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<a href="SvmTheoreticalSpectrumGenerator_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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<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>&#160;<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>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Sandro Andreotti $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Sandro Andreotti $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#ifndef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATOR_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATOR_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;OpenMS/config.h&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TheoreticalSpectrumGenerator_8h.html">OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SimTypes_8h.html">OpenMS/SIMULATION/SimTypes.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SVMWrapper_8h.html">OpenMS/ANALYSIS/SVM/SVMWrapper.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;boost/smart_ptr.hpp&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;{</div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">   69</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> :</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;  {</div>
<div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a44946b9432a4504dfeb43f7ac732d018">   72</a></span>&#160;    <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a>;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    {</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec415b55cb87cb4d8db0e8680d0db11">   82</a></span>&#160;      <a class="code" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">Residue::ResidueType</a> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec415b55cb87cb4d8db0e8680d0db11">residue</a>;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#ac8fa762216a033fdf1c09a9ec3727b56">   83</a></span>&#160;      <a class="code" href="classOpenMS_1_1EmpiricalFormula.html">EmpiricalFormula</a> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#ac8fa762216a033fdf1c09a9ec3727b56">loss</a>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a8253a7962ca1c79b71e6af96589b7720">   84</a></span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a8253a7962ca1c79b71e6af96589b7720">charge</a>;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      <span class="comment">//Default constructor</span></div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a95c9c36699a22aae05300c001affcfaf">   89</a></span>&#160;      <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a95c9c36699a22aae05300c001affcfaf">IonType</a>() :</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        residue((<a class="code" href="classOpenMS_1_1Residue.html">Residue</a>::ResidueType) 0),</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;        loss(),</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        charge(0)</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      {</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      }</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      <span class="comment">//Custom construtor</span></div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec51891c0c625d786abaf92aa5756d0">   97</a></span>&#160;      <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec51891c0c625d786abaf92aa5756d0">IonType</a>(<a class="code" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">Residue::ResidueType</a> residue, <a class="code" href="classOpenMS_1_1EmpiricalFormula.html">EmpiricalFormula</a> loss = <a class="code" href="classOpenMS_1_1EmpiricalFormula.html">EmpiricalFormula</a>(), <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge = 1) :</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;        residue(residue),</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        loss(loss),</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;        charge(charge)</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;      {</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      }</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;      <span class="comment">//Copy constructor</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#aaeac3e60ada7018bd227c3171427b306">  105</a></span>&#160;      <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#aaeac3e60ada7018bd227c3171427b306">IonType</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> &amp; rhs) :</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        residue(rhs.residue),</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        loss(rhs.loss),</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        charge(rhs.charge)</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      {</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      }</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      <span class="comment">//Assignment operator</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#aaad2706cdbe5b8dcee737111988504b0">  113</a></span>&#160;      <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> &amp; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#aaad2706cdbe5b8dcee737111988504b0">operator=</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> &amp; rhs)</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      {</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;        <span class="keywordflow">if</span> (<span class="keyword">this</span> != &amp;rhs)</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        {</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;          residue = rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec415b55cb87cb4d8db0e8680d0db11">residue</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;          