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<a href="CompNovoIdentificationBase_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>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<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: Andreas Bertsch $</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_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATIONBASE_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_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATIONBASE_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="comment">// OpenMS includes</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeptideIdentification_8h.html">OpenMS/METADATA/PeptideIdentification.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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.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="Map_8h.html">OpenMS/DATASTRUCTURES/Map.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ZhangSimilarityScore_8h.html">OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MassDecomposition_8h.html">OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h</a>&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MassDecompositionAlgorithm_8h.html">OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h</a>&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="CompNovoIonScoringBase_8h.html">OpenMS/ANALYSIS/DENOVO/CompNovoIonScoringBase.h</a>&gt;</span></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;<span class="comment">// stl includes</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;{</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html">   58</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> :</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;  {</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;    <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> &amp; source);</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a>();</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;    <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> &amp; source);</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> getIdentifications(std::vector&lt;PeptideIdentification&gt; &amp; ids, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">PeakMap</a> &amp; exp) = 0;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00087"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a7b7c9d2595dd3328e664293d3fec5ef9">   87</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">CompNovoIonScoringBase::IonScore</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    <span class="keywordtype">void</span> filterPermuts_(std::set&lt;String&gt; &amp; permut);</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    <span class="keywordtype">void</span> selectPivotIons_(std::vector&lt;Size&gt; &amp; pivots, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> left, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> right, <a class="code" href="classOpenMS_1_1Map.html">Map&lt;DoubleReal, IonScore&gt;</a> &amp; CID_nodes, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; CID_orig_spec, <a class="code" href="classdouble.html">DoubleReal</a> precursor_weight, <span class="keywordtype">bool</span> full_range = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;    <span class="keywordtype">void</span> filterDecomps_(std::vector&lt;MassDecomposition&gt; &amp; decomps);</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    <span class="keywordtype">void</span> getDecompositions_(std::vector&lt;MassDecomposition&gt; &amp; decomps, <a class="code" href="classdouble.html">DoubleReal</a> mass, <span class="keywordtype">bool</span> no_caching = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;    <span class="keywordtype">void</span> permute_(<a class="code" href="classOpenMS_1_1String.html">String</a> prefix, <a class="code" href="classOpenMS_1_1String.html">String</a> s, std::set&lt;String&gt; &amp; permutations);</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> countMissedCleavagesTryptic_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; peptide) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;    <span class="keywordtype">void</span> getCIDSpectrumLight_(<a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; sequence, <a class="code" href="classdouble.html">DoubleReal</a> prefix, <a class="code" href="classdouble.html">DoubleReal</a> suffix);</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    <span class="keywordtype">void</span> getCIDSpectrum_(<a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; spec, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; sequence, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> charge, <a class="code" href="classdouble.html">DoubleReal</a> prefix = 0.0, <a class="code" href="classdouble.html">DoubleReal</a> suffix = 0.0);</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;    <span class="keywordtype">void</span> initIsotopeDistributions_();</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> estimatePrecursorWeight_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; ETD_spec, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp; charge);</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;    <span class="keywordtype">void</span> windowMower_(<a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; spec, <a