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<a href="PILISNeutralLossModel_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>
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<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_PILISNEUTRALLOSSMODEL_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_PILISNEUTRALLOSSMODEL_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="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="Types_8h.html">OpenMS/CONCEPT/Types.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</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="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></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="l00049"></a><span class="lineno"> 49</span>  <span class="keyword">class </span>AASequence;</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISNeutralLossModel.html"> 62</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> :</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  {</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISNeutralLossModel.html#a1c929c4590965c51a408eb67ae209bd9"> 65</a></span>  <span class="keyword">friend</span> <span class="keyword">class </span>PILISNeutralLossModelGenerator;</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a>();</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> & model);</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>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a>();</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html">PILISNeutralLossModel</a> & mode);</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classdouble.html">DoubleReal</a> train(<span class="keyword">const</span> <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="classdouble.html">DoubleReal</a> ion_weight, <a class="code" href="classunsigned_01int.html">UInt</a> charge, <a class="code" href="classdouble.html">DoubleReal</a> peptide_weight);</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keywordtype">void</span> getIons(std::vector<RichPeak1D> & peaks, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide, <a class="code" href="classdouble.html">DoubleReal</a> initial_prob);</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>  <span class="keywordtype">void</span> setHMM(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> & model);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> & getHMM() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">void</span> generateModel();</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>();</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="keyword">protected</span>:</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>  <a class="code" href="classdouble.html">DoubleReal</a> getIntensitiesFromSpectrum_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> & train_spec, <a class="code" href="classOpenMS_1_1Map.html">Map<String, DoubleReal></a> & pre_ints, <a class="code" href="classdouble.html">DoubleReal</a> ion_weight, <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="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> trainIons_(<a class="code" href="classdouble.html">DoubleReal</a> initial_probability, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Map.html">Map<String, DoubleReal></a> & intensities, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keywordtype">void</span> getIons_(<a class="code" href="classOpenMS_1_1Map.html">Map<String, DoubleReal></a> & intensities, <a class="code" href="classdouble.html">DoubleReal</a> initial_probability, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & precursor);</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <span class="keywordtype">void</span> enableIonStates_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> & peptide);</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISNeutralLossModel.html#aae14d225fc5014125234ebfbe43a6310"> 122</a></span>  <a class="code" href="classOpenMS_1_1HiddenMarkovModel.html">HiddenMarkovModel</a> <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html#aae14d225fc5014125234ebfbe43a6310">hmm_precursor_</a>;</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1PILISNeutralLossModel.html#a7473da8adff84da7ad7e59cf458894c9"> 125</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1PILISNeutralLossModel.html#a7473da8adff84da7ad7e59cf458894c9">num_explicit_</a>;</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordtype">void</span> updateMembers_();</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"> 130</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="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_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="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_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="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1PILISNeutralLossModel_html_aae14d225fc5014125234ebfbe43a6310"><div class="ttname"><a href="classOpenMS_1_1PILISNeutralLossModel.html#aae14d225fc5014125234ebfbe43a6310">OpenMS::PILISNeutralLossModel::hmm_precursor_</a></div><div class="ttdeci">HiddenMarkovModel hmm_precursor_</div><div class="ttdoc">precursor model used </div><div class="ttdef"><b>Definition:</b> PILISNeutralLossModel.h:122</div></div>
<div class="ttc" id="classOpenMS_1_1PILISNeutralLossModel_html_a7473da8adff84da7ad7e59cf458894c9"><div class="ttname"><a href="classOpenMS_1_1PILISNeutralLossModel.html#a7473da8adff84da7ad7e59cf458894c9">OpenMS::PILISNeutralLossModel::num_explicit_</a></div><div class="ttdeci">UInt num_explicit_</div><div class="ttdef"><b>Definition:</b> PILISNeutralLossModel.h:125</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_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< RichPeak1D ></a></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_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_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map< String, DoubleReal ></a></div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></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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