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<a href="EmgScoring_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>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
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<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hannes Roest $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Hannes Roest $</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;<span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGSCORING_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGSCORING_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;boost/math/special_functions/fpclassify.hpp&gt;</span> <span class="comment">// for isnan</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="EmgFitter1D_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgFitter1D.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="EmgModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgModel.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="GaussFilter_8h.html">OpenMS/FILTERING/SMOOTHING/GaussFilter.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MRMFeature_8h.html">OpenMS/KERNEL/MRMFeature.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="MRMTransitionGroup_8h.html">OpenMS/KERNEL/MRMTransitionGroup.h</a>&gt;</span></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;<span class="preprocessor">#include &lt;<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>&gt;</span></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;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;{</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html">   60</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1EmgScoring.html">EmgScoring</a></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;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;  <span class="keyword">public</span> :</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#a4f0f27fd34b37c2dc3c7d3899bfc5416">   65</a></span>&#160;    <a class="code" href="classOpenMS_1_1EmgScoring.html#a4f0f27fd34b37c2dc3c7d3899bfc5416">EmgScoring</a>() { }</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#ad49694f2bdd78da9094a2b462f2f4c04">   67</a></span>&#160;    <a class="code" href="classOpenMS_1_1EmgScoring.html#ad49694f2bdd78da9094a2b462f2f4c04">~EmgScoring</a>() { }</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#ad60792208a31598df5aed3dad7aff339">   69</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1EmgScoring.html#ad60792208a31598df5aed3dad7aff339">setFitterParam</a>(<a class="code" href="classOpenMS_1_1Param.html">Param</a> param)</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    {</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;      <a class="code" href="classOpenMS_1_1EmgScoring.html#a59563b21cd93a3acf9a2bb89d6a3cfec">fitter_emg1D_</a>.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param);</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    }</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#a8dad78b01108d834ef591c7aae60a0d1">   74</a></span>&#160;    <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1EmgScoring.html#a8dad78b01108d834ef591c7aae60a0d1">getDefaults</a>()</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    {</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;      <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1EmgScoring.html#a59563b21cd93a3acf9a2bb89d6a3cfec">fitter_emg1D_</a>.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a>();</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    }</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">typename</span> SpectrumType, <span class="keyword">class</span> TransitionT&gt;</div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#a91a12a6c61f55d0f433b2630f1d0fd9a">   81</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1EmgScoring.html#a91a12a6c61f55d0f433b2630f1d0fd9a">calcElutionFitScore</a>(<a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> &amp; mrmfeature, <a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup&lt;SpectrumType, TransitionT&gt;</a> &amp; transition_group)</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    {</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      std::vector&lt;double&gt; fit_scores;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="keywordtype">double</span> avg_score = 0;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      <span class="keywordtype">bool</span> smooth_data = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> &lt; transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</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="comment">// get the id, then find the corresponding transition and features within this peakgroup</span></div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        <a class="code" href="classOpenMS_1_1String.html">String</a> native_id = transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">getChromatograms</a>()[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getNativeID();</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;        <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f = mrmfeature.<a class="code" href="classOpenMS_1_1MRMFeature.html#abdc83f9e7b377996d3508325f2239db0">getFeature</a>(native_id);</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        <a class="code" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>(f.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().size() == 1, <span class="stringliteral">&quot;Convex hulls need to have exactly one hull point structure&quot;</span>);</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;        <span class="comment">// TODO what if score is -1 ?? e.g. if it is undefined</span></div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        <span class="keywordtype">double</span> fscore = <a class="code" href="classOpenMS_1_1EmgScoring.html#a42879f0a3b43a93723909ec94e135e2e">elutionModelFit</a>(f.