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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_330fe73d44ce641f33dd6036f80161a5.html">ANALYSIS</a></li><li class="navelem"><a class="el" href="dir_27fc9ff688aa3473aa59af3b6445a925.html">ID</a></li> </ul>
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<a href="PILISModel_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_ANALYSIS_ID_PILISMODEL_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_ID_PILISMODEL_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="Map_8h.html">OpenMS/DATASTRUCTURES/Map.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="Types_8h.html">OpenMS/CONCEPT/Types.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="HiddenMarkovModel_8h.html">OpenMS/ANALYSIS/ID/HiddenMarkovModel.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="ProtonDistributionModel_8h.html">OpenMS/ANALYSIS/ID/ProtonDistributionModel.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="TheoreticalSpectrumGenerator_8h.html">OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="SpectrumAlignment_8h.html">OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="TextFile_8h.html">OpenMS/FORMAT/TextFile.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <<a class="code" href="PILISNeutralLossModel_8h.html">OpenMS/ANALYSIS/ID/PILISNeutralLossModel.h</a>></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> {</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">class </span>AASequence;</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html"> 67</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a> :</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  {</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a>();</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a> & model);</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a>();</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PILISModel.html">PILISModel</a> & mode);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="keywordtype">void</span> train(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> &, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide, <a class="code" href="classunsigned_01int.html">UInt</a> charge);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordtype">void</span> readFromFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename);</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>  <span class="keywordtype">void</span> writeGraphMLFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename);</div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordtype">void</span> writeToFile(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & filename);</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="comment">//</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordtype">void</span> init(<span class="keywordtype">bool</span> generate_models = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keywordtype">void</span> getSpectrum(<a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> & spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide, <a class="code" href="classunsigned_01int.html">UInt</a> charge);</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>();</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordtype">bool</span> getInitialTransitionProbabilities_(std::vector<DoubleReal> & bb_init,</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  std::vector<DoubleReal> & cr_init,</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  std::vector<DoubleReal> & sc_init,</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <a class="code" href="classdouble.html">DoubleReal</a> & precursor_init,</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  <span class="keyword">const</span> std::vector<DoubleReal> & bb_charges,</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keyword">const</span> std::vector<DoubleReal> & sc_charges,</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide);</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <a class="code" href="classdouble.html">DoubleReal</a> getAvailableBackboneCharge_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & ion, <a class="code" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">Residue::ResidueType</a> res_type, <span class="keywordtype">int</span> charge);</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> addPeaks_(<a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keywordtype">int</span> charge, <a class="code" href="classdouble.html">DoubleReal</a> mz_offset, <a class="code" href="classdouble.html">DoubleReal</a> intensity, <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> & spectrum, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IsotopeDistribution.html">IsotopeDistribution</a> & <span class="keywordtype">id</span>, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> & name);</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> parseHMMModel_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1StringList.html#a67945f8464b125c988ded2dd2cfdf782">TextFile::ConstIterator</a> & begin, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1StringList.html#a67945f8464b125c988ded2dd2cfdf782">TextFile::ConstIterator</a> & end, <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> & hmm, <a