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<a href="FeatureFinderAlgorithmPicked_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="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Oliver Kohlbacher, Stephan Aiche $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Marc Sturm $</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_FEATUREFINDERALGORITHMPICKED_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_FEATUREFINDERALGORITHMPICKED_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;<a class="code" href="FeatureFinderAlgorithm_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureFinderAlgorithmPickedHelperStructs_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="TraceFitter_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/TraceFitter.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="EGHTraceFitter_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/EGHTraceFitter.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="GaussTraceFitter_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/GaussTraceFitter.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="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.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="FeatureXMLFile_8h.html">OpenMS/FORMAT/FeatureXMLFile.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="TextFile_8h.html">OpenMS/FORMAT/TextFile.h</a>&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="IsotopeDistribution_8h.html">OpenMS/CHEMISTRY/IsotopeDistribution.h</a>&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="StatisticFunctions_8h.html">OpenMS/MATH/STATISTICS/StatisticFunctions.h</a>&gt;</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MathFunctions_8h.html">OpenMS/MATH/MISC/MathFunctions.h</a>&gt;</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Constants_8h.html">OpenMS/CONCEPT/Constants.h</a>&gt;</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Element_8h.html">OpenMS/CHEMISTRY/Element.h</a>&gt;</span></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ElementDB_8h.html">OpenMS/CHEMISTRY/ElementDB.h</a>&gt;</span></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="IsotopeDistribution_8h.html">OpenMS/CHEMISTRY/IsotopeDistribution.h</a>&gt;</span></div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="preprocessor">#include &lt;boost/math/special_functions/fpclassify.hpp&gt;</span></div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;<span class="preprocessor">#include &lt;numeric&gt;</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;<span class="preprocessor">#include &lt;algorithm&gt;</span></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;<span class="preprocessor">#include &lt;QtCore/QDir&gt;</span></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="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#include &lt;omp.h&gt;</span></div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;{</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType&gt;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">   84</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a> :</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a>&lt;PeakType, FeatureType&gt;,</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    <span class="keyword">public</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;  {</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f89be2feec82f5414aedc09e488420b">   91</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::MapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f89be2feec82f5414aedc09e488420b">MapType</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abb9911ee4d024e85861f29bbbd0a63ef">   92</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::FeatureMapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abb9911ee4d024e85861f29bbbd0a63ef">FeatureMapType</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">   93</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MapType::SpectrumType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">   94</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#ae2fc906f686ab141e88c57655afd1774">SpectrumType::FloatDataArrays</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">FloatDataArrays</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::param_</a>;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::features_</a>;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::ff_</a>;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::defaults_</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">  103</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">FeatureFinderAlgorithmPickedHelperStructs::Seed</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">  104</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt;PeakType&gt;</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">MassTrace</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">  105</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt;PeakType&gt;</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a>;</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">  106</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a>;</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">  107</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a>;</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;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">  111</a></span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">FeatureFinderAlgorithmPicked</a>() :</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a>&lt;<a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>, FeatureType&gt;(),</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>(),</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a>()</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    {</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <span class="comment">//debugging</span></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;debug&quot;</span>, <span class="stringliteral">&quot;false&quot;</span>, <span class="stringliteral">&quot;When debug mode is activated, several files with intermediate results are written to the folder &#39;debug&#39; (do not use in parallel mode).&quot;</span>);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">&quot;debug&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;true,false&quot;</span>));</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;      <span class="comment">//intensity</span></div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;intensity:bins&quot;</span>, 10, <span class="stringliteral">&quot;Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.\nThis parameter should be decreased, if the algorithm is used on small regions of a map.&quot;</span>);</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">&quot;intensity:bins&quot;</span>, 1);</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;intensity&quot;</span>, <span class="stringliteral">&quot;Settings for the calculation of a score indicating if a peak&#39;s intensity is significant in the local environment (between 0 and 1)&quot;</span>);</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;      <span class="comment">//mass trace search parameters</span></div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;mass_trace:mz_tolerance&quot;</span>, 0.03, <span class="stringliteral">&quot;Tolerated m/z deviation of peaks belonging to the same mass trace.\nIt should be larger than the m/z resolution of the instument.\nThis value must be smaller than that 1/charge_high!&quot;</span>);</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;mass_trace:mz_tolerance&quot;</span>, 0.0);</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;mass_trace:min_spectra&quot;</span>, 10, <span class="stringliteral">&quot;Number of spectra that have to show a similar peak mass in a mass trace.&quot;</span>);</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">&quot;mass_trace:min_spectra&quot;</span>, 1);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;mass_trace:max_missing&quot;</span>, 1, <span class="stringliteral">&quot;Number of consecutive spectra where a high mass deviation or missing peak is acceptable.\nThis parameter should be well below &#39;min_spectra&#39;!&quot;</span>);</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">&quot;mass_trace:max_missing&quot;</span>, 0);</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;mass_trace:slope_bound&quot;</span>, 0.1, <span class="stringliteral">&quot;The maximum slope of mass trace intensities when extending from the highest peak.\nThis parameter is important to seperate overlapping elution peaks.\nIt should be increased if feature elution profiles fluctuate a lot.&quot;</span>);</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;mass_trace:slope_bound&quot;</span>, 0.0);</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;mass_trace&quot;</span>, <span class="stringliteral">&quot;Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).&quot;</span>);</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;      <span class="comment">//Isotopic pattern search parameters</span></div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:charge_low&quot;</span>, 1, <span class="stringliteral">&quot;Lowest charge to search for.&quot;</span>);</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">&quot;isotopic_pattern:charge_low&quot;</span>, 1);</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:charge_high&quot;</span>, 4, <span class="stringliteral">&quot;Highest charge to search for.&quot;</span>);</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">&quot;isotopic_pattern:charge_high&quot;</span>, 1);</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:mz_tolerance&quot;</span>, 0.03, <span class="stringliteral">&quot;Tolerated m/z deviation from the theoretical isotopic pattern.\nIt should be larger than the m/z resolution of the instument.\nThis value must be smaller than that 1/charge_high!&quot;</span>);</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:mz_tolerance&quot;</span>, 0.0);</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage&quot;</span>, 10.0, <span class="stringliteral">&quot;Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage&quot;</span>, 0.0);</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage&quot;</span>, 100.0);</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage_optional&quot;</span>, 0.1, <span class="stringliteral">&quot;Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage_optional&quot;</span>, 0.0);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage_optional&quot;</span>, 100.0);</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:optional_fit_improvement&quot;</span>, 2.0, <span class="stringliteral">&quot;Minimal percental improvement of isotope fit to allow leaving out an optional peak.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:optional_fit_improvement&quot;</span>, 0.0);</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:optional_fit_improvement&quot;</span>, 100.0);</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:mass_window_width&quot;</span>, 25.0, <span class="stringliteral">&quot;Window width in Dalton for precalculation of estimated isotope distributions.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:mass_window_width&quot;</span>, 1.0);</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:mass_window_width&quot;</span>, 200.0);</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_12C&quot;</span>, 98.93, <span class="stringliteral">&quot;Rel. abundance of the light carbon. Modify if labeled.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_12C&quot;</span>, 0.0);</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_12C&quot;</span>, 100.0);</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_14N&quot;</span>, 99.632, <span class="stringliteral">&quot;Rel. abundance of the light nitrogen. Modify if labeled.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_14N&quot;</span>, 0.0);</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_14N&quot;</span>, 100.0);</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">  159</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;isotopic_pattern&quot;</span>, <span class="stringliteral">&quot;Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).&quot;</span>);</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;      <span class="comment">//Seed settings</span></div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;seed:min_score&quot;</span>, 0.8, <span class="stringliteral">&quot;Minimum seed score a peak has to reach to be used as seed.\nThe seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.\nIf your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.&quot;</span>);</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;seed:min_score&quot;</span>, 0.0);</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;seed:min_score&quot;</span>, 1.0);</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;seed&quot;</span>, <span class="stringliteral">&quot;Settings that determine which peaks are considered a seed&quot;</span>);</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      <span class="comment">//Fitting settings</span></div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;fit:epsilon_abs&quot;</span>, 0.0001, <span class="stringliteral">&quot;Absolute epsilon used for convergence of the fit.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;fit:epsilon_abs&quot;</span>, 0.0);</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;fit:epsilon_rel&quot;</span>, 0.0001, <span class="stringliteral">&quot;Relative epsilon used for convergence of the fit.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;fit:epsilon_rel&quot;</span>, 0.0);</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;fit:max_iterations&quot;</span>, 500, <span class="stringliteral">&quot;Maximum number of iterations of the fit.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">&quot;fit:max_iterations&quot;</span>, 1);</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;fit&quot;</span>, <span class="stringliteral">&quot;Settings for the model fitting&quot;</span>);</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;      <span class="comment">//Feature settings</span></div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:min_score&quot;</span>, 0.7, <span class="stringliteral">&quot;Feature score threshold for a feature to be reported.\nThe feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.&quot;</span>);</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;feature:min_score&quot;</span>, 0.0);</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;feature:min_score&quot;</span>, 1.0);</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:min_isotope_fit&quot;</span>, 0.8, <span class="stringliteral">&quot;Minimum isotope fit of the feature before model fitting.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;feature:min_isotope_fit&quot;</span>, 0.0);</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;feature:min_isotope_fit&quot;</span>, 1.0);</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:min_trace_score&quot;</span>, 0.5, <span class="stringliteral">&quot;Trace score threshold.\nTraces below this threshold are removed after the model fitting.\nThis parameter is important for features that overlap in m/z dimension.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;feature:min_trace_score&quot;</span>, 0.0);</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;feature:min_trace_score&quot;</span>, 1.0);</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:min_rt_span&quot;</span>, 0.333, <span class="stringliteral">&quot;Minimum RT span in relation to extended area that has to remain after model fitting.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;feature:min_rt_span&quot;</span>, 0.0);</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;feature:min_rt_span&quot;</span>, 1.0);</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:max_rt_span&quot;</span>, 2.5, <span class="stringliteral">&quot;Maximum RT span in relation to extended area that the model is allowed to have.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;feature:max_rt_span&quot;</span>, 0.5);</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:rt_shape&quot;</span>, <span class="stringliteral">&quot;symmetric&quot;</span>, <span class="stringliteral">&quot;Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">&quot;feature:rt_shape&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;symmetric,asymmetric&quot;</span>));</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:max_intersection&quot;</span>, 0.35, <span class="stringliteral">&quot;Maximum allowed intersection of features.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;feature:max_intersection&quot;</span>, 0.0);</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;feature:max_intersection&quot;</span>, 1.0);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;feature:reported_mz&quot;</span>, <span class="stringliteral">&quot;monoisotopic&quot;</span>, <span class="stringliteral">&quot;The mass type that is reported for features.\n&#39;maximum&#39; returns the m/z value of the highest mass trace.\n&#39;average&#39; returns the intensity-weighted average m/z value of all contained peaks.\n&#39;monoisotopic&#39; returns the monoisotopic m/z value derived from the fitted isotope model.&quot;</span>);</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">&quot;feature:reported_mz&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;maximum,average,monoisotopic&quot;</span>));</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;feature&quot;</span>, <span class="stringliteral">&quot;Settings for the features (intensity, quality assessment, ...)&quot;</span>);</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;      <span class="comment">//user-specified seed settings</span></div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;user-seed:rt_tolerance&quot;</span>, 5.0, <span class="stringliteral">&quot;Allowed RT deviation of seeds from the user-specified seed position.&quot;</span>);</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;user-seed:rt_tolerance&quot;</span>, 0.0);</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;user-seed:mz_tolerance&quot;</span>, 1.1, <span class="stringliteral">&quot;Allowed m/z deviation of seeds from the user-specified seed position.&quot;</span>);</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;user-seed:mz_tolerance&quot;</span>, 0.0);</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;user-seed:min_score&quot;</span>, 0.5, <span class="stringliteral">&quot;Overwrites &#39;seed:min_score&#39; for user-specified seeds. The cutoff is typically a bit lower in this case.&quot;</span>);</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;user-seed:min_score&quot;</span>, 0.0);</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">&quot;user-seed:min_score&quot;</span>, 1.0);</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">setSectionDescription</a>(<span class="stringliteral">&quot;user-seed&quot;</span>, <span class="stringliteral">&quot;Settings for user-specified seeds.&quot;</span>);</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;      <span class="comment">//debug settings</span></div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;debug:pseudo_rt_shift&quot;</span>, 500.0, <span class="stringliteral">&quot;Pseudo RT shift used when .&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;debug:pseudo_rt_shift&quot;</span>, 1.0);</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>();</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;    }</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;    <span class="comment">// docu in base class</span></div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a683154793bbb12ab5d16db81209606b0">  212</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a683154793bbb12ab5d16db81209606b0">setSeeds</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapType</a>&amp; seeds)</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;    {</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a> = seeds;</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;</div>
<div class="line"><a name="l00218"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">  218</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">run</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="comment">//-------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;      <span class="comment">//General initialization</span></div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;      <span class="comment">//quality estimation</span></div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> min_feature_score = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:min_score&quot;</span>);</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;      <span class="comment">//charges to look at</span></div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> charge_low = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:charge_low&quot;</span>);</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> charge_high = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:charge_high&quot;</span>);</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;      <span class="comment">//fitting settings</span></div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> max_iterations = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;fit:max_iterations&quot;</span>);</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> epsilon_abs = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;fit:epsilon_abs&quot;</span>);</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> epsilon_rel = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;fit:epsilon_rel&quot;</span>);</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_isotopes = 20;</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;      <span class="comment">// check if non-natural isotopic abundances are set. If so modify</span></div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> abundance_12C = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_12C&quot;</span>);</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> abundance_14N = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_14N&quot;</span>);</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Element.html">Element</a>* carbon_const = <a class="code" href="classOpenMS_1_1ElementDB.html#ae141930c87ab8851ec484bc1fd0ccb90">ElementDB::getInstance</a>()-&gt;<a class="code" href="classOpenMS_1_1ElementDB.html#a62508929fb2f7f12cfbd486272f1b480">getElement</a>(<span class="stringliteral">&quot;Carbon&quot;</span>);</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;      <a class="code" href="classOpenMS_1_1Element.html">Element</a>* carbon = <span class="keyword">const_cast&lt;</span><a class="code" href="classOpenMS_1_1Element.html">Element</a>*<span class="keyword">&gt;</span>(carbon_const);</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="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_12C&quot;</span>) != <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_12C&quot;</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">  245</span>&#160;        max_isotopes += 1000;</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;        <a class="code" href="classOpenMS_1_1IsotopeDistribution.html">IsotopeDistribution</a> isotopes;</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;        std::vector&lt;std::pair&lt;Size, double&gt; &gt; container;</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;        container.push_back(std::make_pair(12, abundance_12C / 100.0));</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;        container.push_back(std::make_pair(13, 1.0 - (abundance_12C / 100.0)));</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;        isotopes.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#ad66e45f6a7c4a7224810862a41545b1b">set</a>(container);</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;        carbon-&gt;<a class="code" href="classOpenMS_1_1Element.html#af005f66c79814a28924d954f0150ec44">setIsotopeDistribution</a>(isotopes);</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;</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Element.html">Element</a>* nitrogen_const = <a class="code" href="classOpenMS_1_1ElementDB.html#ae141930c87ab8851ec484bc1fd0ccb90">ElementDB::getInstance</a>()-&gt;<a class="code" href="classOpenMS_1_1ElementDB.html#a62508929fb2f7f12cfbd486272f1b480">getElement</a>(<span class="stringliteral">&quot;Nitrogen&quot;</span>);</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;      <a class="code" href="classOpenMS_1_1Element.html">Element</a>* nitrogen = <span class="keyword">const_cast&lt;</span><a class="code" href="classOpenMS_1_1Element.html">Element</a>*<span class="keyword">&gt;</span>(nitrogen_const);</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="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_14N&quot;</span>) != <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:abundance_14N&quot;</span>))</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;      {</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;        max_isotopes += 1000;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;        <a class="code" href="classOpenMS_1_1IsotopeDistribution.html">IsotopeDistribution</a> isotopes;</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;        std::vector&lt;std::pair&lt;Size, double&gt; &gt; container;</div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;        container.push_back(std::make_pair(14, abundance_14N / 100.0));</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;        container.push_back(std::make_pair(15, 1.0 - (abundance_14N / 100.0)));</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;        isotopes.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#ad66e45f6a7c4a7224810862a41545b1b">set</a>(container);</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;        nitrogen-&gt;<a class="code" href="classOpenMS_1_1Element.html#af005f66c79814a28924d954f0150ec44">setIsotopeDistribution</a>(isotopes);</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;      }</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;      <span class="comment">// initialize trace fitter parameters here to avoid</span></div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;      <span class="comment">// bug https://sourceforge.net/apps/trac/open-ms/ticket/147</span></div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;      <a class="code" href="classOpenMS_1_1Param.html">Param</a> trace_fitter_params;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;      trace_fitter_params.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;max_iteration&quot;</span>, max_iterations);</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;      trace_fitter_params.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;epsilon_abs&quot;</span>, epsilon_abs);</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;      trace_fitter_params.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;epsilon_rel&quot;</span>, epsilon_rel);</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;      <span class="comment">//copy the input map</span></div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a> = *(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;::map_</a>);</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;      <span class="comment">//flag for user-specified seed mode</span></div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;      <span class="keywordtype">bool</span> user_seeds = (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a>.size() &gt; 0);</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;      <span class="keywordflow">if</span> (user_seeds)</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;      {</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a>.<a class="code" href="classOpenMS_1_1FeatureMap.html#a604ce6f3380b18acbebda3c1ed14e70c">sortByMZ</a>();</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;      }</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> user_rt_tol = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;user-seed:rt_tolerance&quot;</span>);</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> user_mz_tol = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;user-seed:mz_tolerance&quot;</span>);</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> user_seed_score = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;user-seed:min_score&quot;</span>);</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;      <span class="comment">//reserve space for calculated scores</span></div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> charge_count = charge_high - charge_low + 1;</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++s)</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;      {</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> scan_size = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>();</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays().<a class="code" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">resize</a>(3 + 2 * charge_count);</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[0].setName(<span class="stringliteral">&quot;trace_score&quot;</span>);</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[0].assign(scan_size, 0.0);</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[1].setName(<span class="stringliteral">&quot;intensity_score&quot;</span>);</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[1].assign(scan_size, 0.0);</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[2].setName(<span class="stringliteral">&quot;local_max&quot;</span>);</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[2].assign(scan_size, 0.0);</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;        <span class="comment">//create isotope pattern score arrays</span></div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;        <a class="code" href="classunsigned_01int.html">UInt</a> charge = charge_low;</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 3; i &lt; 3 + charge_count; ++i)</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;        {</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[i].setName(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;pattern_score_&quot;</span>) + charge);</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[i].assign(scan_size, 0.0);</div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;          ++charge;</div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;        }</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;        <span class="comment">//create overall score arrays</span></div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;        charge = charge_low;</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 3 + charge_count; i &lt; 3 + 2 * charge_count; ++i)</div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;        {</div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[i].setName(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;overall_score_&quot;</span>) + charge);</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[i].assign(scan_size, 0.0);</div>
<div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;          ++charge;</div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;        }</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;      }</div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;      <span class="keywordtype">int</span> gl_progress = 0;</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a> = ((<a class="code" href="classOpenMS_1_1String.html">String</a>)(<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;debug&quot;</span>)) == <span class="stringliteral">&quot;true&quot;</span>);</div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;      <span class="comment">//clean up / create folders for debug information</span></div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>)</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;      {</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;        QDir dir(<span class="stringliteral">&quot;.&quot;</span>);</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;        dir.mkpath(<span class="stringliteral">&quot;debug/features&quot;</span>);</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a>.open(<span class="stringliteral">&quot;debug/log.txt&quot;</span>);</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;      }</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;      <span class="comment">//Step 1:</span></div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;      <span class="comment">//Precalculate intensity scores for peaks</span></div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;Precalculating intensity thresholds ...&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;      <span class="comment">//new scope to make local variables disappear</span></div>
<div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;      {</div>
<div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a>, <span class="stringliteral">&quot;Precalculating intensity scores&quot;</span>);</div>
<div class="line"><a name="l00336"></a><span class="lineno">  336</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> rt_start = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9244f3b9aefde24a9b246a8396c3bb84">getMinRT</a>();</div>
<div class="line"><a name="l00337"></a><span class="lineno">  337</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> mz_start = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d8aab759e082ef93475344071fb7809">getMinMZ</a>();</div>
<div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a> = (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#af67f955c87166e64d9361815dc3760b5">getMaxRT</a>() - rt_start) / (<a class="code" href="classdouble.html">DoubleReal</a>)<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a>;</div>
<div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a> = (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a87d8ffa067f5ee283997ac69b197234f">getMaxMZ</a>() - mz_start) / (<a class="code" href="classdouble.html">DoubleReal</a>)<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a>;</div>
<div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a>.resize(intensity_bins_);</div>
<div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> rt = 0; rt &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a>; ++rt)</div>
<div class="line"><a name="l00342"></a><span class="lineno">  342</span>&#160;        {</div>
<div class="line"><a name="l00343"></a><span class="lineno">  343</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a>[rt].resize(intensity_bins_);</div>
<div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> min_rt = rt_start + rt * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a>;</div>
<div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> max_rt = rt_start + (rt + 1) * intensity_rt_step_;</div>
<div class="line"><a name="l00346"></a><span class="lineno">  346</span>&#160;          std::vector&lt;DoubleReal&gt; tmp;</div>
<div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> mz = 0; mz &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a>; ++mz)</div>
<div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;          {</div>
<div class="line"><a name="l00349"></a><span class="lineno">  349</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(rt * intensity_bins_ + mz);</div>
<div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> min_mz = mz_start + mz * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a>;</div>
<div class="line"><a name="l00351"></a><span class="lineno">  351</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> max_mz = mz_start + (mz + 1) * intensity_mz_step_;</div>