loss = rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#ac8fa762216a033fdf1c09a9ec3727b56">loss</a>;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;          charge = rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a8253a7962ca1c79b71e6af96589b7720">charge</a>;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        }</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      }</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a62ce8a924eb20bede64a656ed861d401">  124</a></span>&#160;      <span class="keywordtype">bool</span> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a62ce8a924eb20bede64a656ed861d401">operator&lt;</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> &amp; rhs)<span class="keyword"> const</span></div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;        <span class="keywordflow">if</span> (residue != rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec415b55cb87cb4d8db0e8680d0db11">residue</a>)</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;          <span class="keywordflow">return</span> residue &lt; rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec415b55cb87cb4d8db0e8680d0db11">residue</a>;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (loss.getString() != rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#ac8fa762216a033fdf1c09a9ec3727b56">loss</a>.<a class="code" href="classOpenMS_1_1EmpiricalFormula.html#a3ef7b2a7d3d55c9d6212c6ec339d288b">getString</a>())</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;          <span class="keywordflow">return</span> loss.getString() &lt; rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#ac8fa762216a033fdf1c09a9ec3727b56">loss</a>.<a class="code" href="classOpenMS_1_1EmpiricalFormula.html#a3ef7b2a7d3d55c9d6212c6ec339d288b">getString</a>();</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;          <span class="keywordflow">return</span> charge &lt; rhs.<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a8253a7962ca1c79b71e6af96589b7720">charge</a>;</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      }</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;    };</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">  138</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">DescriptorSet</a></div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;    {</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a219e3595adfebceeb3c7314473b797a1">  140</a></span>&#160;      <span class="keyword">typedef</span> std::vector&lt;svm_node&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a219e3595adfebceeb3c7314473b797a1">DescriptorSetType</a>;</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a63885d5a4dcdd00de84eb173b534ca37">  141</a></span>&#160;      <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a219e3595adfebceeb3c7314473b797a1">DescriptorSetType</a> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a63885d5a4dcdd00de84eb173b534ca37">descriptors</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;    };</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">  146</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">SvmModelParameterSet</a></div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;    {</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <span class="comment">//pointers to the svm classification models (one per ion_type)</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#ac909a523d5d9e9f376b54d30cf5657bb">  149</a></span>&#160;      std::vector&lt;boost::shared_ptr&lt;SVMWrapper&gt; &gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#ac909a523d5d9e9f376b54d30cf5657bb">class_models</a>;</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      <span class="comment">//pointers to the svm regression models (one per ion_type)</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a4b96023be9755df936a0c1cf232ab90f">  152</a></span>&#160;      std::vector&lt;boost::shared_ptr&lt;SVMWrapper&gt; &gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a4b96023be9755df936a0c1cf232ab90f">reg_models</a>;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      <span class="comment">//The intensity for each ion type for the SVC mode</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a0ce1a4c0a78c845b05edea330797146c">  155</a></span>&#160;      std::map&lt;Residue::ResidueType, DoubleReal&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a0ce1a4c0a78c845b05edea330797146c">static_intensities</a>;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;      <span class="comment">//The selected primary IonTypes</span></div>
<div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#af5d722ded8fabc9b2c92462509ce1d71">  158</a></span>&#160;      std::vector&lt;IonType&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#af5d722ded8fabc9b2c92462509ce1d71">ion_types</a>;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;      <span class="comment">//The selected secondary IonTypes</span></div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a7696e414607eec643bdf2fae973e6588">  161</a></span>&#160;      std::map&lt;IonType, std::vector&lt;IonType&gt; &gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a7696e414607eec643bdf2fae973e6588">secondary_types</a>;</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;      <span class="comment">//The number of intensity levels</span></div>
<div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#ab829af012a40789aa761c1f1b2da5b33">  164</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#ab829af012a40789aa761c1f1b2da5b33">number_intensity_levels</a>;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;      <span class="comment">//The number of regions for every spectrum</span></div>
