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<a href="ProteinResolver_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: David Wojnar $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: David Wojnar $</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_ANALYSIS_QUANTITATION_PROTEINRESOLVER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_QUANTITATION_PROTEINRESOLVER_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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="FASTAFile_8h.html">OpenMS/FORMAT/FASTAFile.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="ProteinIdentification_8h.html">OpenMS/METADATA/ProteinIdentification.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="EnzymaticDigestion_8h.html">OpenMS/CHEMISTRY/EnzymaticDigestion.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> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinResolver.html"> 59</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a> :</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  {</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">public</span>:</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="comment">//default construtor</span></div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a>();</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="comment">//copy constructor</span></div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a> & rhs);</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="comment">//assignment operator</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a> & rhs);</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="comment">//destructor</span></div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1ProteinResolver.html">ProteinResolver</a>();</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html">ProteinEntry</a>;</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a>;</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html">ISDGroup</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html">MSDGroup</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html">ResolverResult</a>;</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="comment">//represents a protein from fasta file</span></div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html"> 85</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html">ProteinEntry</a></div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  {</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a6322cf02bec71a24fe59faedfb6bbf94"> 87</a></span>  std::list<PeptideEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a6322cf02bec71a24fe59faedfb6bbf94">peptides</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a5b9117518b49bf02daa5aa4f6f2b30ec"> 88</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a5b9117518b49bf02daa5aa4f6f2b30ec">traversed</a>;</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#ad721de7b53051c9dc6e7a2bd02007ec3"> 89</a></span>  <a class="code" href="structOpenMS_1_1FASTAFile_1_1FASTAEntry.html">FASTAFile::FASTAEntry</a> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#ad721de7b53051c9dc6e7a2bd02007ec3">fasta_entry</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a7aead736a07eaf25623ad7bfa1f0ee2d"> 90</a></span>  <span class="keyword">enum</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a7aead736a07eaf25623ad7bfa1f0ee2d">type</a> {primary, secondary, primary_indistinguishable, secondary_indistinguishable} protein_type;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a912b8ba7b2a6ccc272b1423bcb9d769b"> 91</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a912b8ba7b2a6ccc272b1423bcb9d769b">weight</a>; <span class="comment">//monoisotopic</span></div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a83039f410d4eb8d068eacfc9ccb6479b"> 92</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a83039f410d4eb8d068eacfc9ccb6479b">coverage</a>; <span class="comment">//in percent</span></div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="comment">//if Protein is indistinguishable all his fellows are in the list indis</span></div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a1d2857d7c4205425ebe4038acc4687ac"> 94</a></span>  std::list<ProteinEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a1d2857d7c4205425ebe4038acc4687ac">indis</a>;</div>
<div class="line"><a name="l00095"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#aebd5628481ed5dc73597551a57eeceac"> 95</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#aebd5628481ed5dc73597551a57eeceac">index</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#ab4439f5b5f6561a8de1ca12373ed8cba"> 96</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#ab4439f5b5f6561a8de1ca12373ed8cba">msd_group</a>; <span class="comment">//index</span></div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#af8a50eaec9fefeb80d97a50abb42445b"> 97</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#af8a50eaec9fefeb80d97a50abb42445b">isd_group</a>; <span class="comment">//index</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#aaaeb94a83f054924c5922db9c16da84f"> 98</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#aaaeb94a83f054924c5922db9c16da84f">number_of_experimental_peptides</a>;</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> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="comment">//represents a peptide. First in silco. If experimental is set to true it is MS/MS derived.