<div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;            <span class="comment">//std::cout &lt;&lt; &quot;rt range: &quot; &lt;&lt; min_rt &lt;&lt; &quot; - &quot; &lt;&lt; max_rt &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00353"></a><span class="lineno">  353</span>&#160;            <span class="comment">//std::cout &lt;&lt; &quot;mz range: &quot; &lt;&lt; min_mz &lt;&lt; &quot; - &quot; &lt;&lt; max_mz &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00354"></a><span class="lineno">  354</span>&#160;            tmp.clear();</div>
<div class="line"><a name="l00355"></a><span class="lineno">  355</span>&#160;            <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1Internal_1_1AreaIterator.html">MapType::ConstAreaIterator</a> it = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#aa23ed32415e6667bd2737377c24c16fb">areaBeginConst</a>(min_rt, max_rt, min_mz, max_mz); it != <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a5f9d4faff212e67330d60f958f0ce4bc">areaEndConst</a>(); ++it)</div>
<div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;            {</div>
<div class="line"><a name="l00357"></a><span class="lineno">  357</span>&#160;              tmp.push_back(it-&gt;getIntensity());</div>
<div class="line"><a name="l00358"></a><span class="lineno">  358</span>&#160;            }</div>
<div class="line"><a name="l00359"></a><span class="lineno">  359</span>&#160;            <span class="comment">//init vector</span></div>
<div class="line"><a name="l00360"></a><span class="lineno">  360</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a>[rt][mz].assign(21, 0.0);</div>
<div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;            <span class="comment">//store quantiles (20)</span></div>
<div class="line"><a name="l00362"></a><span class="lineno">  362</span>&#160;            <span class="keywordflow">if</span> (!tmp.empty())</div>
<div class="line"><a name="l00363"></a><span class="lineno">  363</span>&#160;            {</div>
<div class="line"><a name="l00364"></a><span class="lineno">  364</span>&#160;              std::sort(tmp.begin(), tmp.end());</div>
<div class="line"><a name="l00365"></a><span class="lineno">  365</span>&#160;              <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; 21; ++i)</div>
<div class="line"><a name="l00366"></a><span class="lineno">  366</span>&#160;              {</div>
<div class="line"><a name="l00367"></a><span class="lineno">  367</span>&#160;                <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>) std::floor(0.05 * i * (tmp.size() - 1));</div>
<div class="line"><a name="l00368"></a><span class="lineno">  368</span>&#160;                <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a>[rt][mz][i] = tmp[index];</div>
<div class="line"><a name="l00369"></a><span class="lineno">  369</span>&#160;              }</div>
<div class="line"><a name="l00370"></a><span class="lineno">  370</span>&#160;            }</div>
<div class="line"><a name="l00371"></a><span class="lineno">  371</span>&#160;          }</div>
<div class="line"><a name="l00372"></a><span class="lineno">  372</span>&#160;        }</div>
<div class="line"><a name="l00373"></a><span class="lineno">  373</span>&#160;</div>
<div class="line"><a name="l00374"></a><span class="lineno">  374</span>&#160;        <span class="comment">//store intensity score in PeakInfo</span></div>
<div class="line"><a name="l00375"></a><span class="lineno">  375</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++s)</div>
<div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;        {</div>
<div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++p)</div>
<div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;          {</div>
<div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[1][p] = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a>(s, p);</div>
<div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;          }</div>
<div class="line"><a name="l00381"></a><span class="lineno">  381</span>&#160;        }</div>
<div class="line"><a name="l00382"></a><span class="lineno">  382</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00383"></a><span class="lineno">  383</span>&#160;      }</div>
<div class="line"><a name="l00384"></a><span class="lineno">  384</span>&#160;</div>
<div class="line"><a name="l00385"></a><span class="lineno">  385</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00386"></a><span class="lineno">  386</span>&#160;      <span class="comment">//Step 2:</span></div>
<div class="line"><a name="l00387"></a><span class="lineno">  387</span>&#160;      <span class="comment">//Precalculate mass trace scores and local trace maximum for each peak</span></div>
<div class="line"><a name="l00388"></a><span class="lineno">  388</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00389"></a><span class="lineno">  389</span>&#160;      <span class="comment">//new scope to make local variables disappear</span></div>
<div class="line"><a name="l00390"></a><span class="lineno">  390</span>&#160;      {</div>
<div class="line"><a name="l00391"></a><span class="lineno">  391</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end_iteration = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - std::min((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00392"></a><span class="lineno">  392</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(min_spectra_, end_iteration, <span class="stringliteral">&quot;Precalculating mass trace scores&quot;</span>);</div>
<div class="line"><a name="l00393"></a><span class="lineno">  393</span>&#160;        <span class="comment">// skip first and last scans since we cannot extend the mass traces there</span></div>
<div class="line"><a name="l00394"></a><span class="lineno">  394</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = min_spectra_; s &lt; end_iteration; ++s)</div>
<div class="line"><a name="l00395"></a><span class="lineno">  395</span>&#160;        {</div>
<div class="line"><a name="l00396"></a><span class="lineno">  396</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(s);</div>
<div class="line"><a name="l00397"></a><span class="lineno">  397</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s];</div>
<div class="line"><a name="l00398"></a><span class="lineno">  398</span>&#160;          <span class="comment">//iterate over all peaks of the scan</span></div>
<div class="line"><a name="l00399"></a><span class="lineno">  399</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spectrum.size(); ++p)</div>
<div class="line"><a name="l00400"></a><span class="lineno">  400</span>&#160;          {</div>
<div class="line"><a name="l00401"></a><span class="lineno">  401</span>&#160;            std::vector&lt;DoubleReal&gt; scores;</div>
<div class="line"><a name="l00402"></a><span class="lineno">  402</span>&#160;            scores.reserve(2 * min_spectra_);</div>
<div class="line"><a name="l00403"></a><span class="lineno">  403</span>&#160;</div>
<div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> pos = spectrum[p].getMZ();</div>
<div class="line"><a name="l00405"></a><span class="lineno">  405</span>&#160;            <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> inte = spectrum[p].getIntensity();</div>
<div class="line"><a name="l00406"></a><span class="lineno">  406</span>&#160;</div>
<div class="line"><a name="l00407"></a><span class="lineno">  407</span>&#160;            <span class="comment">//if(debug_) log_ &lt;&lt; std::endl &lt;&lt; &quot;Peak: &quot; &lt;&lt; pos &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00408"></a><span class="lineno">  408</span>&#160;            <span class="keywordtype">bool</span> is_max_peak = <span class="keyword">true</span>; <span class="comment">//checking the maximum intensity peaks -&gt; use them later as feature seeds.</span></div>
<div class="line"><a name="l00409"></a><span class="lineno">  409</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i &lt;= <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>; ++i)</div>
<div class="line"><a name="l00410"></a><span class="lineno">  410</span>&#160;            {</div>
<div class="line"><a name="l00411"></a><span class="lineno">  411</span>&#160;              <span class="keywordflow">try</span></div>
<div class="line"><a name="l00412"></a><span class="lineno">  412</span>&#160;              {</div>
<div class="line"><a name="l00413"></a><span class="lineno">  413</span>&#160;                <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_index = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s + i].findNearest(pos);</div>
<div class="line"><a name="l00414"></a><span class="lineno">  414</span>&#160;                <a class="code" href="classdouble.html">DoubleReal</a> position_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(pos, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s + i][spec_index].getMZ(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a>);</div>
<div class="line"><a name="l00415"></a><span class="lineno">  415</span>&#160;                <span class="keywordflow">if</span> (position_score &gt; 0 &amp;&amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s + i][spec_index].getIntensity() &gt; inte) is_max_peak = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;                scores.push_back(position_score);</div>
<div class="line"><a name="l00417"></a><span class="lineno">  417</span>&#160;              }</div>
<div class="line"><a name="l00418"></a><span class="lineno">  418</span>&#160;              <span class="keywordflow">catch</span> (...) <span class="comment">//no peaks in the spectrum</span></div>
<div class="line"><a name="l00419"></a><span class="lineno">  419</span>&#160;              {</div>
<div class="line"><a name="l00420"></a><span class="lineno">  420</span>&#160;                scores.push_back(0.0);</div>
<div class="line"><a name="l00421"></a><span class="lineno">  421</span>&#160;              }</div>
<div class="line"><a name="l00422"></a><span class="lineno">  422</span>&#160;            }</div>
<div class="line"><a name="l00423"></a><span class="lineno">  423</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i &lt;= <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>; ++i)</div>
<div class="line"><a name="l00424"></a><span class="lineno">  424</span>&#160;            {</div>
<div class="line"><a name="l00425"></a><span class="lineno">  425</span>&#160;              <span class="keywordflow">try</span></div>
<div class="line"><a name="l00426"></a><span class="lineno">  426</span>&#160;              {</div>
<div class="line"><a name="l00427"></a><span class="lineno">  427</span>&#160;                <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_index = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s - i].findNearest(pos);</div>
<div class="line"><a name="l00428"></a><span class="lineno">  428</span>&#160;                <a class="code" href="classdouble.html">DoubleReal</a> position_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(pos, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s - i][spec_index].getMZ(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a>);</div>
<div class="line"><a name="l00429"></a><span class="lineno">  429</span>&#160;                <span class="keywordflow">if</span> (position_score &gt; 0 &amp;&amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s - i][spec_index].getIntensity() &gt; inte) is_max_peak = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00430"></a><span class="lineno">  430</span>&#160;                scores.push_back(position_score);</div>
<div class="line"><a name="l00431"></a><span class="lineno">  431</span>&#160;              }</div>
<div class="line"><a name="l00432"></a><span class="lineno">  432</span>&#160;              <span class="keywordflow">catch</span> (...) <span class="comment">//no peaks in the spectrum</span></div>
<div class="line"><a name="l00433"></a><span class="lineno">  433</span>&#160;              {</div>
<div class="line"><a name="l00434"></a><span class="lineno">  434</span>&#160;                scores.push_back(0.0);</div>
<div class="line"><a name="l00435"></a><span class="lineno">  435</span>&#160;              }</div>
<div class="line"><a name="l00436"></a><span class="lineno">  436</span>&#160;            }</div>
<div class="line"><a name="l00437"></a><span class="lineno">  437</span>&#160;            <span class="comment">//Calculate a consensus score out of the scores calculated before</span></div>
<div class="line"><a name="l00438"></a><span class="lineno">  438</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> trace_score = std::accumulate(scores.begin(), scores.end(), 0.0) / scores.size();</div>
<div class="line"><a name="l00439"></a><span class="lineno">  439</span>&#160;</div>
<div class="line"><a name="l00440"></a><span class="lineno">  440</span>&#160;            <span class="comment">//store final score for later use</span></div>
<div class="line"><a name="l00441"></a><span class="lineno">  441</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[0][p] = trace_score;</div>
<div class="line"><a name="l00442"></a><span class="lineno">  442</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays()[2][p] = is_max_peak;</div>
<div class="line"><a name="l00443"></a><span class="lineno">  443</span>&#160;          }</div>
<div class="line"><a name="l00444"></a><span class="lineno">  444</span>&#160;        }</div>
<div class="line"><a name="l00445"></a><span class="lineno">  445</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00446"></a><span class="lineno">  446</span>&#160;      }</div>
<div class="line"><a name="l00447"></a><span class="lineno">  447</span>&#160;</div>
<div class="line"><a name="l00448"></a><span class="lineno">  448</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00449"></a><span class="lineno">  449</span>&#160;      <span class="comment">//Step 2.5:</span></div>
<div class="line"><a name="l00450"></a><span class="lineno">  450</span>&#160;      <span class="comment">//Precalculate isotope distributions for interesting mass ranges</span></div>
<div class="line"><a name="l00451"></a><span class="lineno">  451</span>&#160;      <span class="comment">//---------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00452"></a><span class="lineno">  452</span>&#160;      <span class="comment">//new scope to make local variables disappear</span></div>
<div class="line"><a name="l00453"></a><span class="lineno">  453</span>&#160;      {</div>
<div class="line"><a name="l00454"></a><span class="lineno">  454</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> max_mass = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a87d8ffa067f5ee283997ac69b197234f">getMaxMZ</a>() * charge_high;</div>
<div class="line"><a name="l00455"></a><span class="lineno">  455</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_isotopes = std::ceil(max_mass / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a>) + 1;</div>
<div class="line"><a name="l00456"></a><span class="lineno">  456</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, num_isotopes, <span class="stringliteral">&quot;Precalculating isotope distributions&quot;</span>);</div>
<div class="line"><a name="l00457"></a><span class="lineno">  457</span>&#160;</div>
<div class="line"><a name="l00458"></a><span class="lineno">  458</span>&#160;        <span class="comment">//reserve enough space</span></div>
<div class="line"><a name="l00459"></a><span class="lineno">  459</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>.resize(num_isotopes);</div>
<div class="line"><a name="l00460"></a><span class="lineno">  460</span>&#160;</div>
<div class="line"><a name="l00461"></a><span class="lineno">  461</span>&#160;        <span class="comment">//calculate distribution if necessary</span></div>
<div class="line"><a name="l00462"></a><span class="lineno">  462</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = 0; index &lt; num_isotopes; ++index)</div>
<div class="line"><a name="l00463"></a><span class="lineno">  463</span>&#160;        {</div>
<div class="line"><a name="l00464"></a><span class="lineno">  464</span>&#160;          <span class="comment">//if(debug_) log_ &lt;&lt; &quot;Calculating iso dist for mass: &quot; &lt;&lt; 0.5*mass_window_width_ + index * mass_window_width_ &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00465"></a><span class="lineno">  465</span>&#160;          <a class="code" href="classOpenMS_1_1IsotopeDistribution.html">IsotopeDistribution</a> d;</div>
<div class="line"><a name="l00466"></a><span class="lineno">  466</span>&#160;          d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a261a831dc055b354545a8c0e48f57cad">setMaxIsotope</a>(max_isotopes);</div>
<div class="line"><a name="l00467"></a><span class="lineno">  467</span>&#160;          d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a2a548700db35cba3fec126772ef27c72">estimateFromPeptideWeight</a>(0.5 * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a> + index * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a>);</div>
<div class="line"><a name="l00468"></a><span class="lineno">  468</span>&#160;          <span class="comment">//trim left and right. And store the number of isotopes on the left, to reconstruct the monoisotopic peak</span></div>
<div class="line"><a name="l00469"></a><span class="lineno">  469</span>&#160;          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> size_before = d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>();</div>
<div class="line"><a name="l00470"></a><span class="lineno">  470</span>&#160;          d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#adf5dffb508ec1b791c73f990ff92a3dd">trimLeft</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">intensity_percentage_optional_</a>);</div>
<div class="line"><a name="l00471"></a><span class="lineno">  471</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].trimmed_left = size_before - d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>();</div>
<div class="line"><a name="l00472"></a><span class="lineno">  472</span>&#160;          d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a055e732ad7e3eed9cce0d279ae7af3a6">trimRight</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">intensity_percentage_optional_</a>);</div>
<div class="line"><a name="l00473"></a><span class="lineno">  473</span>&#160;</div>
<div class="line"><a name="l00474"></a><span class="lineno">  474</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a6d64276a665c3c0dca8fb4ade3c8b477">IsotopeDistribution::Iterator</a> it = d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#a2387033802383edbdc95f9bbb12a707e">begin</a>(); it != d.<a class="code" href="classOpenMS_1_1IsotopeDistribution.html#ab45dae688fc5d8983727abffa4389003">end</a>(); ++it)</div>
<div class="line"><a name="l00475"></a><span class="lineno">  475</span>&#160;          {</div>
<div class="line"><a name="l00476"></a><span class="lineno">  476</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity.push_back(it-&gt;second);</div>
<div class="line"><a name="l00477"></a><span class="lineno">  477</span>&#160;            <span class="comment">//if(debug_) log_ &lt;&lt; &quot; - &quot; &lt;&lt; it-&gt;second &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00478"></a><span class="lineno">  478</span>&#160;          }</div>
<div class="line"><a name="l00479"></a><span class="lineno">  479</span>&#160;</div>
<div class="line"><a name="l00480"></a><span class="lineno">  480</span>&#160;          <span class="comment">//determine the number of optional peaks at the beginning/end</span></div>
<div class="line"><a name="l00481"></a><span class="lineno">  481</span>&#160;          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> begin = 0;</div>
<div class="line"><a name="l00482"></a><span class="lineno">  482</span>&#160;          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end = 0;</div>
<div class="line"><a name="l00483"></a><span class="lineno">  483</span>&#160;          <span class="keywordtype">bool</span> is_begin = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00484"></a><span class="lineno">  484</span>&#160;          <span class="keywordtype">bool</span> is_end = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00485"></a><span class="lineno">  485</span>&#160;</div>
<div class="line"><a name="l00486"></a><span class="lineno">  486</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity.size(); ++i)</div>
<div class="line"><a name="l00487"></a><span class="lineno">  487</span>&#160;          {</div>
<div class="line"><a name="l00488"></a><span class="lineno">  488</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity[i] &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">intensity_percentage_</a>)</div>
<div class="line"><a name="l00489"></a><span class="lineno">  489</span>&#160;            {</div>
<div class="line"><a name="l00490"></a><span class="lineno">  490</span>&#160;              <span class="keywordflow">if</span> (!is_end &amp;&amp; !is_begin) is_end = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00491"></a><span class="lineno">  491</span>&#160;              <span class="keywordflow">if</span> (is_begin) ++begin;</div>
<div class="line"><a name="l00492"></a><span class="lineno">  492</span>&#160;              <span class="keywordflow">else</span> <span class="keywordflow">if</span> (is_end) ++end;</div>
<div class="line"><a name="l00493"></a><span class="lineno">  493</span>&#160;            }</div>
<div class="line"><a name="l00494"></a><span class="lineno">  494</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (is_begin)</div>
<div class="line"><a name="l00495"></a><span class="lineno">  495</span>&#160;            {</div>
<div class="line"><a name="l00496"></a><span class="lineno">  496</span>&#160;              is_begin = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00497"></a><span class="lineno">  497</span>&#160;            }</div>
<div class="line"><a name="l00498"></a><span class="lineno">  498</span>&#160;          }</div>
<div class="line"><a name="l00499"></a><span class="lineno">  499</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].optional_begin = begin;</div>
<div class="line"><a name="l00500"></a><span class="lineno">  500</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].optional_end = end;</div>
<div class="line"><a name="l00501"></a><span class="lineno">  501</span>&#160;          <span class="comment">//scale the distibution to a maximum of 1</span></div>
<div class="line"><a name="l00502"></a><span class="lineno">  502</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> max = 0.0;</div>
<div class="line"><a name="l00503"></a><span class="lineno">  503</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity.size(); ++i)</div>
<div class="line"><a name="l00504"></a><span class="lineno">  504</span>&#160;          {</div>
<div class="line"><a name="l00505"></a><span class="lineno">  505</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity[i] &gt; max)</div>
<div class="line"><a name="l00506"></a><span class="lineno">  506</span>&#160;            {</div>
<div class="line"><a name="l00507"></a><span class="lineno">  507</span>&#160;              max = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity[i];</div>
<div class="line"><a name="l00508"></a><span class="lineno">  508</span>&#160;            }</div>
<div class="line"><a name="l00509"></a><span class="lineno">  509</span>&#160;          }</div>
<div class="line"><a name="l00510"></a><span class="lineno">  510</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].max = max;</div>
<div class="line"><a name="l00511"></a><span class="lineno">  511</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity.size(); ++i)</div>
<div class="line"><a name="l00512"></a><span class="lineno">  512</span>&#160;          {</div>
<div class="line"><a name="l00513"></a><span class="lineno">  513</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index].intensity[i] /= max;</div>
<div class="line"><a name="l00514"></a><span class="lineno">  514</span>&#160;          }</div>
<div class="line"><a name="l00515"></a><span class="lineno">  515</span>&#160;</div>
<div class="line"><a name="l00516"></a><span class="lineno">  516</span>&#160;          <span class="comment">//if(debug_) log_ &lt;&lt; &quot; - optinal begin/end:&quot; &lt;&lt; begin &lt;&lt; &quot; / &quot; &lt;&lt; end &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00517"></a><span class="lineno">  517</span>&#160;        }</div>
<div class="line"><a name="l00518"></a><span class="lineno">  518</span>&#160;</div>
<div class="line"><a name="l00519"></a><span class="lineno">  519</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00520"></a><span class="lineno">  520</span>&#160;      }</div>
<div class="line"><a name="l00521"></a><span class="lineno">  521</span>&#160;</div>
<div class="line"><a name="l00522"></a><span class="lineno">  522</span>&#160;      <span class="comment">//-------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00523"></a><span class="lineno">  523</span>&#160;      <span class="comment">//Step 3:</span></div>
<div class="line"><a name="l00524"></a><span class="lineno">  524</span>&#160;      <span class="comment">//Charge loop (create seeds and features for each charge separately)</span></div>
<div class="line"><a name="l00525"></a><span class="lineno">  525</span>&#160;      <span class="comment">//-------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00526"></a><span class="lineno">  526</span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> plot_nr_global = -1; <span class="comment">//counter for the number of plots (debug info)</span></div>
<div class="line"><a name="l00527"></a><span class="lineno">  527</span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> feature_nr_global = 0; <span class="comment">//counter for the number of features (debug info)</span></div>
<div class="line"><a name="l00528"></a><span class="lineno">  528</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = charge_low; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> &lt;= charge_high; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>)</div>
<div class="line"><a name="l00529"></a><span class="lineno">  529</span>&#160;      {</div>
<div class="line"><a name="l00530"></a><span class="lineno">  530</span>&#160;        <a class="code" href="classunsigned_01int.html">UInt</a> meta_index_isotope = 3 + <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> - charge_low;</div>
<div class="line"><a name="l00531"></a><span class="lineno">  531</span>&#160;        <a class="code" href="classunsigned_01int.html">UInt</a> meta_index_overall = 3 + charge_count + <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> - charge_low;</div>
<div class="line"><a name="l00532"></a><span class="lineno">  532</span>&#160;</div>
<div class="line"><a name="l00533"></a><span class="lineno">  533</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> feature_candidates = 0;</div>
<div class="line"><a name="l00534"></a><span class="lineno">  534</span>&#160;        std::vector&lt;Seed&gt; seeds;</div>
<div class="line"><a name="l00535"></a><span class="lineno">  535</span>&#160;</div>
<div class="line"><a name="l00536"></a><span class="lineno">  536</span>&#160;        <span class="comment">//-----------------------------------------------------------</span></div>
<div class="line"><a name="l00537"></a><span class="lineno">  537</span>&#160;        <span class="comment">//Step 3.1: Precalculate IsotopePattern score</span></div>
<div class="line"><a name="l00538"></a><span class="lineno">  538</span>&#160;        <span class="comment">//-----------------------------------------------------------</span></div>
<div class="line"><a name="l00539"></a><span class="lineno">  539</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Calculating isotope pattern scores for charge &quot;</span>) + <a class="code" href="classOpenMS_1_1String.html">String</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>));</div>
<div class="line"><a name="l00540"></a><span class="lineno">  540</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++s)</div>
<div class="line"><a name="l00541"></a><span class="lineno">  541</span>&#160;        {</div>
<div class="line"><a name="l00542"></a><span class="lineno">  542</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(s);</div>
<div class="line"><a name="l00543"></a><span class="lineno">  543</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s];</div>
<div class="line"><a name="l00544"></a><span class="lineno">  544</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; spectrum.size(); ++p)</div>
<div class="line"><a name="l00545"></a><span class="lineno">  545</span>&#160;          {</div>
<div class="line"><a name="l00546"></a><span class="lineno">  546</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> mz = spectrum[p].getMZ();</div>
<div class="line"><a name="l00547"></a><span class="lineno">  547</span>&#160;</div>
<div class="line"><a name="l00548"></a><span class="lineno">  548</span>&#160;            <span class="comment">//get isotope distribution for this mass</span></div>
<div class="line"><a name="l00549"></a><span class="lineno">  549</span>&#160;            <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">TheoreticalIsotopePattern</a>&amp; isotopes = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">getIsotopeDistribution_</a>(mz * <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00550"></a><span class="lineno">  550</span>&#160;            <span class="comment">//determine highest peak in isotope distribution</span></div>
<div class="line"><a name="l00551"></a><span class="lineno">  551</span>&#160;            <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_isotope = std::max_element(isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.begin(), isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.end()) - isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.begin();</div>
<div class="line"><a name="l00552"></a><span class="lineno">  552</span>&#160;            <span class="comment">//Look up expected isotopic peaks (in the current spectrum or adjacent spectra)</span></div>
<div class="line"><a name="l00553"></a><span class="lineno">  553</span>&#160;            <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak_index = spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a830e58a22131827d85007a70e3069a5f">findNearest</a>(mz - ((<a class="code" href="classdouble.html">DoubleReal</a>)(isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() + 1) / c));</div>
<div class="line"><a name="l00554"></a><span class="lineno">  554</span>&#160;            <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a> pattern(isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00555"></a><span class="lineno">  555</span>&#160;</div>
<div class="line"><a name="l00556"></a><span class="lineno">  556</span>&#160;            <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</div>
<div class="line"><a name="l00557"></a><span class="lineno">  557</span>&#160;            {</div>
<div class="line"><a name="l00558"></a><span class="lineno">  558</span>&#160;              <a class="code" href="classdouble.html">DoubleReal</a> isotope_pos = mz + ((<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)i - max_isotope) / <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>;</div>
<div class="line"><a name="l00559"></a><span class="lineno">  559</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">findIsotope_</a>(isotope_pos, s, pattern, i, peak_index);</div>
<div class="line"><a name="l00560"></a><span class="lineno">  560</span>&#160;            }</div>
<div class="line"><a name="l00561"></a><span class="lineno">  561</span>&#160;</div>
<div class="line"><a name="l00562"></a><span class="lineno">  562</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> pattern_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">isotopeScore_</a>(isotopes, pattern, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00563"></a><span class="lineno">  563</span>&#160;</div>
<div class="line"><a name="l00564"></a><span class="lineno">  564</span>&#160;            <span class="comment">//update pattern scores of all contained peaks (if necessary)</span></div>
<div class="line"><a name="l00565"></a><span class="lineno">  565</span>&#160;            <span class="keywordflow">if</span> (pattern_score &gt; 0.0)</div>
<div class="line"><a name="l00566"></a><span class="lineno">  566</span>&#160;            {</div>
<div class="line"><a name="l00567"></a><span class="lineno">  567</span>&#160;              <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; pattern.peak.size(); ++i)</div>
<div class="line"><a name="l00568"></a><span class="lineno">  568</span>&#160;              {</div>
<div class="line"><a name="l00569"></a><span class="lineno">  569</span>&#160;                <span class="keywordflow">if</span> (pattern.peak[i] &gt;= 0 &amp;&amp; pattern_score &gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[pattern.spectrum[i]].getFloatDataArrays()[meta_index_isotope][pattern.peak[i]])</div>
<div class="line"><a name="l00570"></a><span class="lineno">  570</span>&#160;                {</div>
<div class="line"><a name="l00571"></a><span class="lineno">  571</span>&#160;                  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[pattern.spectrum[i]].getFloatDataArrays()[meta_index_isotope][pattern.peak[i]] = pattern_score;</div>
<div class="line"><a name="l00572"></a><span class="lineno">  572</span>&#160;                }</div>
<div class="line"><a name="l00573"></a><span class="lineno">  573</span>&#160;              }</div>
<div class="line"><a name="l00574"></a><span class="lineno">  574</span>&#160;            }</div>
<div class="line"><a name="l00575"></a><span class="lineno">  575</span>&#160;          }</div>
<div class="line"><a name="l00576"></a><span class="lineno">  576</span>&#160;        }</div>
<div class="line"><a name="l00577"></a><span class="lineno">  577</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00578"></a><span class="lineno">  578</span>&#160;        <span class="comment">//-----------------------------------------------------------</span></div>
<div class="line"><a name="l00579"></a><span class="lineno">  579</span>&#160;        <span class="comment">//Step 3.2:</span></div>
<div class="line"><a name="l00580"></a><span class="lineno">  580</span>&#160;        <span class="comment">//Find seeds for this charge</span></div>
<div class="line"><a name="l00581"></a><span class="lineno">  581</span>&#160;        <span class="comment">//-----------------------------------------------------------</span></div>
<div class="line"><a name="l00582"></a><span class="lineno">  582</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end_of_iteration = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - std::min((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00583"></a><span class="lineno">  583</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(min_spectra_, end_of_iteration, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Finding seeds for charge &quot;</span>) + <a class="code" href="classOpenMS_1_1String.html">String</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>));</div>
<div class="line"><a name="l00584"></a><span class="lineno">  584</span>&#160;</div>
<div class="line"><a name="l00585"></a><span class="lineno">  585</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> min_seed_score = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;seed:min_score&quot;</span>);</div>
<div class="line"><a name="l00586"></a><span class="lineno">  586</span>&#160;        <span class="comment">//do nothing for the first few and last few spectra as the scans required to search for traces are missing</span></div>
<div class="line"><a name="l00587"></a><span class="lineno">  587</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = min_spectra_; s &lt; end_of_iteration; ++s)</div>
<div class="line"><a name="l00588"></a><span class="lineno">  588</span>&#160;        {</div>
<div class="line"><a name="l00589"></a><span class="lineno">  589</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(s);</div>
<div class="line"><a name="l00590"></a><span class="lineno">  590</span>&#160;</div>
<div class="line"><a name="l00591"></a><span class="lineno">  591</span>&#160;          <span class="comment">//iterate over peaks</span></div>