class="code" href="classdouble.html">DoubleReal</a> windowsize, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> no_peaks);</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> compareSpectra_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; s1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> &amp; s2);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> getModifiedAASequence_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; sequence);</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> getModifiedStringFromAASequence_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1AASequence.html">AASequence</a> &amp; sequence);</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#adc6ddd4883b749e4fc2cb7600c41103b">  136</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;char, const Residue *&gt;</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#adc6ddd4883b749e4fc2cb7600c41103b">name_to_residue_</a>;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#ab935c51dfc71c9f00e6bdd21a1932c6f">  139</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;const Residue *, char&gt;</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#ab935c51dfc71c9f00e6bdd21a1932c6f">residue_to_name_</a>;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a478012ec394ab8b0d4d4ea97ba16e37f">  142</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;Size, std::vector&lt;DoubleReal&gt;</a> &gt; <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a478012ec394ab8b0d4d4ea97ba16e37f">isotope_distributions_</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#aa8c6a0786e4331831d8e6f3729594207">  145</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;char, DoubleReal&gt;</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#aa8c6a0786e4331831d8e6f3729594207">aa_to_weight_</a>;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a43ef3d7b1af3fddb3c210d380b3e534f">  147</a></span>&#160;    <a class="code" href="classOpenMS_1_1MassDecompositionAlgorithm.html">MassDecompositionAlgorithm</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a43ef3d7b1af3fddb3c210d380b3e534f">mass_decomp_algorithm_</a>;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#abb2ee242a9ea3383ede3b04f3c581e5c">  149</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#abb2ee242a9ea3383ede3b04f3c581e5c">min_aa_weight_</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#acbe94f316242ea59d88b8a42421f0a8f">  151</a></span>&#160;    <a class="code" href="classOpenMS_1_1ZhangSimilarityScore.html">ZhangSimilarityScore</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#acbe94f316242ea59d88b8a42421f0a8f">zhang_</a>;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;</div>
<div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#aa34c4934ed81b76bd18a61b2ae05a008">  153</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;Size, Map&lt;Size, std::set&lt;String&gt;</a> &gt; &gt; <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#aa34c4934ed81b76bd18a61b2ae05a008">subspec_to_sequences_</a>;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;</div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a185649daf5577a9a653481339ad31050">  155</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a185649daf5577a9a653481339ad31050">max_number_aa_per_decomp_</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a269e179e59449e35188ff860d9b17cc2">  157</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a269e179e59449e35188ff860d9b17cc2">tryptic_only_</a>;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a03d038e2ce9f971ebd73bcb86f417dc8">  159</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a03d038e2ce9f971ebd73bcb86f417dc8">fragment_mass_tolerance_</a>;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a56e61563cf61e1757a66f9575e2b0ff9">  161</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a56e61563cf61e1757a66f9575e2b0ff9">max_number_pivot_</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a13a6f47c92acba9ea98495e4fb4c4830">  163</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a13a6f47c92acba9ea98495e4fb4c4830">decomp_weights_precision_</a>;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;</div>
<div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#af94fd718c0472e5e3ed00fb040ee5b83">  165</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#af94fd718c0472e5e3ed00fb040ee5b83">max_mz_</a>;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00167"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#ac01809ade272d4adc00e2d22fd6a9070">  167</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#ac01809ade272d4adc00e2d22fd6a9070">min_mz_</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a2970ec507616bc85b77e16693874ea3a">  169</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a2970ec507616bc85b77e16693874ea3a">max_decomp_weight_</a>;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a9f258945e665b399255257e2011b9da2">  171</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a9f258945e665b399255257e2011b9da2">max_subscore_number_</a>;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a134a7298252b07d758400714f8d0fb32">  173</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a134a7298252b07d758400714f8d0fb32">max_isotope_</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a899270a4fe96f27b6955a953491b3b5c">  175</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;DoubleReal, std::vector&lt;MassDecomposition&gt;</a> &gt; <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a899270a4fe96f27b6955a953491b3b5c">decomp_cache_</a>;</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;</div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase.html#a9f3b121bc4966a49c6e36572f4f2ae9b">  177</a></span>&#160;    <a class="code" href="classOpenMS_1_1Map.html">Map&lt;String, std::set&lt;String&gt;</a> &gt; <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase.html#a9f3b121bc4966a49c6e36572f4f2ae9b">permute_cache_</a>;</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;</div>