</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html"> 102</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a></div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  {</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ab882919cab417d1efe5ab6fd9074b692"> 104</a></span>  std::list<ProteinEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ab882919cab417d1efe5ab6fd9074b692">proteins</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a5b9117518b49bf02daa5aa4f6f2b30ec"> 105</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a5b9117518b49bf02daa5aa4f6f2b30ec">traversed</a>;</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a3d81a52752fe56b49914dbe273521b5d"> 106</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a3d81a52752fe56b49914dbe273521b5d">sequence</a>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ae7900f239dbb57aa72bf9e981d017554"> 107</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ae7900f239dbb57aa72bf9e981d017554">peptide_identification</a>;</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a26b016002a1a5373fce4c0f92bad35fd"> 108</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a26b016002a1a5373fce4c0f92bad35fd">peptide_hit</a>;</div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#aebd5628481ed5dc73597551a57eeceac"> 109</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#aebd5628481ed5dc73597551a57eeceac">index</a>;</div>
<div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ab4439f5b5f6561a8de1ca12373ed8cba"> 110</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ab4439f5b5f6561a8de1ca12373ed8cba">msd_group</a>; <span class="comment">//index</span></div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#af8a50eaec9fefeb80d97a50abb42445b"> 111</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#af8a50eaec9fefeb80d97a50abb42445b">isd_group</a>; <span class="comment">//index</span></div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a7f8b522c458a047a75a3b8e8144754e7"> 112</a></span>  <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a7f8b522c458a047a75a3b8e8144754e7">experimental</a>;</div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a2bf8eeb17dafb3d8ed1b08810fba2440"> 113</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a2bf8eeb17dafb3d8ed1b08810fba2440">intensity</a>;</div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a7577605afce9ba7b268a887f627bea52"> 114</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a7577605afce9ba7b268a887f627bea52">origin</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  };</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">//representation of an msd group. contains peptides, proteins and a pointer to its ISD group</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html"> 118</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html">MSDGroup</a></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  {</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#ab882919cab417d1efe5ab6fd9074b692"> 120</a></span>  std::list<ProteinEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#ab882919cab417d1efe5ab6fd9074b692">proteins</a>;</div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a6322cf02bec71a24fe59faedfb6bbf94"> 121</a></span>  std::list<PeptideEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a6322cf02bec71a24fe59faedfb6bbf94">peptides</a>;</div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#aebd5628481ed5dc73597551a57eeceac"> 122</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#aebd5628481ed5dc73597551a57eeceac">index</a>;</div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a9395f92099bec1e7437f7daca27c4769"> 123</a></span>  <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html">ISDGroup</a> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a9395f92099bec1e7437f7daca27c4769">isd_group</a>;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a6eb5ed9acec069fce443a8bd7619e1c4"> 124</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a6eb5ed9acec069fce443a8bd7619e1c4">number_of_decoy</a>;</div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a95107d2442593bf8bc03ddb9535b9299"> 125</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a95107d2442593bf8bc03ddb9535b9299">number_of_target</a>;</div>
<div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a83564c20c8bf07c48ddc93d9f4ef4cb4"> 126</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a83564c20c8bf07c48ddc93d9f4ef4cb4">number_of_target_plus_decoy</a>;</div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a2bf8eeb17dafb3d8ed1b08810fba2440"> 127</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a2bf8eeb17dafb3d8ed1b08810fba2440">intensity</a>; <span class="comment">// intensity of the MSD Group. Defined as the median of the peptide intensities.</span></div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  };</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html"> 130</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html">ISDGroup</a></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_1ProteinResolver_1_1ISDGroup.html#ab882919cab417d1efe5ab6fd9074b692"> 132</a></span>  std::list<ProteinEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#ab882919cab417d1efe5ab6fd9074b692">proteins</a>;</div>
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#a6322cf02bec71a24fe59faedfb6bbf94"> 133</a></span>  std::list<PeptideEntry *> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#a6322cf02bec71a24fe59faedfb6bbf94">peptides</a>;</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#aebd5628481ed5dc73597551a57eeceac"> 134</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#aebd5628481ed5dc73597551a57eeceac">index</a>;</div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#a4304e3bc8216e6de88fe0e44aae1fe86"> 135</a></span>  std::list<Size> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#a4304e3bc8216e6de88fe0e44aae1fe86">msd_groups</a>;</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  };</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> </div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html"> 138</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html">ResolverResult</a></div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  {</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#ad15a1566a31388ea3f510fa42a64023b"> 140</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#ad15a1566a31388ea3f510fa42a64023b">identifier</a>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a459a8a309d0833ae269ec33c782e9f8e"> 