<div class="line"><a name="l00592"></a><span class="lineno">  592</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++p)</div>
<div class="line"><a name="l00593"></a><span class="lineno">  593</span>&#160;          {</div>
<div class="line"><a name="l00594"></a><span class="lineno">  594</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">FloatDataArrays</a>&amp; meta = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays();</div>
<div class="line"><a name="l00595"></a><span class="lineno">  595</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> overall_score = std::pow(meta[0][p] * meta[1][p] * meta[meta_index_isotope][p], 1.0f / 3.0f);</div>
<div class="line"><a name="l00596"></a><span class="lineno">  596</span>&#160;            meta[meta_index_overall][p] = overall_score;</div>
<div class="line"><a name="l00597"></a><span class="lineno">  597</span>&#160;</div>
<div class="line"><a name="l00598"></a><span class="lineno">  598</span>&#160;            <span class="comment">//add seed to vector if certain conditions are fulfilled</span></div>
<div class="line"><a name="l00599"></a><span class="lineno">  599</span>&#160;            <span class="keywordflow">if</span> (meta[2][p] != 0.0) <span class="comment">// local maximum of mass trace is prerequisite for all features</span></div>
<div class="line"><a name="l00600"></a><span class="lineno">  600</span>&#160;            {</div>
<div class="line"><a name="l00601"></a><span class="lineno">  601</span>&#160;              <span class="comment">//automatic seeds: overall score greater than the min seed score</span></div>
<div class="line"><a name="l00602"></a><span class="lineno">  602</span>&#160;              <span class="keywordflow">if</span> (!user_seeds &amp;&amp; overall_score &gt;= min_seed_score)</div>
<div class="line"><a name="l00603"></a><span class="lineno">  603</span>&#160;              {</div>
<div class="line"><a name="l00604"></a><span class="lineno">  604</span>&#160;                <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">Seed</a> seed;</div>
<div class="line"><a name="l00605"></a><span class="lineno">  605</span>&#160;                seed.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a> = s;</div>
<div class="line"><a name="l00606"></a><span class="lineno">  606</span>&#160;                seed.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> = p;</div>
<div class="line"><a name="l00607"></a><span class="lineno">  607</span>&#160;                seed.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#a2bf8eeb17dafb3d8ed1b08810fba2440">intensity</a> = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s][p].getIntensity();</div>
<div class="line"><a name="l00608"></a><span class="lineno">  608</span>&#160;                seeds.push_back(seed);</div>
<div class="line"><a name="l00609"></a><span class="lineno">  609</span>&#160;              }</div>
<div class="line"><a name="l00610"></a><span class="lineno">  610</span>&#160;              <span class="comment">//user-specified seeds: overall score greater than USER min seed score</span></div>
<div class="line"><a name="l00611"></a><span class="lineno">  611</span>&#160;              <span class="keywordflow">else</span> <span class="keywordflow">if</span> (user_seeds &amp;&amp; overall_score &gt;= user_seed_score)</div>
<div class="line"><a name="l00612"></a><span class="lineno">  612</span>&#160;              {</div>
<div class="line"><a name="l00613"></a><span class="lineno">  613</span>&#160;                <span class="comment">//only consider seeds, if they are near a user-specified seed</span></div>
<div class="line"><a name="l00614"></a><span class="lineno">  614</span>&#160;                FeatureType tmp;</div>
<div class="line"><a name="l00615"></a><span class="lineno">  615</span>&#160;                tmp.setMZ(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s][p].getMZ() - user_mz_tol);</div>
<div class="line"><a name="l00616"></a><span class="lineno">  616</span>&#160;                <span class="keywordflow">for</span> (<span class="keyword">typename</span> FeatureMapType::const_iterator it = std::lower_bound(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a>.begin(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a>.end(), tmp, <span class="keyword">typename</span> FeatureType::MZLess()); it &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a>.end(); ++it)</div>
<div class="line"><a name="l00617"></a><span class="lineno">  617</span>&#160;                {</div>
<div class="line"><a name="l00618"></a><span class="lineno">  618</span>&#160;                  <span class="keywordflow">if</span> (it-&gt;getMZ() &gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s][p].getMZ() + user_mz_tol)</div>
<div class="line"><a name="l00619"></a><span class="lineno">  619</span>&#160;                  {</div>
<div class="line"><a name="l00620"></a><span class="lineno">  620</span>&#160;                    <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00621"></a><span class="lineno">  621</span>&#160;                  }</div>
<div class="line"><a name="l00622"></a><span class="lineno">  622</span>&#160;                  <span class="keywordflow">if</span> (fabs(it-&gt;getMZ() - <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s][p].getMZ()) &lt; user_mz_tol &amp;&amp;</div>
<div class="line"><a name="l00623"></a><span class="lineno">  623</span>&#160;                      fabs(it-&gt;getRT() - <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getRT()) &lt; user_rt_tol)</div>
<div class="line"><a name="l00624"></a><span class="lineno">  624</span>&#160;                  {</div>
<div class="line"><a name="l00625"></a><span class="lineno">  625</span>&#160;                    <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">Seed</a> seed;</div>
<div class="line"><a name="l00626"></a><span class="lineno">  626</span>&#160;                    seed.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a> = s;</div>
<div class="line"><a name="l00627"></a><span class="lineno">  627</span>&#160;                    seed.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> = p;</div>
<div class="line"><a name="l00628"></a><span class="lineno">  628</span>&#160;                    seed.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#a2bf8eeb17dafb3d8ed1b08810fba2440">intensity</a> = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s][p].getIntensity();</div>
<div class="line"><a name="l00629"></a><span class="lineno">  629</span>&#160;                    seeds.push_back(seed);</div>
<div class="line"><a name="l00630"></a><span class="lineno">  630</span>&#160;                    <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00631"></a><span class="lineno">  631</span>&#160;                  }</div>
<div class="line"><a name="l00632"></a><span class="lineno">  632</span>&#160;                }</div>
<div class="line"><a name="l00633"></a><span class="lineno">  633</span>&#160;              }</div>
<div class="line"><a name="l00634"></a><span class="lineno">  634</span>&#160;            }</div>
<div class="line"><a name="l00635"></a><span class="lineno">  635</span>&#160;          }</div>
<div class="line"><a name="l00636"></a><span class="lineno">  636</span>&#160;        }</div>
<div class="line"><a name="l00637"></a><span class="lineno">  637</span>&#160;        <span class="comment">//sort seeds according to intensity</span></div>
<div class="line"><a name="l00638"></a><span class="lineno">  638</span>&#160;        std::sort(seeds.rbegin(), seeds.rend());</div>
<div class="line"><a name="l00639"></a><span class="lineno">  639</span>&#160;        <span class="comment">//create and store seeds map and selected peak map</span></div>
<div class="line"><a name="l00640"></a><span class="lineno">  640</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>)</div>
<div class="line"><a name="l00641"></a><span class="lineno">  641</span>&#160;        {</div>
<div class="line"><a name="l00642"></a><span class="lineno">  642</span>&#160;          <span class="comment">//seeds</span></div>
<div class="line"><a name="l00643"></a><span class="lineno">  643</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> seed_map;</div>
<div class="line"><a name="l00644"></a><span class="lineno">  644</span>&#160;          seed_map.reserve(seeds.size());</div>
<div class="line"><a name="l00645"></a><span class="lineno">  645</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; seeds.size(); ++i)</div>
<div class="line"><a name="l00646"></a><span class="lineno">  646</span>&#160;          {</div>
<div class="line"><a name="l00647"></a><span class="lineno">  647</span>&#160;            <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum = seeds[i].spectrum;</div>
<div class="line"><a name="l00648"></a><span class="lineno">  648</span>&#160;            <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak = seeds[i].peak;</div>
<div class="line"><a name="l00649"></a><span class="lineno">  649</span>&#160;            <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">FloatDataArrays</a>&amp; meta = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum].getFloatDataArrays();</div>
<div class="line"><a name="l00650"></a><span class="lineno">  650</span>&#160;            <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> tmp;</div>
<div class="line"><a name="l00651"></a><span class="lineno">  651</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(seeds[i].intensity);</div>
<div class="line"><a name="l00652"></a><span class="lineno">  652</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">setOverallQuality</a>(meta[meta_index_overall][peak]);</div>
<div class="line"><a name="l00653"></a><span class="lineno">  653</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum].getRT());</div>
<div class="line"><a name="l00654"></a><span class="lineno">  654</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum][peak].getMZ());</div>
<div class="line"><a name="l00655"></a><span class="lineno">  655</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;intensity_score&quot;</span>, meta[1][peak]);</div>
<div class="line"><a name="l00656"></a><span class="lineno">  656</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;pattern_score&quot;</span>, meta[meta_index_isotope][peak]);</div>
<div class="line"><a name="l00657"></a><span class="lineno">  657</span>&#160;            tmp.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;trace_score&quot;</span>, meta[0][peak]);</div>
<div class="line"><a name="l00658"></a><span class="lineno">  658</span>&#160;            seed_map.push_back(tmp);</div>
<div class="line"><a name="l00659"></a><span class="lineno">  659</span>&#160;          }</div>
<div class="line"><a name="l00660"></a><span class="lineno">  660</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a>().<a class="code" href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">store</a>(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;debug/seeds_&quot;</span>) + <a class="code" href="classOpenMS_1_1String.html">String</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>) + <span class="stringliteral">&quot;.featureXML&quot;</span>, seed_map);</div>
<div class="line"><a name="l00661"></a><span class="lineno">  661</span>&#160;        }</div>
<div class="line"><a name="l00662"></a><span class="lineno">  662</span>&#160;</div>
<div class="line"><a name="l00663"></a><span class="lineno">  663</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00664"></a><span class="lineno">  664</span>&#160;        std::cout &lt;&lt; <span class="stringliteral">&quot;Found &quot;</span> &lt;&lt; seeds.size() &lt;&lt; <span class="stringliteral">&quot; seeds for charge &quot;</span> &lt;&lt; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> &lt;&lt; <span class="stringliteral">&quot;.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00665"></a><span class="lineno">  665</span>&#160;</div>
<div class="line"><a name="l00666"></a><span class="lineno">  666</span>&#160;        <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00667"></a><span class="lineno">  667</span>&#160;        <span class="comment">//Step 3.3:</span></div>
<div class="line"><a name="l00668"></a><span class="lineno">  668</span>&#160;        <span class="comment">//Extension of seeds</span></div>
<div class="line"><a name="l00669"></a><span class="lineno">  669</span>&#160;        <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00670"></a><span class="lineno">  670</span>&#160;</div>
<div class="line"><a name="l00671"></a><span class="lineno">  671</span>&#160;        <span class="comment">// We do not want to store features whose seeds lie within other</span></div>
<div class="line"><a name="l00672"></a><span class="lineno">  672</span>&#160;        <span class="comment">// features with higher intensity. We thus store this information in</span></div>
<div class="line"><a name="l00673"></a><span class="lineno">  673</span>&#160;        <span class="comment">// the map seeds_in_features which contains for each seed i a vector</span></div>
<div class="line"><a name="l00674"></a><span class="lineno">  674</span>&#160;        <span class="comment">// of other seeds that are contained in the corresponding feature i.</span></div>
<div class="line"><a name="l00675"></a><span class="lineno">  675</span>&#160;        <span class="comment">//</span></div>
<div class="line"><a name="l00676"></a><span class="lineno">  676</span>&#160;        <span class="comment">// The features are stored in an temporary feature map until it is</span></div>
<div class="line"><a name="l00677"></a><span class="lineno">  677</span>&#160;        <span class="comment">// decided whether they are contained within a seed of higher</span></div>
<div class="line"><a name="l00678"></a><span class="lineno">  678</span>&#160;        <span class="comment">// intensity.</span></div>
<div class="line"><a name="l00679"></a><span class="lineno">  679</span>&#160;        std::map&lt;Size, std::vector&lt;Size&gt; &gt; seeds_in_features;</div>
<div class="line"><a name="l00680"></a><span class="lineno">  680</span>&#160;        <span class="keyword">typedef</span> std::map&lt;Size, FeatureType&gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abb9911ee4d024e85861f29bbbd0a63ef">FeatureMapType</a>;</div>
<div class="line"><a name="l00681"></a><span class="lineno">  681</span>&#160;        FeatureMapType tmp_feature_map;</div>
<div class="line"><a name="l00682"></a><span class="lineno">  682</span>&#160;        gl_progress = 0;</div>
<div class="line"><a name="l00683"></a><span class="lineno">  683</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, seeds.size(), <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Extending seeds for charge &quot;</span>) + <a class="code" href="classOpenMS_1_1String.html">String</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>));</div>
<div class="line"><a name="l00684"></a><span class="lineno">  684</span>&#160;<span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00685"></a><span class="lineno">  685</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#pragma omp parallel for</span></div>
<div class="line"><a name="l00686"></a><span class="lineno">  686</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00687"></a><span class="lineno">  687</span>&#160;<span class="preprocessor"></span>        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> i = 0; i &lt; (<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>)seeds.size(); ++i)</div>
<div class="line"><a name="l00688"></a><span class="lineno">  688</span>&#160;        {</div>
<div class="line"><a name="l00689"></a><span class="lineno">  689</span>&#160;          <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00690"></a><span class="lineno">  690</span>&#160;          <span class="comment">//Step 3.3.1:</span></div>
<div class="line"><a name="l00691"></a><span class="lineno">  691</span>&#160;          <span class="comment">//Extend all mass traces</span></div>
<div class="line"><a name="l00692"></a><span class="lineno">  692</span>&#160;          <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00693"></a><span class="lineno">  693</span>&#160;</div>
<div class="line"><a name="l00694"></a><span class="lineno">  694</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[seeds[i].spectrum];</div>
<div class="line"><a name="l00695"></a><span class="lineno">  695</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>&amp; peak = spectrum[seeds[i].peak];</div>
<div class="line"><a name="l00696"></a><span class="lineno">  696</span>&#160;</div>
<div class="line"><a name="l00697"></a><span class="lineno">  697</span>&#160;          <a class="code" href="OpenSwathChromatogramExtractor_8C.html#ad1b6cd7c1daf3c44f94b28a904153b46">IF_MASTERTHREAD</a></div>
<div class="line"><a name="l00698"></a><span class="lineno">  698</span>&#160;          {</div>
<div class="line"><a name="l00699"></a><span class="lineno">  699</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(gl_progress++);</div>
<div class="line"><a name="l00700"></a><span class="lineno">  700</span>&#160;</div>
<div class="line"><a name="l00701"></a><span class="lineno">  701</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>)</div>
<div class="line"><a name="l00702"></a><span class="lineno">  702</span>&#160;            {</div>
<div class="line"><a name="l00703"></a><span class="lineno">  703</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; std::endl &lt;&lt; <span class="stringliteral">&quot;Seed &quot;</span> &lt;&lt; i &lt;&lt; <span class="stringliteral">&quot;:&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00704"></a><span class="lineno">  704</span>&#160;              <span class="comment">//If the intensity is zero this seed is already uses in another feature</span></div>
<div class="line"><a name="l00705"></a><span class="lineno">  705</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Int: &quot;</span> &lt;&lt; peak.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() &lt;&lt; std::endl;</div>
<div class="line"><a name="l00706"></a><span class="lineno">  706</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - RT: &quot;</span> &lt;&lt; spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() &lt;&lt; std::endl;</div>
<div class="line"><a name="l00707"></a><span class="lineno">  707</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - MZ: &quot;</span> &lt;&lt; peak.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() &lt;&lt; std::endl;</div>
<div class="line"><a name="l00708"></a><span class="lineno">  708</span>&#160;            }</div>
<div class="line"><a name="l00709"></a><span class="lineno">  709</span>&#160;          }</div>
<div class="line"><a name="l00710"></a><span class="lineno">  710</span>&#160;</div>
<div class="line"><a name="l00711"></a><span class="lineno">  711</span>&#160;          <span class="comment">//----------------------------------------------------------------</span></div>
<div class="line"><a name="l00712"></a><span class="lineno">  712</span>&#160;          <span class="comment">//Find best fitting isotope pattern for this charge (using averagine)</span></div>
<div class="line"><a name="l00713"></a><span class="lineno">  713</span>&#160;          <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a> best_pattern(0);</div>
<div class="line"><a name="l00714"></a><span class="lineno">  714</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> isotope_fit_quality = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">findBestIsotopeFit_</a>(seeds[i], <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, best_pattern);</div>
<div class="line"><a name="l00715"></a><span class="lineno">  715</span>&#160;</div>
<div class="line"><a name="l00716"></a><span class="lineno">  716</span>&#160;          <span class="keywordflow">if</span> (isotope_fit_quality &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">min_isotope_fit_</a>)</div>
<div class="line"><a name="l00717"></a><span class="lineno">  717</span>&#160;          {</div>
<div class="line"><a name="l00718"></a><span class="lineno">  718</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">abort_</a>(seeds[i], <span class="stringliteral">&quot;Could not find good enough isotope pattern containing the seed&quot;</span>);</div>
<div class="line"><a name="l00719"></a><span class="lineno">  719</span>&#160;            <span class="comment">//continue;</span></div>
<div class="line"><a name="l00720"></a><span class="lineno">  720</span>&#160;          }</div>
<div class="line"><a name="l00721"></a><span class="lineno">  721</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00722"></a><span class="lineno">  722</span>&#160;          {</div>
<div class="line"><a name="l00723"></a><span class="lineno">  723</span>&#160;</div>
<div class="line"><a name="l00724"></a><span class="lineno">  724</span>&#160;            <span class="comment">//extend the convex hull in RT dimension (starting from the trace peaks)</span></div>
<div class="line"><a name="l00725"></a><span class="lineno">  725</span>&#160;            <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a> traces;</div>
<div class="line"><a name="l00726"></a><span class="lineno">  726</span>&#160;            traces.reserve(best_pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>.size());</div>
<div class="line"><a name="l00727"></a><span class="lineno">  727</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">extendMassTraces_</a>(best_pattern, traces, meta_index_overall);</div>
<div class="line"><a name="l00728"></a><span class="lineno">  728</span>&#160;</div>
<div class="line"><a name="l00729"></a><span class="lineno">  729</span>&#160;            <span class="comment">//check if the traces are still valid</span></div>
<div class="line"><a name="l00730"></a><span class="lineno">  730</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> seed_mz = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[seeds[i].spectrum][seeds[i].peak].getMZ();</div>
<div class="line"><a name="l00731"></a><span class="lineno">  731</span>&#160;</div>
<div class="line"><a name="l00732"></a><span class="lineno">  732</span>&#160;            <span class="keywordflow">if</span> (!traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a7e409d85407a4cfbc76fdc4aac06f185">isValid</a>(seed_mz, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a>))</div>
<div class="line"><a name="l00733"></a><span class="lineno">  733</span>&#160;            {</div>
<div class="line"><a name="l00734"></a><span class="lineno">  734</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">abort_</a>(seeds[i], <span class="stringliteral">&quot;Could not extend seed&quot;</span>);</div>
<div class="line"><a name="l00735"></a><span class="lineno">  735</span>&#160;              <span class="comment">//continue;</span></div>
<div class="line"><a name="l00736"></a><span class="lineno">  736</span>&#160;            }</div>
<div class="line"><a name="l00737"></a><span class="lineno">  737</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l00738"></a><span class="lineno">  738</span>&#160;            {</div>
<div class="line"><a name="l00739"></a><span class="lineno">  739</span>&#160;</div>
<div class="line"><a name="l00740"></a><span class="lineno">  740</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00741"></a><span class="lineno">  741</span>&#160;              <span class="comment">//Step 3.3.2:</span></div>
<div class="line"><a name="l00742"></a><span class="lineno">  742</span>&#160;              <span class="comment">//Gauss/EGH fit (first fit to find the feature boundaries)</span></div>
<div class="line"><a name="l00743"></a><span class="lineno">  743</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00744"></a><span class="lineno">  744</span>&#160;              <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> plot_nr = -1;</div>
<div class="line"><a name="l00745"></a><span class="lineno">  745</span>&#160;</div>
<div class="line"><a name="l00746"></a><span class="lineno">  746</span>&#160;<span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00747"></a><span class="lineno">  747</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#pragma omp critical (FeatureFinderAlgorithmPicked_PLOTNR)</span></div>
<div class="line"><a name="l00748"></a><span class="lineno">  748</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00749"></a><span class="lineno">  749</span>&#160;<span class="preprocessor"></span>              {</div>
<div class="line"><a name="l00750"></a><span class="lineno">  750</span>&#160;                plot_nr = ++plot_nr_global;</div>
<div class="line"><a name="l00751"></a><span class="lineno">  751</span>&#160;              }</div>
<div class="line"><a name="l00752"></a><span class="lineno">  752</span>&#160;</div>
<div class="line"><a name="l00753"></a><span class="lineno">  753</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00754"></a><span class="lineno">  754</span>&#160;</div>
<div class="line"><a name="l00755"></a><span class="lineno">  755</span>&#160;              <span class="comment">//TODO try fit with baseline term once more</span></div>
<div class="line"><a name="l00756"></a><span class="lineno">  756</span>&#160;              <span class="comment">//baseline estimate</span></div>
<div class="line"><a name="l00757"></a><span class="lineno">  757</span>&#160;              traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac342b58a6d6d5e6fae39d3300c37178d">updateBaseline</a>();</div>
<div class="line"><a name="l00758"></a><span class="lineno">  758</span>&#160;              traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a> = 0.75 * traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a>;</div>
<div class="line"><a name="l00759"></a><span class="lineno">  759</span>&#160;</div>
<div class="line"><a name="l00760"></a><span class="lineno">  760</span>&#160;              traces[traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>].updateMaximum();</div>
<div class="line"><a name="l00761"></a><span class="lineno">  761</span>&#160;</div>
<div class="line"><a name="l00762"></a><span class="lineno">  762</span>&#160;              <span class="comment">// choose fitter</span></div>
<div class="line"><a name="l00763"></a><span class="lineno">  763</span>&#160;              <span class="keywordtype">double</span> egh_tau = 0.0;</div>
<div class="line"><a name="l00764"></a><span class="lineno">  764</span>&#160;              <a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter&lt;PeakType&gt;</a>* fitter = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad832d6128e519d1c6a7fefd89158c37e">chooseTraceFitter_</a>(egh_tau);</div>
<div class="line"><a name="l00765"></a><span class="lineno">  765</span>&#160;</div>
<div class="line"><a name="l00766"></a><span class="lineno">  766</span>&#160;              fitter-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(trace_fitter_params);</div>
<div class="line"><a name="l00767"></a><span class="lineno">  767</span>&#160;              fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">fit</a>(traces);</div>
<div class="line"><a name="l00768"></a><span class="lineno">  768</span>&#160;</div>
<div class="line"><a name="l00769"></a><span class="lineno">  769</span>&#160;<span class="preprocessor">#if 0</span></div>
<div class="line"><a name="l00770"></a><span class="lineno">  770</span>&#160;<span class="preprocessor"></span>              <a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter&lt;PeakType&gt;</a>* alt_fitter = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1GaussTraceFitter.html">GaussTraceFitter&lt;PeakType&gt;</a>();</div>
<div class="line"><a name="l00771"></a><span class="lineno">  771</span>&#160;              <a class="code" href="classOpenMS_1_1Param.html">Param</a> alt_p;</div>
<div class="line"><a name="l00772"></a><span class="lineno">  772</span>&#160;              alt_p.setValue(<span class="stringliteral">&quot;max_iteration&quot;</span>, max_iterations);</div>
<div class="line"><a name="l00773"></a><span class="lineno">  773</span>&#160;              alt_p.setValue(<span class="stringliteral">&quot;epsilon_abs&quot;</span>, epsilon_abs);</div>
<div class="line"><a name="l00774"></a><span class="lineno">  774</span>&#160;              alt_p.setValue(<span class="stringliteral">&quot;epsilon_rel&quot;</span>, epsilon_rel);</div>
<div class="line"><a name="l00775"></a><span class="lineno">  775</span>&#160;</div>
<div class="line"><a name="l00776"></a><span class="lineno">  776</span>&#160;              alt_fitter-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(alt_p);</div>
<div class="line"><a name="l00777"></a><span class="lineno">  777</span>&#160;              alt_fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">fit</a>(traces);</div>
<div class="line"><a name="l00778"></a><span class="lineno">  778</span>&#160;</div>
<div class="line"><a name="l00779"></a><span class="lineno">  779</span>&#160;              <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;EGH:   &quot;</span> &lt;&lt; fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>() &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">getHeight</a>() &lt;&lt; std::endl;</div>
<div class="line"><a name="l00780"></a><span class="lineno">  780</span>&#160;              <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;GAUSS: &quot;</span> &lt;&lt; alt_fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>() &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; alt_fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">getHeight</a>() &lt;&lt; std::endl;</div>
<div class="line"><a name="l00781"></a><span class="lineno">  781</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00782"></a><span class="lineno">  782</span>&#160;<span class="preprocessor"></span>              <span class="comment">// what should come out</span></div>
<div class="line"><a name="l00783"></a><span class="lineno">  783</span>&#160;              <span class="comment">// left &quot;sigma&quot;</span></div>
<div class="line"><a name="l00784"></a><span class="lineno">  784</span>&#160;              <span class="comment">// right &quot;sigma&quot;</span></div>
<div class="line"><a name="l00785"></a><span class="lineno">  785</span>&#160;              <span class="comment">// x0 .. &quot;center&quot; position of RT fit</span></div>
<div class="line"><a name="l00786"></a><span class="lineno">  786</span>&#160;              <span class="comment">// height .. &quot;height&quot; of RT fit</span></div>
<div class="line"><a name="l00787"></a><span class="lineno">  787</span>&#160;</div>
<div class="line"><a name="l00788"></a><span class="lineno">  788</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00789"></a><span class="lineno">  789</span>&#160;</div>
<div class="line"><a name="l00790"></a><span class="lineno">  790</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00791"></a><span class="lineno">  791</span>&#160;              <span class="comment">//Step 3.3.3:</span></div>
<div class="line"><a name="l00792"></a><span class="lineno">  792</span>&#160;              <span class="comment">//Crop feature according to RT fit (2.5*sigma) and remove badly fitting traces</span></div>
<div class="line"><a name="l00793"></a><span class="lineno">  793</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00794"></a><span class="lineno">  794</span>&#160;              <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a> new_traces;</div>
<div class="line"><a name="l00795"></a><span class="lineno">  795</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">cropFeature_</a>(fitter, traces, new_traces);</div>
<div class="line"><a name="l00796"></a><span class="lineno">  796</span>&#160;</div>
<div class="line"><a name="l00797"></a><span class="lineno">  797</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00798"></a><span class="lineno">  798</span>&#160;              <span class="comment">//Step 3.3.4:</span></div>
<div class="line"><a name="l00799"></a><span class="lineno">  799</span>&#160;              <span class="comment">//Check if feature is ok</span></div>
<div class="line"><a name="l00800"></a><span class="lineno">  800</span>&#160;              <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00801"></a><span class="lineno">  801</span>&#160;              <a class="code" href="classOpenMS_1_1String.html">String</a> error_msg = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l00802"></a><span class="lineno">  802</span>&#160;</div>
<div class="line"><a name="l00803"></a><span class="lineno">  803</span>&#160;              <a class="code" href="classdouble.html">DoubleReal</a> fit_score = 0.0;</div>
<div class="line"><a name="l00804"></a><span class="lineno">  804</span>&#160;              <a class="code" href="classdouble.html">DoubleReal</a> correlation = 0.0;</div>
<div class="line"><a name="l00805"></a><span class="lineno">  805</span>&#160;              <a class="code" href="classdouble.html">DoubleReal</a> final_score = 0.0;</div>
<div class="line"><a name="l00806"></a><span class="lineno">  806</span>&#160;</div>
<div class="line"><a name="l00807"></a><span class="lineno">  807</span>&#160;              <span class="keywordtype">bool</span> feature_ok = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">checkFeatureQuality_</a>(fitter, new_traces, seed_mz, min_feature_score, error_msg, fit_score, correlation, final_score);</div>
<div class="line"><a name="l00808"></a><span class="lineno">  808</span>&#160;<span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00809"></a><span class="lineno">  809</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#pragma omp critical (FeatureFinderAlgorithmPicked_DEBUG)</span></div>
<div class="line"><a name="l00810"></a><span class="lineno">  810</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00811"></a><span class="lineno">  811</span>&#160;<span class="preprocessor"></span>              {</div>
<div class="line"><a name="l00812"></a><span class="lineno">  812</span>&#160;                <span class="comment">//write debug output of feature</span></div>
<div class="line"><a name="l00813"></a><span class="lineno">  813</span>&#160;                <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>)</div>
<div class="line"><a name="l00814"></a><span class="lineno">  814</span>&#160;                {</div>
<div class="line"><a name="l00815"></a><span class="lineno">  815</span>&#160;                  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4">writeFeatureDebugInfo_</a>(fitter, traces, new_traces, feature_ok, error_msg, final_score, plot_nr, peak);</div>
<div class="line"><a name="l00816"></a><span class="lineno">  816</span>&#160;                }</div>
<div class="line"><a name="l00817"></a><span class="lineno">  817</span>&#160;              }</div>
<div class="line"><a name="l00818"></a><span class="lineno">  818</span>&#160;              traces = new_traces;</div>
<div class="line"><a name="l00819"></a><span class="lineno">  819</span>&#160;</div>
<div class="line"><a name="l00820"></a><span class="lineno">  820</span>&#160;</div>
<div class="line"><a name="l00821"></a><span class="lineno">  821</span>&#160;              <span class="comment">//validity output</span></div>
<div class="line"><a name="l00822"></a><span class="lineno">  822</span>&#160;              <span class="keywordflow">if</span> (!feature_ok)</div>
<div class="line"><a name="l00823"></a><span class="lineno">  823</span>&#160;              {</div>
<div class="line"><a name="l00824"></a><span class="lineno">  824</span>&#160;                <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">abort_</a>(seeds[i], error_msg);</div>
<div class="line"><a name="l00825"></a><span class="lineno">  825</span>&#160;                <span class="comment">//continue;</span></div>
<div class="line"><a name="l00826"></a><span class="lineno">  826</span>&#160;              }</div>
<div class="line"><a name="l00827"></a><span class="lineno">  827</span>&#160;              <span class="keywordflow">else</span></div>
<div class="line"><a name="l00828"></a><span class="lineno">  828</span>&#160;              {</div>