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>()[0].getHullPoints(), smooth_data);</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;        fit_scores.push_back(fscore);</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;        avg_score += fscore;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      }</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      avg_score /= transition_group.<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>();</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;      <span class="keywordflow">return</span> avg_score;</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">// Fxn from FeatureFinderAlgorithmMRM</span></div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="comment">// TODO: check whether we can leave out some of the steps here, e.g. gaussian smoothing</span></div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#a42879f0a3b43a93723909ec94e135e2e">  106</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1EmgScoring.html#a42879f0a3b43a93723909ec94e135e2e">elutionModelFit</a>(<a class="code" href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">ConvexHull2D::PointArrayType</a> current_section, <span class="keywordtype">bool</span> smooth_data)</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;    {</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;      <span class="comment">// We need at least 2 datapoints in order to create a fit</span></div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      <span class="keywordflow">if</span> (current_section.size() &lt; 2)</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;        <span class="keywordflow">return</span> -1;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      }</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      <span class="comment">// local PeakType is a small hack since here we *need* data of type</span></div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      <span class="comment">// Peak1D, otherwise our fitter will not accept it.</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> LocalPeakType;</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;      <span class="comment">// -- cut line 301 of FeatureFinderAlgorithmMRM</span></div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;      std::vector&lt;LocalPeakType&gt; data_to_fit;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;      <a class="code" href="classOpenMS_1_1EmgScoring.html#a38a8356e73763a34e70aa5fad809eba0">prepareFit_</a>(current_section, data_to_fit, smooth_data);</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * model_rt = 0;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> quality = <a class="code" href="classOpenMS_1_1EmgScoring.html#aee04cc30033052b32c9c91fb9e3aeb4d">fitRT_</a>(data_to_fit, model_rt);</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;      <span class="comment">// cut line 354 of FeatureFinderAlgorithmMRM</span></div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      <span class="keyword">delete</span> model_rt;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;      <span class="keywordflow">return</span> quality;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    }</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;  <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> LocalPeakType&gt;</div>
<div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#aee04cc30033052b32c9c91fb9e3aeb4d">  133</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1EmgScoring.html#aee04cc30033052b32c9c91fb9e3aeb4d">fitRT_</a>(std::vector&lt;LocalPeakType&gt; &amp; rt_input_data, <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * &amp; model)</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;    {</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> quality;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      <span class="comment">//Param param;</span></div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;      <span class="comment">/*EmgFitter</span></div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;<span class="comment">       param.setValue( &quot;tolerance_stdev_bounding_box&quot;, tolerance_stdev_box_);</span></div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;<span class="comment">       param.setValue( &quot;statistics:mean&quot;, rt_stat_.mean() );</span></div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;<span class="comment">       param.setValue( &quot;statistics:variance&quot;, rt_stat_.variance() );</span></div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;<span class="comment">       param.setValue( &quot;interpolation_step&quot;, interpolation_step_rt_ );</span></div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;<span class="comment">       param.setValue( &quot;max_iteration&quot;, max_iteration_);</span></div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;<span class="comment">       param.setValue( &quot;deltaAbsError&quot;, deltaAbsError_);</span></div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;<span class="comment">       param.setValue( &quot;deltaRelError&quot;, deltaRelError_);</span></div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;<span class="comment">       */</span></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">// Set parameter for fitter</span></div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;      <span class="comment">//fitter_emg1D.setParameters(param);</span></div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;      <span class="comment">// Construct model for rt</span></div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      quality = <a class="code" href="classOpenMS_1_1EmgScoring.html#a59563b21cd93a3acf9a2bb89d6a3cfec">fitter_emg1D_</a>.