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">  186</a></span>&#160;    <span class="keyword">class </span><a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">Permut</a></div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;    {</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;<span class="keyword">private</span>:</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#ad8e8227baac7ad39c8691a1065bfe25a">  190</a></span>&#160;      <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#ad8e8227baac7ad39c8691a1065bfe25a">Permut</a>() :</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;        score_(0)</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;      {</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;      }</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a89a85742d682ca8981a5e593eb83a236">  197</a></span>&#160;      <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a89a85742d682ca8981a5e593eb83a236">Permut</a>(<span class="keyword">const</span> std::set&lt;String&gt;::const_iterator &amp; permut, <a class="code" href="classdouble.html">DoubleReal</a> s) :</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;        permut_(permut),</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;        score_(s)</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;      {</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;      }</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;</div>
<div class="line"><a name="l00203"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#aaeebdb6cb032b8b1f20ee286fca925c3">  203</a></span>&#160;      <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#aaeebdb6cb032b8b1f20ee286fca925c3">Permut</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">Permut</a> &amp; rhs) :</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;        permut_(rhs.permut_),</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;        score_(rhs.score_)</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;      {</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;      }</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;</div>
<div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a882e900918bce595fc453d97dd126e95">  209</a></span>&#160;      <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a882e900918bce595fc453d97dd126e95">~Permut</a>()</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;      {</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;      }</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;</div>
<div class="line"><a name="l00213"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a0c48921f3cbfb9061bd1181de0c798fb">  213</a></span>&#160;      <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">Permut</a> &amp; <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a0c48921f3cbfb9061bd1181de0c798fb">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">Permut</a> &amp; rhs)</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      {</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;        <span class="keywordflow">if</span> (&amp;rhs != <span class="keyword">this</span>)</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;        {</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;          permut_ = rhs.<a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#abab6ee264843d8d40e1ee5463b327a91">permut_</a>;</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;          score_ = rhs.<a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a86eb7a5fef1847e4651de4491b9a361d">score_</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> *<span class="keyword">this</span>;</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"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a2e90063f2009e879cd980fedb5d11dac">  223</a></span>&#160;      <span class="keyword">const</span> std::set&lt;String&gt;::const_iterator &amp; <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a2e90063f2009e879cd980fedb5d11dac">getPermut</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;        <span class="keywordflow">return</span> permut_;</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;      }</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;</div>
<div class="line"><a name="l00228"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#aaa402ac745c7c5354890e7b26cd5c4b6">  228</a></span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#aaa402ac745c7c5354890e7b26cd5c4b6">setPermut</a>(<span class="keyword">const</span> std::set&lt;String&gt;::const_iterator &amp; it)</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;      {</div>
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<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;      }</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div>