<div class="line"><a name="l00829"></a><span class="lineno">  829</span>&#160;</div>
<div class="line"><a name="l00830"></a><span class="lineno">  830</span>&#160;                <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00831"></a><span class="lineno">  831</span>&#160;                <span class="comment">//Step 3.3.5:</span></div>
<div class="line"><a name="l00832"></a><span class="lineno">  832</span>&#160;                <span class="comment">//Feature creation</span></div>
<div class="line"><a name="l00833"></a><span class="lineno">  833</span>&#160;                <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00834"></a><span class="lineno">  834</span>&#160;                <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f;</div>
<div class="line"><a name="l00835"></a><span class="lineno">  835</span>&#160;                <span class="comment">//set label</span></div>
<div class="line"><a name="l00836"></a><span class="lineno">  836</span>&#160;                f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(3, plot_nr);</div>
<div class="line"><a name="l00837"></a><span class="lineno">  837</span>&#160;                f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">setCharge</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00838"></a><span class="lineno">  838</span>&#160;                f.<a class="code" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">setOverallQuality</a>(final_score);</div>
<div class="line"><a name="l00839"></a><span class="lineno">  839</span>&#160;                f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;score_fit&quot;</span>, fit_score);</div>
<div class="line"><a name="l00840"></a><span class="lineno">  840</span>&#160;                f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;score_correlation&quot;</span>, correlation);</div>
<div class="line"><a name="l00841"></a><span class="lineno">  841</span>&#160;                f.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>());</div>
<div class="line"><a name="l00842"></a><span class="lineno">  842</span>&#160;                f.<a class="code" href="classOpenMS_1_1BaseFeature.html#a908f7d0328c34d70706d48af082d4751">setWidth</a>(fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#aa1e7b6cd685312da3c92644d8fe71aac">getFWHM</a>());</div>
<div class="line"><a name="l00843"></a><span class="lineno">  843</span>&#160;</div>
<div class="line"><a name="l00844"></a><span class="lineno">  844</span>&#160;                <span class="comment">// Extract some of the model parameters.</span></div>
<div class="line"><a name="l00845"></a><span class="lineno">  845</span>&#160;                <span class="keywordflow">if</span> (egh_tau != 0.0)</div>
<div class="line"><a name="l00846"></a><span class="lineno">  846</span>&#160;                {</div>
<div class="line"><a name="l00847"></a><span class="lineno">  847</span>&#160;                  egh_tau = (<span class="keyword">static_cast&lt;</span><a class="code" href="classOpenMS_1_1EGHTraceFitter.html">EGHTraceFitter&lt;PeakType&gt;</a>*<span class="keyword">&gt;</span>(fitter))-&gt;getTau();</div>
<div class="line"><a name="l00848"></a><span class="lineno">  848</span>&#160;                  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;EGH_tau&quot;</span>, egh_tau);</div>
<div class="line"><a name="l00849"></a><span class="lineno">  849</span>&#160;                  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;EGH_height&quot;</span>, (<span class="keyword">static_cast&lt;</span><a class="code" href="classOpenMS_1_1EGHTraceFitter.html">EGHTraceFitter&lt;PeakType&gt;</a>*<span class="keyword">&gt;</span>(fitter))-&gt;getHeight());</div>
<div class="line"><a name="l00850"></a><span class="lineno">  850</span>&#160;                  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;EGH_sigma&quot;</span>, (<span class="keyword">static_cast&lt;</span><a class="code" href="classOpenMS_1_1EGHTraceFitter.html">EGHTraceFitter&lt;PeakType&gt;</a>*<span class="keyword">&gt;</span>(fitter))-&gt;getSigmaSquare());</div>
<div class="line"><a name="l00851"></a><span class="lineno">  851</span>&#160;                }</div>
<div class="line"><a name="l00852"></a><span class="lineno">  852</span>&#160;</div>
<div class="line"><a name="l00853"></a><span class="lineno">  853</span>&#160;                <span class="comment">// Calculate the mass of the feature: maximum, average, monoisotopic</span></div>
<div class="line"><a name="l00854"></a><span class="lineno">  854</span>&#160;                <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">reported_mz_</a> == <span class="stringliteral">&quot;maximum&quot;</span>)</div>
<div class="line"><a name="l00855"></a><span class="lineno">  855</span>&#160;                {</div>
<div class="line"><a name="l00856"></a><span class="lineno">  856</span>&#160;                  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(traces[traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#abd839e76d16452338866dd6bf6290c72">getTheoreticalmaxPosition</a>()].getAvgMZ());</div>
<div class="line"><a name="l00857"></a><span class="lineno">  857</span>&#160;                }</div>
<div class="line"><a name="l00858"></a><span class="lineno">  858</span>&#160;                <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">reported_mz_</a> == <span class="stringliteral">&quot;average&quot;</span>)</div>
<div class="line"><a name="l00859"></a><span class="lineno">  859</span>&#160;                {</div>
<div class="line"><a name="l00860"></a><span class="lineno">  860</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> total_intensity = 0.0;</div>
<div class="line"><a name="l00861"></a><span class="lineno">  861</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> average_mz = 0.0;</div>
<div class="line"><a name="l00862"></a><span class="lineno">  862</span>&#160;                  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> t = 0; t &lt; traces.size(); ++t)</div>
<div class="line"><a name="l00863"></a><span class="lineno">  863</span>&#160;                  {</div>
<div class="line"><a name="l00864"></a><span class="lineno">  864</span>&#160;                    <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; traces[t].peaks.size(); ++p)</div>
<div class="line"><a name="l00865"></a><span class="lineno">  865</span>&#160;                    {</div>
<div class="line"><a name="l00866"></a><span class="lineno">  866</span>&#160;                      average_mz += traces[t].peaks[p].second-&gt;getMZ() * traces[t].peaks[p].second-&gt;getIntensity();</div>
<div class="line"><a name="l00867"></a><span class="lineno">  867</span>&#160;                      total_intensity += traces[t].peaks[p].second-&gt;getIntensity();</div>
<div class="line"><a name="l00868"></a><span class="lineno">  868</span>&#160;                    }</div>
<div class="line"><a name="l00869"></a><span class="lineno">  869</span>&#160;                  }</div>
<div class="line"><a name="l00870"></a><span class="lineno">  870</span>&#160;                  average_mz /= total_intensity;</div>
<div class="line"><a name="l00871"></a><span class="lineno">  871</span>&#160;                  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(average_mz);</div>
<div class="line"><a name="l00872"></a><span class="lineno">  872</span>&#160;                }</div>
<div class="line"><a name="l00873"></a><span class="lineno">  873</span>&#160;                <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">reported_mz_</a> == <span class="stringliteral">&quot;monoisotopic&quot;</span>)</div>
<div class="line"><a name="l00874"></a><span class="lineno">  874</span>&#160;                {</div>
<div class="line"><a name="l00875"></a><span class="lineno">  875</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> mono_mz = traces[traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#abd839e76d16452338866dd6bf6290c72">getTheoreticalmaxPosition</a>()].getAvgMZ();</div>
<div class="line"><a name="l00876"></a><span class="lineno">  876</span>&#160;                  mono_mz -= (<a class="code" href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">Constants::PROTON_MASS_U</a> / <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>) * (traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#abd839e76d16452338866dd6bf6290c72">getTheoreticalmaxPosition</a>() + best_pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">theoretical_pattern</a>.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#abe90dc4ba735b87228bfe913b490f9f2">trimmed_left</a>);</div>
<div class="line"><a name="l00877"></a><span class="lineno">  877</span>&#160;                  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(mono_mz);</div>
<div class="line"><a name="l00878"></a><span class="lineno">  878</span>&#160;                }</div>
<div class="line"><a name="l00879"></a><span class="lineno">  879</span>&#160;</div>
<div class="line"><a name="l00880"></a><span class="lineno">  880</span>&#160;                <span class="comment">// Calculate intensity based on model only</span></div>
<div class="line"><a name="l00881"></a><span class="lineno">  881</span>&#160;                <span class="comment">// - the model does not include the baseline, so we ignore it here</span></div>
<div class="line"><a name="l00882"></a><span class="lineno">  882</span>&#160;                <span class="comment">// - as we scaled the isotope distribution to</span></div>
<div class="line"><a name="l00883"></a><span class="lineno">  883</span>&#160;                f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(</div>
<div class="line"><a name="l00884"></a><span class="lineno">  884</span>&#160;                  fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">getFeatureIntensityContribution</a>() <span class="comment">// was 2.5 * fitter-&gt;getHeight() * sigma</span></div>
<div class="line"><a name="l00885"></a><span class="lineno">  885</span>&#160;                  / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">getIsotopeDistribution_</a>(f.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>()).max);</div>
<div class="line"><a name="l00886"></a><span class="lineno">  886</span>&#160;</div>
<div class="line"><a name="l00887"></a><span class="lineno">  887</span>&#160;                <span class="comment">// we do not need the fitter anymore</span></div>
<div class="line"><a name="l00888"></a><span class="lineno">  888</span>&#160;                <span class="keyword">delete</span> fitter;</div>
<div class="line"><a name="l00889"></a><span class="lineno">  889</span>&#160;</div>
<div class="line"><a name="l00890"></a><span class="lineno">  890</span>&#160;                <span class="comment">//add convex hulls of mass traces</span></div>
<div class="line"><a name="l00891"></a><span class="lineno">  891</span>&#160;                <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; traces.size(); ++j)</div>
<div class="line"><a name="l00892"></a><span class="lineno">  892</span>&#160;                {</div>
<div class="line"><a name="l00893"></a><span class="lineno">  893</span>&#160;                  f.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().push_back(traces[j].getConvexhull());</div>
<div class="line"><a name="l00894"></a><span class="lineno">  894</span>&#160;                }</div>
<div class="line"><a name="l00895"></a><span class="lineno">  895</span>&#160;</div>
<div class="line"><a name="l00896"></a><span class="lineno">  896</span>&#160;<span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00897"></a><span class="lineno">  897</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#pragma omp critical (FeatureFinderAlgorithmPicked_TMPFEATUREMAP)</span></div>
<div class="line"><a name="l00898"></a><span class="lineno">  898</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00899"></a><span class="lineno">  899</span>&#160;<span class="preprocessor"></span>                {</div>
<div class="line"><a name="l00900"></a><span class="lineno">  900</span>&#160;                  tmp_feature_map[i] = f;</div>
<div class="line"><a name="l00901"></a><span class="lineno">  901</span>&#160;                }</div>
<div class="line"><a name="l00902"></a><span class="lineno">  902</span>&#160;</div>
<div class="line"><a name="l00903"></a><span class="lineno">  903</span>&#160;                <span class="comment">//----------------------------------------------------------------</span></div>
<div class="line"><a name="l00904"></a><span class="lineno">  904</span>&#160;                <span class="comment">//Remember all seeds that lie inside the convex hull of the new feature</span></div>
<div class="line"><a name="l00905"></a><span class="lineno">  905</span>&#160;                <a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> bb = f.<a class="code" href="classOpenMS_1_1Feature.html#ab071fe5bd7b2f969e4f9ed5d7467da1e">getConvexHull</a>().<a class="code" href="classOpenMS_1_1ConvexHull2D.html#a88c6186ce22fc5eae73df90899695229">getBoundingBox</a>();</div>
<div class="line"><a name="l00906"></a><span class="lineno">  906</span>&#160;                <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = i + 1; j &lt; seeds.size(); ++j)</div>
<div class="line"><a name="l00907"></a><span class="lineno">  907</span>&#160;                {</div>
<div class="line"><a name="l00908"></a><span class="lineno">  908</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> rt = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[seeds[j].spectrum].getRT();</div>
<div class="line"><a name="l00909"></a><span class="lineno">  909</span>&#160;                  <a class="code" href="classdouble.html">DoubleReal</a> mz = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[seeds[j].spectrum][seeds[j].peak].getMZ();</div>
<div class="line"><a name="l00910"></a><span class="lineno">  910</span>&#160;                  <span class="keywordflow">if</span> (bb.<a class="code" href="classOpenMS_1_1DBoundingBox.html#ac55b302033b5b9d7c78a223db8cfaffb">encloses</a>(rt, mz) &amp;&amp; f.<a class="code" href="classOpenMS_1_1Feature.html#a57c4a49592647cc2db0dc517ed9a1a02">encloses</a>(rt, mz))</div>
<div class="line"><a name="l00911"></a><span class="lineno">  911</span>&#160;                  {</div>
<div class="line"><a name="l00912"></a><span class="lineno">  912</span>&#160;<span class="preprocessor">#ifdef _OPENMP</span></div>
<div class="line"><a name="l00913"></a><span class="lineno">  913</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#pragma omp critical (FeatureFinderAlgorithmPicked_SEEDSINFEATURES)</span></div>
<div class="line"><a name="l00914"></a><span class="lineno">  914</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00915"></a><span class="lineno">  915</span>&#160;<span class="preprocessor"></span>                    {</div>
<div class="line"><a name="l00916"></a><span class="lineno">  916</span>&#160;                      seeds_in_features[i].push_back(j);</div>
<div class="line"><a name="l00917"></a><span class="lineno">  917</span>&#160;                    }</div>
<div class="line"><a name="l00918"></a><span class="lineno">  918</span>&#160;                  }</div>
<div class="line"><a name="l00919"></a><span class="lineno">  919</span>&#160;                }</div>
<div class="line"><a name="l00920"></a><span class="lineno">  920</span>&#160;              }</div>
<div class="line"><a name="l00921"></a><span class="lineno">  921</span>&#160;            }</div>
<div class="line"><a name="l00922"></a><span class="lineno">  922</span>&#160;          } <span class="comment">// three if/else statements instead of continue (disallowed in OpenMP)</span></div>
<div class="line"><a name="l00923"></a><span class="lineno">  923</span>&#160;        } <span class="comment">// end of OPENMP over seeds</span></div>
<div class="line"><a name="l00924"></a><span class="lineno">  924</span>&#160;</div>
<div class="line"><a name="l00925"></a><span class="lineno">  925</span>&#160;        <span class="comment">// Here we have to evaluate which seeds are already contained in</span></div>
<div class="line"><a name="l00926"></a><span class="lineno">  926</span>&#160;        <span class="comment">// features of seeds with higher intensities. Only if the seed is not</span></div>
<div class="line"><a name="l00927"></a><span class="lineno">  927</span>&#160;        <span class="comment">// used in any feature with higher intensity, we can add it to the</span></div>
<div class="line"><a name="l00928"></a><span class="lineno">  928</span>&#160;        <span class="comment">// features_ list.</span></div>
<div class="line"><a name="l00929"></a><span class="lineno">  929</span>&#160;        std::vector&lt;Size&gt; seeds_contained;</div>
<div class="line"><a name="l00930"></a><span class="lineno">  930</span>&#160;        <span class="keywordflow">for</span> (<span class="keyword">typename</span> std::map&lt;Size, FeatureType&gt;::iterator iter = tmp_feature_map.begin(); iter != tmp_feature_map.end(); ++iter)</div>
<div class="line"><a name="l00931"></a><span class="lineno">  931</span>&#160;        {</div>
<div class="line"><a name="l00932"></a><span class="lineno">  932</span>&#160;          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> seed_nr = iter-&gt;first;</div>
<div class="line"><a name="l00933"></a><span class="lineno">  933</span>&#160;          <span class="keywordtype">bool</span> is_used = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00934"></a><span class="lineno">  934</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; seeds_contained.size(); ++i)</div>
<div class="line"><a name="l00935"></a><span class="lineno">  935</span>&#160;          {</div>
<div class="line"><a name="l00936"></a><span class="lineno">  936</span>&#160;            <span class="keywordflow">if</span> (seed_nr == seeds_contained[i]) { is_used = <span class="keyword">true</span>; <span class="keywordflow">break</span>; }</div>
<div class="line"><a name="l00937"></a><span class="lineno">  937</span>&#160;          }</div>
<div class="line"><a name="l00938"></a><span class="lineno">  938</span>&#160;          <span class="keywordflow">if</span> (!is_used)</div>
<div class="line"><a name="l00939"></a><span class="lineno">  939</span>&#160;          {</div>
<div class="line"><a name="l00940"></a><span class="lineno">  940</span>&#160;            ++feature_candidates;</div>
<div class="line"><a name="l00941"></a><span class="lineno">  941</span>&#160;</div>
<div class="line"><a name="l00942"></a><span class="lineno">  942</span>&#160;            <span class="comment">//re-set label</span></div>
<div class="line"><a name="l00943"></a><span class="lineno">  943</span>&#160;            iter-&gt;second.setMetaValue(3, feature_nr_global);</div>
<div class="line"><a name="l00944"></a><span class="lineno">  944</span>&#160;            ++feature_nr_global;</div>
<div class="line"><a name="l00945"></a><span class="lineno">  945</span>&#160;            <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;push_back(iter-&gt;second);</div>
<div class="line"><a name="l00946"></a><span class="lineno">  946</span>&#160;</div>
<div class="line"><a name="l00947"></a><span class="lineno">  947</span>&#160;            std::vector&lt;Size&gt; curr_seed = seeds_in_features[seed_nr];</div>
<div class="line"><a name="l00948"></a><span class="lineno">  948</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; curr_seed.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00949"></a><span class="lineno">  949</span>&#160;            {</div>
<div class="line"><a name="l00950"></a><span class="lineno">  950</span>&#160;              seeds_contained.push_back(curr_seed[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>]);</div>
<div class="line"><a name="l00951"></a><span class="lineno">  951</span>&#160;</div>
<div class="line"><a name="l00952"></a><span class="lineno">  952</span>&#160;            }</div>
<div class="line"><a name="l00953"></a><span class="lineno">  953</span>&#160;          }</div>
<div class="line"><a name="l00954"></a><span class="lineno">  954</span>&#160;        }</div>
<div class="line"><a name="l00955"></a><span class="lineno">  955</span>&#160;</div>
<div class="line"><a name="l00956"></a><span class="lineno">  956</span>&#160;        <a class="code" href="OpenSwathChromatogramExtractor_8C.html#ad1b6cd7c1daf3c44f94b28a904153b46">IF_MASTERTHREAD</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00957"></a><span class="lineno">  957</span>&#160;        std::cout &lt;&lt; <span class="stringliteral">&quot;Found &quot;</span> &lt;&lt; feature_candidates &lt;&lt; <span class="stringliteral">&quot; feature candidates for charge &quot;</span> &lt;&lt; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> &lt;&lt; <span class="stringliteral">&quot;.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00958"></a><span class="lineno">  958</span>&#160;      }</div>
<div class="line"><a name="l00959"></a><span class="lineno">  959</span>&#160;      <span class="comment">// END OPENMP</span></div>
<div class="line"><a name="l00960"></a><span class="lineno">  960</span>&#160;</div>
<div class="line"><a name="l00961"></a><span class="lineno">  961</span>&#160;      <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00962"></a><span class="lineno">  962</span>&#160;      <span class="comment">//Step 4:</span></div>
<div class="line"><a name="l00963"></a><span class="lineno">  963</span>&#160;      <span class="comment">//Resolve contradicting and overlapping features</span></div>
<div class="line"><a name="l00964"></a><span class="lineno">  964</span>&#160;      <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l00965"></a><span class="lineno">  965</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size() * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size(), <span class="stringliteral">&quot;Resolving overlapping features&quot;</span>);</div>
<div class="line"><a name="l00966"></a><span class="lineno">  966</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;Resolving intersecting features (&quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size() &lt;&lt; <span class="stringliteral">&quot; candidates)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00967"></a><span class="lineno">  967</span>&#160;      <span class="comment">//sort features according to m/z in order to speed up the resolution</span></div>
<div class="line"><a name="l00968"></a><span class="lineno">  968</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;<a class="code" href="classOpenMS_1_1FeatureMap.html#a604ce6f3380b18acbebda3c1ed14e70c">sortByMZ</a>();</div>
<div class="line"><a name="l00969"></a><span class="lineno">  969</span>&#160;      <span class="comment">//precalculate BBs and maximum mz span</span></div>
<div class="line"><a name="l00970"></a><span class="lineno">  970</span>&#160;      std::vector&lt;DBoundingBox&lt;2&gt; &gt; bbs(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size());</div>
<div class="line"><a name="l00971"></a><span class="lineno">  971</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> max_mz_span = 0.0;</div>
<div class="line"><a name="l00972"></a><span class="lineno">  972</span>&#160;</div>
<div class="line"><a name="l00973"></a><span class="lineno">  973</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size(); ++i)</div>
<div class="line"><a name="l00974"></a><span class="lineno">  974</span>&#160;      {</div>
<div class="line"><a name="l00975"></a><span class="lineno">  975</span>&#160;        bbs[i] = (*features_)[i].getConvexHull().getBoundingBox();</div>
<div class="line"><a name="l00976"></a><span class="lineno">  976</span>&#160;        <span class="keywordflow">if</span> (bbs[i].height() &gt; max_mz_span)</div>
<div class="line"><a name="l00977"></a><span class="lineno">  977</span>&#160;        {</div>
<div class="line"><a name="l00978"></a><span class="lineno">  978</span>&#160;          max_mz_span = bbs[i].height();</div>
<div class="line"><a name="l00979"></a><span class="lineno">  979</span>&#160;        }</div>
<div class="line"><a name="l00980"></a><span class="lineno">  980</span>&#160;      }</div>
<div class="line"><a name="l00981"></a><span class="lineno">  981</span>&#160;</div>
<div class="line"><a name="l00982"></a><span class="lineno">  982</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> removed(0);</div>
<div class="line"><a name="l00983"></a><span class="lineno">  983</span>&#160;      <span class="comment">//intersect</span></div>
<div class="line"><a name="l00984"></a><span class="lineno">  984</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size(); ++i)</div>
<div class="line"><a name="l00985"></a><span class="lineno">  985</span>&#160;      {</div>
<div class="line"><a name="l00986"></a><span class="lineno">  986</span>&#160;        <a class="code" href="classOpenMS_1_1Feature.html">Feature</a>&amp; f1((*<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>)[i]);</div>
<div class="line"><a name="l00987"></a><span class="lineno">  987</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = i + 1; j &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size(); ++j)</div>
<div class="line"><a name="l00988"></a><span class="lineno">  988</span>&#160;        {</div>
<div class="line"><a name="l00989"></a><span class="lineno">  989</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(i * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size() + j);</div>
<div class="line"><a name="l00990"></a><span class="lineno">  990</span>&#160;          <a class="code" href="classOpenMS_1_1Feature.html">Feature</a>&amp; f2((*<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>)[j]);</div>
<div class="line"><a name="l00991"></a><span class="lineno">  991</span>&#160;          <span class="comment">//features that are more than 2 times the maximum m/z span apart do not overlap =&gt; abort</span></div>
<div class="line"><a name="l00992"></a><span class="lineno">  992</span>&#160;          <span class="keywordflow">if</span> (f2.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() - f1.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() &gt; 2.0 * max_mz_span) <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00993"></a><span class="lineno">  993</span>&#160;          <span class="comment">//do nothing if one of the features is already removed</span></div>
<div class="line"><a name="l00994"></a><span class="lineno">  994</span>&#160;          <span class="keywordflow">if</span> (f1.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() == 0.0 || f2.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() == 0.0) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00995"></a><span class="lineno">  995</span>&#160;          <span class="comment">//do nothing if the overall convex hulls do not overlap</span></div>
<div class="line"><a name="l00996"></a><span class="lineno">  996</span>&#160;          <span class="keywordflow">if</span> (!bbs[i].intersects(bbs[j])) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00997"></a><span class="lineno">  997</span>&#160;          <span class="comment">//act depending on the intersection</span></div>
<div class="line"><a name="l00998"></a><span class="lineno">  998</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> intersection = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#acc97fb931afc9e8f86fe9e40683a5a6c">intersection_</a>(f1, f2);</div>
<div class="line"><a name="l00999"></a><span class="lineno">  999</span>&#160;</div>
<div class="line"><a name="l01000"></a><span class="lineno"> 1000</span>&#160;          <span class="keywordflow">if</span> (intersection &gt;= <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">max_feature_intersection_</a>)</div>
<div class="line"><a name="l01001"></a><span class="lineno"> 1001</span>&#160;          {</div>
<div class="line"><a name="l01002"></a><span class="lineno"> 1002</span>&#160;            ++removed;</div>
<div class="line"><a name="l01003"></a><span class="lineno"> 1003</span>&#160;</div>
<div class="line"><a name="l01004"></a><span class="lineno"> 1004</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Intersection (&quot;</span> &lt;&lt; (i + 1) &lt;&lt; <span class="stringliteral">&quot;/&quot;</span> &lt;&lt; (j + 1) &lt;&lt; <span class="stringliteral">&quot;): &quot;</span> &lt;&lt; intersection &lt;&lt; std::endl;</div>
<div class="line"><a name="l01005"></a><span class="lineno"> 1005</span>&#160;            <span class="keywordflow">if</span> (f1.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>() == f2.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>())</div>
<div class="line"><a name="l01006"></a><span class="lineno"> 1006</span>&#160;            {</div>
<div class="line"><a name="l01007"></a><span class="lineno"> 1007</span>&#160;              <span class="keywordflow">if</span> (f1.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() * f1.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>() &gt; f2.<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() * f2.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>())</div>
<div class="line"><a name="l01008"></a><span class="lineno"> 1008</span>&#160;              {</div>
<div class="line"><a name="l01009"></a><span class="lineno"> 1009</span>&#160;                <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - same charge -&gt; removing duplicate &quot;</span> &lt;&lt; (j + 1) &lt;&lt; std::endl;</div>
<div class="line"><a name="l01010"></a><span class="lineno"> 1010</span>&#160;                f1.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(f2);</div>
<div class="line"><a name="l01011"></a><span class="lineno"> 1011</span>&#160;                f2.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0.0);</div>
<div class="line"><a name="l01012"></a><span class="lineno"> 1012</span>&#160;              }</div>
<div class="line"><a name="l01013"></a><span class="lineno"> 1013</span>&#160;              <span class="keywordflow">else</span></div>
<div class="line"><a name="l01014"></a><span class="lineno"> 1014</span>&#160;              {</div>
<div class="line"><a name="l01015"></a><span class="lineno"> 1015</span>&#160;                <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - same charge -&gt; removing duplicate &quot;</span> &lt;&lt; (i + 1) &lt;&lt; std::endl;</div>
<div class="line"><a name="l01016"></a><span class="lineno"> 1016</span>&#160;                f2.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(f1);</div>
<div class="line"><a name="l01017"></a><span class="lineno"> 1017</span>&#160;                f1.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0.0);</div>
<div class="line"><a name="l01018"></a><span class="lineno"> 1018</span>&#160;              }</div>
<div class="line"><a name="l01019"></a><span class="lineno"> 1019</span>&#160;            }</div>
<div class="line"><a name="l01020"></a><span class="lineno"> 1020</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (f2.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>() % f1.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>() == 0)</div>
<div class="line"><a name="l01021"></a><span class="lineno"> 1021</span>&#160;            {</div>
<div class="line"><a name="l01022"></a><span class="lineno"> 1022</span>&#160;              <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - different charge (one is the multiple of the other) -&gt; removing lower charge &quot;</span> &lt;&lt; (i + 1) &lt;&lt; std::endl;</div>
<div class="line"><a name="l01023"></a><span class="lineno"> 1023</span>&#160;              f2.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(f1);</div>
<div class="line"><a name="l01024"></a><span class="lineno"> 1024</span>&#160;              f1.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0.0);</div>
<div class="line"><a name="l01025"></a><span class="lineno"> 1025</span>&#160;            }</div>
<div class="line"><a name="l01026"></a><span class="lineno"> 1026</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (f1.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>() % f2.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>() == 0)</div>
<div class="line"><a name="l01027"></a><span class="lineno"> 1027</span>&#160;            {</div>
<div class="line"><a name="l01028"></a><span class="lineno"> 1028</span>&#160;              <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - different charge (one is the multiple of the other) -&gt; removing lower charge &quot;</span> &lt;&lt; (i + 1) &lt;&lt; std::endl;</div>
<div class="line"><a name="l01029"></a><span class="lineno"> 1029</span>&#160;              f1.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(f2);</div>
<div class="line"><a name="l01030"></a><span class="lineno"> 1030</span>&#160;              f2.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0.0);</div>
<div class="line"><a name="l01031"></a><span class="lineno"> 1031</span>&#160;            }</div>
<div class="line"><a name="l01032"></a><span class="lineno"> 1032</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l01033"></a><span class="lineno"> 1033</span>&#160;            {</div>
<div class="line"><a name="l01034"></a><span class="lineno"> 1034</span>&#160;              <span class="keywordflow">if</span> (f1.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>() &gt; f2.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>())</div>
<div class="line"><a name="l01035"></a><span class="lineno"> 1035</span>&#160;              {</div>
<div class="line"><a name="l01036"></a><span class="lineno"> 1036</span>&#160;                <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - different charge -&gt; removing lower score &quot;</span> &lt;&lt; (j + 1) &lt;&lt; std::endl;</div>
<div class="line"><a name="l01037"></a><span class="lineno"> 1037</span>&#160;                f1.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(f2);</div>
<div class="line"><a name="l01038"></a><span class="lineno"> 1038</span>&#160;                f2.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0.0);</div>
<div class="line"><a name="l01039"></a><span class="lineno"> 1039</span>&#160;              }</div>
<div class="line"><a name="l01040"></a><span class="lineno"> 1040</span>&#160;              <span class="keywordflow">else</span></div>
<div class="line"><a name="l01041"></a><span class="lineno"> 1041</span>&#160;              {</div>
<div class="line"><a name="l01042"></a><span class="lineno"> 1042</span>&#160;                <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - different charge -&gt; removing lower score &quot;</span> &lt;&lt; (i + 1) &lt;&lt; std::endl;</div>
<div class="line"><a name="l01043"></a><span class="lineno"> 1043</span>&#160;                f2.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(f1);</div>
<div class="line"><a name="l01044"></a><span class="lineno"> 1044</span>&#160;                f1.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0.0);</div>
<div class="line"><a name="l01045"></a><span class="lineno"> 1045</span>&#160;              }</div>
<div class="line"><a name="l01046"></a><span class="lineno"> 1046</span>&#160;            }</div>
<div class="line"><a name="l01047"></a><span class="lineno"> 1047</span>&#160;          }</div>
<div class="line"><a name="l01048"></a><span class="lineno"> 1048</span>&#160;        }</div>
<div class="line"><a name="l01049"></a><span class="lineno"> 1049</span>&#160;      }</div>
<div class="line"><a name="l01050"></a><span class="lineno"> 1050</span>&#160;      <a class="code" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a> &lt;&lt; <span class="stringliteral">&quot;Removed &quot;</span> &lt;&lt; removed &lt;&lt; <span class="stringliteral">&quot; overlapping features.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01051"></a><span class="lineno"> 1051</span>&#160;      <span class="comment">//finally remove features with intensity 0</span></div>
<div class="line"><a name="l01052"></a><span class="lineno"> 1052</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> tmp;</div>
<div class="line"><a name="l01053"></a><span class="lineno"> 1053</span>&#160;      tmp.reserve(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size());</div>
