864710eb01a99aa"> 232</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a51db91c41ce0919dd864710eb01a99aa">rt_</a>, mz_;</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#af71274961d8487036283991f2ba652a1"> 235</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#af71274961d8487036283991f2ba652a1">charge_</a>;</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#af03ad2b8299753b5d1e1b88dde2d7188"> 238</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#af03ad2b8299753b5d1e1b88dde2d7188">search_id_</a>;</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a9e325af3cdc9e77753f1042b18c6676f"> 241</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a9e325af3cdc9e77753f1042b18c6676f">prot_id_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div>
<div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#ab11b7dd5f2f6ffc800af0152f5c2e69a"> 244</a></span>  <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">date_</a>;</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span> </div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#ac47b1fa6e7b9aaab7558c6887cdcf497"> 247</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1PepXMLFile.html#ac47b1fa6e7b9aaab7558c6887cdcf497">hydrogen_mass_</a>;</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a93a2d66d67637792143b1b2bc2b65b3d"> 250</a></span>  std::vector<std::pair<String, Size> > <a class="code" href="classOpenMS_1_1PepXMLFile.html#a93a2d66d67637792143b1b2bc2b65b3d">current_modifications_</a>;</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div>
<div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#ab15bace4e9b1d69bcbb4c123bd679c9c"> 253</a></span>  std::vector<AminoAcidModification> <a class="code" href="classOpenMS_1_1PepXMLFile.html#ab15bace4e9b1d69bcbb4c123bd679c9c">fixed_modifications_</a>;</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> </div>
<div class="line"><a name="l00256"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PepXMLFile.html#a44cdb39bffdb662fe69039cb91a72c9c"> 256</a></span>  std::vector<AminoAcidModification> <a class="code" href="classOpenMS_1_1PepXMLFile.html#a44cdb39bffdb662fe69039cb91a72c9c">variable_modifications_</a>;</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> </div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  };</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> </div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> <span class="preprocessor">#endif // OPENMS_FORMAT_PEPXMLFILE_H</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="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_abed7308e50a9e78e80be417ee1e070cd"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#abed7308e50a9e78e80be417ee1e070cd">OpenMS::PepXMLFile::AminoAcidModification::operator=</a></div><div class="ttdeci">AminoAcidModification & operator=(const AminoAcidModification &rhs)</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:161</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_1PepXMLFile_html_a6ecfd3d5770da70f19ca938d6f71d804"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a6ecfd3d5770da70f19ca938d6f71d804">OpenMS::PepXMLFile::current_proteins_</a></div><div class="ttdeci">std::vector< std::vector< ProteinIdentification >::iterator > current_proteins_</div><div class="ttdoc">References to currently active ProteinIdentifications. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:214</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a113b9d8040e40cf4386efc3796fbebfb"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a113b9d8040e40cf4386efc3796fbebfb">OpenMS::PepXMLFile::AminoAcidModification::AminoAcidModification</a></div><div class="ttdeci">AminoAcidModification()</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a20485bae7a3bd7b2fcd5d491b4cf51c9"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a20485bae7a3bd7b2fcd5d491b4cf51c9">OpenMS::PepXMLFile::exp_name_</a></div><div class="ttdeci">String exp_name_</div><div class="ttdoc">Name of the associated experiment (filename of the data file, extension will be removed) ...</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:187</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_aaecddb731d6a7b2f86d458429a6a8529"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#aaecddb731d6a7b2f86d458429a6a8529">OpenMS::PepXMLFile::proteins_</a></div><div class="ttdeci">std::vector< ProteinIdentification > * proteins_</div><div class="ttdoc">Pointer to the list of identified proteins. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:178</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html">OpenMS::Internal::XMLHandler</a></div><div class="ttdoc">Base class for XML handlers. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:89</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="AASequence_8h_html"><div class="ttname"><a href="AASequence_8h.html">AASequence.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_aba244924723289b66a604a9826e8dcd5"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#aba244924723289b66a604a9826e8dcd5">OpenMS::PepXMLFile::hydrogen_</a></div><div class="ttdeci">Element hydrogen_</div><div class="ttdoc">Hydrogen data (for mass types) </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:202</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_aa4ca080975281a5791c1c7ee3ee6f8ab"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#aa4ca080975281a5791c1c7ee3ee6f8ab">OpenMS::PepXMLFile::AminoAcidModification::terminus</a></div><div class="ttdeci">String terminus</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:139</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_ae5ac0e145939c4a27382de2ef68c387d"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#ae5ac0e145939c4a27382de2ef68c387d">OpenMS::PepXMLFile::AminoAcidModification::massdiff</a></div><div class="ttdeci">String massdiff</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:135</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a539c9d482294ce72ce5d0a60560d8d30"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a539c9d482294ce72ce5d0a60560d8d30">OpenMS::PepXMLFile::AminoAcidModification::AminoAcidModification</a></div><div class="ttdeci">AminoAcidModification(const AminoAcidModification &rhs)</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_ab15bace4e9b1d69bcbb4c123bd679c9c"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#ab15bace4e9b1d69bcbb4c123bd679c9c">OpenMS::PepXMLFile::fixed_modifications_</a></div><div class="ttdeci">std::vector< AminoAcidModification > fixed_modifications_</div><div class="ttdoc">Fixed aminoacid modifications. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:253</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_ac3d586e03dbf806c042823615bb112d7"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#ac3d586e03dbf806c042823615bb112d7">OpenMS::PepXMLFile::params_</a></div><div class="ttdeci">ProteinIdentification::SearchParameters params_</div><div class="ttdoc">Search parameters of the current identification run. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:217</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="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a3b22574bce9d616fec5a607b2391a2f8"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a3b22574bce9d616fec5a607b2391a2f8">OpenMS::PepXMLFile::AminoAcidModification::mass</a></div><div class="ttdeci">DoubleReal mass</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:136</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html">OpenMS::PepXMLFile</a></div><div class="ttdoc">Used to load and store PepXML files. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a3e597f3665d43b306ba043ca6913d706"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a3e597f3665d43b306ba043ca6913d706">OpenMS::PepXMLFile::current_sequence_</a></div><div class="ttdeci">String current_sequence_</div><div class="ttdoc">Sequence of the current peptide hit. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:229</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html">OpenMS::PepXMLFile::AminoAcidModification</a></div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:132</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a76d2b0133d83c43dfd8a19286ac55325"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a76d2b0133d83c43dfd8a19286ac55325">OpenMS::PepXMLFile::AminoAcidModification::description</a></div><div class="ttdeci">String description</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a27d0704c17599647c1ebd10fe406f69c"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a27d0704c17599647c1ebd10fe406f69c">OpenMS::PepXMLFile::seen_experiment_</a></div><div class="ttdeci">bool seen_experiment_</div><div class="ttdoc">Have we seen the experiment of interest at all? </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:208</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_ab727f118bb1450b2204ed4b5bf2d1ab6"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#ab727f118bb1450b2204ed4b5bf2d1ab6">OpenMS::PepXMLFile::use_precursor_data_</a></div><div class="ttdeci">bool use_precursor_data_</div><div class="ttdoc">Get RT and m/z for peptide ID from precursor scan (should only matter for RT)? </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:193</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="ProteinIdentification_8h_html"><div class="ttname"><a href="ProteinIdentification_8h.html">ProteinIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Element_html"><div class="ttname"><a href="classOpenMS_1_1Element.html">OpenMS::Element</a></div><div class="ttdoc">Representation of an element. </div><div class="ttdef"><b>Definition:</b> Element.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinIdentification_html_ac1976fd756a09ae4e26fe6b32fcb396c"><div class="ttname"><a href="classOpenMS_1_1ProteinIdentification.html#ac1976fd756a09ae4e26fe6b32fcb396c">OpenMS::ProteinIdentification::DigestionEnzyme</a></div><div class="ttdeci">DigestionEnzyme</div><div class="ttdef"><b>Definition:</b> ProteinIdentification.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_af03ad2b8299753b5d1e1b88dde2d7188"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#af03ad2b8299753b5d1e1b88dde2d7188">OpenMS::PepXMLFile::search_id_</a></div><div class="ttdeci">UInt search_id_</div><div class="ttdoc">ID of current search result. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:238</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="XMLFile_8h_html"><div class="ttname"><a href="XMLFile_8h.html">XMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_ac47b1fa6e7b9aaab7558c6887cdcf497"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#ac47b1fa6e7b9aaab7558c6887cdcf497">OpenMS::PepXMLFile::hydrogen_mass_</a></div><div class="ttdeci">DoubleReal hydrogen_mass_</div><div class="ttdoc">Mass of a hydrogen atom (monoisotopic/average depending on case) </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_add5c0d058e0cee825f46ec0aeeec89da"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#add5c0d058e0cee825f46ec0aeeec89da">OpenMS::PepXMLFile::scan_map_</a></div><div class="ttdeci">std::map< Size, Size > scan_map_</div><div class="ttdoc">Mapping between scan number in the pepXML file and index in the corresponding MSExperiment. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:196</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a6f28b892172fe0ec098cb6781e58c7f4"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a6f28b892172fe0ec098cb6781e58c7f4">OpenMS::PepXMLFile::peptides_</a></div><div class="ttdeci">std::vector< PeptideIdentification > * peptides_</div><div class="ttdoc">Pointer to the list of identified peptides. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:181</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a59a0e004888af308552b44e57832a5a9"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a59a0e004888af308552b44e57832a5a9">OpenMS::PepXMLFile::enzyme_</a></div><div class="ttdeci">ProteinIdentification::DigestionEnzyme enzyme_</div><div class="ttdoc">Enyzme associated with the current identification run. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:220</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_ae16b642f67c5b8385bb2d967257129ed"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#ae16b642f67c5b8385bb2d967257129ed">OpenMS::PepXMLFile::wrong_experiment_</a></div><div class="ttdeci">bool wrong_experiment_</div><div class="ttdoc">Do current entries belong to the experiment of interest (for pepXML files that bundle results from di...