<div class="line"><a name="l00233"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#acb78adb3e494a969c6c56c3a9071705d">  233</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#acb78adb3e494a969c6c56c3a9071705d">getScore</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;<span class="keyword">      </span>{</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;        <span class="keywordflow">return</span> score_;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;      }</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;</div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a2e9b7c12f6d8fa7415aa0aca69208f42">  238</a></span>&#160;      <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a2e9b7c12f6d8fa7415aa0aca69208f42">setScore</a>(<a class="code" href="classdouble.html">DoubleReal</a> score)</div>
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<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;        score_ = score;</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;      }</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#abab6ee264843d8d40e1ee5463b327a91">  245</a></span>&#160;      std::set&lt;String&gt;::const_iterator <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#abab6ee264843d8d40e1ee5463b327a91">permut_</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno"><a class="line" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a86eb7a5fef1847e4651de4491b9a361d">  246</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a86eb7a5fef1847e4651de4491b9a361d">score_</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    };</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;  };</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="namespaceOpenMS_1_1Internal.html">  251</a></span>&#160;  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;  {</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenMS_1_1Internal.html#a6193961c4f72625df769be5d1cfd24fd">PermutScoreComparator</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">CompNovoIdentificationBase::Permut</a> &amp; p1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">CompNovoIdentificationBase::Permut</a> &amp; p2);</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;  }</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;}</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_acb78adb3e494a969c6c56c3a9071705d"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#acb78adb3e494a969c6c56c3a9071705d">OpenMS::CompNovoIdentificationBase::Permut::getScore</a></div><div class="ttdeci">DoubleReal getScore() const </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:233</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_1CompNovoIdentificationBase_1_1Permut_html_abab6ee264843d8d40e1ee5463b327a91"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#abab6ee264843d8d40e1ee5463b327a91">OpenMS::CompNovoIdentificationBase::Permut::permut_</a></div><div class="ttdeci">std::set&lt; String &gt;::const_iterator permut_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_adc6ddd4883b749e4fc2cb7600c41103b"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#adc6ddd4883b749e4fc2cb7600c41103b">OpenMS::CompNovoIdentificationBase::name_to_residue_</a></div><div class="ttdeci">Map&lt; char, const Residue * &gt; name_to_residue_</div><div class="ttdoc">mapping for the internal representation character to the actual residue </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:136</div></div>
<div class="ttc" id="CompNovoIonScoringBase_8h_html"><div class="ttname"><a href="CompNovoIonScoringBase_8h.html">CompNovoIonScoringBase.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_ab935c51dfc71c9f00e6bdd21a1932c6f"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#ab935c51dfc71c9f00e6bdd21a1932c6f">OpenMS::CompNovoIdentificationBase::residue_to_name_</a></div><div class="ttdeci">Map&lt; const Residue *, char &gt; residue_to_name_</div><div class="ttdoc">mapping of the actual residue to the internal representing character </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:139</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_aaeebdb6cb032b8b1f20ee286fca925c3"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#aaeebdb6cb032b8b1f20ee286fca925c3">OpenMS::CompNovoIdentificationBase::Permut::Permut</a></div><div class="ttdeci">Permut(const Permut &amp;rhs)</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:203</div></div>
<div class="ttc" id="MassDecomposition_8h_html"><div class="ttname"><a href="MassDecomposition_8h.html">MassDecomposition.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_a2e90063f2009e879cd980fedb5d11dac"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a2e90063f2009e879cd980fedb5d11dac">OpenMS::CompNovoIdentificationBase::Permut::getPermut</a></div><div class="ttdeci">const std::set&lt; String &gt;::const_iterator &amp; getPermut() const </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:223</div></div>