<div class="line"><a name="l01054"></a><span class="lineno"> 1054</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size(); ++i)</div>
<div class="line"><a name="l01055"></a><span class="lineno"> 1055</span>&#160;      {</div>
<div class="line"><a name="l01056"></a><span class="lineno"> 1056</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;operator[](i).getIntensity() != 0.0)</div>
<div class="line"><a name="l01057"></a><span class="lineno"> 1057</span>&#160;        {</div>
<div class="line"><a name="l01058"></a><span class="lineno"> 1058</span>&#160;          tmp.push_back(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;operator[](i));</div>
<div class="line"><a name="l01059"></a><span class="lineno"> 1059</span>&#160;        }</div>
<div class="line"><a name="l01060"></a><span class="lineno"> 1060</span>&#160;      }</div>
<div class="line"><a name="l01061"></a><span class="lineno"> 1061</span>&#160;      tmp.<a class="code" href="classOpenMS_1_1FeatureMap.html#a3554cb60a93215ed6c61b257a67efcc3">swapFeaturesOnly</a>(*<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>);</div>
<div class="line"><a name="l01062"></a><span class="lineno"> 1062</span>&#160;      <span class="comment">//sort features by intensity</span></div>
<div class="line"><a name="l01063"></a><span class="lineno"> 1063</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;<a class="code" href="classOpenMS_1_1FeatureMap.html#a93f1c9f620403aec160d98e83e125502">sortByIntensity</a>(<span class="keyword">true</span>);</div>
<div class="line"><a name="l01064"></a><span class="lineno"> 1064</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l01065"></a><span class="lineno"> 1065</span>&#160;      std::cout &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size() &lt;&lt; <span class="stringliteral">&quot; features left.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01066"></a><span class="lineno"> 1066</span>&#160;</div>
<div class="line"><a name="l01067"></a><span class="lineno"> 1067</span>&#160;      <span class="comment">//Abort reasons</span></div>
<div class="line"><a name="l01068"></a><span class="lineno"> 1068</span>&#160;      std::cout &lt;&lt; std::endl;</div>
<div class="line"><a name="l01069"></a><span class="lineno"> 1069</span>&#160;      std::cout &lt;&lt; <span class="stringliteral">&quot;Abort reasons during feature construction:&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01070"></a><span class="lineno"> 1070</span>&#160;      <span class="keywordflow">for</span> (std::map&lt;String, UInt&gt;::const_iterator it = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">aborts_</a>.begin(); it != <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">aborts_</a>.end(); ++it)</div>
<div class="line"><a name="l01071"></a><span class="lineno"> 1071</span>&#160;      {</div>
<div class="line"><a name="l01072"></a><span class="lineno"> 1072</span>&#160;        std::cout &lt;&lt; <span class="stringliteral">&quot;- &quot;</span> &lt;&lt; it-&gt;first &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; it-&gt;second &lt;&lt; std::endl;</div>
<div class="line"><a name="l01073"></a><span class="lineno"> 1073</span>&#160;      }</div>
<div class="line"><a name="l01074"></a><span class="lineno"> 1074</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>)</div>
<div class="line"><a name="l01075"></a><span class="lineno"> 1075</span>&#160;      {</div>
<div class="line"><a name="l01076"></a><span class="lineno"> 1076</span>&#160;        <span class="comment">//store map of abort reasons for failed seeds</span></div>
<div class="line"><a name="l01077"></a><span class="lineno"> 1077</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;&gt;</a> abort_map;</div>
<div class="line"><a name="l01078"></a><span class="lineno"> 1078</span>&#160;        abort_map.reserve(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">abort_reasons_</a>.size());</div>
<div class="line"><a name="l01079"></a><span class="lineno"> 1079</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> counter = 0;</div>
<div class="line"><a name="l01080"></a><span class="lineno"> 1080</span>&#160;        <span class="keywordflow">for</span> (<span class="keyword">typename</span> std::map&lt;Seed, String&gt;::iterator it2 = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">abort_reasons_</a>.begin(); it2 != <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">abort_reasons_</a>.end(); ++it2, ++counter)</div>
<div class="line"><a name="l01081"></a><span class="lineno"> 1081</span>&#160;        {</div>
<div class="line"><a name="l01082"></a><span class="lineno"> 1082</span>&#160;          <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f;</div>
<div class="line"><a name="l01083"></a><span class="lineno"> 1083</span>&#160;          f.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[it2-&gt;first.spectrum].getRT());</div>
<div class="line"><a name="l01084"></a><span class="lineno"> 1084</span>&#160;          f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[it2-&gt;first.spectrum][it2-&gt;first.peak].getMZ());</div>
<div class="line"><a name="l01085"></a><span class="lineno"> 1085</span>&#160;          f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[it2-&gt;first.spectrum][it2-&gt;first.peak].getIntensity());</div>
<div class="line"><a name="l01086"></a><span class="lineno"> 1086</span>&#160;          f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(<span class="stringliteral">&quot;label&quot;</span>, it2-&gt;second);</div>
<div class="line"><a name="l01087"></a><span class="lineno"> 1087</span>&#160;          f.<a class="code" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">setUniqueId</a>(counter); <span class="comment">// ID = index</span></div>
<div class="line"><a name="l01088"></a><span class="lineno"> 1088</span>&#160;          abort_map.push_back(f);</div>
<div class="line"><a name="l01089"></a><span class="lineno"> 1089</span>&#160;        }</div>
<div class="line"><a name="l01090"></a><span class="lineno"> 1090</span>&#160;        abort_map.<a class="code" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">setUniqueId</a>();</div>
<div class="line"><a name="l01091"></a><span class="lineno"> 1091</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureXMLFile.html">FeatureXMLFile</a>().<a class="code" href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">store</a>(<span class="stringliteral">&quot;debug/abort_reasons.featureXML&quot;</span>, abort_map);</div>
<div class="line"><a name="l01092"></a><span class="lineno"> 1092</span>&#160;</div>
<div class="line"><a name="l01093"></a><span class="lineno"> 1093</span>&#160;        <span class="comment">//store input map with calculated scores (without overall score)</span></div>
<div class="line"><a name="l01094"></a><span class="lineno"> 1094</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++s)</div>
<div class="line"><a name="l01095"></a><span class="lineno"> 1095</span>&#160;        {</div>
<div class="line"><a name="l01096"></a><span class="lineno"> 1096</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays().erase(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s].getFloatDataArrays().begin() + 2);</div>
<div class="line"><a name="l01097"></a><span class="lineno"> 1097</span>&#160;        }</div>
<div class="line"><a name="l01098"></a><span class="lineno"> 1098</span>&#160;        <a class="code" href="classOpenMS_1_1MzMLFile.html">MzMLFile</a>().<a class="code" href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">store</a>(<span class="stringliteral">&quot;debug/input.mzML&quot;</span>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>);</div>
<div class="line"><a name="l01099"></a><span class="lineno"> 1099</span>&#160;      }</div>
<div class="line"><a name="l01100"></a><span class="lineno"> 1100</span>&#160;</div>
<div class="line"><a name="l01101"></a><span class="lineno"> 1101</span>&#160;    }</div>
<div class="line"><a name="l01102"></a><span class="lineno"> 1102</span>&#160;</div>
<div class="line"><a name="l01103"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a81483ea6deb5aa7b6e11d0c3c871f532"> 1103</a></span>&#160;    <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;</a>* <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a81483ea6deb5aa7b6e11d0c3c871f532">create</a>()</div>
<div class="line"><a name="l01104"></a><span class="lineno"> 1104</span>&#160;    {</div>
<div class="line"><a name="l01105"></a><span class="lineno"> 1105</span>&#160;      <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">FeatureFinderAlgorithmPicked</a>();</div>
<div class="line"><a name="l01106"></a><span class="lineno"> 1106</span>&#160;    }</div>
<div class="line"><a name="l01107"></a><span class="lineno"> 1107</span>&#160;</div>
<div class="line"><a name="l01108"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af73fd15708e50e77665070023a09cc87"> 1108</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
<div class="line"><a name="l01109"></a><span class="lineno"> 1109</span>&#160;    {</div>
<div class="line"><a name="l01110"></a><span class="lineno"> 1110</span>&#160;      <span class="keywordflow">return</span> <span class="stringliteral">&quot;centroided&quot;</span>;</div>
<div class="line"><a name="l01111"></a><span class="lineno"> 1111</span>&#160;    }</div>
<div class="line"><a name="l01112"></a><span class="lineno"> 1112</span>&#160;</div>
<div class="line"><a name="l01113"></a><span class="lineno"> 1113</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l01115"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab"> 1115</a></span>&#160;    <a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>;</div>
<div class="line"><a name="l01117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35"> 1117</a></span>&#160;    <span class="keyword">mutable</span> std::ofstream <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a>;</div>
<div class="line"><a name="l01119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1"> 1119</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>;</div>
<div class="line"><a name="l01121"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4"> 1121</a></span>&#160;    std::map&lt;String, UInt&gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">aborts_</a>;</div>
<div class="line"><a name="l01123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47"> 1123</a></span>&#160;    std::map&lt;Seed, String&gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">abort_reasons_</a>;</div>
<div class="line"><a name="l01125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d"> 1125</a></span>&#160;    <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a>;</div>
<div class="line"><a name="l01126"></a><span class="lineno"> 1126</span>&#160;</div>
<div class="line"><a name="l01128"></a><span class="lineno"> 1128</span>&#160;</div>
<div class="line"><a name="l01129"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48"> 1129</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a>; </div>
<div class="line"><a name="l01130"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7"> 1130</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a>; </div>
<div class="line"><a name="l01131"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22"> 1131</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>; </div>
<div class="line"><a name="l01132"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b"> 1132</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">max_missing_trace_peaks_</a>; </div>
<div class="line"><a name="l01133"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917"> 1133</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">slope_bound_</a>; </div>
<div class="line"><a name="l01134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d"> 1134</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">intensity_percentage_</a>; </div>
<div class="line"><a name="l01135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7"> 1135</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">intensity_percentage_optional_</a>; </div>
<div class="line"><a name="l01136"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a"> 1136</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">optional_fit_improvement_</a>; </div>
<div class="line"><a name="l01137"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f"> 1137</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a>; </div>
<div class="line"><a name="l01138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e"> 1138</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a>; </div>
<div class="line"><a name="l01139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5"> 1139</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">min_isotope_fit_</a>; </div>
<div class="line"><a name="l01140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc"> 1140</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">min_trace_score_</a>; </div>
<div class="line"><a name="l01141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007"> 1141</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">min_rt_span_</a>; </div>
<div class="line"><a name="l01142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b"> 1142</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">max_rt_span_</a>; </div>
<div class="line"><a name="l01143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00"> 1143</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">max_feature_intersection_</a>; </div>
<div class="line"><a name="l01144"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e"> 1144</a></span>&#160;    <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">reported_mz_</a>; </div>
<div class="line"><a name="l01145"></a><span class="lineno"> 1145</span>&#160;</div>
<div class="line"><a name="l01146"></a><span class="lineno"> 1146</span>&#160;</div>
<div class="line"><a name="l01148"></a><span class="lineno"> 1148</span>&#160;</div>
<div class="line"><a name="l01149"></a><span class="lineno"> 1149</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a>;</div>
<div class="line"><a name="l01152"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89"> 1152</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a>;</div>
<div class="line"><a name="l01154"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0"> 1154</a></span>&#160;    std::vector&lt;std::vector&lt;std::vector&lt;DoubleReal&gt; &gt; &gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a>;</div>
<div class="line"><a name="l01156"></a><span class="lineno"> 1156</span>&#160;</div>
<div class="line"><a name="l01158"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee"> 1158</a></span>&#160;    std::vector&lt;TheoreticalIsotopePattern&gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>;</div>
<div class="line"><a name="l01159"></a><span class="lineno"> 1159</span>&#160;</div>
<div class="line"><a name="l01160"></a><span class="lineno"> 1160</span>&#160;    <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l01161"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d"> 1161</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</div>
<div class="line"><a name="l01162"></a><span class="lineno"> 1162</span>&#160;    {</div>
<div class="line"><a name="l01163"></a><span class="lineno"> 1163</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;mass_trace:mz_tolerance&quot;</span>);</div>
<div class="line"><a name="l01164"></a><span class="lineno"> 1164</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:mz_tolerance&quot;</span>);</div>
<div class="line"><a name="l01165"></a><span class="lineno"> 1165</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a> = (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>) std::floor((<a class="code" href="classdouble.html">DoubleReal</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;mass_trace:min_spectra&quot;</span>) * 0.5);</div>
<div class="line"><a name="l01166"></a><span class="lineno"> 1166</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">max_missing_trace_peaks_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;mass_trace:max_missing&quot;</span>);</div>
<div class="line"><a name="l01167"></a><span class="lineno"> 1167</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">slope_bound_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;mass_trace:slope_bound&quot;</span>);</div>
<div class="line"><a name="l01168"></a><span class="lineno"> 1168</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">intensity_percentage_</a> = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage&quot;</span>) / 100.0;</div>
<div class="line"><a name="l01169"></a><span class="lineno"> 1169</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">intensity_percentage_optional_</a> = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:intensity_percentage_optional&quot;</span>) / 100.0;</div>
<div class="line"><a name="l01170"></a><span class="lineno"> 1170</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">optional_fit_improvement_</a> = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:optional_fit_improvement&quot;</span>) / 100.0;</div>
<div class="line"><a name="l01171"></a><span class="lineno"> 1171</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;isotopic_pattern:mass_window_width&quot;</span>);</div>
<div class="line"><a name="l01172"></a><span class="lineno"> 1172</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a> =  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;intensity:bins&quot;</span>);</div>
<div class="line"><a name="l01173"></a><span class="lineno"> 1173</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">min_isotope_fit_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:min_isotope_fit&quot;</span>);</div>
<div class="line"><a name="l01174"></a><span class="lineno"> 1174</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">min_trace_score_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:min_trace_score&quot;</span>);</div>
<div class="line"><a name="l01175"></a><span class="lineno"> 1175</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">min_rt_span_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:min_rt_span&quot;</span>);</div>
<div class="line"><a name="l01176"></a><span class="lineno"> 1176</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">max_rt_span_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:max_rt_span&quot;</span>);</div>
<div class="line"><a name="l01177"></a><span class="lineno"> 1177</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">max_feature_intersection_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:max_intersection&quot;</span>);</div>
<div class="line"><a name="l01178"></a><span class="lineno"> 1178</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">reported_mz_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:reported_mz&quot;</span>);</div>
<div class="line"><a name="l01179"></a><span class="lineno"> 1179</span>&#160;    }</div>
<div class="line"><a name="l01180"></a><span class="lineno"> 1180</span>&#160;</div>
<div class="line"><a name="l01182"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b"> 1182</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">abort_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">Seed</a>&amp; seed, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; reason)</div>
<div class="line"><a name="l01183"></a><span class="lineno"> 1183</span>&#160;    {</div>
<div class="line"><a name="l01184"></a><span class="lineno"> 1184</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;Abort: &quot;</span> &lt;&lt; reason &lt;&lt; std::endl;</div>
<div class="line"><a name="l01185"></a><span class="lineno"> 1185</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">aborts_</a>[reason]++;</div>
<div class="line"><a name="l01186"></a><span class="lineno"> 1186</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">abort_reasons_</a>[seed] = reason;</div>
<div class="line"><a name="l01187"></a><span class="lineno"> 1187</span>&#160;    }</div>
<div class="line"><a name="l01188"></a><span class="lineno"> 1188</span>&#160;</div>
<div class="line"><a name="l01193"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#acc97fb931afc9e8f86fe9e40683a5a6c"> 1193</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#acc97fb931afc9e8f86fe9e40683a5a6c">intersection_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Feature.html">Feature</a>&amp; f1, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Feature.html">Feature</a>&amp; f2)<span class="keyword"> const</span></div>
<div class="line"><a name="l01194"></a><span class="lineno"> 1194</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01195"></a><span class="lineno"> 1195</span>&#160;      <span class="comment">//calculate the RT range sum of feature 1</span></div>
<div class="line"><a name="l01196"></a><span class="lineno"> 1196</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> s1 = 0.0;</div>
<div class="line"><a name="l01197"></a><span class="lineno"> 1197</span>&#160;      <span class="keyword">const</span> std::vector&lt;ConvexHull2D&gt;&amp; hulls1 = f1.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>();</div>
<div class="line"><a name="l01198"></a><span class="lineno"> 1198</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; hulls1.size(); ++i)</div>
<div class="line"><a name="l01199"></a><span class="lineno"> 1199</span>&#160;      {</div>
<div class="line"><a name="l01200"></a><span class="lineno"> 1200</span>&#160;        s1 += hulls1[i].getBoundingBox().width();</div>
<div class="line"><a name="l01201"></a><span class="lineno"> 1201</span>&#160;      }</div>
<div class="line"><a name="l01202"></a><span class="lineno"> 1202</span>&#160;</div>
<div class="line"><a name="l01203"></a><span class="lineno"> 1203</span>&#160;      <span class="comment">//calculate the RT range sum of feature 2</span></div>
<div class="line"><a name="l01204"></a><span class="lineno"> 1204</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> s2 = 0.0;</div>
<div class="line"><a name="l01205"></a><span class="lineno"> 1205</span>&#160;      <span class="keyword">const</span> std::vector&lt;ConvexHull2D&gt;&amp; hulls2 = f2.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>();</div>
<div class="line"><a name="l01206"></a><span class="lineno"> 1206</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; hulls2.size(); ++j)</div>
<div class="line"><a name="l01207"></a><span class="lineno"> 1207</span>&#160;      {</div>
<div class="line"><a name="l01208"></a><span class="lineno"> 1208</span>&#160;        s2 += hulls2[j].getBoundingBox().width();</div>
<div class="line"><a name="l01209"></a><span class="lineno"> 1209</span>&#160;      }</div>
<div class="line"><a name="l01210"></a><span class="lineno"> 1210</span>&#160;</div>
<div class="line"><a name="l01211"></a><span class="lineno"> 1211</span>&#160;      <span class="comment">//calculate overlap</span></div>
<div class="line"><a name="l01212"></a><span class="lineno"> 1212</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> overlap = 0.0;</div>
<div class="line"><a name="l01213"></a><span class="lineno"> 1213</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; hulls1.size(); ++i)</div>
<div class="line"><a name="l01214"></a><span class="lineno"> 1214</span>&#160;      {</div>
<div class="line"><a name="l01215"></a><span class="lineno"> 1215</span>&#160;        <a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> bb1 = hulls1[i].getBoundingBox();</div>
<div class="line"><a name="l01216"></a><span class="lineno"> 1216</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; hulls2.size(); ++j)</div>
<div class="line"><a name="l01217"></a><span class="lineno"> 1217</span>&#160;        {</div>
<div class="line"><a name="l01218"></a><span class="lineno"> 1218</span>&#160;          <a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> bb2 = hulls2[j].getBoundingBox();</div>
<div class="line"><a name="l01219"></a><span class="lineno"> 1219</span>&#160;          <span class="keywordflow">if</span> (bb1.<a class="code" href="classOpenMS_1_1DBoundingBox.html#af99d7503ed85cda7c0ccc2217f36cee1">intersects</a>(bb2))</div>
<div class="line"><a name="l01220"></a><span class="lineno"> 1220</span>&#160;          {</div>
<div class="line"><a name="l01221"></a><span class="lineno"> 1221</span>&#160;            <span class="keywordflow">if</span> (bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &lt;= bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &amp;&amp;</div>
<div class="line"><a name="l01222"></a><span class="lineno"> 1222</span>&#160;                bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0] &gt;= bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0]) <span class="comment">//bb1 contains bb2</span></div>
<div class="line"><a name="l01223"></a><span class="lineno"> 1223</span>&#160;            {</div>
<div class="line"><a name="l01224"></a><span class="lineno"> 1224</span>&#160;              overlap += bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a1d3473af083e9dd668d782424aa2da05">width</a>();</div>
<div class="line"><a name="l01225"></a><span class="lineno"> 1225</span>&#160;            }</div>
<div class="line"><a name="l01226"></a><span class="lineno"> 1226</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &lt;= bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &amp;&amp;</div>
<div class="line"><a name="l01227"></a><span class="lineno"> 1227</span>&#160;                     bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0] &gt;= bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0]) <span class="comment">//bb2 contains bb1</span></div>
<div class="line"><a name="l01228"></a><span class="lineno"> 1228</span>&#160;            {</div>
<div class="line"><a name="l01229"></a><span class="lineno"> 1229</span>&#160;              overlap += bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a1d3473af083e9dd668d782424aa2da05">width</a>();</div>
<div class="line"><a name="l01230"></a><span class="lineno"> 1230</span>&#160;            }</div>
<div class="line"><a name="l01231"></a><span class="lineno"> 1231</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &lt;= bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &amp;&amp;</div>
<div class="line"><a name="l01232"></a><span class="lineno"> 1232</span>&#160;                     bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0] &lt;= bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0]) <span class="comment">//the end of bb1 overlaps with bb2</span></div>
<div class="line"><a name="l01233"></a><span class="lineno"> 1233</span>&#160;            {</div>
<div class="line"><a name="l01234"></a><span class="lineno"> 1234</span>&#160;              overlap += bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0] - bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0];</div>
<div class="line"><a name="l01235"></a><span class="lineno"> 1235</span>&#160;            }</div>
<div class="line"><a name="l01236"></a><span class="lineno"> 1236</span>&#160;            <span class="keywordflow">else</span> <span class="keywordflow">if</span> (bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &lt;= bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0] &amp;&amp;</div>
<div class="line"><a name="l01237"></a><span class="lineno"> 1237</span>&#160;                     bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0] &lt;= bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0]) <span class="comment">//the end of bb2 overlaps with bb1</span></div>
<div class="line"><a name="l01238"></a><span class="lineno"> 1238</span>&#160;            {</div>
<div class="line"><a name="l01239"></a><span class="lineno"> 1239</span>&#160;              overlap += bb2.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>()[0] - bb1.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>()[0];</div>
<div class="line"><a name="l01240"></a><span class="lineno"> 1240</span>&#160;            }</div>
<div class="line"><a name="l01241"></a><span class="lineno"> 1241</span>&#160;          }</div>
<div class="line"><a name="l01242"></a><span class="lineno"> 1242</span>&#160;        }</div>
<div class="line"><a name="l01243"></a><span class="lineno"> 1243</span>&#160;      }</div>
<div class="line"><a name="l01244"></a><span class="lineno"> 1244</span>&#160;</div>
<div class="line"><a name="l01245"></a><span class="lineno"> 1245</span>&#160;      <span class="keywordflow">return</span> overlap / std::min(s1, s2);</div>
<div class="line"><a name="l01246"></a><span class="lineno"> 1246</span>&#160;    }</div>
<div class="line"><a name="l01247"></a><span class="lineno"> 1247</span>&#160;</div>
<div class="line"><a name="l01249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6"> 1249</a></span>&#160;    <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">TheoreticalIsotopePattern</a>&amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">getIsotopeDistribution_</a>(<a class="code" href="classdouble.html">DoubleReal</a> mass)<span class="keyword"> const</span></div>
<div class="line"><a name="l01250"></a><span class="lineno"> 1250</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01251"></a><span class="lineno"> 1251</span>&#160;      <span class="comment">//calculate index in the vector</span></div>
<div class="line"><a name="l01252"></a><span class="lineno"> 1252</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>) std::floor(mass / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a>);</div>
<div class="line"><a name="l01253"></a><span class="lineno"> 1253</span>&#160;</div>
<div class="line"><a name="l01254"></a><span class="lineno"> 1254</span>&#160;      <span class="keywordflow">if</span> (index &gt;= <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>.size())</div>
<div class="line"><a name="l01255"></a><span class="lineno"> 1255</span>&#160;      {</div>
<div class="line"><a name="l01256"></a><span class="lineno"> 1256</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidValue.html">Exception::InvalidValue</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;IsotopeDistribution not precalculated. Maximum allowed index is &quot;</span> + <a class="code" href="classOpenMS_1_1String.html">String</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>.size()), <a class="code" href="classOpenMS_1_1String.html">String</a>(index));</div>
<div class="line"><a name="l01257"></a><span class="lineno"> 1257</span>&#160;      }</div>
<div class="line"><a name="l01258"></a><span class="lineno"> 1258</span>&#160;</div>
<div class="line"><a name="l01259"></a><span class="lineno"> 1259</span>&#160;      <span class="comment">//Return distribution</span></div>
<div class="line"><a name="l01260"></a><span class="lineno"> 1260</span>&#160;      <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a>[index];</div>
<div class="line"><a name="l01261"></a><span class="lineno"> 1261</span>&#160;    }</div>
<div class="line"><a name="l01262"></a><span class="lineno"> 1262</span>&#160;</div>
<div class="line"><a name="l01270"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e"> 1270</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">findBestIsotopeFit_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">Seed</a>&amp; center, <a class="code" href="classunsigned_01int.html">UInt</a> charge, <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a>&amp; best_pattern)<span class="keyword"> const</span></div>
<div class="line"><a name="l01271"></a><span class="lineno"> 1271</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01272"></a><span class="lineno"> 1272</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;Testing isotope patterns for charge &quot;</span> &lt;&lt; charge &lt;&lt; <span class="stringliteral">&quot;: &quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01273"></a><span class="lineno"> 1273</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>];</div>
<div class="line"><a name="l01274"></a><span class="lineno"> 1274</span>&#160;      <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">TheoreticalIsotopePattern</a>&amp; isotopes = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">getIsotopeDistribution_</a>(spectrum[center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ() * charge);</div>
<div class="line"><a name="l01275"></a><span class="lineno"> 1275</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Seed: &quot;</span> &lt;&lt; center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> &lt;&lt; <span class="stringliteral">&quot; (mz:&quot;</span> &lt;&lt; spectrum[center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01276"></a><span class="lineno"> 1276</span>&#160;</div>
<div class="line"><a name="l01277"></a><span class="lineno"> 1277</span>&#160;      <span class="comment">//Find m/z boundaries of search space (linear search as this is local and we have the center already)</span></div>
<div class="line"><a name="l01278"></a><span class="lineno"> 1278</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> mass_window = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)(isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() + 1) / (<a class="code" href="classdouble.html">DoubleReal</a>)charge;</div>
<div class="line"><a name="l01279"></a><span class="lineno"> 1279</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Mass window: &quot;</span> &lt;&lt; mass_window &lt;&lt; std::endl;</div>
<div class="line"><a name="l01280"></a><span class="lineno"> 1280</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end = center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>;</div>
<div class="line"><a name="l01281"></a><span class="lineno"> 1281</span>&#160;      <span class="keywordflow">while</span> (end &lt; spectrum.size() &amp;&amp;</div>
<div class="line"><a name="l01282"></a><span class="lineno"> 1282</span>&#160;             spectrum[end].getMZ() &lt; spectrum[center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ() + mass_window)</div>
<div class="line"><a name="l01283"></a><span class="lineno"> 1283</span>&#160;      {</div>
<div class="line"><a name="l01284"></a><span class="lineno"> 1284</span>&#160;        ++end;</div>
<div class="line"><a name="l01285"></a><span class="lineno"> 1285</span>&#160;      }</div>
<div class="line"><a name="l01286"></a><span class="lineno"> 1286</span>&#160;      --end;</div>
<div class="line"><a name="l01287"></a><span class="lineno"> 1287</span>&#160;</div>
<div class="line"><a name="l01288"></a><span class="lineno"> 1288</span>&#160;      <span class="comment">//search begin</span></div>
<div class="line"><a name="l01289"></a><span class="lineno"> 1289</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin = center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>;</div>
<div class="line"><a name="l01290"></a><span class="lineno"> 1290</span>&#160;      <span class="keywordflow">while</span> (begin &gt;= 0 &amp;&amp;</div>
<div class="line"><a name="l01291"></a><span class="lineno"> 1291</span>&#160;             spectrum[begin].getMZ() &gt; spectrum[center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ() - mass_window)</div>
<div class="line"><a name="l01292"></a><span class="lineno"> 1292</span>&#160;      {</div>
<div class="line"><a name="l01293"></a><span class="lineno"> 1293</span>&#160;        --begin;</div>
<div class="line"><a name="l01294"></a><span class="lineno"> 1294</span>&#160;      }</div>
<div class="line"><a name="l01295"></a><span class="lineno"> 1295</span>&#160;      ++begin;</div>
<div class="line"><a name="l01296"></a><span class="lineno"> 1296</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Begin: &quot;</span> &lt;&lt; begin &lt;&lt; <span class="stringliteral">&quot; (mz:&quot;</span> &lt;&lt; spectrum[begin].getMZ() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01297"></a><span class="lineno"> 1297</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - End: &quot;</span> &lt;&lt; end &lt;&lt; <span class="stringliteral">&quot; (mz:&quot;</span> &lt;&lt; spectrum[end].getMZ() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01298"></a><span class="lineno"> 1298</span>&#160;</div>
<div class="line"><a name="l01299"></a><span class="lineno"> 1299</span>&#160;      <span class="comment">//fit isotope distribution to peaks</span></div>
<div class="line"><a name="l01300"></a><span class="lineno"> 1300</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> max_score = 0.0;</div>