141</a></span>  std::vector<ISDGroup> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a459a8a309d0833ae269ec33c782e9f8e">isds</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a159e9f34cbc098c1ea4e952f27fb6135"> 142</a></span>  std::vector<MSDGroup> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a159e9f34cbc098c1ea4e952f27fb6135">msds</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a98eb6122f1f05819a3b85287ac5435c0"> 143</a></span>  std::vector<ProteinEntry> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a98eb6122f1f05819a3b85287ac5435c0">protein_entries</a>;</div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a88e1a20751431172eda419c040c1f6d6"> 144</a></span>  std::vector<PeptideEntry> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a88e1a20751431172eda419c040c1f6d6">peptide_entries</a>;</div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a8b52860fe9ebf0f4e256f2d8e5a03363"> 145</a></span>  std::vector<Size> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a8b52860fe9ebf0f4e256f2d8e5a03363">reindexed_peptides</a>;</div>
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7c70a3c528c8ec1e1a1d496569bc4967"> 146</a></span>  std::vector<Size> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7c70a3c528c8ec1e1a1d496569bc4967">reindexed_proteins</a>;</div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7aead736a07eaf25623ad7bfa1f0ee2d"> 147</a></span>  <span class="keyword">enum</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7aead736a07eaf25623ad7bfa1f0ee2d">type</a> {PeptideIdent, Consensus} input_type;</div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7344cdec248f331754514fb7bafd379c"> 148</a></span>  std::vector<PeptideIdentification> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7344cdec248f331754514fb7bafd379c">peptide_identification</a>;</div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#abf5ae0b4e4fd67a5b4d3f0206b0bd3de"> 149</a></span>  <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> * <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#abf5ae0b4e4fd67a5b4d3f0206b0bd3de">consensus_map</a>;</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  };</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> </div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordtype">void</span> resolveConsensus(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus);</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordtype">void</span> resolveID(std::vector<PeptideIdentification> & peptide_identifications);</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> </div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// void writeProteinsAndPeptidesmzTab(std::vector<ProteinEntry>& protein_nodes, std::vector<PeptideEntry>& peptide_nodes, std::vector<Size>& reindexed_proteins, std::vector<Size>& reindexed_peptides, std::vector<PeptideIdentification>& peptide_identifications, String& output );</span></div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> <span class="comment"></span> <span class="comment">// void writePeptideTable(std::vector<PeptideEntry> & peptides, std::vector<Size> & reindexed_peptides, std::vector<PeptideIdentification> & identifications, String & output_file); // not implemented</span></div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> <span class="comment"></span> <span class="comment">// void writePeptideTable(std::vector<PeptideEntry> & peptides, std::vector<Size> & reindexed_peptides, ConsensusMap & consensus, String & output_file); // not implemented</span></div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> <span class="comment"></span> <span class="comment">// void writeProteinTable(std::vector<ProteinEntry> & proteins, std::vector<Size> & reindexed_proteins, String & output_file); // not implemented</span></div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> <span class="comment"></span> <span class="comment">// void writeProteinGroups(std::vector<ISDGroup> & isd_groups, std::vector<MSDGroup> & msd_groups, String & output_file); // not implemented</span></div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keywordtype">void</span> countTargetDecoy(std::vector<MSDGroup> & msd_groups, <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus);</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keywordtype">void</span> countTargetDecoy(std::vector<MSDGroup> & msd_groups, std::vector<PeptideIdentification> & peptide_nodes);</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <span class="keywordtype">void</span> clearResult();</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordtype">void</span> setProteinData(std::vector<FASTAFile::FASTAEntry> & protein_data);</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="keyword">const</span> std::vector<ResolverResult> & getResults();</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="comment">//overloaded functions -- return a const reference to a PeptideIdentification object or a peptideHit either from a consensusMap or a vector<PeptideIdentification></span></div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & getPeptideIdentification(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a> * peptide);</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> & getPeptideHit(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a> * peptide);</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & getPeptideIdentification(<span class="keyword">const</span> std::vector<PeptideIdentification> & peptide_nodes, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a> * peptide);</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> & getPeptideHit(<span class="keyword">const</span> std::vector<PeptideIdentification> & peptide_nodes, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a> * peptide);</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> </div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> </div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinResolver.html#a4c49b96ec457ee2202e74f5ada1e40ff"> 247</a></span>  std::vector<ResolverResult> <a class="code" href="classOpenMS_1_1ProteinResolver.html#a4c49b96ec457ee2202e74f5ada1e40ff">resolver_result_</a>;</div>