</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:205</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_af71274961d8487036283991f2ba652a1"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#af71274961d8487036283991f2ba652a1">OpenMS::PepXMLFile::charge_</a></div><div class="ttdeci">Int charge_</div><div class="ttdoc">Precursor ion charge. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:235</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_ab11b7dd5f2f6ffc800af0152f5c2e69a"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#ab11b7dd5f2f6ffc800af0152f5c2e69a">OpenMS::PepXMLFile::date_</a></div><div class="ttdeci">DateTime date_</div><div class="ttdoc">Date the pepXML file was generated. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:244</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a51db91c41ce0919dd864710eb01a99aa"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a51db91c41ce0919dd864710eb01a99aa">OpenMS::PepXMLFile::rt_</a></div><div class="ttdeci">DoubleReal rt_</div><div class="ttdoc">RT and m/z of current PeptideIdentification. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:232</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_1PepXMLFile_html_a93a2d66d67637792143b1b2bc2b65b3d"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a93a2d66d67637792143b1b2bc2b65b3d">OpenMS::PepXMLFile::current_modifications_</a></div><div class="ttdeci">std::vector< std::pair< String, Size > > current_modifications_</div><div class="ttdoc">The modifications of the current peptide hit (position is 1-based) </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:250</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_1PepXMLFile_html_a9e325af3cdc9e77753f1042b18c6676f"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a9e325af3cdc9e77753f1042b18c6676f">OpenMS::PepXMLFile::prot_id_</a></div><div class="ttdeci">String prot_id_</div><div class="ttdoc">Identifier linking PeptideIdentifications and ProteinIdentifications. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:241</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a44cdb39bffdb662fe69039cb91a72c9c"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a44cdb39bffdb662fe69039cb91a72c9c">OpenMS::PepXMLFile::variable_modifications_</a></div><div class="ttdeci">std::vector< AminoAcidModification > variable_modifications_</div><div class="ttdoc">Variable aminoacid modifications. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:256</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_1PepXMLFile_html_a43a54f0e9678737ac75292aad6e394a6"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a43a54f0e9678737ac75292aad6e394a6">OpenMS::PepXMLFile::peptide_hit_</a></div><div class="ttdeci">PeptideHit peptide_hit_</div><div class="ttdoc">PeptideHit instance currently being processed. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:226</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a4e96a9037f26680129f5f1b128ec71d0"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a4e96a9037f26680129f5f1b128ec71d0">OpenMS::PepXMLFile::current_peptide_</a></div><div class="ttdeci">PeptideIdentification current_peptide_</div><div class="ttdoc">PeptideIdentification instance currently being processed. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:223</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a0883863ca7e426c9b5a4e52124d7a86b"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a0883863ca7e426c9b5a4e52124d7a86b">OpenMS::PepXMLFile::AminoAcidModification::aminoacid</a></div><div class="ttdeci">String aminoacid</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:134</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a689c9221bfb5ffea61465aa5018d421c"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a689c9221bfb5ffea61465aa5018d421c">OpenMS::PepXMLFile::checked_base_name_</a></div><div class="ttdeci">bool checked_base_name_</div><div class="ttdoc">Have we checked the &quot;base_name&quot; attribute in the &quot;msms_run_summary&quot; element? </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:211</div></div>
<div class="ttc" id="Element_8h_html"><div class="ttname"><a href="Element_8h.html">Element.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a5025f2dee8f88a7632f01b5cea7043d9"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a5025f2dee8f88a7632f01b5cea7043d9">OpenMS::PepXMLFile::search_engine_</a></div><div class="ttdeci">String search_engine_</div><div class="ttdoc">Set name of search engine. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1PepXMLFile_html_a4b56759c1db4a79eb15d182c26752227"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a4b56759c1db4a79eb15d182c26752227">OpenMS::PepXMLFile::rt_tol_</a></div><div class="ttdeci">DoubleReal rt_tol_</div><div class="ttdoc">Retention time and mass-to-charge tolerance. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:199</div></div>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a7ac19126de2dfc1781ddfc693fb793ba"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a7ac19126de2dfc1781ddfc693fb793ba">OpenMS::PepXMLFile::AminoAcidModification::~AminoAcidModification</a></div><div class="ttdeci">virtual ~AminoAcidModification()</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:157</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_1PepXMLFile_html_a911a12c1b01a39d866ca2df63ebe71c2"><div class="ttname"><a href="classOpenMS_1_1PepXMLFile.html#a911a12c1b01a39d866ca2df63ebe71c2">OpenMS::PepXMLFile::experiment_</a></div><div class="ttdeci">const MSExperiment * experiment_</div><div class="ttdoc">Pointer to the experiment from which the pepXML file was generated. </div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:184</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>
<div class="ttc" id="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification_html_a9d266d51881fcd2e8ce7fecb8a5ae9ed"><div class="ttname"><a href="structOpenMS_1_1PepXMLFile_1_1AminoAcidModification.html#a9d266d51881fcd2e8ce7fecb8a5ae9ed">OpenMS::PepXMLFile::AminoAcidModification::variable</a></div><div class="ttdeci">bool variable</div><div class="ttdef"><b>Definition:</b> PepXMLFile.h:137</div></div>
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