<div class="line"><a name="l01301"></a><span class="lineno"> 1301</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start = begin; start &lt;= end; ++start)</div>
<div class="line"><a name="l01302"></a><span class="lineno"> 1302</span>&#160;      {</div>
<div class="line"><a name="l01303"></a><span class="lineno"> 1303</span>&#160;        <span class="comment">//find isotope peaks for the current start peak</span></div>
<div class="line"><a name="l01304"></a><span class="lineno"> 1304</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak_index = start;</div>
<div class="line"><a name="l01305"></a><span class="lineno"> 1305</span>&#160;        <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a> pattern(isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l01306"></a><span class="lineno"> 1306</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Fitting at &quot;</span> &lt;&lt; start &lt;&lt; <span class="stringliteral">&quot; (mz:&quot;</span> &lt;&lt; spectrum[start].getMZ() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01307"></a><span class="lineno"> 1307</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso = 0; iso &lt; isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++iso)</div>
<div class="line"><a name="l01308"></a><span class="lineno"> 1308</span>&#160;        {</div>
<div class="line"><a name="l01309"></a><span class="lineno"> 1309</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> pos = spectrum[start].getMZ() + iso / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)charge;</div>
<div class="line"><a name="l01310"></a><span class="lineno"> 1310</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">findIsotope_</a>(pos, center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>, pattern, iso, peak_index);</div>
<div class="line"><a name="l01311"></a><span class="lineno"> 1311</span>&#160;        }</div>
<div class="line"><a name="l01312"></a><span class="lineno"> 1312</span>&#160;</div>
<div class="line"><a name="l01313"></a><span class="lineno"> 1313</span>&#160;        <span class="comment">//check if the seed is contained, otherwise abort</span></div>
<div class="line"><a name="l01314"></a><span class="lineno"> 1314</span>&#160;        <span class="keywordtype">bool</span> seed_contained = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01315"></a><span class="lineno"> 1315</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso = 0; iso &lt; pattern.peak.size(); ++iso)</div>
<div class="line"><a name="l01316"></a><span class="lineno"> 1316</span>&#160;        {</div>
<div class="line"><a name="l01317"></a><span class="lineno"> 1317</span>&#160;          <span class="keywordflow">if</span> (pattern.peak[iso] == (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> &amp;&amp; pattern.spectrum[iso] == center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>)</div>
<div class="line"><a name="l01318"></a><span class="lineno"> 1318</span>&#160;          {</div>
<div class="line"><a name="l01319"></a><span class="lineno"> 1319</span>&#160;            seed_contained = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01320"></a><span class="lineno"> 1320</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01321"></a><span class="lineno"> 1321</span>&#160;          }</div>
<div class="line"><a name="l01322"></a><span class="lineno"> 1322</span>&#160;        }</div>
<div class="line"><a name="l01323"></a><span class="lineno"> 1323</span>&#160;        <span class="keywordflow">if</span> (!seed_contained)</div>
<div class="line"><a name="l01324"></a><span class="lineno"> 1324</span>&#160;        {</div>
<div class="line"><a name="l01325"></a><span class="lineno"> 1325</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - aborting: seed is not contained!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01326"></a><span class="lineno"> 1326</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01327"></a><span class="lineno"> 1327</span>&#160;        }</div>
<div class="line"><a name="l01328"></a><span class="lineno"> 1328</span>&#160;</div>
<div class="line"><a name="l01329"></a><span class="lineno"> 1329</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">isotopeScore_</a>(isotopes, pattern, <span class="keyword">false</span>);</div>
<div class="line"><a name="l01330"></a><span class="lineno"> 1330</span>&#160;</div>
<div class="line"><a name="l01331"></a><span class="lineno"> 1331</span>&#160;        <span class="comment">//check if the seed is still contained, otherwise abort</span></div>
<div class="line"><a name="l01332"></a><span class="lineno"> 1332</span>&#160;        seed_contained = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01333"></a><span class="lineno"> 1333</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso = 0; iso &lt; pattern.peak.size(); ++iso)</div>
<div class="line"><a name="l01334"></a><span class="lineno"> 1334</span>&#160;        {</div>
<div class="line"><a name="l01335"></a><span class="lineno"> 1335</span>&#160;          <span class="keywordflow">if</span> (pattern.peak[iso]     == (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> &amp;&amp;</div>
<div class="line"><a name="l01336"></a><span class="lineno"> 1336</span>&#160;              pattern.spectrum[iso] == center.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>)</div>
<div class="line"><a name="l01337"></a><span class="lineno"> 1337</span>&#160;          {</div>
<div class="line"><a name="l01338"></a><span class="lineno"> 1338</span>&#160;            seed_contained = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01339"></a><span class="lineno"> 1339</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01340"></a><span class="lineno"> 1340</span>&#160;          }</div>
<div class="line"><a name="l01341"></a><span class="lineno"> 1341</span>&#160;        }</div>
<div class="line"><a name="l01342"></a><span class="lineno"> 1342</span>&#160;        <span class="keywordflow">if</span> (!seed_contained)</div>
<div class="line"><a name="l01343"></a><span class="lineno"> 1343</span>&#160;        {</div>
<div class="line"><a name="l01344"></a><span class="lineno"> 1344</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - aborting: seed was removed during isotope fit!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01345"></a><span class="lineno"> 1345</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01346"></a><span class="lineno"> 1346</span>&#160;        }</div>
<div class="line"><a name="l01347"></a><span class="lineno"> 1347</span>&#160;</div>
<div class="line"><a name="l01348"></a><span class="lineno"> 1348</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - final score: &quot;</span> &lt;&lt; score &lt;&lt; std::endl;</div>
<div class="line"><a name="l01349"></a><span class="lineno"> 1349</span>&#160;        <span class="keywordflow">if</span> (score &gt; max_score)</div>
<div class="line"><a name="l01350"></a><span class="lineno"> 1350</span>&#160;        {</div>
<div class="line"><a name="l01351"></a><span class="lineno"> 1351</span>&#160;          max_score = score;</div>
<div class="line"><a name="l01352"></a><span class="lineno"> 1352</span>&#160;          best_pattern = pattern;</div>
<div class="line"><a name="l01353"></a><span class="lineno"> 1353</span>&#160;        }</div>
<div class="line"><a name="l01354"></a><span class="lineno"> 1354</span>&#160;      }</div>
<div class="line"><a name="l01355"></a><span class="lineno"> 1355</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - best score              : &quot;</span> &lt;&lt; max_score &lt;&lt; std::endl;</div>
<div class="line"><a name="l01356"></a><span class="lineno"> 1356</span>&#160;      best_pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">theoretical_pattern</a> = isotopes;</div>
<div class="line"><a name="l01357"></a><span class="lineno"> 1357</span>&#160;      <span class="keywordflow">return</span> max_score;</div>
<div class="line"><a name="l01358"></a><span class="lineno"> 1358</span>&#160;    }</div>
<div class="line"><a name="l01359"></a><span class="lineno"> 1359</span>&#160;</div>
<div class="line"><a name="l01367"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d"> 1367</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">extendMassTraces_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a>&amp; pattern, <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a>&amp; traces, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> meta_index_overall)<span class="keyword"> const</span></div>
<div class="line"><a name="l01368"></a><span class="lineno"> 1368</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01369"></a><span class="lineno"> 1369</span>&#160;      <span class="comment">//find index of the trace with the maximum intensity</span></div>
<div class="line"><a name="l01370"></a><span class="lineno"> 1370</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> max_int =  0.0;</div>
<div class="line"><a name="l01371"></a><span class="lineno"> 1371</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_trace_index = 0;</div>
<div class="line"><a name="l01372"></a><span class="lineno"> 1372</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>.size(); ++p)</div>
<div class="line"><a name="l01373"></a><span class="lineno"> 1373</span>&#160;      {</div>
<div class="line"><a name="l01374"></a><span class="lineno"> 1374</span>&#160;        <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[p] &lt; 0) <span class="keywordflow">continue</span>; <span class="comment">//skip missing and removed traces</span></div>
<div class="line"><a name="l01375"></a><span class="lineno"> 1375</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[p]][pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[p]].getIntensity() &gt; max_int)</div>
<div class="line"><a name="l01376"></a><span class="lineno"> 1376</span>&#160;        {</div>
<div class="line"><a name="l01377"></a><span class="lineno"> 1377</span>&#160;          max_int = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[p]][pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[p]].getIntensity();</div>
<div class="line"><a name="l01378"></a><span class="lineno"> 1378</span>&#160;          max_trace_index = p;</div>
<div class="line"><a name="l01379"></a><span class="lineno"> 1379</span>&#160;        }</div>
<div class="line"><a name="l01380"></a><span class="lineno"> 1380</span>&#160;      }</div>
<div class="line"><a name="l01381"></a><span class="lineno"> 1381</span>&#160;</div>
<div class="line"><a name="l01382"></a><span class="lineno"> 1382</span>&#160;      <span class="comment">//extend the maximum intensity trace to determine the boundaries in RT dimension</span></div>
<div class="line"><a name="l01383"></a><span class="lineno"> 1383</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start_index = pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[max_trace_index];</div>
<div class="line"><a name="l01384"></a><span class="lineno"> 1384</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>* start_peak = &amp;(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[max_trace_index]][pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[max_trace_index]]);</div>
<div class="line"><a name="l01385"></a><span class="lineno"> 1385</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> start_mz = start_peak-&gt;<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>();</div>
<div class="line"><a name="l01386"></a><span class="lineno"> 1386</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> start_rt = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[start_index].getRT();</div>
<div class="line"><a name="l01387"></a><span class="lineno"> 1387</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Trace &quot;</span> &lt;&lt; max_trace_index &lt;&lt; <span class="stringliteral">&quot; (maximum intensity)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01388"></a><span class="lineno"> 1388</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - extending from: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[start_index].getRT() &lt;&lt; <span class="stringliteral">&quot; / &quot;</span> &lt;&lt; start_mz &lt;&lt; <span class="stringliteral">&quot; (int: &quot;</span> &lt;&lt; start_peak-&gt;<a class="code" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01389"></a><span class="lineno"> 1389</span>&#160;      <span class="comment">//initialize the trace and extend</span></div>
<div class="line"><a name="l01390"></a><span class="lineno"> 1390</span>&#160;      <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">MassTrace</a> max_trace;</div>
<div class="line"><a name="l01391"></a><span class="lineno"> 1391</span>&#160;      max_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.push_back(std::make_pair(start_rt, start_peak));</div>
<div class="line"><a name="l01392"></a><span class="lineno"> 1392</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">extendMassTrace_</a>(max_trace, start_index, start_mz, <span class="keyword">false</span>, meta_index_overall);</div>
<div class="line"><a name="l01393"></a><span class="lineno"> 1393</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">extendMassTrace_</a>(max_trace, start_index, start_mz, <span class="keyword">true</span>, meta_index_overall);</div>
<div class="line"><a name="l01394"></a><span class="lineno"> 1394</span>&#160;</div>
<div class="line"><a name="l01395"></a><span class="lineno"> 1395</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt_max = max_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.back().first;</div>
<div class="line"><a name="l01396"></a><span class="lineno"> 1396</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt_min = max_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.begin()-&gt;first;</div>
<div class="line"><a name="l01397"></a><span class="lineno"> 1397</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - rt bounds: &quot;</span> &lt;&lt; rt_min &lt;&lt; <span class="stringliteral">&quot;-&quot;</span> &lt;&lt; rt_max &lt;&lt; std::endl;</div>
<div class="line"><a name="l01398"></a><span class="lineno"> 1398</span>&#160;      <span class="comment">//Abort if too few peak were found</span></div>
<div class="line"><a name="l01399"></a><span class="lineno"> 1399</span>&#160;      <span class="keywordflow">if</span> (!max_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#aac1b70a2ed67ead038c4d3f5ac4d8a81">isValid</a>() || max_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size() &lt; 2 * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a> - <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">max_missing_trace_peaks_</a>)</div>
<div class="line"><a name="l01400"></a><span class="lineno"> 1400</span>&#160;      {</div>
<div class="line"><a name="l01401"></a><span class="lineno"> 1401</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - could not extend trace with maximum intensity =&gt; abort&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01402"></a><span class="lineno"> 1402</span>&#160;        <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l01403"></a><span class="lineno"> 1403</span>&#160;      }</div>
<div class="line"><a name="l01404"></a><span class="lineno"> 1404</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p &lt; pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>.size(); ++p)</div>
<div class="line"><a name="l01405"></a><span class="lineno"> 1405</span>&#160;      {</div>
<div class="line"><a name="l01406"></a><span class="lineno"> 1406</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - Trace &quot;</span> &lt;&lt; p &lt;&lt; std::endl;</div>
<div class="line"><a name="l01407"></a><span class="lineno"> 1407</span>&#160;        <span class="keywordflow">if</span> (p == max_trace_index)</div>
<div class="line"><a name="l01408"></a><span class="lineno"> 1408</span>&#160;        {</div>
<div class="line"><a name="l01409"></a><span class="lineno"> 1409</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - previously extended maximum trace&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01410"></a><span class="lineno"> 1410</span>&#160;          traces.push_back(max_trace);</div>
<div class="line"><a name="l01411"></a><span class="lineno"> 1411</span>&#160;          traces.back().theoretical_int = pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">theoretical_pattern</a>.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>[p];</div>
<div class="line"><a name="l01412"></a><span class="lineno"> 1412</span>&#160;          traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a> = traces.size() - 1;</div>
<div class="line"><a name="l01413"></a><span class="lineno"> 1413</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01414"></a><span class="lineno"> 1414</span>&#160;        }</div>
<div class="line"><a name="l01415"></a><span class="lineno"> 1415</span>&#160;        <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">Seed</a> starting_peak;</div>
<div class="line"><a name="l01416"></a><span class="lineno"> 1416</span>&#160;        starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a> = pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[p];</div>
<div class="line"><a name="l01417"></a><span class="lineno"> 1417</span>&#160;        starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> = pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[p];</div>
<div class="line"><a name="l01418"></a><span class="lineno"> 1418</span>&#160;        <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[p] == -2)</div>
<div class="line"><a name="l01419"></a><span class="lineno"> 1419</span>&#160;        {</div>
<div class="line"><a name="l01420"></a><span class="lineno"> 1420</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - removed during isotope fit&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01421"></a><span class="lineno"> 1421</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01422"></a><span class="lineno"> 1422</span>&#160;        }</div>
<div class="line"><a name="l01423"></a><span class="lineno"> 1423</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[p] == -1)</div>
<div class="line"><a name="l01424"></a><span class="lineno"> 1424</span>&#160;        {</div>
<div class="line"><a name="l01425"></a><span class="lineno"> 1425</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - missing&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01426"></a><span class="lineno"> 1426</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01427"></a><span class="lineno"> 1427</span>&#160;        }</div>
<div class="line"><a name="l01428"></a><span class="lineno"> 1428</span>&#160;        starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#a2bf8eeb17dafb3d8ed1b08810fba2440">intensity</a> = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getIntensity();</div>
<div class="line"><a name="l01429"></a><span class="lineno"> 1429</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - trace seed: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>].getRT() &lt;&lt; <span class="stringliteral">&quot; / &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ() &lt;&lt; <span class="stringliteral">&quot; (int: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getIntensity() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01430"></a><span class="lineno"> 1430</span>&#160;</div>
<div class="line"><a name="l01431"></a><span class="lineno"> 1431</span>&#160;        <span class="comment">//search for nearby maximum of the mass trace as the extension assumes that it starts at the maximum</span></div>
<div class="line"><a name="l01432"></a><span class="lineno"> 1432</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> begin = std::max((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)0, starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a> - <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>);</div>
<div class="line"><a name="l01433"></a><span class="lineno"> 1433</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end = std::min(starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a> + <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>, (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l01434"></a><span class="lineno"> 1434</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> mz = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ();</div>
<div class="line"><a name="l01435"></a><span class="lineno"> 1435</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> inte = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getIntensity();</div>
<div class="line"><a name="l01436"></a><span class="lineno"> 1436</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum_index = begin; spectrum_index &lt; end; ++spectrum_index)</div>
<div class="line"><a name="l01437"></a><span class="lineno"> 1437</span>&#160;        {</div>
<div class="line"><a name="l01438"></a><span class="lineno"> 1438</span>&#160;          <span class="comment">//find better seeds (no-empty scan/low mz diff/higher intensity)</span></div>
<div class="line"><a name="l01439"></a><span class="lineno"> 1439</span>&#160;          <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> peak_index = -1;</div>
<div class="line"><a name="l01440"></a><span class="lineno"> 1440</span>&#160;          <span class="keywordflow">try</span></div>
<div class="line"><a name="l01441"></a><span class="lineno"> 1441</span>&#160;          {</div>
<div class="line"><a name="l01442"></a><span class="lineno"> 1442</span>&#160;            peak_index = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index].findNearest(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ());</div>
<div class="line"><a name="l01443"></a><span class="lineno"> 1443</span>&#160;          }</div>
<div class="line"><a name="l01444"></a><span class="lineno"> 1444</span>&#160;          <span class="keywordflow">catch</span> (...) <span class="comment">//no peaks in the spectrum</span></div>
<div class="line"><a name="l01445"></a><span class="lineno"> 1445</span>&#160;          {</div>
<div class="line"><a name="l01446"></a><span class="lineno"> 1446</span>&#160;            peak_index = -1;</div>
<div class="line"><a name="l01447"></a><span class="lineno"> 1447</span>&#160;          }</div>
<div class="line"><a name="l01448"></a><span class="lineno"> 1448</span>&#160;</div>
<div class="line"><a name="l01449"></a><span class="lineno"> 1449</span>&#160;          <span class="keywordflow">if</span> (peak_index &lt; 0 ||</div>
<div class="line"><a name="l01450"></a><span class="lineno"> 1450</span>&#160;              <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index].getIntensity() &lt;= inte ||</div>
<div class="line"><a name="l01451"></a><span class="lineno"> 1451</span>&#160;              std::fabs(mz - <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index].getMZ()) &gt;= <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a></div>
<div class="line"><a name="l01452"></a><span class="lineno"> 1452</span>&#160;              )</div>
<div class="line"><a name="l01453"></a><span class="lineno"> 1453</span>&#160;          {</div>
<div class="line"><a name="l01454"></a><span class="lineno"> 1454</span>&#160;            <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01455"></a><span class="lineno"> 1455</span>&#160;          }</div>
<div class="line"><a name="l01456"></a><span class="lineno"> 1456</span>&#160;</div>
<div class="line"><a name="l01457"></a><span class="lineno"> 1457</span>&#160;          starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a> = spectrum_index;</div>
<div class="line"><a name="l01458"></a><span class="lineno"> 1458</span>&#160;          starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a> = peak_index;</div>
<div class="line"><a name="l01459"></a><span class="lineno"> 1459</span>&#160;          inte = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index].getIntensity();</div>
<div class="line"><a name="l01460"></a><span class="lineno"> 1460</span>&#160;        }</div>
<div class="line"><a name="l01461"></a><span class="lineno"> 1461</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - extending from: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>].getRT() &lt;&lt; <span class="stringliteral">&quot; / &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getMZ() &lt;&lt; <span class="stringliteral">&quot; (int: &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>].getIntensity() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01462"></a><span class="lineno"> 1462</span>&#160;</div>
<div class="line"><a name="l01463"></a><span class="lineno"> 1463</span>&#160;        <span class="comment">//------------------------------------------------------------------</span></div>
<div class="line"><a name="l01464"></a><span class="lineno"> 1464</span>&#160;        <span class="comment">//Extend seed to a mass trace</span></div>
<div class="line"><a name="l01465"></a><span class="lineno"> 1465</span>&#160;        <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">MassTrace</a> trace;</div>
<div class="line"><a name="l01466"></a><span class="lineno"> 1466</span>&#160;        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>* seed = &amp;(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>][starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">peak</a>]);</div>
<div class="line"><a name="l01467"></a><span class="lineno"> 1467</span>&#160;        <span class="comment">//initialize trace with seed data and extend</span></div>
<div class="line"><a name="l01468"></a><span class="lineno"> 1468</span>&#160;        trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.push_back(std::make_pair(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>].getRT(), seed));</div>
<div class="line"><a name="l01469"></a><span class="lineno"> 1469</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">extendMassTrace_</a>(trace, starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>, seed-&gt;<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>(), <span class="keyword">false</span>, meta_index_overall, rt_min, rt_max);</div>
<div class="line"><a name="l01470"></a><span class="lineno"> 1470</span>&#160;        <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">extendMassTrace_</a>(trace, starting_peak.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">spectrum</a>, seed-&gt;<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>(), <span class="keyword">true</span>, meta_index_overall, rt_min, rt_max);</div>
<div class="line"><a name="l01471"></a><span class="lineno"> 1471</span>&#160;</div>
<div class="line"><a name="l01472"></a><span class="lineno"> 1472</span>&#160;        <span class="comment">//check if enough peaks were found</span></div>
<div class="line"><a name="l01473"></a><span class="lineno"> 1473</span>&#160;        <span class="keywordflow">if</span> (!trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#aac1b70a2ed67ead038c4d3f5ac4d8a81">isValid</a>())</div>
<div class="line"><a name="l01474"></a><span class="lineno"> 1474</span>&#160;        {</div>
<div class="line"><a name="l01475"></a><span class="lineno"> 1475</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - could not extend trace &quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01476"></a><span class="lineno"> 1476</span>&#160;          <span class="comment">//Missing traces in the middle of a pattern are not acceptable =&gt; fix this</span></div>
<div class="line"><a name="l01477"></a><span class="lineno"> 1477</span>&#160;          <span class="keywordflow">if</span> (p &lt; traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>)</div>
<div class="line"><a name="l01478"></a><span class="lineno"> 1478</span>&#160;          {</div>
<div class="line"><a name="l01479"></a><span class="lineno"> 1479</span>&#160;            traces.clear(); <span class="comment">//remove earlier traces</span></div>
<div class="line"><a name="l01480"></a><span class="lineno"> 1480</span>&#160;            <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l01481"></a><span class="lineno"> 1481</span>&#160;          }</div>
<div class="line"><a name="l01482"></a><span class="lineno"> 1482</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (p &gt; traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>)</div>
<div class="line"><a name="l01483"></a><span class="lineno"> 1483</span>&#160;          {</div>
<div class="line"><a name="l01484"></a><span class="lineno"> 1484</span>&#160;            <span class="keywordflow">break</span>; <span class="comment">//no more traces are possible</span></div>
<div class="line"><a name="l01485"></a><span class="lineno"> 1485</span>&#160;          }</div>
<div class="line"><a name="l01486"></a><span class="lineno"> 1486</span>&#160;        }</div>
<div class="line"><a name="l01487"></a><span class="lineno"> 1487</span>&#160;        traces.push_back(trace);</div>
<div class="line"><a name="l01488"></a><span class="lineno"> 1488</span>&#160;        traces.back().theoretical_int = pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">theoretical_pattern</a>.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>[p];</div>
<div class="line"><a name="l01489"></a><span class="lineno"> 1489</span>&#160;      }</div>
<div class="line"><a name="l01490"></a><span class="lineno"> 1490</span>&#160;    }</div>
<div class="line"><a name="l01491"></a><span class="lineno"> 1491</span>&#160;</div>
<div class="line"><a name="l01510"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f"> 1510</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">extendMassTrace_</a>(<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">MassTrace</a>&amp; trace, <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> spectrum_index, <a class="code" href="classdouble.html">DoubleReal</a> mz, <span class="keywordtype">bool</span> increase_rt, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> meta_index_overall, <a class="code" href="classdouble.html">DoubleReal</a> min_rt = 0.0, <a class="code" href="classdouble.html">DoubleReal</a> max_rt = 0.0)<span class="keyword"> const</span></div>
<div class="line"><a name="l01511"></a><span class="lineno"> 1511</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01512"></a><span class="lineno"> 1512</span>&#160;      <span class="comment">//Reverse peaks if we run the method for the second time (to keep them in chronological order)</span></div>
<div class="line"><a name="l01513"></a><span class="lineno"> 1513</span>&#160;      <span class="keywordflow">if</span> (increase_rt)</div>
<div class="line"><a name="l01514"></a><span class="lineno"> 1514</span>&#160;      {</div>
<div class="line"><a name="l01515"></a><span class="lineno"> 1515</span>&#160;        ++spectrum_index;</div>
<div class="line"><a name="l01516"></a><span class="lineno"> 1516</span>&#160;        std::reverse(trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.begin(), trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.end());</div>
<div class="line"><a name="l01517"></a><span class="lineno"> 1517</span>&#160;      }</div>
<div class="line"><a name="l01518"></a><span class="lineno"> 1518</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l01519"></a><span class="lineno"> 1519</span>&#160;      {</div>
<div class="line"><a name="l01520"></a><span class="lineno"> 1520</span>&#160;        --spectrum_index;</div>
<div class="line"><a name="l01521"></a><span class="lineno"> 1521</span>&#160;      }</div>
<div class="line"><a name="l01522"></a><span class="lineno"> 1522</span>&#160;</div>
<div class="line"><a name="l01523"></a><span class="lineno"> 1523</span>&#160;      <span class="comment">//check if boundaries are set</span></div>
<div class="line"><a name="l01524"></a><span class="lineno"> 1524</span>&#160;      <span class="keywordtype">bool</span> boundaries = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01525"></a><span class="lineno"> 1525</span>&#160;      <span class="keywordflow">if</span> (max_rt != min_rt)</div>
<div class="line"><a name="l01526"></a><span class="lineno"> 1526</span>&#160;      {</div>
<div class="line"><a name="l01527"></a><span class="lineno"> 1527</span>&#160;        boundaries = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01528"></a><span class="lineno"> 1528</span>&#160;      }</div>
<div class="line"><a name="l01529"></a><span class="lineno"> 1529</span>&#160;</div>
<div class="line"><a name="l01530"></a><span class="lineno"> 1530</span>&#160;      <span class="comment">//Relax slope theshold if there is a hard boundary for the extension</span></div>
<div class="line"><a name="l01531"></a><span class="lineno"> 1531</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> current_slope_bound = (1.0 + (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)boundaries) * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">slope_bound_</a>;</div>
<div class="line"><a name="l01532"></a><span class="lineno"> 1532</span>&#160;</div>
<div class="line"><a name="l01533"></a><span class="lineno"> 1533</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> delta_count = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a>;</div>
<div class="line"><a name="l01534"></a><span class="lineno"> 1534</span>&#160;      std::vector&lt;DoubleReal&gt; deltas(delta_count - 1, 0);</div>
<div class="line"><a name="l01535"></a><span class="lineno"> 1535</span>&#160;</div>
<div class="line"><a name="l01536"></a><span class="lineno"> 1536</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> last_observed_intensity = trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.back().second-&gt;getIntensity();</div>
<div class="line"><a name="l01537"></a><span class="lineno"> 1537</span>&#160;</div>
<div class="line"><a name="l01538"></a><span class="lineno"> 1538</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> missing_peaks = 0;</div>
<div class="line"><a name="l01539"></a><span class="lineno"> 1539</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peaks_before_extension = trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size();</div>
<div class="line"><a name="l01540"></a><span class="lineno"> 1540</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> abort_reason = <span class="stringliteral">&quot;&quot;</span>;</div>
<div class="line"><a name="l01541"></a><span class="lineno"> 1541</span>&#160;</div>
<div class="line"><a name="l01542"></a><span class="lineno"> 1542</span>&#160;      <span class="keywordflow">while</span> ((!increase_rt &amp;&amp; spectrum_index &gt;= 0) || (increase_rt &amp;&amp; spectrum_index &lt; (<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>)<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>()))</div>
<div class="line"><a name="l01543"></a><span class="lineno"> 1543</span>&#160;      {</div>
<div class="line"><a name="l01544"></a><span class="lineno"> 1544</span>&#160;        <span class="keywordflow">if</span> (boundaries &amp;&amp;</div>
<div class="line"><a name="l01545"></a><span class="lineno"> 1545</span>&#160;            ((!increase_rt &amp;&amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index].getRT() &lt; min_rt) ||</div>
<div class="line"><a name="l01546"></a><span class="lineno"> 1546</span>&#160;             (increase_rt &amp;&amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index].getRT() &gt; max_rt))</div>
<div class="line"><a name="l01547"></a><span class="lineno"> 1547</span>&#160;            )</div>
<div class="line"><a name="l01548"></a><span class="lineno"> 1548</span>&#160;        {</div>
<div class="line"><a name="l01549"></a><span class="lineno"> 1549</span>&#160;          abort_reason = <span class="stringliteral">&quot;Hit upper/lower boundary&quot;</span>;</div>
<div class="line"><a name="l01550"></a><span class="lineno"> 1550</span>&#160;          <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01551"></a><span class="lineno"> 1551</span>&#160;        }</div>
<div class="line"><a name="l01552"></a><span class="lineno"> 1552</span>&#160;</div>
<div class="line"><a name="l01553"></a><span class="lineno"> 1553</span>&#160;        <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> peak_index = -1;</div>
<div class="line"><a name="l01554"></a><span class="lineno"> 1554</span>&#160;</div>
<div class="line"><a name="l01555"></a><span class="lineno"> 1555</span>&#160;        <span class="keywordflow">try</span></div>