<div class="line"><a name="l00248"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ProteinResolver.html#adbb6932604b6b4a6f5dc6526cc2c9048"> 248</a></span>  std::vector<FASTAFile::FASTAEntry> <a class="code" href="classOpenMS_1_1ProteinResolver.html#adbb6932604b6b4a6f5dc6526cc2c9048">protein_data_</a>;</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> </div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordtype">void</span> computeIntensityOfMSD_(std::vector<MSDGroup> & msd_groups);</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="comment">//travers Protein and peptide nodes. Once for building ISD groups and once for building MSD groups</span></div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordtype">void</span> traversProtein_(<a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html">ProteinEntry</a> * prot_node, <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html">ISDGroup</a> & group);</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keywordtype">void</span> traversProtein_(<a class="code" href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html">ProteinEntry</a> * prot_node, <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html">MSDGroup</a> & group);</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="keywordtype">void</span> traversPeptide_(<a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a> * pep_node, <a class="code" href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html">ISDGroup</a> & group);</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordtype">void</span> traversPeptide_(<a class="code" href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">PeptideEntry</a> * pep_node, <a class="code" href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html">MSDGroup</a> & group);</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="comment">//searches given sequence in all nodes and returns its index or nodes.size() if not found.</span></div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> findPeptideEntry_(<a class="code" href="classOpenMS_1_1String.html">String</a> seq, std::vector<PeptideEntry> & nodes);</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="comment">//helper function for findPeptideEntry.</span></div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> binarySearchNodes_(<a class="code" href="classOpenMS_1_1String.html">String</a> & seq, std::vector<PeptideEntry> & nodes, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end);</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="comment">//includes all MSMS derived peptides into the graph --idXML</span></div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> includeMSMSPeptides_(std::vector<PeptideIdentification> & peptide_identifications, std::vector<PeptideEntry> & peptide_nodes);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="comment">//TODO include run information for each peptide</span></div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="comment">//includes all MSMS derived peptides into the graph --consensusXML</span></div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> includeMSMSPeptides_(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & consensus, std::vector<PeptideEntry> & peptide_nodes);</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">//Proteins and Peptides get reindexed, based on whether they belong to msd groups or not. Indexes of Proteins which are in an ISD group but in none of the MSD groups will not be used anymore.</span></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordtype">void</span> reindexingNodes_(std::vector<MSDGroup> & msd_groups, std::vector<Size> & reindexed_proteins, std::vector<Size> & reindexed_peptides);</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <span class="comment">//marks Proteins which have a unique peptide as primary. Uses reindexed vector, thus reindexingNodes has to be called before.</span></div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <span class="keywordtype">void</span> primaryProteins_(std::vector<PeptideEntry> & peptide_nodes, std::vector<Size> & reindexed_peptides);</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordtype">void</span> buildingMSDGroups_(std::vector<MSDGroup> & msd_groups, std::vector<ISDGroup> & isd_groups);</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keywordtype">void</span> buildingISDGroups_(std::vector<ProteinEntry> & protein_nodes, std::vector<PeptideEntry> & peptide_nodes,</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  std::vector<ISDGroup> & isd_groups);</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="comment">//not tested</span></div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="comment">//ProteinResolver::indistinguishableProteins(vector<MSDGroup>& msd_groups);</span></div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> </div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  }; <span class="comment">// class</span></div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> </div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span> } <span class="comment">// namespace</span></div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span> <span class="preprocessor">#endif // OPENMS_ANALYSIS_QUANTITATION_PROTEINRESOLVER_H</span></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ISDGroup_html_ab882919cab417d1efe5ab6fd9074b692"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#ab882919cab417d1efe5ab6fd9074b692">OpenMS::ProteinResolver::ISDGroup::proteins</a></div><div class="ttdeci">std::list< ProteinEntry * > proteins</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:132</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ISDGroup_html"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html">OpenMS::ProteinResolver::ISDGroup</a></div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:130</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_ab882919cab417d1efe5ab6fd9074b692"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#ab882919cab417d1efe5ab6fd9074b692">OpenMS::ProteinResolver::MSDGroup::proteins</a></div><div class="ttdeci">std::list< ProteinEntry * > proteins</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:120</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_aebd5628481ed5dc73597551a57eeceac"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#aebd5628481ed5dc73597551a57eeceac">OpenMS::ProteinResolver::PeptideEntry::index</a></div><div class="ttdeci">Size index</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:109</div></div>