<div class="line"><a name="l00167"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a48cfb7f8c8f7f571b84f5319581ec2ed">  167</a></span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a48cfb7f8c8f7f571b84f5319581ec2ed">number_regions</a>;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;      <span class="comment">//upper limits (required for scaling)</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a7576925395947d63054db15b70beeaac">  170</a></span>&#160;      std::vector&lt;DoubleReal&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a7576925395947d63054db15b70beeaac">feature_max</a>;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;      <span class="comment">//lower limits (required for scaling)</span></div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a04ead88d30f81500407a2e39a3b2fccf">  173</a></span>&#160;      std::vector&lt;DoubleReal&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a04ead88d30f81500407a2e39a3b2fccf">feature_min</a>;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;      <span class="comment">//lower bound for scaling</span></div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a5483c133b5ddb9b0d783edcaadfb4dcb">  176</a></span>&#160;      <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a5483c133b5ddb9b0d783edcaadfb4dcb">scaling_lower</a>;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;      <span class="comment">//upper bound for scaling</span></div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a0ca86ec3f6c7d8d2aa9439b2d25aeaf2">  179</a></span>&#160;      <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a0ca86ec3f6c7d8d2aa9439b2d25aeaf2">scaling_upper</a>;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;      <span class="comment">//border values for binning secondary types intensity</span></div>
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#afb5218f2c1e1a693f2240b3cc8a1cf3f">  182</a></span>&#160;      std::vector&lt;DoubleReal&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#afb5218f2c1e1a693f2240b3cc8a1cf3f">intensity_bin_boarders</a>;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      <span class="comment">//intensity values for binned secondary types intensity</span></div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a84ba76357099f24c8699ac1b7438bbe6">  185</a></span>&#160;      std::vector&lt;DoubleReal&gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a84ba76357099f24c8699ac1b7438bbe6">intensity_bin_values</a>;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      <span class="comment">//conditional probabilities for secondary types</span></div>
<div class="line"><a name="l00188"></a><span class="lineno"><a class="line" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a390f6226cd88d5943f4a1aefc174ddc7">  188</a></span>&#160;      std::map&lt;std::pair&lt;IonType, Size&gt;, std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &gt; <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a390f6226cd88d5943f4a1aefc174ddc7">conditional_prob</a>;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    };</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;    <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a>();</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> &amp; source);</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> &amp; tsg);</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a>();</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;    <span class="keywordtype">void</span> simulate(<a class="code" href="classOpenMS_1_1MSSpectrum.html">RichPeakSpectrum</a> &amp; spectrum, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> &amp; peptide, <span class="keyword">const</span> gsl_rng * rng, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_charge);</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;    <span class="keywordtype">void</span> load();</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;</div>
<div class="line"><a name="l00218"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a7fd878e35881deccde0faca564b096fe">  218</a></span>&#160;    <span class="keyword">const</span> std::vector&lt;IonType&gt; &amp; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a7fd878e35881deccde0faca564b096fe">getIonTypes</a>()</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;    {</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      <span class="keywordflow">return</span> mp_.ion_types;</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;    }</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00224"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ad0f94e7ae2de2380f906f0e3110d58cc">  224</a></span>&#160;    <span class="keyword">typedef</span> std::map&lt;IonType, DoubleReal&gt; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ad0f94e7ae2de2380f906f0e3110d58cc">IntensityMap</a>;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;</div>
<div class="line"><a name="l00227"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab4f4b9381d8d1c6ede3ef66028cd6b42">  227</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab4f4b9381d8d1c6ede3ef66028cd6b42">precursor_charge_</a>;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;</div>
<div class="line"><a name="l00230"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a442a4d1a69906395b7ac683b15344229">  230</a></span>&#160;    <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">SvmModelParameterSet</a> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a442a4d1a69906395b7ac683b15344229">mp_</a>;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;</div>