<div class="line"><a name="l01556"></a><span class="lineno"> 1556</span>&#160;        {</div>
<div class="line"><a name="l01557"></a><span class="lineno"> 1557</span>&#160;          peak_index = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index].findNearest(mz);</div>
<div class="line"><a name="l01558"></a><span class="lineno"> 1558</span>&#160;        }</div>
<div class="line"><a name="l01559"></a><span class="lineno"> 1559</span>&#160;        <span class="keywordflow">catch</span> (...) <span class="comment">//no peaks in the spectrum</span></div>
<div class="line"><a name="l01560"></a><span class="lineno"> 1560</span>&#160;        {</div>
<div class="line"><a name="l01561"></a><span class="lineno"> 1561</span>&#160;          peak_index = -1;</div>
<div class="line"><a name="l01562"></a><span class="lineno"> 1562</span>&#160;        }</div>
<div class="line"><a name="l01563"></a><span class="lineno"> 1563</span>&#160;</div>
<div class="line"><a name="l01564"></a><span class="lineno"> 1564</span>&#160;        <span class="comment">// check if the peak is &quot;missing&quot;</span></div>
<div class="line"><a name="l01565"></a><span class="lineno"> 1565</span>&#160;        <span class="keywordflow">if</span> (</div>
<div class="line"><a name="l01566"></a><span class="lineno"> 1566</span>&#160;          peak_index &lt; 0 <span class="comment">// no peak found</span></div>
<div class="line"><a name="l01567"></a><span class="lineno"> 1567</span>&#160;           || <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index].getFloatDataArrays()[meta_index_overall][peak_index] &lt; 0.01 <span class="comment">// overall score is to low</span></div>
<div class="line"><a name="l01568"></a><span class="lineno"> 1568</span>&#160;           || <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(mz, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index].getMZ(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a>) == 0.0 <span class="comment">// deviation of mz is too big</span></div>
<div class="line"><a name="l01569"></a><span class="lineno"> 1569</span>&#160;          )</div>
<div class="line"><a name="l01570"></a><span class="lineno"> 1570</span>&#160;        {</div>
<div class="line"><a name="l01571"></a><span class="lineno"> 1571</span>&#160;          ++missing_peaks;</div>
<div class="line"><a name="l01572"></a><span class="lineno"> 1572</span>&#160;</div>
<div class="line"><a name="l01573"></a><span class="lineno"> 1573</span>&#160;          <span class="keywordflow">if</span> (missing_peaks &gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">max_missing_trace_peaks_</a>)</div>
<div class="line"><a name="l01574"></a><span class="lineno"> 1574</span>&#160;          {</div>
<div class="line"><a name="l01575"></a><span class="lineno"> 1575</span>&#160;            abort_reason = <span class="stringliteral">&quot;too many peaks missing&quot;</span>;</div>
<div class="line"><a name="l01576"></a><span class="lineno"> 1576</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01577"></a><span class="lineno"> 1577</span>&#160;          }</div>
<div class="line"><a name="l01578"></a><span class="lineno"> 1578</span>&#160;        }</div>
<div class="line"><a name="l01579"></a><span class="lineno"> 1579</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01580"></a><span class="lineno"> 1580</span>&#160;        {</div>
<div class="line"><a name="l01581"></a><span class="lineno"> 1581</span>&#160;          missing_peaks = 0;</div>
<div class="line"><a name="l01582"></a><span class="lineno"> 1582</span>&#160;</div>
<div class="line"><a name="l01583"></a><span class="lineno"> 1583</span>&#160;          <span class="comment">//add found peak to trace</span></div>
<div class="line"><a name="l01584"></a><span class="lineno"> 1584</span>&#160;          trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.push_back(std::make_pair(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index].getRT(), &amp;(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index])));</div>
<div class="line"><a name="l01585"></a><span class="lineno"> 1585</span>&#160;</div>
<div class="line"><a name="l01586"></a><span class="lineno"> 1586</span>&#160;          <span class="comment">//update deltas and intensities</span></div>
<div class="line"><a name="l01587"></a><span class="lineno"> 1587</span>&#160;          deltas.push_back((<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index].getIntensity() - last_observed_intensity) / last_observed_intensity);</div>
<div class="line"><a name="l01588"></a><span class="lineno"> 1588</span>&#160;          last_observed_intensity = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index][peak_index].getIntensity();</div>
<div class="line"><a name="l01589"></a><span class="lineno"> 1589</span>&#160;</div>
<div class="line"><a name="l01590"></a><span class="lineno"> 1590</span>&#160;          <span class="comment">//Abort if the average delta is too big (as intensity increases then)</span></div>
<div class="line"><a name="l01591"></a><span class="lineno"> 1591</span>&#160;          <a class="code" href="classdouble.html">DoubleReal</a> average_delta = std::accumulate(deltas.end() - delta_count, deltas.end(), 0.0) / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)delta_count;</div>
<div class="line"><a name="l01592"></a><span class="lineno"> 1592</span>&#160;          <span class="keywordflow">if</span> (average_delta &gt; current_slope_bound)</div>
<div class="line"><a name="l01593"></a><span class="lineno"> 1593</span>&#160;          {</div>
<div class="line"><a name="l01594"></a><span class="lineno"> 1594</span>&#160;            abort_reason = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Average delta above threshold: &quot;</span>) + average_delta + <span class="stringliteral">&quot;/&quot;</span> + current_slope_bound;</div>
<div class="line"><a name="l01595"></a><span class="lineno"> 1595</span>&#160;</div>
<div class="line"><a name="l01596"></a><span class="lineno"> 1596</span>&#160;            <span class="comment">//remove last peaks as we extended too far</span></div>
<div class="line"><a name="l01597"></a><span class="lineno"> 1597</span>&#160;            <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <span class="keyword">remove</span> = std::min((<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>)(trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size() - peaks_before_extension), delta_count - 1);</div>
<div class="line"><a name="l01598"></a><span class="lineno"> 1598</span>&#160;            trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.erase(trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.end() - <span class="keyword">remove</span>, trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.end());</div>
<div class="line"><a name="l01599"></a><span class="lineno"> 1599</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01600"></a><span class="lineno"> 1600</span>&#160;          }</div>
<div class="line"><a name="l01601"></a><span class="lineno"> 1601</span>&#160;        }</div>
<div class="line"><a name="l01602"></a><span class="lineno"> 1602</span>&#160;</div>
<div class="line"><a name="l01603"></a><span class="lineno"> 1603</span>&#160;        <span class="comment">//increase/decrease scan index</span></div>
<div class="line"><a name="l01604"></a><span class="lineno"> 1604</span>&#160;        <span class="keywordflow">if</span> (increase_rt) ++spectrum_index;</div>
<div class="line"><a name="l01605"></a><span class="lineno"> 1605</span>&#160;        <span class="keywordflow">else</span> --spectrum_index;</div>
<div class="line"><a name="l01606"></a><span class="lineno"> 1606</span>&#160;      }</div>
<div class="line"><a name="l01607"></a><span class="lineno"> 1607</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - Added &quot;</span> &lt;&lt; (trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size() - peaks_before_extension) &lt;&lt; <span class="stringliteral">&quot; peaks (abort: &quot;</span> &lt;&lt; abort_reason &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01608"></a><span class="lineno"> 1608</span>&#160;    }</div>
<div class="line"><a name="l01609"></a><span class="lineno"> 1609</span>&#160;</div>
<div class="line"><a name="l01611"></a><span class="lineno"> 1611</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l01612"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5c38e77e9286e4faf58e56afce913ee2"> 1612</a></span>&#160;    <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5c38e77e9286e4faf58e56afce913ee2">nearest_</a>(<a class="code" href="classdouble.html">DoubleReal</a> pos, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spec, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start)<span class="keyword"> const</span></div>
<div class="line"><a name="l01613"></a><span class="lineno"> 1613</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01614"></a><span class="lineno"> 1614</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = start;</div>
<div class="line"><a name="l01615"></a><span class="lineno"> 1615</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> distance = std::fabs(pos - spec[index].getMZ());</div>
<div class="line"><a name="l01616"></a><span class="lineno"> 1616</span>&#160;      ++index;</div>
<div class="line"><a name="l01617"></a><span class="lineno"> 1617</span>&#160;      <span class="keywordflow">while</span> (index &lt; spec.size())</div>
<div class="line"><a name="l01618"></a><span class="lineno"> 1618</span>&#160;      {</div>
<div class="line"><a name="l01619"></a><span class="lineno"> 1619</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> new_distance = std::fabs(pos - spec[index].getMZ());</div>
<div class="line"><a name="l01620"></a><span class="lineno"> 1620</span>&#160;        <span class="keywordflow">if</span> (new_distance &lt; distance)</div>
<div class="line"><a name="l01621"></a><span class="lineno"> 1621</span>&#160;        {</div>
<div class="line"><a name="l01622"></a><span class="lineno"> 1622</span>&#160;          distance = new_distance;</div>
<div class="line"><a name="l01623"></a><span class="lineno"> 1623</span>&#160;          ++index;</div>
<div class="line"><a name="l01624"></a><span class="lineno"> 1624</span>&#160;        }</div>
<div class="line"><a name="l01625"></a><span class="lineno"> 1625</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l01626"></a><span class="lineno"> 1626</span>&#160;        {</div>
<div class="line"><a name="l01627"></a><span class="lineno"> 1627</span>&#160;          <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01628"></a><span class="lineno"> 1628</span>&#160;        }</div>
<div class="line"><a name="l01629"></a><span class="lineno"> 1629</span>&#160;      }</div>
<div class="line"><a name="l01630"></a><span class="lineno"> 1630</span>&#160;      <span class="keywordflow">return</span> --index;</div>
<div class="line"><a name="l01631"></a><span class="lineno"> 1631</span>&#160;    }</div>
<div class="line"><a name="l01632"></a><span class="lineno"> 1632</span>&#160;</div>
<div class="line"><a name="l01642"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973"> 1642</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">findIsotope_</a>(<a class="code" href="classdouble.html">DoubleReal</a> pos, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum_index, <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a>&amp; pattern, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> pattern_index, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>&amp; peak_index)<span class="keyword"> const</span></div>
<div class="line"><a name="l01643"></a><span class="lineno"> 1643</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01644"></a><span class="lineno"> 1644</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - Isotope &quot;</span> &lt;&lt; pattern_index &lt;&lt; <span class="stringliteral">&quot;: &quot;</span>;</div>
<div class="line"><a name="l01645"></a><span class="lineno"> 1645</span>&#160;</div>
<div class="line"><a name="l01646"></a><span class="lineno"> 1646</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> intensity = 0.0;</div>
<div class="line"><a name="l01647"></a><span class="lineno"> 1647</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> pos_score = 0.0;</div>
<div class="line"><a name="l01648"></a><span class="lineno"> 1648</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> matches = 0;</div>
<div class="line"><a name="l01649"></a><span class="lineno"> 1649</span>&#160;</div>
<div class="line"><a name="l01650"></a><span class="lineno"> 1650</span>&#160;      <span class="comment">//search in the center spectrum</span></div>
<div class="line"><a name="l01651"></a><span class="lineno"> 1651</span>&#160;      <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index];</div>
<div class="line"><a name="l01652"></a><span class="lineno"> 1652</span>&#160;      peak_index = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5c38e77e9286e4faf58e56afce913ee2">nearest_</a>(pos, spectrum, peak_index);</div>
<div class="line"><a name="l01653"></a><span class="lineno"> 1653</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> mz_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(pos, spectrum[peak_index].getMZ(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a>);</div>
<div class="line"><a name="l01654"></a><span class="lineno"> 1654</span>&#160;      pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a7d03330cd21316709f10c3e9ca55f95c">theoretical_mz</a>[pattern_index] = pos;</div>
<div class="line"><a name="l01655"></a><span class="lineno"> 1655</span>&#160;</div>
<div class="line"><a name="l01656"></a><span class="lineno"> 1656</span>&#160;      <span class="keywordflow">if</span> (mz_score != 0.0)</div>
<div class="line"><a name="l01657"></a><span class="lineno"> 1657</span>&#160;      {</div>
<div class="line"><a name="l01658"></a><span class="lineno"> 1658</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(spectrum[peak_index].getIntensity(), 1) &lt;&lt; <span class="stringliteral">&quot; &quot;</span>;</div>
<div class="line"><a name="l01659"></a><span class="lineno"> 1659</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern_index] = peak_index;</div>
<div class="line"><a name="l01660"></a><span class="lineno"> 1660</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[pattern_index] = spectrum_index;</div>
<div class="line"><a name="l01661"></a><span class="lineno"> 1661</span>&#160;        intensity += spectrum[peak_index].getIntensity();</div>
<div class="line"><a name="l01662"></a><span class="lineno"> 1662</span>&#160;        pos_score += mz_score;</div>
<div class="line"><a name="l01663"></a><span class="lineno"> 1663</span>&#160;        ++matches;</div>
<div class="line"><a name="l01664"></a><span class="lineno"> 1664</span>&#160;      }</div>
<div class="line"><a name="l01665"></a><span class="lineno"> 1665</span>&#160;</div>
<div class="line"><a name="l01666"></a><span class="lineno"> 1666</span>&#160;      <span class="comment">//previous spectrum</span></div>
<div class="line"><a name="l01667"></a><span class="lineno"> 1667</span>&#160;      <span class="keywordflow">if</span> (spectrum_index != 0 &amp;&amp; !<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index - 1].empty())</div>
<div class="line"><a name="l01668"></a><span class="lineno"> 1668</span>&#160;      {</div>
<div class="line"><a name="l01669"></a><span class="lineno"> 1669</span>&#160;        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum_before = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index - 1];</div>
<div class="line"><a name="l01670"></a><span class="lineno"> 1670</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index_before = spectrum_before.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a830e58a22131827d85007a70e3069a5f">findNearest</a>(pos);</div>
<div class="line"><a name="l01671"></a><span class="lineno"> 1671</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> mz_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(pos, spectrum_before[index_before].getMZ(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a>);</div>
<div class="line"><a name="l01672"></a><span class="lineno"> 1672</span>&#160;        <span class="keywordflow">if</span> (mz_score != 0.0)</div>
<div class="line"><a name="l01673"></a><span class="lineno"> 1673</span>&#160;        {</div>
<div class="line"><a name="l01674"></a><span class="lineno"> 1674</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(spectrum_before[index_before].getIntensity(), 1) &lt;&lt; <span class="stringliteral">&quot;b &quot;</span>;</div>
<div class="line"><a name="l01675"></a><span class="lineno"> 1675</span>&#160;          intensity += spectrum_before[index_before].getIntensity();</div>
<div class="line"><a name="l01676"></a><span class="lineno"> 1676</span>&#160;          pos_score += mz_score;</div>
<div class="line"><a name="l01677"></a><span class="lineno"> 1677</span>&#160;          ++matches;</div>
<div class="line"><a name="l01678"></a><span class="lineno"> 1678</span>&#160;</div>
<div class="line"><a name="l01679"></a><span class="lineno"> 1679</span>&#160;          <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern_index] == -1)</div>
<div class="line"><a name="l01680"></a><span class="lineno"> 1680</span>&#160;          {</div>
<div class="line"><a name="l01681"></a><span class="lineno"> 1681</span>&#160;            pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern_index] = index_before;</div>
<div class="line"><a name="l01682"></a><span class="lineno"> 1682</span>&#160;            pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[pattern_index] = spectrum_index - 1;</div>
<div class="line"><a name="l01683"></a><span class="lineno"> 1683</span>&#160;          }</div>
<div class="line"><a name="l01684"></a><span class="lineno"> 1684</span>&#160;        }</div>
<div class="line"><a name="l01685"></a><span class="lineno"> 1685</span>&#160;      }</div>
<div class="line"><a name="l01686"></a><span class="lineno"> 1686</span>&#160;      <span class="comment">//next spectrum</span></div>
<div class="line"><a name="l01687"></a><span class="lineno"> 1687</span>&#160;      <span class="keywordflow">if</span> (spectrum_index != <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - 1 &amp;&amp; !<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index + 1].<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l01688"></a><span class="lineno"> 1688</span>&#160;      {</div>
<div class="line"><a name="l01689"></a><span class="lineno"> 1689</span>&#160;        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>&amp; spectrum_after = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum_index + 1];</div>
<div class="line"><a name="l01690"></a><span class="lineno"> 1690</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index_after = spectrum_after.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a830e58a22131827d85007a70e3069a5f">findNearest</a>(pos);</div>
<div class="line"><a name="l01691"></a><span class="lineno"> 1691</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> mz_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(pos, spectrum_after[index_after].getMZ(), <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a>);</div>
<div class="line"><a name="l01692"></a><span class="lineno"> 1692</span>&#160;        <span class="keywordflow">if</span> (mz_score != 0.0)</div>
<div class="line"><a name="l01693"></a><span class="lineno"> 1693</span>&#160;        {</div>
<div class="line"><a name="l01694"></a><span class="lineno"> 1694</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(spectrum_after[index_after].getIntensity(), 1) &lt;&lt; <span class="stringliteral">&quot;a &quot;</span>;</div>
<div class="line"><a name="l01695"></a><span class="lineno"> 1695</span>&#160;          intensity += spectrum_after[index_after].getIntensity();</div>
<div class="line"><a name="l01696"></a><span class="lineno"> 1696</span>&#160;          pos_score += mz_score;</div>
<div class="line"><a name="l01697"></a><span class="lineno"> 1697</span>&#160;          ++matches;</div>
<div class="line"><a name="l01698"></a><span class="lineno"> 1698</span>&#160;</div>
<div class="line"><a name="l01699"></a><span class="lineno"> 1699</span>&#160;          <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern_index] == -1)</div>
<div class="line"><a name="l01700"></a><span class="lineno"> 1700</span>&#160;          {</div>
<div class="line"><a name="l01701"></a><span class="lineno"> 1701</span>&#160;            pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern_index] = index_after;</div>
<div class="line"><a name="l01702"></a><span class="lineno"> 1702</span>&#160;            pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">spectrum</a>[pattern_index] = spectrum_index + 1;</div>
<div class="line"><a name="l01703"></a><span class="lineno"> 1703</span>&#160;          }</div>
<div class="line"><a name="l01704"></a><span class="lineno"> 1704</span>&#160;        }</div>
<div class="line"><a name="l01705"></a><span class="lineno"> 1705</span>&#160;      }</div>
<div class="line"><a name="l01706"></a><span class="lineno"> 1706</span>&#160;      <span class="comment">//no isotope found</span></div>
<div class="line"><a name="l01707"></a><span class="lineno"> 1707</span>&#160;      <span class="keywordflow">if</span> (matches == 0)</div>
<div class="line"><a name="l01708"></a><span class="lineno"> 1708</span>&#160;      {</div>
<div class="line"><a name="l01709"></a><span class="lineno"> 1709</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; missing&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01710"></a><span class="lineno"> 1710</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern_index] = -1;</div>
<div class="line"><a name="l01711"></a><span class="lineno"> 1711</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>[pattern_index] = 0.0;</div>
<div class="line"><a name="l01712"></a><span class="lineno"> 1712</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>[pattern_index] = 0.0;</div>
<div class="line"><a name="l01713"></a><span class="lineno"> 1713</span>&#160;      }</div>
<div class="line"><a name="l01714"></a><span class="lineno"> 1714</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l01715"></a><span class="lineno"> 1715</span>&#160;      {</div>
<div class="line"><a name="l01716"></a><span class="lineno"> 1716</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;=&gt; &quot;</span> &lt;&lt; intensity / matches &lt;&lt; std::endl;</div>
<div class="line"><a name="l01717"></a><span class="lineno"> 1717</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>[pattern_index] = pos_score / matches;</div>
<div class="line"><a name="l01718"></a><span class="lineno"> 1718</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>[pattern_index] = intensity / matches;</div>
<div class="line"><a name="l01719"></a><span class="lineno"> 1719</span>&#160;      }</div>
<div class="line"><a name="l01720"></a><span class="lineno"> 1720</span>&#160;    }</div>
<div class="line"><a name="l01721"></a><span class="lineno"> 1721</span>&#160;</div>
<div class="line"><a name="l01723"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60"> 1723</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a>(<a class="code" href="classdouble.html">DoubleReal</a> pos1, <a class="code" href="classdouble.html">DoubleReal</a> pos2, <a class="code" href="classdouble.html">DoubleReal</a> allowed_deviation)<span class="keyword"> const</span></div>
<div class="line"><a name="l01724"></a><span class="lineno"> 1724</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01725"></a><span class="lineno"> 1725</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> diff = fabs(pos1 - pos2);</div>
<div class="line"><a name="l01726"></a><span class="lineno"> 1726</span>&#160;      <span class="keywordflow">if</span> (diff &lt;= 0.5 * allowed_deviation)</div>
<div class="line"><a name="l01727"></a><span class="lineno"> 1727</span>&#160;      {</div>
<div class="line"><a name="l01728"></a><span class="lineno"> 1728</span>&#160;        <span class="keywordflow">return</span> 0.1 * (0.5 * allowed_deviation - diff) / (0.5 * allowed_deviation) + 0.9;</div>
<div class="line"><a name="l01729"></a><span class="lineno"> 1729</span>&#160;      }</div>
<div class="line"><a name="l01730"></a><span class="lineno"> 1730</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (diff &lt;= allowed_deviation)</div>
<div class="line"><a name="l01731"></a><span class="lineno"> 1731</span>&#160;      {</div>
<div class="line"><a name="l01732"></a><span class="lineno"> 1732</span>&#160;        <span class="keywordflow">return</span> 0.9 * (allowed_deviation - diff) / (0.5 * allowed_deviation);</div>
<div class="line"><a name="l01733"></a><span class="lineno"> 1733</span>&#160;      }</div>
<div class="line"><a name="l01734"></a><span class="lineno"> 1734</span>&#160;      <span class="keywordflow">return</span> 0.0;</div>
<div class="line"><a name="l01735"></a><span class="lineno"> 1735</span>&#160;    }</div>
<div class="line"><a name="l01736"></a><span class="lineno"> 1736</span>&#160;</div>
<div class="line"><a name="l01738"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e"> 1738</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">isotopeScore_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">TheoreticalIsotopePattern</a>&amp; isotopes, <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">IsotopePattern</a>&amp; pattern, <span class="keywordtype">bool</span> consider_mz_distances)<span class="keyword"> const</span></div>
<div class="line"><a name="l01739"></a><span class="lineno"> 1739</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01740"></a><span class="lineno"> 1740</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - fitting &quot;</span> &lt;&lt; pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.size() &lt;&lt; <span class="stringliteral">&quot; peaks&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01741"></a><span class="lineno"> 1741</span>&#160;      <span class="comment">//Abort if a core peak is missing</span></div>
<div class="line"><a name="l01742"></a><span class="lineno"> 1742</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso = 0 + isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#af2e76e2f5a4b1549e43a4dac9a3c35c2">optional_begin</a>; iso &lt; pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>.size() - isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a511873304a043cc9222285de3a2c2913">optional_end</a>; ++iso)</div>
<div class="line"><a name="l01743"></a><span class="lineno"> 1743</span>&#160;      {</div>
<div class="line"><a name="l01744"></a><span class="lineno"> 1744</span>&#160;        <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[iso] == -1)</div>
<div class="line"><a name="l01745"></a><span class="lineno"> 1745</span>&#160;        {</div>
<div class="line"><a name="l01746"></a><span class="lineno"> 1746</span>&#160;          <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - aborting: core peak is missing&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01747"></a><span class="lineno"> 1747</span>&#160;          <span class="keywordflow">return</span> 0.0;</div>
<div class="line"><a name="l01748"></a><span class="lineno"> 1748</span>&#160;        }</div>
<div class="line"><a name="l01749"></a><span class="lineno"> 1749</span>&#160;      }</div>
<div class="line"><a name="l01750"></a><span class="lineno"> 1750</span>&#160;      <span class="comment">//Find best isotope fit</span></div>
<div class="line"><a name="l01751"></a><span class="lineno"> 1751</span>&#160;      <span class="comment">// - try to leave out optional isotope peaks to improve the fit</span></div>
<div class="line"><a name="l01752"></a><span class="lineno"> 1752</span>&#160;      <span class="comment">// - do not allow gaps inside the pattern</span></div>
<div class="line"><a name="l01753"></a><span class="lineno"> 1753</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> best_int_score = 0.01; <span class="comment">//Not 0 as this would result in problems when checking for the percental improvement</span></div>
<div class="line"><a name="l01754"></a><span class="lineno"> 1754</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> best_begin = 0;</div>
<div class="line"><a name="l01755"></a><span class="lineno"> 1755</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#af2e76e2f5a4b1549e43a4dac9a3c35c2">optional_begin</a>; i &gt; 0; --i)</div>
<div class="line"><a name="l01756"></a><span class="lineno"> 1756</span>&#160;      {</div>
<div class="line"><a name="l01757"></a><span class="lineno"> 1757</span>&#160;        <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[i - 1] == -1)</div>
<div class="line"><a name="l01758"></a><span class="lineno"> 1758</span>&#160;        {</div>
<div class="line"><a name="l01759"></a><span class="lineno"> 1759</span>&#160;          best_begin = i;</div>
<div class="line"><a name="l01760"></a><span class="lineno"> 1760</span>&#160;          <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01761"></a><span class="lineno"> 1761</span>&#160;        }</div>
<div class="line"><a name="l01762"></a><span class="lineno"> 1762</span>&#160;      }</div>
<div class="line"><a name="l01763"></a><span class="lineno"> 1763</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> best_end = 0;</div>
<div class="line"><a name="l01764"></a><span class="lineno"> 1764</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a511873304a043cc9222285de3a2c2913">optional_end</a>; i &gt; 0; --i)</div>
<div class="line"><a name="l01765"></a><span class="lineno"> 1765</span>&#160;      {</div>
<div class="line"><a name="l01766"></a><span class="lineno"> 1766</span>&#160;        <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>.size() - i] == -1)</div>
<div class="line"><a name="l01767"></a><span class="lineno"> 1767</span>&#160;        {</div>
<div class="line"><a name="l01768"></a><span class="lineno"> 1768</span>&#160;          best_end = i;</div>
<div class="line"><a name="l01769"></a><span class="lineno"> 1769</span>&#160;          <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01770"></a><span class="lineno"> 1770</span>&#160;        }</div>
<div class="line"><a name="l01771"></a><span class="lineno"> 1771</span>&#160;      }</div>
<div class="line"><a name="l01772"></a><span class="lineno"> 1772</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - best_begin/end: &quot;</span> &lt;&lt; best_begin &lt;&lt; <span class="stringliteral">&quot;/&quot;</span> &lt;&lt; best_end &lt;&lt; std::endl;</div>
<div class="line"><a name="l01773"></a><span class="lineno"> 1773</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> b = best_begin; b &lt;= isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#af2e76e2f5a4b1549e43a4dac9a3c35c2">optional_begin</a>; ++b)</div>
<div class="line"><a name="l01774"></a><span class="lineno"> 1774</span>&#160;      {</div>
<div class="line"><a name="l01775"></a><span class="lineno"> 1775</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> e = best_end; e &lt;= isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a511873304a043cc9222285de3a2c2913">optional_end</a>; ++e)</div>
<div class="line"><a name="l01776"></a><span class="lineno"> 1776</span>&#160;        {</div>
<div class="line"><a name="l01777"></a><span class="lineno"> 1777</span>&#160;          <span class="comment">//Make sure we have more than 2 peaks (unless in the first loop interation, there we allow two points)</span></div>
<div class="line"><a name="l01778"></a><span class="lineno"> 1778</span>&#160;          <span class="keywordflow">if</span> (isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - b - e &gt; 2 || (b == best_begin &amp;&amp;</div>
<div class="line"><a name="l01779"></a><span class="lineno"> 1779</span>&#160;                                              e == best_end &amp;&amp;</div>
<div class="line"><a name="l01780"></a><span class="lineno"> 1780</span>&#160;                                              isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - b - e &gt; 1))</div>
<div class="line"><a name="l01781"></a><span class="lineno"> 1781</span>&#160;          {</div>
<div class="line"><a name="l01782"></a><span class="lineno"> 1782</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> int_score = <a class="code" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">Math::pearsonCorrelationCoefficient</a>(isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.begin() + b, isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.end() - e, pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.begin() + b, pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>.end() - e);</div>
<div class="line"><a name="l01783"></a><span class="lineno"> 1783</span>&#160;            <span class="keywordflow">if</span> (boost::math::isnan(int_score)) int_score = 0.0;</div>
<div class="line"><a name="l01784"></a><span class="lineno"> 1784</span>&#160;            <span class="keywordflow">if</span> (isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - b - e == 2 &amp;&amp; int_score &gt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">min_isotope_fit_</a>) int_score = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">min_isotope_fit_</a>; <span class="comment">//special case for the first loop iteration (otherwise the score is 1)</span></div>
<div class="line"><a name="l01785"></a><span class="lineno"> 1785</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - fit (&quot;</span> &lt;&lt; b &lt;&lt; <span class="stringliteral">&quot;/&quot;</span> &lt;&lt; e &lt;&lt; <span class="stringliteral">&quot;): &quot;</span> &lt;&lt; int_score;</div>
<div class="line"><a name="l01786"></a><span class="lineno"> 1786</span>&#160;            <span class="keywordflow">if</span> (int_score / best_int_score &gt;= 1.0 + <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">optional_fit_improvement_</a>)</div>
<div class="line"><a name="l01787"></a><span class="lineno"> 1787</span>&#160;            {</div>
<div class="line"><a name="l01788"></a><span class="lineno"> 1788</span>&#160;              <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - new best fit &quot;</span>;</div>
<div class="line"><a name="l01789"></a><span class="lineno"> 1789</span>&#160;              best_int_score = int_score;</div>
<div class="line"><a name="l01790"></a><span class="lineno"> 1790</span>&#160;              best_begin = b;</div>
<div class="line"><a name="l01791"></a><span class="lineno"> 1791</span>&#160;              best_end = e;</div>
<div class="line"><a name="l01792"></a><span class="lineno"> 1792</span>&#160;            }</div>
<div class="line"><a name="l01793"></a><span class="lineno"> 1793</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01794"></a><span class="lineno"> 1794</span>&#160;          }</div>
<div class="line"><a name="l01795"></a><span class="lineno"> 1795</span>&#160;        }</div>
<div class="line"><a name="l01796"></a><span class="lineno"> 1796</span>&#160;      }</div>
<div class="line"><a name="l01797"></a><span class="lineno"> 1797</span>&#160;</div>
<div class="line"><a name="l01798"></a><span class="lineno"> 1798</span>&#160;      <span class="comment">//if the best fit is empty, abort</span></div>
<div class="line"><a name="l01799"></a><span class="lineno"> 1799</span>&#160;      <span class="keywordflow">if</span> (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>.size() - best_begin - best_end == 0)</div>
<div class="line"><a name="l01800"></a><span class="lineno"> 1800</span>&#160;      {</div>
<div class="line"><a name="l01801"></a><span class="lineno"> 1801</span>&#160;        <span class="keywordflow">return</span> 0.0;</div>
<div class="line"><a name="l01802"></a><span class="lineno"> 1802</span>&#160;      }</div>
<div class="line"><a name="l01803"></a><span class="lineno"> 1803</span>&#160;</div>
<div class="line"><a name="l01804"></a><span class="lineno"> 1804</span>&#160;      <span class="comment">//remove left out peaks from the beginning</span></div>
<div class="line"><a name="l01805"></a><span class="lineno"> 1805</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; best_begin; ++i)</div>