<div class="ttc" id="group__Concept_html_gab685845059e8a2c92743427d9a698c70"><div class="ttname"><a href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">OpenMS::Real</a></div><div class="ttdeci">float Real</div><div class="ttdoc">Real type. </div><div class="ttdef"><b>Definition:</b> Types.h:109</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a7c70a3c528c8ec1e1a1d496569bc4967"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7c70a3c528c8ec1e1a1d496569bc4967">OpenMS::ProteinResolver::ResolverResult::reindexed_proteins</a></div><div class="ttdeci">std::vector< Size > * reindexed_proteins</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:146</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_ab4439f5b5f6561a8de1ca12373ed8cba"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ab4439f5b5f6561a8de1ca12373ed8cba">OpenMS::ProteinResolver::PeptideEntry::msd_group</a></div><div class="ttdeci">Size msd_group</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:110</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="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_a9395f92099bec1e7437f7daca27c4769"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a9395f92099bec1e7437f7daca27c4769">OpenMS::ProteinResolver::MSDGroup::isd_group</a></div><div class="ttdeci">ISDGroup * isd_group</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:123</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ISDGroup_html_aebd5628481ed5dc73597551a57eeceac"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#aebd5628481ed5dc73597551a57eeceac">OpenMS::ProteinResolver::ISDGroup::index</a></div><div class="ttdeci">Size index</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:134</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a7344cdec248f331754514fb7bafd379c"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7344cdec248f331754514fb7bafd379c">OpenMS::ProteinResolver::ResolverResult::peptide_identification</a></div><div class="ttdeci">std::vector< PeptideIdentification > * peptide_identification</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:148</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_a26b016002a1a5373fce4c0f92bad35fd"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a26b016002a1a5373fce4c0f92bad35fd">OpenMS::ProteinResolver::PeptideEntry::peptide_hit</a></div><div class="ttdeci">Size peptide_hit</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:108</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a88e1a20751431172eda419c040c1f6d6"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a88e1a20751431172eda419c040c1f6d6">OpenMS::ProteinResolver::ResolverResult::peptide_entries</a></div><div class="ttdeci">std::vector< PeptideEntry > * peptide_entries</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:144</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_a6322cf02bec71a24fe59faedfb6bbf94"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a6322cf02bec71a24fe59faedfb6bbf94">OpenMS::ProteinResolver::ProteinEntry::peptides</a></div><div class="ttdeci">std::list< PeptideEntry * > peptides</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:87</div></div>
<div class="ttc" id="FASTAFile_8h_html"><div class="ttname"><a href="FASTAFile_8h.html">FASTAFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_af8a50eaec9fefeb80d97a50abb42445b"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#af8a50eaec9fefeb80d97a50abb42445b">OpenMS::ProteinResolver::ProteinEntry::isd_group</a></div><div class="ttdeci">Size isd_group</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:97</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_a2bf8eeb17dafb3d8ed1b08810fba2440"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a2bf8eeb17dafb3d8ed1b08810fba2440">OpenMS::ProteinResolver::MSDGroup::intensity</a></div><div class="ttdeci">Real intensity</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:127</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_ad15a1566a31388ea3f510fa42a64023b"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#ad15a1566a31388ea3f510fa42a64023b">OpenMS::ProteinResolver::ResolverResult::identifier</a></div><div class="ttdeci">String identifier</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:140</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html">OpenMS::ProteinResolver::MSDGroup</a></div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinResolver_html_adbb6932604b6b4a6f5dc6526cc2c9048"><div class="ttname"><a href="classOpenMS_1_1ProteinResolver.html#adbb6932604b6b4a6f5dc6526cc2c9048">OpenMS::ProteinResolver::protein_data_</a></div><div class="ttdeci">std::vector< FASTAFile::FASTAEntry > protein_data_</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:248</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_a6eb5ed9acec069fce443a8bd7619e1c4"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a6eb5ed9acec069fce443a8bd7619e1c4">OpenMS::ProteinResolver::MSDGroup::number_of_decoy</a></div><div class="ttdeci">Size