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<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="classOpenMS_1_1CompNovoIdentificationBase_html_af94fd718c0472e5e3ed00fb040ee5b83"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#af94fd718c0472e5e3ed00fb040ee5b83">OpenMS::CompNovoIdentificationBase::max_mz_</a></div><div class="ttdeci">DoubleReal max_mz_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:165</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_1CompNovoIdentificationBase_html_a134a7298252b07d758400714f8d0fb32"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a134a7298252b07d758400714f8d0fb32">OpenMS::CompNovoIdentificationBase::max_isotope_</a></div><div class="ttdeci">Size max_isotope_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:173</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a13a6f47c92acba9ea98495e4fb4c4830"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a13a6f47c92acba9ea98495e4fb4c4830">OpenMS::CompNovoIdentificationBase::decomp_weights_precision_</a></div><div class="ttdeci">DoubleReal decomp_weights_precision_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:163</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_a86eb7a5fef1847e4651de4491b9a361d"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a86eb7a5fef1847e4651de4491b9a361d">OpenMS::CompNovoIdentificationBase::Permut::score_</a></div><div class="ttdeci">DoubleReal score_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:246</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a7b7c9d2595dd3328e664293d3fec5ef9"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a7b7c9d2595dd3328e664293d3fec5ef9">OpenMS::CompNovoIdentificationBase::IonScore</a></div><div class="ttdeci">CompNovoIonScoringBase::IonScore IonScore</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:87</div></div>
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<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a2970ec507616bc85b77e16693874ea3a"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a2970ec507616bc85b77e16693874ea3a">OpenMS::CompNovoIdentificationBase::max_decomp_weight_</a></div><div class="ttdeci">DoubleReal max_decomp_weight_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:169</div></div>
<div class="ttc" id="classOpenMS_1_1ZhangSimilarityScore_html"><div class="ttname"><a href="classOpenMS_1_1ZhangSimilarityScore.html">OpenMS::ZhangSimilarityScore</a></div><div class="ttdoc">Similarity score of Zhang. </div><div class="ttdef"><b>Definition:</b> ZhangSimilarityScore.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_acbe94f316242ea59d88b8a42421f0a8f"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#acbe94f316242ea59d88b8a42421f0a8f">OpenMS::CompNovoIdentificationBase::zhang_</a></div><div class="ttdeci">ZhangSimilarityScore zhang_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:151</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Internal_html_a6193961c4f72625df769be5d1cfd24fd"><div class="ttname"><a href="namespaceOpenMS_1_1Internal.html#a6193961c4f72625df769be5d1cfd24fd">OpenMS::Internal::PermutScoreComparator</a></div><div class="ttdeci">bool PermutScoreComparator(const CompNovoIdentificationBase::Permut &amp;p1, const CompNovoIdentificationBase::Permut &amp;p2)</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_ac01809ade272d4adc00e2d22fd6a9070"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#ac01809ade272d4adc00e2d22fd6a9070">OpenMS::CompNovoIdentificationBase::min_mz_</a></div><div class="ttdeci">DoubleReal min_mz_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:167</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_a882e900918bce595fc453d97dd126e95"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a882e900918bce595fc453d97dd126e95">OpenMS::CompNovoIdentificationBase::Permut::~Permut</a></div><div class="ttdeci">virtual ~Permut()</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:209</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_a89a85742d682ca8981a5e593eb83a236"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a89a85742d682ca8981a5e593eb83a236">OpenMS::CompNovoIdentificationBase::Permut::Permut</a></div><div class="ttdeci">Permut(const std::set&lt; String &gt;::const_iterator &amp;permut, DoubleReal s)</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_aa8c6a0786e4331831d8e6f3729594207"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#aa8c6a0786e4331831d8e6f3729594207">OpenMS::CompNovoIdentificationBase::aa_to_weight_</a></div><div class="ttdeci">Map&lt; char, DoubleReal &gt; aa_to_weight_</div><div class="ttdoc">masses of the amino acids </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:145</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a478012ec394ab8b0d4d4ea97ba16e37f"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a478012ec394ab8b0d4d4ea97ba16e37f">OpenMS::CompNovoIdentificationBase::isotope_distributions_</a></div><div class="ttdeci">Map&lt; Size, std::vector&lt; DoubleReal &gt; &gt; isotope_distributions_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:142</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a185649daf5577a9a653481339ad31050"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a185649daf5577a9a653481339ad31050">OpenMS::CompNovoIdentificationBase::max_number_aa_per_decomp_</a></div><div class="ttdeci">Size max_number_aa_per_decomp_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_a0c48921f3cbfb9061bd1181de0c798fb"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a0c48921f3cbfb9061bd1181de0c798fb">OpenMS::CompNovoIdentificationBase::Permut::operator=</a></div><div class="ttdeci">Permut &amp; operator=(const Permut &amp;rhs)</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:213</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a56e61563cf61e1757a66f9575e2b0ff9"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a56e61563cf61e1757a66f9575e2b0ff9">OpenMS::CompNovoIdentificationBase::max_number_pivot_</a></div><div class="ttdeci">Size max_number_pivot_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:161</div></div>
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<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_aaa402ac745c7c5354890e7b26cd5c4b6"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#aaa402ac745c7c5354890e7b26cd5c4b6">OpenMS::CompNovoIdentificationBase::Permut::setPermut</a></div><div class="ttdeci">void setPermut(const std::set&lt; String &gt;::const_iterator &amp;it)</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:228</div></div>