class="code" href="classOpenMS_1_1Param.html">Param</a> & param);</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> writeParameters_(std::ostream & os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> & param);</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#acb9723c2cddccf401f9e257d66ee3182"> 140</a></span>  <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#acb9723c2cddccf401f9e257d66ee3182">hmm_</a>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a4dfbdb017bcdf678b0aefe87e0deabb1"> 143</a></span>  <a class="code" href="classOpenMS_1_1ProtonDistributionModel.html">ProtonDistributionModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a4dfbdb017bcdf678b0aefe87e0deabb1">prot_dist_</a>;</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#ac889eab4b469ef0c20a8dea67a9943bf"> 146</a></span>  <a class="code" href="classOpenMS_1_1TheoreticalSpectrumGenerator.html">TheoreticalSpectrumGenerator</a> <a class="code" href="classOpenMS_1_1PILISModel.html#ac889eab4b469ef0c20a8dea67a9943bf">tsg_</a>;</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a2dd81c85c0b7f68b59750ae4441f7da4"> 149</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1PILISModel.html#a2dd81c85c0b7f68b59750ae4441f7da4">valid_</a>;</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#ac0003a92036eb4ea6fb9cda839de39c2"> 152</a></span>  <a class="code" href="classOpenMS_1_1Map.html">Map<DoubleReal, std::vector<RichPeak1D></a> > <a class="code" href="classOpenMS_1_1PILISModel.html#ac0003a92036eb4ea6fb9cda839de39c2">peaks_</a>;</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a983ce6398bc396acd87b002e82f0cd31"> 155</a></span>  <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a983ce6398bc396acd87b002e82f0cd31">spectra_aligner_</a>;</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#ab2e7eaa60e55467678b4a5c242149e3f"> 158</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#ab2e7eaa60e55467678b4a5c242149e3f">precursor_model_cr_</a>;</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
<div class="line"><a name="l00160"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a0466fe7e46a643eff23d4c18a5f73109"> 160</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a0466fe7e46a643eff23d4c18a5f73109">precursor_model_cd_</a>;</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#ab8b6f3019439fd05b05c28955656cf18"> 162</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#ab8b6f3019439fd05b05c28955656cf18">a_ion_losses_cr_</a>;</div>
<div class="line"><a name="l00163"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a247bed7e8d513ca9228adce009745876"> 163</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a247bed7e8d513ca9228adce009745876">a_ion_losses_cd_</a>;</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> </div>
<div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a52332404d3a2ae14fb514afa7de6147d"> 165</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a52332404d3a2ae14fb514afa7de6147d">b_ion_losses_cr_</a>;</div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#aa8b718f19c3a87d8dbad332a3413e210"> 166</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#aa8b718f19c3a87d8dbad332a3413e210">b_ion_losses_cd_</a>;</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> </div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a3c26ce28250d6c86104b4b63c88e57ff"> 168</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a3c26ce28250d6c86104b4b63c88e57ff">b2_ion_losses_cr_</a>;</div>
<div class="line"><a name="l00169"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#ae122f0f5e830157c2391592cec982a32"> 169</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#ae122f0f5e830157c2391592cec982a32">b2_ion_losses_cd_</a>;</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span> </div>
<div class="line"><a name="l00171"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#a83884268eede3ebf762e9e1aa09133f6"> 171</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#a83884268eede3ebf762e9e1aa09133f6">y_ion_losses_cr_</a>;</div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISModel.html#ab05610e65ad0b611e333e49fa552d6b8"> 172</a></span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> <a class="code" href="classOpenMS_1_1PILISModel.html#ab05610e65ad0b611e333e49fa552d6b8">y_ion_losses_cd_</a>;</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  };</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> }</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_a52332404d3a2ae14fb514afa7de6147d"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a52332404d3a2ae14fb514afa7de6147d">OpenMS::PILISModel::b_ion_losses_cr_</a></div><div class="ttdeci">PILISNeutralLossModel b_ion_losses_cr_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:165</div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="Types_8h_html"><div class="ttname"><a href="Types_8h.html">Types.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="classOpenMS_1_1PILISModel_html_a3c26ce28250d6c86104b4b63c88e57ff"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a3c26ce28250d6c86104b4b63c88e57ff">OpenMS::PILISModel::b2_ion_losses_cr_</a></div><div class="ttdeci">PILISNeutralLossModel b2_ion_losses_cr_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:168</div></div>
