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<a href="PeptideIdentification_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: Nico Pfeifer $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</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_METADATA_PEPTIDEIDENTIFICATION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_METADATA_PEPTIDEIDENTIFICATION_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="PeptideHit_8h.html">OpenMS/METADATA/PeptideHit.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="MetaInfoInterface_8h.html">OpenMS/METADATA/MetaInfoInterface.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="ProteinHit_8h.html">OpenMS/METADATA/ProteinHit.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <string></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <map></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> {</div>
<div class="line"><a name="l00063"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html"> 63</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> :</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a></div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  {</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html#a274bec67c485db1aae67a8d12d2ca296"> 69</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> <a class="code" href="classOpenMS_1_1PeptideIdentification.html#a274bec67c485db1aae67a8d12d2ca296">HitType</a>;</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>();</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>();</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & source);</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & source);</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">bool</span> operator==(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & rhs) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordtype">bool</span> operator!=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> & rhs) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">const</span> std::vector<PeptideHit> & getHits() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keywordtype">void</span> insertHit(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> & hit);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">void</span> setHits(<span class="keyword">const</span> std::vector<PeptideHit> & hits);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <a class="code" href="classdouble.html">DoubleReal</a> getSignificanceThreshold() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordtype">void</span> setSignificanceThreshold(<a class="code" href="classdouble.html">DoubleReal</a> value);</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> getScoreType() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">void</span> setScoreType(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & type);</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="keywordtype">bool</span> isHigherScoreBetter() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">void</span> setHigherScoreBetter(<span class="keywordtype">bool</span> value);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & getIdentifier() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">void</span> setIdentifier(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & <span class="keywordtype">id</span>);</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordtype">void</span> assignRanks();</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keywordtype">void</span> sort();</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">bool</span> empty() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</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="l00131"></a><span class="lineno"> 131</span>  <span class="keywordtype">void</span> getReferencingHits(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & protein_accession, std::vector<PeptideHit> & peptide_hits) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span> </div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="keywordtype">void</span> getReferencingHits(<span class="keyword">const</span> std::vector<String> & accessions, std::vector<PeptideHit> & peptide_hits) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordtype">void</span> getReferencingHits(<span class="keyword">const</span> std::vector<ProteinHit> & protein_hits, std::vector<PeptideHit> & peptide_hits) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">void</span> getNonReferencingHits(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & protein_accession, std::vector<PeptideHit> & peptide_hits) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordtype">void</span> getNonReferencingHits(<span class="keyword">const</span> std::vector<String> & accessions, std::vector<PeptideHit> & peptide_hits) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordtype">void</span> getNonReferencingHits(<span class="keyword">const</span> std::vector<ProteinHit> & protein_hits, std::vector<PeptideHit> & peptide_hits) <span class="keyword">const</span>;</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> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html#ae1d43a6f8bee9f364bea98c12662e966"> 146</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PeptideIdentification.html#ae1d43a6f8bee9f364bea98c12662e966">id_</a>; </div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html#a79d4455f471fcdd3e195cf29f2fdb36f"> 147</a></span>  std::vector<PeptideHit> <a class="code" href="classOpenMS_1_1PeptideIdentification.html#a79d4455f471fcdd3e195cf29f2fdb36f">hits_</a>; </div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html#abc04134b209607b000cf0981101fb72c"> 148</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1PeptideIdentification.html#abc04134b209607b000cf0981101fb72c">significance_threshold_</a>; </div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html#a53c5ab78a58e8242d9007d2319a5ad3e"> 149</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1PeptideIdentification.html#a53c5ab78a58e8242d9007d2319a5ad3e">score_type_</a>; </div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PeptideIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada"> 150</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada">higher_score_better_</a>; </div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  };</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> </div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> } <span class="comment">//namespace OpenMS</span></div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="preprocessor">#endif // OPENMS_METADATA_PEPTIDEIDENTIFICATION_H</span></div>
<div class="ttc" id="ProteinHit_8h_html"><div class="ttname"><a href="ProteinHit_8h.html">ProteinHit.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_a53c5ab78a58e8242d9007d2319a5ad3e"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#a53c5ab78a58e8242d9007d2319a5ad3e">OpenMS::PeptideIdentification::score_type_</a></div><div class="ttdeci">String score_type_</div><div class="ttdoc">The score type (Mascot, Sequest, e-value, p-value) </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:149</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_a79d4455f471fcdd3e195cf29f2fdb36f"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#a79d4455f471fcdd3e195cf29f2fdb36f">OpenMS::PeptideIdentification::hits_</a></div><div class="ttdeci">std::vector< PeptideHit > hits_</div><div class="ttdoc">A list containing the peptide hits. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:147</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="MetaInfoInterface_8h_html"><div class="ttname"><a href="MetaInfoInterface_8h.html">MetaInfoInterface.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_a274bec67c485db1aae67a8d12d2ca296"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#a274bec67c485db1aae67a8d12d2ca296">OpenMS::PeptideIdentification::HitType</a></div><div class="ttdeci">PeptideHit HitType</div><div class="ttdoc">Hit type definition. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_ae1d43a6f8bee9f364bea98c12662e966"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#ae1d43a6f8bee9f364bea98c12662e966">OpenMS::PeptideIdentification::id_</a></div><div class="ttdeci">String id_</div><div class="ttdoc">Identifier by which ProteinIdentification and PeptideIdentification are matched. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:146</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_abc04134b209607b000cf0981101fb72c"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#abc04134b209607b000cf0981101fb72c">OpenMS::PeptideIdentification::significance_threshold_</a></div><div class="ttdeci">DoubleReal significance_threshold_</div><div class="ttdoc">the peptide significance threshold </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:148</div></div>
<div class="ttc" id="PeptideHit_8h_html"><div class="ttname"><a href="PeptideHit_8h.html">PeptideHit.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html_a9e5d348a14e5fe639d88db39f0ff7ada"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html#a9e5d348a14e5fe639d88db39f0ff7ada">OpenMS::PeptideIdentification::higher_score_better_</a></div><div class="ttdeci">bool higher_score_better_</div><div class="ttdoc">The score orientation. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:150</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:19 using doxygen 1.8.5</font></TD>
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