<div class="ttc" id="PeptideIdentification_8h_html"><div class="ttname"><a href="PeptideIdentification_8h.html">PeptideIdentification.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html">OpenMS::CompNovoIdentificationBase</a></div><div class="ttdoc">run with CompNovoIdentificationBase </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:58</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="classOpenMS_1_1CompNovoIdentificationBase_html_aa34c4934ed81b76bd18a61b2ae05a008"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#aa34c4934ed81b76bd18a61b2ae05a008">OpenMS::CompNovoIdentificationBase::subspec_to_sequences_</a></div><div class="ttdeci">Map&lt; Size, Map&lt; Size, std::set&lt; String &gt; &gt; &gt; subspec_to_sequences_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:153</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a9f3b121bc4966a49c6e36572f4f2ae9b"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a9f3b121bc4966a49c6e36572f4f2ae9b">OpenMS::CompNovoIdentificationBase::permute_cache_</a></div><div class="ttdeci">Map&lt; String, std::set&lt; String &gt; &gt; permute_cache_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:177</div></div>
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<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a43ef3d7b1af3fddb3c210d380b3e534f"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a43ef3d7b1af3fddb3c210d380b3e534f">OpenMS::CompNovoIdentificationBase::mass_decomp_algorithm_</a></div><div class="ttdeci">MassDecompositionAlgorithm mass_decomp_algorithm_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:147</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_1CompNovoIdentificationBase_html_a899270a4fe96f27b6955a953491b3b5c"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a899270a4fe96f27b6955a953491b3b5c">OpenMS::CompNovoIdentificationBase::decomp_cache_</a></div><div class="ttdeci">Map&lt; DoubleReal, std::vector&lt; MassDecomposition &gt; &gt; decomp_cache_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:175</div></div>
<div class="ttc" id="classOpenMS_1_1MassDecompositionAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1MassDecompositionAlgorithm.html">OpenMS::MassDecompositionAlgorithm</a></div><div class="ttdoc">Mass decomposition algorithm, given a mass it suggests possible compositions. </div><div class="ttdef"><b>Definition:</b> MassDecompositionAlgorithm.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a9f258945e665b399255257e2011b9da2"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a9f258945e665b399255257e2011b9da2">OpenMS::CompNovoIdentificationBase::max_subscore_number_</a></div><div class="ttdeci">Size max_subscore_number_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:171</div></div>
<div class="ttc" id="ZhangSimilarityScore_8h_html"><div class="ttname"><a href="ZhangSimilarityScore_8h.html">ZhangSimilarityScore.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">OpenMS::CompNovoIdentificationBase::Permut</a></div><div class="ttdoc">Simple class to store permutations and a score. </div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:186</div></div>
<div class="ttc" id="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore_html"><div class="ttname"><a href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">OpenMS::CompNovoIonScoringBase::IonScore</a></div><div class="ttdef"><b>Definition:</b> CompNovoIonScoringBase.h:66</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_1CompNovoIdentificationBase_1_1Permut_html_a2e9b7c12f6d8fa7415aa0aca69208f42"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#a2e9b7c12f6d8fa7415aa0aca69208f42">OpenMS::CompNovoIdentificationBase::Permut::setScore</a></div><div class="ttdeci">void setScore(DoubleReal score)</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:238</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a269e179e59449e35188ff860d9b17cc2"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a269e179e59449e35188ff860d9b17cc2">OpenMS::CompNovoIdentificationBase::tryptic_only_</a></div><div class="ttdeci">bool tryptic_only_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut_html_ad8e8227baac7ad39c8691a1065bfe25a"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html#ad8e8227baac7ad39c8691a1065bfe25a">OpenMS::CompNovoIdentificationBase::Permut::Permut</a></div><div class="ttdeci">Permut()</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_a03d038e2ce9f971ebd73bcb86f417dc8"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#a03d038e2ce9f971ebd73bcb86f417dc8">OpenMS::CompNovoIdentificationBase::fragment_mass_tolerance_</a></div><div class="ttdeci">DoubleReal fragment_mass_tolerance_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:159</div></div>
<div class="ttc" id="classOpenMS_1_1CompNovoIdentificationBase_html_abb2ee242a9ea3383ede3b04f3c581e5c"><div class="ttname"><a href="classOpenMS_1_1CompNovoIdentificationBase.html#abb2ee242a9ea3383ede3b04f3c581e5c">OpenMS::CompNovoIdentificationBase::min_aa_weight_</a></div><div class="ttdeci">DoubleReal min_aa_weight_</div><div class="ttdef"><b>Definition:</b> CompNovoIdentificationBase.h:149</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 11:19:12 using doxygen 1.8.5</font></TD>
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