<div class="line"><a name="l00233"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a6488f3ef2246dcc142791a66eab4bf7a">  233</a></span>&#160;    <span class="keyword">static</span> std::map&lt;String, Size&gt; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a6488f3ef2246dcc142791a66eab4bf7a">aa_to_index_</a>;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;</div>
<div class="line"><a name="l00236"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#aaf924b0e5c8dd84daeb1705aaf1d01bc">  236</a></span>&#160;    <span class="keyword">static</span> std::map&lt;String, DoubleReal&gt; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#aaf924b0e5c8dd84daeb1705aaf1d01bc">hydrophobicity_</a>;</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;</div>
<div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a08803b692e19f653b8c0a1a62fcda611">  239</a></span>&#160;    <span class="keyword">static</span> std::map&lt;String, DoubleReal&gt; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a08803b692e19f653b8c0a1a62fcda611">helicity_</a>;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;</div>
<div class="line"><a name="l00242"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a3af386eefaea14316abc3da0c3a6bbee">  242</a></span>&#160;    <span class="keyword">static</span> std::map&lt;String, DoubleReal&gt; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a3af386eefaea14316abc3da0c3a6bbee">basicity_</a>;</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ae6c6c1213fef424b3e47b9f16e0afed1">  245</a></span>&#160;    std::map&lt;IonType, bool&gt; <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ae6c6c1213fef424b3e47b9f16e0afed1">hide_type_</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">void</span> scaleSingleFeature_(<span class="keywordtype">double</span> &amp; value, <span class="keywordtype">double</span> feature_min, <span class="keywordtype">double</span> feature_max, <span class="keywordtype">double</span> lower = -1.0, <span class="keywordtype">double</span> upper = 1.0);</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;    <span class="keywordtype">void</span> scaleDescriptorSet_(<a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">DescriptorSet</a> &amp; desc, <span class="keywordtype">double</span> lower, <span class="keywordtype">double</span> upper);</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> generateDescriptorSet_(<a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> peptide, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> position, <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> type, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_charge, <a class="code" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">DescriptorSet</a> &amp; desc_set);</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> ResidueTypeToString_(<a class="code" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">Residue::ResidueType</a> type);</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> initializeMaps_();</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;</div>
<div class="line"><a name="l00263"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab1cb112813b80accd3a3adf8aac0f8c8">  263</a></span>&#160;    <span class="keyword">static</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab1cb112813b80accd3a3adf8aac0f8c8">initializedMaps_</a>;</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;    <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;  };</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;</div>
<div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a01b2ecfa118e5ad632ece3b09987856c">  268</a></span>&#160;  <span class="keywordtype">void</span> <span class="keyword">inline</span> <a class="code" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a01b2ecfa118e5ad632ece3b09987856c">SvmTheoreticalSpectrumGenerator::scaleSingleFeature_</a>(<span class="keywordtype">double</span> &amp; value, <span class="keywordtype">double</span> lower, <span class="keywordtype">double</span> upper, <span class="keywordtype">double</span> feature_min, <span class="keywordtype">double</span> feature_max)</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;  {</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;    <span class="keywordtype">double</span> prev = value;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;    <span class="keywordflow">if</span> (feature_max == feature_min)</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;    {</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;      <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;    }</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;    <span class="keywordflow">if</span> (value &lt;= feature_min)</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;    {</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;      value = lower;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;    }</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;    <span class="keywordflow">else</span> <span class="keywordflow">if</span> (value &gt;= feature_max)</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;    {</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;      value = upper;</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;    }</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;    <span class="keywordflow">else</span></div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;    {</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;      value = lower + (upper - lower) *</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;              (value - feature_min) /</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;              (feature_max - feature_min);</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;    }</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;    <span class="keywordflow">if</span> (value &lt; 