<div class="ttc" id="classOpenMS_1_1PILISNeutralLossModel_html"><div class="ttname"><a href="classOpenMS_1_1PILISNeutralLossModel.html">OpenMS::PILISNeutralLossModel</a></div><div class="ttdoc">This class implements the simulation of the spectra from PILIS. </div><div class="ttdef"><b>Definition:</b> PILISNeutralLossModel.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_aa8b718f19c3a87d8dbad332a3413e210"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#aa8b718f19c3a87d8dbad332a3413e210">OpenMS::PILISModel::b_ion_losses_cd_</a></div><div class="ttdeci">PILISNeutralLossModel b_ion_losses_cd_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:166</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_ae122f0f5e830157c2391592cec982a32"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#ae122f0f5e830157c2391592cec982a32">OpenMS::PILISModel::b2_ion_losses_cd_</a></div><div class="ttdeci">PILISNeutralLossModel b2_ion_losses_cd_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:169</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_ab05610e65ad0b611e333e49fa552d6b8"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#ab05610e65ad0b611e333e49fa552d6b8">OpenMS::PILISModel::y_ion_losses_cd_</a></div><div class="ttdeci">PILISNeutralLossModel y_ion_losses_cd_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:172</div></div>
<div class="ttc" id="classOpenMS_1_1ProtonDistributionModel_html"><div class="ttname"><a href="classOpenMS_1_1ProtonDistributionModel.html">OpenMS::ProtonDistributionModel</a></div><div class="ttdoc">A proton distribution model to calculate the proton distribution over charged peptides. </div><div class="ttdef"><b>Definition:</b> ProtonDistributionModel.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html">OpenMS::IsotopeDistribution</a></div><div class="ttdoc">Isotope distribution class. </div><div class="ttdef"><b>Definition:</b> IsotopeDistribution.h:61</div></div>
<div class="ttc" id="Map_8h_html"><div class="ttname"><a href="Map_8h.html">Map.h</a></div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1TheoreticalSpectrumGenerator_html"><div class="ttname"><a href="classOpenMS_1_1TheoreticalSpectrumGenerator.html">OpenMS::TheoreticalSpectrumGenerator</a></div><div class="ttdoc">Generates theoretical spectra with various options. </div><div class="ttdef"><b>Definition:</b> TheoreticalSpectrumGenerator.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1AASequence_html"><div class="ttname"><a href="classOpenMS_1_1AASequence.html">OpenMS::AASequence</a></div><div class="ttdoc">Representation of a peptide/protein sequence. </div><div class="ttdef"><b>Definition:</b> AASequence.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_a83884268eede3ebf762e9e1aa09133f6"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a83884268eede3ebf762e9e1aa09133f6">OpenMS::PILISModel::y_ion_losses_cr_</a></div><div class="ttdeci">PILISNeutralLossModel y_ion_losses_cr_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:171</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="classOpenMS_1_1StringList_html_a67945f8464b125c988ded2dd2cfdf782"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a67945f8464b125c988ded2dd2cfdf782">OpenMS::StringList::ConstIterator</a></div><div class="ttdeci">const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> StringList.h:67</div></div>
<div class="ttc" id="PILISNeutralLossModel_8h_html"><div class="ttname"><a href="PILISNeutralLossModel_8h.html">PILISNeutralLossModel.h</a></div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_aacf12ce6c8657d87174c792d19c318bf"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">OpenMS::OptimizationFunctions::evaluate</a></div><div class="ttdeci">int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)</div><div class="ttdoc">Driver function for the evaluation of function and jacobian. </div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_ac0003a92036eb4ea6fb9cda839de39c2"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#ac0003a92036eb4ea6fb9cda839de39c2">OpenMS::PILISModel::peaks_</a></div><div class="ttdeci">Map< DoubleReal, std::vector< RichPeak1D > > peaks_</div><div class="ttdoc">stores the peaks of a spectrum </div><div class="ttdef"><b>Definition:</b> PILISModel.h:152</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_acb9723c2cddccf401f9e257d66ee3182"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#acb9723c2cddccf401f9e257d66ee3182">OpenMS::PILISModel::hmm_</a></div><div class="ttdeci">HiddenMarkovModel hmm_</div><div class="ttdoc">base model used </div><div class="ttdef"><b>Definition:</b> PILISModel.h:140</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< RichPeak1D ></a></div></div>