<a class="code" href="classOpenMS_1_1EmgFitter1D.html#a250458ea3a48557d8a6ccaa2df1ee1ec">fit1d</a>(rt_input_data, model);</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">  153</span>&#160;      <span class="comment">// Check quality</span></div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      <span class="keywordflow">if</span> (boost::math::isnan(quality)) quality = -1.0;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;      <span class="keywordflow">return</span> quality;</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;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;    <span class="comment">// Fxn from FeatureFinderAlgorithmMRM</span></div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    <span class="comment">// TODO: check whether we can leave out some of the steps here, e.g. gaussian smoothing</span></div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> LocalPeakType&gt;</div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="classOpenMS_1_1EmgScoring.html#a38a8356e73763a34e70aa5fad809eba0">  161</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1EmgScoring.html#a38a8356e73763a34e70aa5fad809eba0">prepareFit_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">ConvexHull2D::PointArrayType</a> &amp; current_section, std::vector&lt;LocalPeakType&gt; &amp; data_to_fit, <span class="keywordtype">bool</span> smooth_data)</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">// typedef Peak1D LocalPeakType;</span></div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;      <a class="code" href="classOpenMS_1_1MSSpectrum.html">PeakSpectrum</a> filter_spec;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      <span class="comment">// first smooth the data to prevent outliers from destroying the fit</span></div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;      <span class="keywordflow">for</span> (ConvexHull2D::PointArrayType::const_iterator it = current_section.begin(); it != current_section.end(); it++)</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      {</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;        LocalPeakType p;</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;        p.setMZ(it-&gt;getX());</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        p.setIntensity(it-&gt;getY());</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;        filter_spec.push_back(p);</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">  173</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;      <span class="comment">// add two peaks at the beginning and at the end for better fit</span></div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;      <span class="comment">// therefore calculate average distance first</span></div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;      std::vector&lt;DoubleReal&gt; distances;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 1; j &lt; filter_spec.size(); ++j)</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;        distances.push_back(filter_spec[j].getMZ() - filter_spec[j - 1].getMZ());</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;      <a class="code" href="classdouble.html">DoubleReal</a> dist_average = std::accumulate(distances.begin(), distances.end(), 0.0) / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>) distances.size();</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;      <span class="comment">// append peaks</span></div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      <a class="code" href="classOpenMS_1_1Peak1D.html">Peak1D</a> new_peak;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0);</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.back().getMZ() + dist_average);</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      filter_spec.push_back(new_peak);</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.back().getMZ() + dist_average);</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      filter_spec.push_back(new_peak);</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.back().getMZ() + dist_average);</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;      filter_spec.push_back(new_peak);</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;      <span class="comment">// prepend peaks</span></div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.front().getMZ() - dist_average);</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      filter_spec.insert(filter_spec.begin(), new_peak);</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.front().getMZ() - dist_average);</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;      filter_spec.insert(filter_spec.begin(), new_peak);</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;      new_peak.<a class="code" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">setMZ</a>(filter_spec.front().getMZ() - dist_average);</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;      filter_spec.insert(filter_spec.begin(), new_peak);</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;      <span class="comment">// To get an estimate of the peak quality, we probably should not smooth</span></div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;      <span class="comment">// and/or transform the data.