0)</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;    {</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;      std::cerr &lt;&lt; <span class="stringliteral">&quot;negative value!! &quot;</span> &lt;&lt; value &lt;&lt; <span class="stringliteral">&quot;  l: &quot;</span> &lt;&lt; lower &lt;&lt; <span class="stringliteral">&quot; u: &quot;</span> &lt;&lt; upper &lt;&lt; <span class="stringliteral">&quot; fm: &quot;</span> &lt;&lt; feature_min &lt;&lt; <span class="stringliteral">&quot; fma: &quot;</span> &lt;&lt; feature_max &lt;&lt; <span class="stringliteral">&quot;  prev: &quot;</span> &lt;&lt; prev &lt;&lt; std::endl;</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;    }</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;  }</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;<span class="preprocessor">#endif // #ifdef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORTRAINER_H</span></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">OpenMS::SvmTheoreticalSpectrumGenerator::IonType</a></div><div class="ttdoc">nested class </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_a6488f3ef2246dcc142791a66eab4bf7a"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a6488f3ef2246dcc142791a66eab4bf7a">OpenMS::SvmTheoreticalSpectrumGenerator::aa_to_index_</a></div><div class="ttdeci">static std::map&lt; String, Size &gt; aa_to_index_</div><div class="ttdoc">map AA to integers </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:233</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_a3af386eefaea14316abc3da0c3a6bbee"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a3af386eefaea14316abc3da0c3a6bbee">OpenMS::SvmTheoreticalSpectrumGenerator::basicity_</a></div><div class="ttdeci">static std::map&lt; String, DoubleReal &gt; basicity_</div><div class="ttdoc">basicity values for each AA </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:242</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="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a7696e414607eec643bdf2fae973e6588"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a7696e414607eec643bdf2fae973e6588">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::secondary_types</a></div><div class="ttdeci">std::map&lt; IonType, std::vector&lt; IonType &gt; &gt; secondary_types</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:161</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a48cfb7f8c8f7f571b84f5319581ec2ed"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a48cfb7f8c8f7f571b84f5319581ec2ed">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::number_regions</a></div><div class="ttdeci">Size number_regions</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:167</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a0ca86ec3f6c7d8d2aa9439b2d25aeaf2"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a0ca86ec3f6c7d8d2aa9439b2d25aeaf2">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::scaling_upper</a></div><div class="ttdeci">double scaling_upper</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:179</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a04ead88d30f81500407a2e39a3b2fccf"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a04ead88d30f81500407a2e39a3b2fccf">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::feature_min</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; feature_min</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:173</div></div>
<div class="ttc" id="SimTypes_8h_html"><div class="ttname"><a href="SimTypes_8h.html">SimTypes.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_a95c9c36699a22aae05300c001affcfaf"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a95c9c36699a22aae05300c001affcfaf">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::IonType</a></div><div class="ttdeci">IonType()</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_ad0f94e7ae2de2380f906f0e3110d58cc"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ad0f94e7ae2de2380f906f0e3110d58cc">OpenMS::SvmTheoreticalSpectrumGenerator::IntensityMap</a></div><div class="ttdeci">std::map&lt; IonType, DoubleReal &gt; IntensityMap</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:224</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_afec415b55cb87cb4d8db0e8680d0db11"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec415b55cb87cb4d8db0e8680d0db11">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::residue</a></div><div class="ttdeci">Residue::ResidueType residue</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:82</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="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet_html_a219e3595adfebceeb3c7314473b797a1"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a219e3595adfebceeb3c7314473b797a1">OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet::DescriptorSetType</a></div><div class="ttdeci">std::vector&lt; svm_node &gt; DescriptorSetType</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:140</div></div>