<div class="ttc" id="TheoreticalSpectrumGenerator_8h_html"><div class="ttname"><a href="TheoreticalSpectrumGenerator_8h.html">TheoreticalSpectrumGenerator.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html">OpenMS::PILISModel</a></div><div class="ttdoc">This class implements the simulation of the spectra from PILIS. </div><div class="ttdef"><b>Definition:</b> PILISModel.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumAlignment_html"><div class="ttname"><a href="classOpenMS_1_1SpectrumAlignment.html">OpenMS::SpectrumAlignment</a></div><div class="ttdoc">Aligns the peaks of two spectra. </div><div class="ttdef"><b>Definition:</b> SpectrumAlignment.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_ac889eab4b469ef0c20a8dea67a9943bf"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#ac889eab4b469ef0c20a8dea67a9943bf">OpenMS::PILISModel::tsg_</a></div><div class="ttdeci">TheoreticalSpectrumGenerator tsg_</div><div class="ttdoc">theoretical spectrum generator (needed for training/aligning and spectrum intensity extraction) ...</div><div class="ttdef"><b>Definition:</b> PILISModel.h:146</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_a4dfbdb017bcdf678b0aefe87e0deabb1"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a4dfbdb017bcdf678b0aefe87e0deabb1">OpenMS::PILISModel::prot_dist_</a></div><div class="ttdeci">ProtonDistributionModel prot_dist_</div><div class="ttdoc">proton distribution model </div><div class="ttdef"><b>Definition:</b> PILISModel.h:143</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_ab2e7eaa60e55467678b4a5c242149e3f"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#ab2e7eaa60e55467678b4a5c242149e3f">OpenMS::PILISModel::precursor_model_cr_</a></div><div class="ttdeci">PILISNeutralLossModel precursor_model_cr_</div><div class="ttdoc">precursor model used </div><div class="ttdef"><b>Definition:</b> PILISModel.h:158</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_a983ce6398bc396acd87b002e82f0cd31"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a983ce6398bc396acd87b002e82f0cd31">OpenMS::PILISModel::spectra_aligner_</a></div><div class="ttdeci">SpectrumAlignment spectra_aligner_</div><div class="ttdoc">the alignment algorithm used </div><div class="ttdef"><b>Definition:</b> PILISModel.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_a0466fe7e46a643eff23d4c18a5f73109"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a0466fe7e46a643eff23d4c18a5f73109">OpenMS::PILISModel::precursor_model_cd_</a></div><div class="ttdeci">PILISNeutralLossModel precursor_model_cd_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:160</div></div>
<div class="ttc" id="HiddenMarkovModel_8h_html"><div class="ttname"><a href="HiddenMarkovModel_8h.html">HiddenMarkovModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Residue_html_a7651af21f9cf8ed6445415903fc6cb48"><div class="ttname"><a href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">OpenMS::Residue::ResidueType</a></div><div class="ttdeci">ResidueType</div><div class="ttdef"><b>Definition:</b> Residue.h:361</div></div>
<div class="ttc" id="ProtonDistributionModel_8h_html"><div class="ttname"><a href="ProtonDistributionModel_8h.html">ProtonDistributionModel.h</a></div></div>
<div class="ttc" id="TextFile_8h_html"><div class="ttname"><a href="TextFile_8h.html">TextFile.h</a></div></div>
<div class="ttc" id="SpectrumAlignment_8h_html"><div class="ttname"><a href="SpectrumAlignment_8h.html">SpectrumAlignment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1HiddenMarkovModel_html"><div class="ttname"><a href="classOpenMS_1_1HiddenMarkovModel.html">OpenMS::HiddenMarkovModel</a></div><div class="ttdoc">Hidden Markov Model implementation of PILIS. </div><div class="ttdef"><b>Definition:</b> HiddenMarkovModel.h:134</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="classOpenMS_1_1PILISModel_html_a2dd81c85c0b7f68b59750ae4441f7da4"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a2dd81c85c0b7f68b59750ae4441f7da4">OpenMS::PILISModel::valid_</a></div><div class="ttdeci">bool valid_</div><div class="ttdoc">true if the instance is valid </div><div class="ttdef"><b>Definition:</b> PILISModel.h:149</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_a247bed7e8d513ca9228adce009745876"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#a247bed7e8d513ca9228adce009745876">OpenMS::PILISModel::a_ion_losses_cd_</a></div><div class="ttdeci">PILISNeutralLossModel a_ion_losses_cd_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:163</div></div>
<div class="ttc" id="classOpenMS_1_1PILISModel_html_ab8b6f3019439fd05b05c28955656cf18"><div class="ttname"><a href="classOpenMS_1_1PILISModel.html#ab8b6f3019439fd05b05c28955656cf18">OpenMS::PILISModel::a_ion_losses_cr_</a></div><div class="ttdeci">PILISNeutralLossModel a_ion_losses_cr_</div><div class="ttdef"><b>Definition:</b> PILISModel.h:162</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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