</span></div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;      <span class="keywordflow">if</span> (smooth_data)</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;        <a class="code" href="classOpenMS_1_1GaussFilter.html">GaussFilter</a> filter;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;        <a class="code" href="classOpenMS_1_1Param.html">Param</a> filter_param(filter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a>());</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;        filter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(filter_param);</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        filter_param.setValue(<span class="stringliteral">&quot;gaussian_width&quot;</span>, 4 * dist_average);</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;        filter.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(filter_param);</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;        filter.<a class="code" href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">filter</a>(filter_spec);</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">  213</span>&#160;      <span class="comment">// transform the data for fitting and fit RT profile</span></div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j != filter_spec.size(); ++j)</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;      {</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;        LocalPeakType p;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;        p.setPosition(filter_spec[j].getMZ());</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;        p.setIntensity(filter_spec[j].getIntensity());</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        data_to_fit.push_back(p);</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      }</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_1EmgScoring.html#a59563b21cd93a3acf9a2bb89d6a3cfec">  223</a></span>&#160;    <a class="code" href="classOpenMS_1_1EmgFitter1D.html">EmgFitter1D</a> <a class="code" href="classOpenMS_1_1EmgScoring.html#a59563b21cd93a3acf9a2bb89d6a3cfec">fitter_emg1D_</a>;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;  };</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;}</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;<span class="preprocessor">#endif </span><span class="comment">/* EMGSCORING_H_ */</span><span class="preprocessor"></span></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a93a8dc068053ec44ee7e45864ef969f7"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a></div><div class="ttdeci">const double k</div></div>
<div class="ttc" id="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a02f02fa9832ca3e8d47c575a39803a2a"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">OpenMS::DefaultParamHandler::getDefaults</a></div><div class="ttdeci">const Param &amp; getDefaults() const </div><div class="ttdoc">Non-mutable access to the default parameters. </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="MRMFeature_8h_html"><div class="ttname"><a href="MRMFeature_8h.html">MRMFeature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MRMTransitionGroup::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html">OpenMS::EmgScoring</a></div><div class="ttdoc">Scoring of an elution peak using an exponentially modified gaussian distribution model. </div><div class="ttdef"><b>Definition:</b> EmgScoring.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html_a84fbe2b625d0885f5e93397ed2122202"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">OpenMS::MRMTransitionGroup::getChromatograms</a></div><div class="ttdeci">const std::vector&lt; SpectrumType &gt; &amp; getChromatograms() const </div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:148</div></div>
<div class="ttc" id="group__Conditions_html_ga45a74ea28109e7e1ed992fbd2ee97778"><div class="ttname"><a href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a></div><div class="ttdeci">#define OPENMS_PRECONDITION(condition, message)</div><div class="ttdoc">Precondition macro. </div><div class="ttdef"><b>Definition:</b> Macros.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html_abdcce0f11b8d73a2b4da5b1a00457d7b"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#abdcce0f11b8d73a2b4da5b1a00457d7b">OpenMS::ConvexHull2D::PointArrayType</a></div><div class="ttdeci">std::vector&lt; PointType &gt; PointArrayType</div><div class="ttdef"><b>Definition:</b> ConvexHull2D.h:79</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_a59563b21cd93a3acf9a2bb89d6a3cfec"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#a59563b21cd93a3acf9a2bb89d6a3cfec">OpenMS::EmgScoring::fitter_emg1D_</a></div><div class="ttdeci">EmgFitter1D fitter_emg1D_</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:223</div></div>
<div class="ttc" id="classOpenMS_1_1EmgFitter1D_html"><div class="ttname"><a href="classOpenMS_1_1EmgFitter1D.html">OpenMS::EmgFitter1D</a></div><div class="ttdoc">Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL...</div><div class="ttdef"><b>Definition:</b> EmgFitter1D.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1EmgFitter1D_html_a250458ea3a48557d8a6ccaa2df1ee1ec"><div class="ttname"><a href="classOpenMS_1_1EmgFitter1D.html#a250458ea3a48557d8a6ccaa2df1ee1ec">OpenMS::EmgFitter1D::fit1d</a></div><div class="ttdeci">QualityType fit1d(const RawDataArrayType &amp;range, InterpolationModel *&amp;model)</div><div class="ttdoc">return interpolation model </div></div>