number_of_decoy</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:124</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_aebd5628481ed5dc73597551a57eeceac"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#aebd5628481ed5dc73597551a57eeceac">OpenMS::ProteinResolver::ProteinEntry::index</a></div><div class="ttdeci">Size index</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:95</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_ae7900f239dbb57aa72bf9e981d017554"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ae7900f239dbb57aa72bf9e981d017554">OpenMS::ProteinResolver::PeptideEntry::peptide_identification</a></div><div class="ttdeci">Size peptide_identification</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:107</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a8b52860fe9ebf0f4e256f2d8e5a03363"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a8b52860fe9ebf0f4e256f2d8e5a03363">OpenMS::ProteinResolver::ResolverResult::reindexed_peptides</a></div><div class="ttdeci">std::vector< Size > * reindexed_peptides</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:145</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_a6322cf02bec71a24fe59faedfb6bbf94"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a6322cf02bec71a24fe59faedfb6bbf94">OpenMS::ProteinResolver::MSDGroup::peptides</a></div><div class="ttdeci">std::list< PeptideEntry * > peptides</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:121</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_a1d2857d7c4205425ebe4038acc4687ac"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a1d2857d7c4205425ebe4038acc4687ac">OpenMS::ProteinResolver::ProteinEntry::indis</a></div><div class="ttdeci">std::list< ProteinEntry * > indis</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:94</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_aebd5628481ed5dc73597551a57eeceac"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#aebd5628481ed5dc73597551a57eeceac">OpenMS::ProteinResolver::MSDGroup::index</a></div><div class="ttdeci">Size index</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:122</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_a83564c20c8bf07c48ddc93d9f4ef4cb4"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a83564c20c8bf07c48ddc93d9f4ef4cb4">OpenMS::ProteinResolver::MSDGroup::number_of_target_plus_decoy</a></div><div class="ttdeci">Size number_of_target_plus_decoy</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:126</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_a5b9117518b49bf02daa5aa4f6f2b30ec"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a5b9117518b49bf02daa5aa4f6f2b30ec">OpenMS::ProteinResolver::PeptideEntry::traversed</a></div><div class="ttdeci">bool traversed</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinResolver_html"><div class="ttname"><a href="classOpenMS_1_1ProteinResolver.html">OpenMS::ProteinResolver</a></div><div class="ttdoc">Helper class for peptide and protein quantification based on feature data annotated with IDs...</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:59</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_af8a50eaec9fefeb80d97a50abb42445b"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#af8a50eaec9fefeb80d97a50abb42445b">OpenMS::ProteinResolver::PeptideEntry::isd_group</a></div><div class="ttdeci">Size isd_group</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:111</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_aaaeb94a83f054924c5922db9c16da84f"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#aaaeb94a83f054924c5922db9c16da84f">OpenMS::ProteinResolver::ProteinEntry::number_of_experimental_peptides</a></div><div class="ttdeci">Size number_of_experimental_peptides</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:98</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="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a98eb6122f1f05819a3b85287ac5435c0"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a98eb6122f1f05819a3b85287ac5435c0">OpenMS::ProteinResolver::ResolverResult::protein_entries</a></div><div class="ttdeci">std::vector< ProteinEntry > * protein_entries</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:143</div></div>
<div class="ttc" id="EnzymaticDigestion_8h_html"><div class="ttname"><a href="EnzymaticDigestion_8h.html">EnzymaticDigestion.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a7aead736a07eaf25623ad7bfa1f0ee2d"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a7aead736a07eaf25623ad7bfa1f0ee2d">OpenMS::ProteinResolver::ResolverResult::type</a></div><div class="ttdeci">type</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:147</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_a7577605afce9ba7b268a887f627bea52"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a7577605afce9ba7b268a887f627bea52">OpenMS::ProteinResolver::PeptideEntry::origin</a></div><div class="ttdeci">String origin</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:114</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_ab4439f5b5f6561a8de1ca12373ed8cba"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#ab4439f5b5f6561a8de1ca12373ed8cba">OpenMS::ProteinResolver::ProteinEntry::msd_group</a></div><div class="ttdeci">Size msd_group</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:96</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_a83039f410d4eb8d068eacfc9ccb6479b"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a83039f410d4eb8d068eacfc9ccb6479b">OpenMS::ProteinResolver::ProteinEntry::coverage</a></div><div class="ttdeci">Real coverage</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:92</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ISDGroup_html_a6322cf02bec71a24fe59faedfb6bbf94"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#a6322cf02bec71a24fe59faedfb6bbf94">OpenMS::ProteinResolver::ISDGroup::peptides</a></div><div class="ttdeci">std::list< PeptideEntry * > peptides</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:133</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ISDGroup_html_a4304e3bc8216e6de88fe0e44aae1fe86"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ISDGroup.html#a4304e3bc8216e6de88fe0e44aae1fe86">OpenMS::ProteinResolver::ISDGroup::msd_groups</a></div><div class="ttdeci">std::list< Size > msd_groups</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:135</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="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html">OpenMS::ProteinResolver::ProteinEntry</a></div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:85</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_a7f8b522c458a047a75a3b8e8144754e7"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a7f8b522c458a047a75a3b8e8144754e7">OpenMS::ProteinResolver::PeptideEntry::experimental</a></div><div class="ttdeci">bool experimental</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:112</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_ad721de7b53051c9dc6e7a2bd02007ec3"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#ad721de7b53051c9dc6e7a2bd02007ec3">OpenMS::ProteinResolver::ProteinEntry::fasta_entry</a></div><div class="ttdeci">FASTAFile::FASTAEntry * fasta_entry</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:89</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html">OpenMS::ProteinResolver::ResolverResult</a></div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:138</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_abf5ae0b4e4fd67a5b4d3f0206b0bd3de"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#abf5ae0b4e4fd67a5b4d3f0206b0bd3de">OpenMS::ProteinResolver::ResolverResult::consensus_map</a></div><div class="ttdeci">ConsensusMap * consensus_map</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:149</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_a3d81a52752fe56b49914dbe273521b5d"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a3d81a52752fe56b49914dbe273521b5d">OpenMS::ProteinResolver::PeptideEntry::sequence</a></div><div class="ttdeci">String sequence</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:106</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_a912b8ba7b2a6ccc272b1423bcb9d769b"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a912b8ba7b2a6ccc272b1423bcb9d769b">OpenMS::ProteinResolver::ProteinEntry::weight</a></div><div class="ttdeci">DoubleReal weight</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:91</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1MSDGroup_html_a95107d2442593bf8bc03ddb9535b9299"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1MSDGroup.html#a95107d2442593bf8bc03ddb9535b9299">OpenMS::ProteinResolver::MSDGroup::number_of_target</a></div><div class="ttdeci">Size number_of_target</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1ProteinResolver_html_a4c49b96ec457ee2202e74f5ada1e40ff"><div class="ttname"><a href="classOpenMS_1_1ProteinResolver.html#a4c49b96ec457ee2202e74f5ada1e40ff">OpenMS::ProteinResolver::resolver_result_</a></div><div class="ttdeci">std::vector< ResolverResult > resolver_result_</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:247</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="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a159e9f34cbc098c1ea4e952f27fb6135"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a159e9f34cbc098c1ea4e952f27fb6135">OpenMS::ProteinResolver::ResolverResult::msds</a></div><div class="ttdeci">std::vector< MSDGroup > * msds</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:142</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_a5b9117518b49bf02daa5aa4f6f2b30ec"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a5b9117518b49bf02daa5aa4f6f2b30ec">OpenMS::ProteinResolver::ProteinEntry::traversed</a></div><div class="ttdeci">bool traversed</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:88</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ResolverResult_html_a459a8a309d0833ae269ec33c782e9f8e"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ResolverResult.html#a459a8a309d0833ae269ec33c782e9f8e">OpenMS::ProteinResolver::ResolverResult::isds</a></div><div class="ttdeci">std::vector< ISDGroup > * isds</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:141</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html">OpenMS::ProteinResolver::PeptideEntry</a></div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:102</div></div>
<div class="ttc" id="structOpenMS_1_1FASTAFile_1_1FASTAEntry_html"><div class="ttname"><a href="structOpenMS_1_1FASTAFile_1_1FASTAEntry.html">OpenMS::FASTAFile::FASTAEntry</a></div><div class="ttdoc">FASTA entry type (identifier, description and sequence) </div><div class="ttdef"><b>Definition:</b> FASTAFile.h:61</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_a2bf8eeb17dafb3d8ed1b08810fba2440"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#a2bf8eeb17dafb3d8ed1b08810fba2440">OpenMS::ProteinResolver::PeptideEntry::intensity</a></div><div class="ttdeci">Real intensity</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:113</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1PeptideEntry_html_ab882919cab417d1efe5ab6fd9074b692"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1PeptideEntry.html#ab882919cab417d1efe5ab6fd9074b692">OpenMS::ProteinResolver::PeptideEntry::proteins</a></div><div class="ttdeci">std::list< ProteinEntry * > proteins</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:104</div></div>
<div class="ttc" id="structOpenMS_1_1ProteinResolver_1_1ProteinEntry_html_a7aead736a07eaf25623ad7bfa1f0ee2d"><div class="ttname"><a href="structOpenMS_1_1ProteinResolver_1_1ProteinEntry.html#a7aead736a07eaf25623ad7bfa1f0ee2d">OpenMS::ProteinResolver::ProteinEntry::type</a></div><div class="ttdeci">type</div><div class="ttdef"><b>Definition:</b> ProteinResolver.h:90</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.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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