<div class="ttc" id="classOpenMS_1_1Residue_html"><div class="ttname"><a href="classOpenMS_1_1Residue.html">OpenMS::Residue</a></div><div class="ttdoc">Representation of a residue. </div><div class="ttdef"><b>Definition:</b> Residue.h:64</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a0ce1a4c0a78c845b05edea330797146c"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a0ce1a4c0a78c845b05edea330797146c">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::static_intensities</a></div><div class="ttdeci">std::map&lt; Residue::ResidueType, DoubleReal &gt; static_intensities</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1EmpiricalFormula_html"><div class="ttname"><a href="classOpenMS_1_1EmpiricalFormula.html">OpenMS::EmpiricalFormula</a></div><div class="ttdoc">Representation of an empirical formula. </div><div class="ttdef"><b>Definition:</b> EmpiricalFormula.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">OpenMS::SvmTheoreticalSpectrumGenerator</a></div><div class="ttdoc">Simulates ms2 spectra with support vector machines. </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:69</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_ac8fa762216a033fdf1c09a9ec3727b56"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#ac8fa762216a033fdf1c09a9ec3727b56">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::loss</a></div><div class="ttdeci">EmpiricalFormula loss</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; RichPeak1D &gt;</a></div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet</a></div><div class="ttdoc">Simple container storing the model parameters required for simulation. </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:146</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_afb5218f2c1e1a693f2240b3cc8a1cf3f"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#afb5218f2c1e1a693f2240b3cc8a1cf3f">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::intensity_bin_boarders</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; intensity_bin_boarders</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer_html"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">OpenMS::SvmTheoreticalSpectrumGeneratorTrainer</a></div><div class="ttdoc">Train SVM models that are used by SvmTheoreticalSpectrumGenerator. </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGeneratorTrainer.h:62</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet_html"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet</a></div><div class="ttdoc">A set of descriptors for a single training row. </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:138</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_1SvmTheoreticalSpectrumGenerator_html_ab1cb112813b80accd3a3adf8aac0f8c8"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab1cb112813b80accd3a3adf8aac0f8c8">OpenMS::SvmTheoreticalSpectrumGenerator::initializedMaps_</a></div><div class="ttdeci">static bool initializedMaps_</div><div class="ttdoc">flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized ...</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:263</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_aaeac3e60ada7018bd227c3171427b306"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#aaeac3e60ada7018bd227c3171427b306">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::IonType</a></div><div class="ttdeci">IonType(const IonType &amp;rhs)</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1EmpiricalFormula_html_a3ef7b2a7d3d55c9d6212c6ec339d288b"><div class="ttname"><a href="classOpenMS_1_1EmpiricalFormula.html#a3ef7b2a7d3d55c9d6212c6ec339d288b">OpenMS::EmpiricalFormula::getString</a></div><div class="ttdeci">String getString() const </div><div class="ttdoc">returns the formula as a string (charges are not included) </div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a4b96023be9755df936a0c1cf232ab90f"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a4b96023be9755df936a0c1cf232ab90f">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::reg_models</a></div><div class="ttdeci">std::vector&lt; boost::shared_ptr&lt; SVMWrapper &gt; &gt; reg_models</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:152</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_a01b2ecfa118e5ad632ece3b09987856c"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a01b2ecfa118e5ad632ece3b09987856c">OpenMS::SvmTheoreticalSpectrumGenerator::scaleSingleFeature_</a></div><div class="ttdeci">void scaleSingleFeature_(double &amp;value, double feature_min, double feature_max, double lower=-1.0, double upper=1.0)</div><div class="ttdoc">scale value to the intervall [lower,max] given the maximal and minimal entries for a feature ...</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:268</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_a7fd878e35881deccde0faca564b096fe"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a7fd878e35881deccde0faca564b096fe">OpenMS::SvmTheoreticalSpectrumGenerator::getIonTypes</a></div><div class="ttdeci">const std::vector&lt; IonType &gt; &amp; getIonTypes()</div><div class="ttdoc">return the set of ion types that are modeled by the loaded SVMs </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:218</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a7576925395947d63054db15b70beeaac"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a7576925395947d63054db15b70beeaac">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::feature_max</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; feature_max</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:170</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="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_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_ac909a523d5d9e9f376b54d30cf5657bb"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#ac909a523d5d9e9f376b54d30cf5657bb">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::class_models</a></div><div class="ttdeci">std::vector&lt; boost::shared_ptr&lt; SVMWrapper &gt; &gt; class_models</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:149</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_ab4f4b9381d8d1c6ede3ef66028cd6b42"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab4f4b9381d8d1c6ede3ef66028cd6b42">OpenMS::SvmTheoreticalSpectrumGenerator::precursor_charge_</a></div><div class="ttdeci">Size precursor_charge_</div><div class="ttdoc">charge of the precursors used for training </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:227</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet_html_a63885d5a4dcdd00de84eb173b534ca37"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#a63885d5a4dcdd00de84eb173b534ca37">OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet::descriptors</a></div><div class="ttdeci">DescriptorSetType descriptors</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_a442a4d1a69906395b7ac683b15344229"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a442a4d1a69906395b7ac683b15344229">OpenMS::SvmTheoreticalSpectrumGenerator::mp_</a></div><div class="ttdeci">SvmModelParameterSet mp_</div><div class="ttdoc">set of model parameters read from model file </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:230</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a84ba76357099f24c8699ac1b7438bbe6"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a84ba76357099f24c8699ac1b7438bbe6">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::intensity_bin_values</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; intensity_bin_values</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:185</div></div>
<div class="ttc" id="SVMWrapper_8h_html"><div class="ttname"><a href="SVMWrapper_8h.html">SVMWrapper.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_ae6c6c1213fef424b3e47b9f16e0afed1"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ae6c6c1213fef424b3e47b9f16e0afed1">OpenMS::SvmTheoreticalSpectrumGenerator::hide_type_</a></div><div class="ttdeci">std::map&lt; IonType, bool &gt; hide_type_</div><div class="ttdoc">whether ion types are hidden or not </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:245</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_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_ab829af012a40789aa761c1f1b2da5b33"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#ab829af012a40789aa761c1f1b2da5b33">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::number_intensity_levels</a></div><div class="ttdeci">Size number_intensity_levels</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:164</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_a8253a7962ca1c79b71e6af96589b7720"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a8253a7962ca1c79b71e6af96589b7720">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::charge</a></div><div class="ttdeci">Int charge</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:84</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_aaad2706cdbe5b8dcee737111988504b0"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#aaad2706cdbe5b8dcee737111988504b0">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::operator=</a></div><div class="ttdeci">IonType &amp; operator=(const IonType &amp;rhs)</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:113</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a390f6226cd88d5943f4a1aefc174ddc7"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a390f6226cd88d5943f4a1aefc174ddc7">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::conditional_prob</a></div><div class="ttdeci">std::map&lt; std::pair&lt; IonType, Size &gt;, std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &gt; conditional_prob</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:188</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_afec51891c0c625d786abaf92aa5756d0"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#afec51891c0c625d786abaf92aa5756d0">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::IonType</a></div><div class="ttdeci">IonType(Residue::ResidueType residue, EmpiricalFormula loss=EmpiricalFormula(), Int charge=1)</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:97</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType_html_a62ce8a924eb20bede64a656ed861d401"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#a62ce8a924eb20bede64a656ed861d401">OpenMS::SvmTheoreticalSpectrumGenerator::IonType::operator&lt;</a></div><div class="ttdeci">bool operator&lt;(const IonType &amp;rhs) const </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_aaf924b0e5c8dd84daeb1705aaf1d01bc"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#aaf924b0e5c8dd84daeb1705aaf1d01bc">OpenMS::SvmTheoreticalSpectrumGenerator::hydrophobicity_</a></div><div class="ttdeci">static std::map&lt; String, DoubleReal &gt; hydrophobicity_</div><div class="ttdoc">hydrophobicity values for each AA </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:236</div></div>
<div class="ttc" id="classOpenMS_1_1SvmTheoreticalSpectrumGenerator_html_a08803b692e19f653b8c0a1a62fcda611"><div class="ttname"><a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a08803b692e19f653b8c0a1a62fcda611">OpenMS::SvmTheoreticalSpectrumGenerator::helicity_</a></div><div class="ttdeci">static std::map&lt; String, DoubleReal &gt; helicity_</div><div class="ttdoc">helicity values for each AA </div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:239</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_af5d722ded8fabc9b2c92462509ce1d71"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#af5d722ded8fabc9b2c92462509ce1d71">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::ion_types</a></div><div class="ttdeci">std::vector&lt; IonType &gt; ion_types</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:158</div></div>
<div class="ttc" id="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet_html_a5483c133b5ddb9b0d783edcaadfb4dcb"><div class="ttname"><a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html#a5483c133b5ddb9b0d783edcaadfb4dcb">OpenMS::SvmTheoreticalSpectrumGenerator::SvmModelParameterSet::scaling_lower</a></div><div class="ttdeci">double scaling_lower</div><div class="ttdef"><b>Definition:</b> SvmTheoreticalSpectrumGenerator.h:176</div></div>
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