<div class="ttc" id="GaussFilter_8h_html"><div class="ttname"><a href="GaussFilter_8h.html">GaussFilter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab9c4ce5d172a75d6de2c6f5f1847c9ab"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">OpenMS::Peak1D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType mz)</div><div class="ttdoc">Mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak1D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak1D.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &amp;param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html">OpenMS::MRMTransitionGroup</a></div><div class="ttdoc">The representation of a transition group that has information about the individual chromatograms as w...</div><div class="ttdef"><b>Definition:</b> MRMTransitionGroup.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1InterpolationModel_html"><div class="ttname"><a href="classOpenMS_1_1InterpolationModel.html">OpenMS::InterpolationModel</a></div><div class="ttdoc">Abstract class for 1D-models that are approximated using linear interpolation. </div><div class="ttdef"><b>Definition:</b> InterpolationModel.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; Peak1D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ad99bb8ba2103d6c52ee10ae6369b46e7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">OpenMS::Feature::getConvexHulls</a></div><div class="ttdeci">const std::vector&lt; ConvexHull2D &gt; &amp; getConvexHulls() const </div><div class="ttdoc">Non-mutable access to the convex hulls. </div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html">OpenMS::Peak1D</a></div><div class="ttdoc">A 1-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_ad60792208a31598df5aed3dad7aff339"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#ad60792208a31598df5aed3dad7aff339">OpenMS::EmgScoring::setFitterParam</a></div><div class="ttdeci">void setFitterParam(Param param)</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:69</div></div>
<div class="ttc" id="MRMTransitionGroup_8h_html"><div class="ttname"><a href="MRMTransitionGroup_8h.html">MRMTransitionGroup.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_ad49694f2bdd78da9094a2b462f2f4c04"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#ad49694f2bdd78da9094a2b462f2f4c04">OpenMS::EmgScoring::~EmgScoring</a></div><div class="ttdeci">~EmgScoring()</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_a42879f0a3b43a93723909ec94e135e2e"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#a42879f0a3b43a93723909ec94e135e2e">OpenMS::EmgScoring::elutionModelFit</a></div><div class="ttdeci">double elutionModelFit(ConvexHull2D::PointArrayType current_section, bool smooth_data)</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="EmgFitter1D_8h_html"><div class="ttname"><a href="EmgFitter1D_8h.html">EmgFitter1D.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html">OpenMS::GaussFilter</a></div><div class="ttdoc">This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...</div><div class="ttdef"><b>Definition:</b> GaussFilter.h:73</div></div>
<div class="ttc" id="EmgModel_8h_html"><div class="ttname"><a href="EmgModel_8h.html">EmgModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeature_html_abdc83f9e7b377996d3508325f2239db0"><div class="ttname"><a href="classOpenMS_1_1MRMFeature.html#abdc83f9e7b377996d3508325f2239db0">OpenMS::MRMFeature::getFeature</a></div><div class="ttdeci">Feature &amp; getFeature(String key)</div><div class="ttdoc">get a specified feature </div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_a91a12a6c61f55d0f433b2630f1d0fd9a"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#a91a12a6c61f55d0f433b2630f1d0fd9a">OpenMS::EmgScoring::calcElutionFitScore</a></div><div class="ttdeci">double calcElutionFitScore(MRMFeature &amp;mrmfeature, MRMTransitionGroup&lt; SpectrumType, TransitionT &gt; &amp;transition_group)</div><div class="ttdoc">calculate the elution profile fit score </div><div class="ttdef"><b>Definition:</b> EmgScoring.h:81</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_1EmgScoring_html_a38a8356e73763a34e70aa5fad809eba0"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#a38a8356e73763a34e70aa5fad809eba0">OpenMS::EmgScoring::prepareFit_</a></div><div class="ttdeci">void prepareFit_(const ConvexHull2D::PointArrayType &amp;current_section, std::vector&lt; LocalPeakType &gt; &amp;data_to_fit, bool smooth_data)</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:161</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_a4f0f27fd34b37c2dc3c7d3899bfc5416"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#a4f0f27fd34b37c2dc3c7d3899bfc5416">OpenMS::EmgScoring::EmgScoring</a></div><div class="ttdeci">EmgScoring()</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeature_html"><div class="ttname"><a href="classOpenMS_1_1MRMFeature.html">OpenMS::MRMFeature</a></div><div class="ttdoc">A multi-chromatogram MRM feature. </div><div class="ttdef"><b>Definition:</b> MRMFeature.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_a8dad78b01108d834ef591c7aae60a0d1"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#a8dad78b01108d834ef591c7aae60a0d1">OpenMS::EmgScoring::getDefaults</a></div><div class="ttdeci">Param getDefaults()</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1EmgScoring_html_aee04cc30033052b32c9c91fb9e3aeb4d"><div class="ttname"><a href="classOpenMS_1_1EmgScoring.html#aee04cc30033052b32c9c91fb9e3aeb4d">OpenMS::EmgScoring::fitRT_</a></div><div class="ttdeci">double fitRT_(std::vector&lt; LocalPeakType &gt; &amp;rt_input_data, InterpolationModel *&amp;model)</div><div class="ttdef"><b>Definition:</b> EmgScoring.h:133</div></div>
<div class="ttc" id="classOpenMS_1_1GaussFilter_html_ab978eb8c2316573b1753199c8af2b041"><div class="ttname"><a href="classOpenMS_1_1GaussFilter.html#ab978eb8c2316573b1753199c8af2b041">OpenMS::GaussFilter::filter</a></div><div class="ttdeci">void filter(MSSpectrum&lt; PeakType &gt; &amp;spectrum)</div><div class="ttdoc">Smoothes an MSSpectrum containing profile data. </div><div class="ttdef"><b>Definition:</b> GaussFilter.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a7f6aab5a7dfbdd1c062a4352a29361f3"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">OpenMS::DefaultParamHandler::getParameters</a></div><div class="ttdeci">const Param &amp; getParameters() const </div><div class="ttdoc">Non-mutable access to the parameters. </div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
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