<div class="line"><a name="l01806"></a><span class="lineno"> 1806</span>&#160;      {</div>
<div class="line"><a name="l01807"></a><span class="lineno"> 1807</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[i] = -2;</div>
<div class="line"><a name="l01808"></a><span class="lineno"> 1808</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>[i] = 0.0;</div>
<div class="line"><a name="l01809"></a><span class="lineno"> 1809</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>[i] = 0.0;</div>
<div class="line"><a name="l01810"></a><span class="lineno"> 1810</span>&#160;      }</div>
<div class="line"><a name="l01811"></a><span class="lineno"> 1811</span>&#160;      <span class="comment">//remove left out peaks from the end</span></div>
<div class="line"><a name="l01812"></a><span class="lineno"> 1812</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; best_end; ++i)</div>
<div class="line"><a name="l01813"></a><span class="lineno"> 1813</span>&#160;      {</div>
<div class="line"><a name="l01814"></a><span class="lineno"> 1814</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">peak</a>[isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - 1 - i] = -2;</div>
<div class="line"><a name="l01815"></a><span class="lineno"> 1815</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">intensity</a>[isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - 1 - i] = 0.0;</div>
<div class="line"><a name="l01816"></a><span class="lineno"> 1816</span>&#160;        pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>[isotopes.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() - 1 - i] = 0.0;</div>
<div class="line"><a name="l01817"></a><span class="lineno"> 1817</span>&#160;      }</div>
<div class="line"><a name="l01818"></a><span class="lineno"> 1818</span>&#160;      <span class="comment">//calculate m/z score (if required)</span></div>
<div class="line"><a name="l01819"></a><span class="lineno"> 1819</span>&#160;      <span class="keywordflow">if</span> (consider_mz_distances)</div>
<div class="line"><a name="l01820"></a><span class="lineno"> 1820</span>&#160;      {</div>
<div class="line"><a name="l01821"></a><span class="lineno"> 1821</span>&#160;        best_int_score *= std::accumulate(pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>.begin() + best_begin, pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>.end() - best_end, 0.0) / (pattern.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">mz_score</a>.size() - best_begin - best_end);</div>
<div class="line"><a name="l01822"></a><span class="lineno"> 1822</span>&#160;      }</div>
<div class="line"><a name="l01823"></a><span class="lineno"> 1823</span>&#160;</div>
<div class="line"><a name="l01824"></a><span class="lineno"> 1824</span>&#160;      <span class="comment">//return final score</span></div>
<div class="line"><a name="l01825"></a><span class="lineno"> 1825</span>&#160;      <a class="code" href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</a>(best_int_score &gt;= 0.0, (<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Internal error: Isotope score (&quot;</span>) + best_int_score + <span class="stringliteral">&quot;) should be &gt;=0.0&quot;</span>).c_str())</div>
<div class="line"><a name="l01826"></a><span class="lineno"> 1826</span>&#160;      <a class="code" href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</a>(best_int_score &lt;= 1.0, (<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Internal error: Isotope score (&quot;</span>) + best_int_score + <span class="stringliteral">&quot;) should be &lt;=1.0&quot;</span>).c_str())</div>
<div class="line"><a name="l01827"></a><span class="lineno"> 1827</span>&#160;      <span class="keywordflow">return</span> best_int_score;</div>
<div class="line"><a name="l01828"></a><span class="lineno"> 1828</span>&#160;    }</div>
<div class="line"><a name="l01829"></a><span class="lineno"> 1829</span>&#160;</div>
<div class="line"><a name="l01840"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97"> 1840</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a>(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak)<span class="keyword"> const</span></div>
<div class="line"><a name="l01841"></a><span class="lineno"> 1841</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01842"></a><span class="lineno"> 1842</span>&#160;      <span class="comment">// calculate (half) bin numbers</span></div>
<div class="line"><a name="l01843"></a><span class="lineno"> 1843</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> intensity  = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum][peak].getIntensity();</div>
<div class="line"><a name="l01844"></a><span class="lineno"> 1844</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum].getRT();</div>
<div class="line"><a name="l01845"></a><span class="lineno"> 1845</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> mz = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[spectrum][peak].getMZ();</div>
<div class="line"><a name="l01846"></a><span class="lineno"> 1846</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> rt_min = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9244f3b9aefde24a9b246a8396c3bb84">getMinRT</a>();</div>
<div class="line"><a name="l01847"></a><span class="lineno"> 1847</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> mz_min = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d8aab759e082ef93475344071fb7809">getMinMZ</a>();</div>
<div class="line"><a name="l01848"></a><span class="lineno"> 1848</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> rt_bin = std::min(2 * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a> - 1, (<a class="code" href="classunsigned_01int.html">UInt</a>) std::floor((rt - rt_min) / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a> * 2.0));</div>
<div class="line"><a name="l01849"></a><span class="lineno"> 1849</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> mz_bin = std::min(2 * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a> - 1, (<a class="code" href="classunsigned_01int.html">UInt</a>) std::floor((mz - mz_min) / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a> * 2.0));</div>
<div class="line"><a name="l01850"></a><span class="lineno"> 1850</span>&#160;      <span class="comment">// determine mz bins</span></div>
<div class="line"><a name="l01851"></a><span class="lineno"> 1851</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> ml, mh;</div>
<div class="line"><a name="l01852"></a><span class="lineno"> 1852</span>&#160;      <span class="keywordflow">if</span> (mz_bin == 0 || mz_bin == 2 * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a> - 1)</div>
<div class="line"><a name="l01853"></a><span class="lineno"> 1853</span>&#160;      {</div>
<div class="line"><a name="l01854"></a><span class="lineno"> 1854</span>&#160;        ml = mz_bin / 2;</div>
<div class="line"><a name="l01855"></a><span class="lineno"> 1855</span>&#160;        mh = mz_bin / 2;</div>
<div class="line"><a name="l01856"></a><span class="lineno"> 1856</span>&#160;      }</div>
<div class="line"><a name="l01857"></a><span class="lineno"> 1857</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="group__MathFunctionsMisc.html#gadaeb3f406822442307da5b2b94c40885">Math::isOdd</a>(mz_bin))</div>
<div class="line"><a name="l01858"></a><span class="lineno"> 1858</span>&#160;      {</div>
<div class="line"><a name="l01859"></a><span class="lineno"> 1859</span>&#160;        ml = mz_bin / 2;</div>
<div class="line"><a name="l01860"></a><span class="lineno"> 1860</span>&#160;        mh = mz_bin / 2 + 1;</div>
<div class="line"><a name="l01861"></a><span class="lineno"> 1861</span>&#160;      }</div>
<div class="line"><a name="l01862"></a><span class="lineno"> 1862</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l01863"></a><span class="lineno"> 1863</span>&#160;      {</div>
<div class="line"><a name="l01864"></a><span class="lineno"> 1864</span>&#160;        ml = mz_bin / 2 - 1;</div>
<div class="line"><a name="l01865"></a><span class="lineno"> 1865</span>&#160;        mh = mz_bin / 2;</div>
<div class="line"><a name="l01866"></a><span class="lineno"> 1866</span>&#160;      }</div>
<div class="line"><a name="l01867"></a><span class="lineno"> 1867</span>&#160;      <span class="comment">// determine rt bins</span></div>
<div class="line"><a name="l01868"></a><span class="lineno"> 1868</span>&#160;      <a class="code" href="classunsigned_01int.html">UInt</a> rl, rh;</div>
<div class="line"><a name="l01869"></a><span class="lineno"> 1869</span>&#160;      <span class="keywordflow">if</span> (rt_bin == 0 || rt_bin == 2 * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a> - 1)</div>
<div class="line"><a name="l01870"></a><span class="lineno"> 1870</span>&#160;      {</div>
<div class="line"><a name="l01871"></a><span class="lineno"> 1871</span>&#160;        rl = rt_bin / 2;</div>
<div class="line"><a name="l01872"></a><span class="lineno"> 1872</span>&#160;        rh = rt_bin / 2;</div>
<div class="line"><a name="l01873"></a><span class="lineno"> 1873</span>&#160;      }</div>
<div class="line"><a name="l01874"></a><span class="lineno"> 1874</span>&#160;      <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="group__MathFunctionsMisc.html#gadaeb3f406822442307da5b2b94c40885">Math::isOdd</a>(rt_bin))</div>
<div class="line"><a name="l01875"></a><span class="lineno"> 1875</span>&#160;      {</div>
<div class="line"><a name="l01876"></a><span class="lineno"> 1876</span>&#160;        rl = rt_bin / 2;</div>
<div class="line"><a name="l01877"></a><span class="lineno"> 1877</span>&#160;        rh = rt_bin / 2 + 1;</div>
<div class="line"><a name="l01878"></a><span class="lineno"> 1878</span>&#160;      }</div>
<div class="line"><a name="l01879"></a><span class="lineno"> 1879</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l01880"></a><span class="lineno"> 1880</span>&#160;      {</div>
<div class="line"><a name="l01881"></a><span class="lineno"> 1881</span>&#160;        rl = rt_bin / 2 - 1;</div>
<div class="line"><a name="l01882"></a><span class="lineno"> 1882</span>&#160;        rh = rt_bin / 2;</div>
<div class="line"><a name="l01883"></a><span class="lineno"> 1883</span>&#160;      }</div>
<div class="line"><a name="l01884"></a><span class="lineno"> 1884</span>&#160;      <span class="comment">// calculate distances to surrounding bin centers (normalized to [0,1])</span></div>
<div class="line"><a name="l01885"></a><span class="lineno"> 1885</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> drl = std::fabs(rt_min + (0.5 + rl) * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a> - rt) / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a>;</div>
<div class="line"><a name="l01886"></a><span class="lineno"> 1886</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> drh = std::fabs(rt_min + (0.5 + rh) * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a> - rt) / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a>;</div>
<div class="line"><a name="l01887"></a><span class="lineno"> 1887</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> dml = std::fabs(mz_min + (0.5 + ml) * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a> - mz) / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a>;</div>
<div class="line"><a name="l01888"></a><span class="lineno"> 1888</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> dmh = std::fabs(mz_min + (0.5 + mh) * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a> - mz) / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a>;</div>
<div class="line"><a name="l01889"></a><span class="lineno"> 1889</span>&#160;      <span class="comment">// Calculate weights for the intensity scores based on the distances to the</span></div>
<div class="line"><a name="l01890"></a><span class="lineno"> 1890</span>&#160;      <span class="comment">// bin center(the nearer to better)</span></div>
<div class="line"><a name="l01891"></a><span class="lineno"> 1891</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> d1 = std::sqrt(std::pow(1.0 - drl, 2) + std::pow(1.0 - dml, 2));</div>
<div class="line"><a name="l01892"></a><span class="lineno"> 1892</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> d2 = std::sqrt(std::pow(1.0 - drh, 2) + std::pow(1.0 - dml, 2));</div>
<div class="line"><a name="l01893"></a><span class="lineno"> 1893</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> d3 = std::sqrt(std::pow(1.0 - drl, 2) + std::pow(1.0 - dmh, 2));</div>
<div class="line"><a name="l01894"></a><span class="lineno"> 1894</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> d4 = std::sqrt(std::pow(1.0 - drh, 2) + std::pow(1.0 - dmh, 2));</div>
<div class="line"><a name="l01895"></a><span class="lineno"> 1895</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> d_sum = d1 + d2 + d3 + d4;</div>
<div class="line"><a name="l01896"></a><span class="lineno"> 1896</span>&#160;      <span class="comment">// Final score .. intensityScore in the surrounding bins, weighted by the distance of the</span></div>
<div class="line"><a name="l01897"></a><span class="lineno"> 1897</span>&#160;      <span class="comment">// bin center to the peak</span></div>
<div class="line"><a name="l01898"></a><span class="lineno"> 1898</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <span class="keyword">final</span> = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a>(rl, ml, intensity) * (d1 / d_sum)</div>
<div class="line"><a name="l01899"></a><span class="lineno"> 1899</span>&#160;                         + <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a>(rh, ml, intensity) * (d2 / d_sum)</div>
<div class="line"><a name="l01900"></a><span class="lineno"> 1900</span>&#160;                         + <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a>(rl, mh, intensity) * (d3 / d_sum)</div>
<div class="line"><a name="l01901"></a><span class="lineno"> 1901</span>&#160;                         + <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a>(rh, mh, intensity) * (d4 / d_sum);</div>
<div class="line"><a name="l01902"></a><span class="lineno"> 1902</span>&#160;</div>
<div class="line"><a name="l01903"></a><span class="lineno"> 1903</span>&#160;      <a class="code" href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</a>(<span class="keyword">final</span> &gt;= 0.0, (<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Internal error: Intensity score (&quot;</span>) + <span class="keyword">final</span> + <span class="stringliteral">&quot;) should be &gt;=0.0&quot;</span>).c_str())</div>
<div class="line"><a name="l01904"></a><span class="lineno"> 1904</span>&#160;      <a class="code" href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</a>(<span class="keyword">final</span> &lt;= 1.0001, (<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;Internal error: Intensity score (&quot;</span>) + <span class="keyword">final</span> + <span class="stringliteral">&quot;) should be &lt;=1.0&quot;</span>).c_str())</div>
<div class="line"><a name="l01905"></a><span class="lineno"> 1905</span>&#160;      <span class="keywordflow">return</span> <span class="keyword">final</span>;</div>
<div class="line"><a name="l01906"></a><span class="lineno"> 1906</span>&#160;    }</div>
<div class="line"><a name="l01907"></a><span class="lineno"> 1907</span>&#160;</div>
<div class="line"><a name="l01914"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad832d6128e519d1c6a7fefd89158c37e"> 1914</a></span>&#160;    <a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter&lt;PeakType&gt;</a>* <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad832d6128e519d1c6a7fefd89158c37e">chooseTraceFitter_</a>(<span class="keywordtype">double</span>&amp; tau)</div>
<div class="line"><a name="l01915"></a><span class="lineno"> 1915</span>&#160;    {</div>
<div class="line"><a name="l01916"></a><span class="lineno"> 1916</span>&#160;      <span class="comment">// choose fitter</span></div>
<div class="line"><a name="l01917"></a><span class="lineno"> 1917</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;feature:rt_shape&quot;</span>) == <span class="stringliteral">&quot;asymmetric&quot;</span>)</div>
<div class="line"><a name="l01918"></a><span class="lineno"> 1918</span>&#160;      {</div>
<div class="line"><a name="l01919"></a><span class="lineno"> 1919</span>&#160;        <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;use asymmetric rt peak shape&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01920"></a><span class="lineno"> 1920</span>&#160;        tau = -1.0;</div>
<div class="line"><a name="l01921"></a><span class="lineno"> 1921</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1EGHTraceFitter.html">EGHTraceFitter&lt;PeakType&gt;</a>();</div>
<div class="line"><a name="l01922"></a><span class="lineno"> 1922</span>&#160;      }</div>
<div class="line"><a name="l01923"></a><span class="lineno"> 1923</span>&#160;      <span class="keywordflow">else</span> <span class="comment">// if (param_.getValue(&quot;feature:rt_shape&quot;) == &quot;symmetric&quot;)</span></div>
<div class="line"><a name="l01924"></a><span class="lineno"> 1924</span>&#160;      {</div>
<div class="line"><a name="l01925"></a><span class="lineno"> 1925</span>&#160;        <a class="code" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a> &lt;&lt; <span class="stringliteral">&quot;use symmetric rt peak shape&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01926"></a><span class="lineno"> 1926</span>&#160;        <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1GaussTraceFitter.html">GaussTraceFitter&lt;PeakType&gt;</a>();</div>
<div class="line"><a name="l01927"></a><span class="lineno"> 1927</span>&#160;      }</div>
<div class="line"><a name="l01928"></a><span class="lineno"> 1928</span>&#160;    }</div>
<div class="line"><a name="l01929"></a><span class="lineno"> 1929</span>&#160;</div>
<div class="line"><a name="l01930"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3430a3cac3d46d0420ab99024264359f"> 1930</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3430a3cac3d46d0420ab99024264359f">intensityScore_</a>(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> rt_bin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> mz_bin, <a class="code" href="classdouble.html">DoubleReal</a> intensity)<span class="keyword"> const</span></div>
<div class="line"><a name="l01931"></a><span class="lineno"> 1931</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l01932"></a><span class="lineno"> 1932</span>&#160;      <span class="comment">// interpolate score value according to quantiles(20)</span></div>
<div class="line"><a name="l01933"></a><span class="lineno"> 1933</span>&#160;      <span class="keyword">const</span> std::vector&lt;DoubleReal&gt;&amp; quantiles20 = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a>[rt_bin][mz_bin];</div>
<div class="line"><a name="l01934"></a><span class="lineno"> 1934</span>&#160;      <span class="comment">// get iterator pointing to quantile that is &gt;= intensity</span></div>
<div class="line"><a name="l01935"></a><span class="lineno"> 1935</span>&#160;      std::vector&lt;DoubleReal&gt;::const_iterator it = std::lower_bound(quantiles20.begin(), quantiles20.end(), intensity);</div>
<div class="line"><a name="l01936"></a><span class="lineno"> 1936</span>&#160;      <span class="comment">// bigger than the biggest value =&gt; return 1.0</span></div>
<div class="line"><a name="l01937"></a><span class="lineno"> 1937</span>&#160;      <span class="keywordflow">if</span> (it == quantiles20.end())</div>
<div class="line"><a name="l01938"></a><span class="lineno"> 1938</span>&#160;      {</div>
<div class="line"><a name="l01939"></a><span class="lineno"> 1939</span>&#160;        <span class="keywordflow">return</span> 1.0;</div>
<div class="line"><a name="l01940"></a><span class="lineno"> 1940</span>&#160;      }</div>
<div class="line"><a name="l01941"></a><span class="lineno"> 1941</span>&#160;      <span class="comment">// interpolate inside the bin</span></div>
<div class="line"><a name="l01942"></a><span class="lineno"> 1942</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> bin_score = 0.0;</div>
<div class="line"><a name="l01943"></a><span class="lineno"> 1943</span>&#160;      <span class="keywordflow">if</span> (it == quantiles20.begin())</div>
<div class="line"><a name="l01944"></a><span class="lineno"> 1944</span>&#160;      {</div>
<div class="line"><a name="l01945"></a><span class="lineno"> 1945</span>&#160;        bin_score = 0.05 * intensity / *it;</div>
<div class="line"><a name="l01946"></a><span class="lineno"> 1946</span>&#160;      }</div>
<div class="line"><a name="l01947"></a><span class="lineno"> 1947</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l01948"></a><span class="lineno"> 1948</span>&#160;      {</div>
<div class="line"><a name="l01949"></a><span class="lineno"> 1949</span>&#160;        <span class="comment">// (intensity - vigintile_low) / (vigintile_high - vigintile_low)</span></div>
<div class="line"><a name="l01950"></a><span class="lineno"> 1950</span>&#160;        bin_score = 0.05 * (intensity - *(it - 1)) / (*it - *(it - 1));</div>
<div class="line"><a name="l01951"></a><span class="lineno"> 1951</span>&#160;      }</div>
<div class="line"><a name="l01952"></a><span class="lineno"> 1952</span>&#160;</div>
<div class="line"><a name="l01953"></a><span class="lineno"> 1953</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> <span class="keyword">final</span> = bin_score +</div>
<div class="line"><a name="l01954"></a><span class="lineno"> 1954</span>&#160;                         0.05 * ((it - quantiles20.begin()) - 1.0); <span class="comment">// determine position of lower bound in the vector</span></div>
<div class="line"><a name="l01955"></a><span class="lineno"> 1955</span>&#160;</div>
<div class="line"><a name="l01956"></a><span class="lineno"> 1956</span>&#160;      <span class="comment">//fix numerical problems</span></div>
<div class="line"><a name="l01957"></a><span class="lineno"> 1957</span>&#160;      <span class="keywordflow">if</span> (<span class="keyword">final</span> &lt; 0.0) <span class="keyword">final</span> = 0.0;</div>
<div class="line"><a name="l01958"></a><span class="lineno"> 1958</span>&#160;      <span class="keywordflow">if</span> (<span class="keyword">final</span> &gt; 1.0) <span class="keyword">final</span> = 1.0;</div>
<div class="line"><a name="l01959"></a><span class="lineno"> 1959</span>&#160;</div>
<div class="line"><a name="l01960"></a><span class="lineno"> 1960</span>&#160;      <span class="comment">// final = 1/20 * [ index(vigintile_low) + (intensity-vigintile_low) / (vigintile_high - vigintile_low) ]</span></div>
<div class="line"><a name="l01961"></a><span class="lineno"> 1961</span>&#160;      <span class="keywordflow">return</span> <span class="keyword">final</span>;</div>
<div class="line"><a name="l01962"></a><span class="lineno"> 1962</span>&#160;    }</div>
<div class="line"><a name="l01963"></a><span class="lineno"> 1963</span>&#160;</div>
<div class="line"><a name="l01970"></a><span class="lineno"> 1970</span>&#160;</div>
<div class="line"><a name="l01979"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a"> 1979</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">cropFeature_</a>(<a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter&lt;PeakType&gt;</a>* fitter,</div>
<div class="line"><a name="l01980"></a><span class="lineno"> 1980</span>&#160;                      <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a>&amp; traces,</div>
<div class="line"><a name="l01981"></a><span class="lineno"> 1981</span>&#160;                      <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a>&amp; new_traces)</div>
<div class="line"><a name="l01982"></a><span class="lineno"> 1982</span>&#160;    {</div>
<div class="line"><a name="l01983"></a><span class="lineno"> 1983</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> low_bound = fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a10ddb3b8cc795c598f76db017b9ca322">getLowerRTBound</a>();</div>
<div class="line"><a name="l01984"></a><span class="lineno"> 1984</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> high_bound = fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a0ab9bd668829f0fc9608bd56560ac1ae">getUpperRTBound</a>();</div>
<div class="line"><a name="l01985"></a><span class="lineno"> 1985</span>&#160;</div>
<div class="line"><a name="l01986"></a><span class="lineno"> 1986</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;    =&gt; RT bounds: &quot;</span> &lt;&lt; low_bound &lt;&lt; <span class="stringliteral">&quot; - &quot;</span> &lt;&lt; high_bound &lt;&lt; std::endl;</div>
<div class="line"><a name="l01987"></a><span class="lineno"> 1987</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> t = 0; t &lt; traces.size(); ++t)</div>
<div class="line"><a name="l01988"></a><span class="lineno"> 1988</span>&#160;      {</div>
<div class="line"><a name="l01989"></a><span class="lineno"> 1989</span>&#160;        <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">MassTrace</a>&amp; trace = traces[t];</div>
<div class="line"><a name="l01990"></a><span class="lineno"> 1990</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;   - Trace &quot;</span> &lt;&lt; t &lt;&lt; <span class="stringliteral">&quot;: (&quot;</span> &lt;&lt; trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a7db81fa54d4743c867872ac5b0938247">theoretical_int</a> &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l01991"></a><span class="lineno"> 1991</span>&#160;</div>
<div class="line"><a name="l01992"></a><span class="lineno"> 1992</span>&#160;        <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">MassTrace</a> new_trace;</div>
<div class="line"><a name="l01993"></a><span class="lineno"> 1993</span>&#160;        <span class="comment">//compute average relative deviation and correlation</span></div>
<div class="line"><a name="l01994"></a><span class="lineno"> 1994</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> deviation = 0.0;</div>
<div class="line"><a name="l01995"></a><span class="lineno"> 1995</span>&#160;        std::vector&lt;DoubleReal&gt; v_theo, v_real;</div>
<div class="line"><a name="l01996"></a><span class="lineno"> 1996</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; trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l01997"></a><span class="lineno"> 1997</span>&#160;        {</div>
<div class="line"><a name="l01998"></a><span class="lineno"> 1998</span>&#160;          <span class="comment">//consider peaks when inside RT bounds only</span></div>
<div class="line"><a name="l01999"></a><span class="lineno"> 1999</span>&#160;          <span class="keywordflow">if</span> (trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].first &gt;= low_bound &amp;&amp; trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].first &lt;= high_bound)</div>
<div class="line"><a name="l02000"></a><span class="lineno"> 2000</span>&#160;          {</div>
<div class="line"><a name="l02001"></a><span class="lineno"> 2001</span>&#160;            new_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.push_back(trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>]);</div>
<div class="line"><a name="l02002"></a><span class="lineno"> 2002</span>&#160;</div>
<div class="line"><a name="l02003"></a><span class="lineno"> 2003</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> theo = traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a> + fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">computeTheoretical</a>(trace, <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>);</div>
<div class="line"><a name="l02004"></a><span class="lineno"> 2004</span>&#160;</div>
<div class="line"><a name="l02005"></a><span class="lineno"> 2005</span>&#160;            v_theo.push_back(theo);</div>
<div class="line"><a name="l02006"></a><span class="lineno"> 2006</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> real = trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].second-&gt;getIntensity();</div>
<div class="line"><a name="l02007"></a><span class="lineno"> 2007</span>&#160;            v_real.push_back(real);</div>
<div class="line"><a name="l02008"></a><span class="lineno"> 2008</span>&#160;            deviation += std::fabs(real - theo) / theo;</div>
<div class="line"><a name="l02009"></a><span class="lineno"> 2009</span>&#160;          }</div>
<div class="line"><a name="l02010"></a><span class="lineno"> 2010</span>&#160;        }</div>
<div class="line"><a name="l02011"></a><span class="lineno"> 2011</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> fit_score = 0.0;</div>
<div class="line"><a name="l02012"></a><span class="lineno"> 2012</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> correlation = 0.0;</div>
<div class="line"><a name="l02013"></a><span class="lineno"> 2013</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> final_score = 0.0;</div>
<div class="line"><a name="l02014"></a><span class="lineno"> 2014</span>&#160;        <span class="keywordflow">if</span> (!new_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.empty())</div>
<div class="line"><a name="l02015"></a><span class="lineno"> 2015</span>&#160;        {</div>
<div class="line"><a name="l02016"></a><span class="lineno"> 2016</span>&#160;          fit_score = deviation / new_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size();</div>
<div class="line"><a name="l02017"></a><span class="lineno"> 2017</span>&#160;          correlation = std::max(0.0, <a class="code" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">Math::pearsonCorrelationCoefficient</a>(v_theo.begin(), v_theo.end(), v_real.begin(), v_real.end()));</div>
<div class="line"><a name="l02018"></a><span class="lineno"> 2018</span>&#160;          final_score = std::sqrt(correlation * std::max(0.0, 1.0 - fit_score));</div>
<div class="line"><a name="l02019"></a><span class="lineno"> 2019</span>&#160;        }</div>
<div class="line"><a name="l02020"></a><span class="lineno"> 2020</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;     - peaks: &quot;</span> &lt;&lt; new_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size() &lt;&lt; <span class="stringliteral">&quot; / &quot;</span> &lt;&lt; trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size() &lt;&lt; <span class="stringliteral">&quot; - relative deviation: &quot;</span> &lt;&lt; fit_score &lt;&lt; <span class="stringliteral">&quot; - correlation: &quot;</span> &lt;&lt; correlation &lt;&lt; <span class="stringliteral">&quot; - final score: &quot;</span> &lt;&lt; correlation &lt;&lt; std::endl;</div>
<div class="line"><a name="l02021"></a><span class="lineno"> 2021</span>&#160;        <span class="comment">//remove badly fitting traces</span></div>
<div class="line"><a name="l02022"></a><span class="lineno"> 2022</span>&#160;        <span class="keywordflow">if</span> (!new_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#aac1b70a2ed67ead038c4d3f5ac4d8a81">isValid</a>() || final_score &lt; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">min_trace_score_</a>)</div>
<div class="line"><a name="l02023"></a><span class="lineno"> 2023</span>&#160;        {</div>
<div class="line"><a name="l02024"></a><span class="lineno"> 2024</span>&#160;          <span class="keywordflow">if</span> (t &lt; traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>)</div>
<div class="line"><a name="l02025"></a><span class="lineno"> 2025</span>&#160;          {</div>
<div class="line"><a name="l02026"></a><span class="lineno"> 2026</span>&#160;            new_traces = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a>();</div>
<div class="line"><a name="l02027"></a><span class="lineno"> 2027</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;     - removed this and previous traces due to bad fit&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l02028"></a><span class="lineno"> 2028</span>&#160;            new_traces.clear(); <span class="comment">//remove earlier traces</span></div>
<div class="line"><a name="l02029"></a><span class="lineno"> 2029</span>&#160;            <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l02030"></a><span class="lineno"> 2030</span>&#160;          }</div>
<div class="line"><a name="l02031"></a><span class="lineno"> 2031</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (t == traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>)</div>
<div class="line"><a name="l02032"></a><span class="lineno"> 2032</span>&#160;          {</div>
<div class="line"><a name="l02033"></a><span class="lineno"> 2033</span>&#160;            new_traces = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a>();</div>
<div class="line"><a name="l02034"></a><span class="lineno"> 2034</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;     - aborting (max trace was removed)&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l02035"></a><span class="lineno"> 2035</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l02036"></a><span class="lineno"> 2036</span>&#160;          }</div>
<div class="line"><a name="l02037"></a><span class="lineno"> 2037</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (t &gt; traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>)</div>
<div class="line"><a name="l02038"></a><span class="lineno"> 2038</span>&#160;          {</div>
<div class="line"><a name="l02039"></a><span class="lineno"> 2039</span>&#160;            <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;     - removed due to bad fit =&gt; omitting the rest&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l02040"></a><span class="lineno"> 2040</span>&#160;            <span class="keywordflow">break</span>; <span class="comment">//no more traces are possible</span></div>
<div class="line"><a name="l02041"></a><span class="lineno"> 2041</span>&#160;          }</div>
<div class="line"><a name="l02042"></a><span class="lineno"> 2042</span>&#160;        }</div>
<div class="line"><a name="l02043"></a><span class="lineno"> 2043</span>&#160;        <span class="comment">//add new trace</span></div>
<div class="line"><a name="l02044"></a><span class="lineno"> 2044</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02045"></a><span class="lineno"> 2045</span>&#160;        {</div>
<div class="line"><a name="l02046"></a><span class="lineno"> 2046</span>&#160;          new_trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a7db81fa54d4743c867872ac5b0938247">theoretical_int</a> = trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a7db81fa54d4743c867872ac5b0938247">theoretical_int</a>;</div>
<div class="line"><a name="l02047"></a><span class="lineno"> 2047</span>&#160;          new_traces.push_back(new_trace);</div>
<div class="line"><a name="l02048"></a><span class="lineno"> 2048</span>&#160;          <span class="keywordflow">if</span> (t == traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a>)</div>
<div class="line"><a name="l02049"></a><span class="lineno"> 2049</span>&#160;          {</div>
<div class="line"><a name="l02050"></a><span class="lineno"> 2050</span>&#160;            new_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">max_trace</a> = new_traces.size() - 1;</div>
<div class="line"><a name="l02051"></a><span class="lineno"> 2051</span>&#160;          }</div>
<div class="line"><a name="l02052"></a><span class="lineno"> 2052</span>&#160;        }</div>
<div class="line"><a name="l02053"></a><span class="lineno"> 2053</span>&#160;      }</div>
<div class="line"><a name="l02054"></a><span class="lineno"> 2054</span>&#160;      new_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a> = traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a>;</div>
<div class="line"><a name="l02055"></a><span class="lineno"> 2055</span>&#160;    }</div>
<div class="line"><a name="l02056"></a><span class="lineno"> 2056</span>&#160;</div>
<div class="line"><a name="l02080"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d"> 2080</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">checkFeatureQuality_</a>(<a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter&lt;PeakType&gt;</a>* fitter,</div>
<div class="line"><a name="l02081"></a><span class="lineno"> 2081</span>&#160;                              <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a>&amp; feature_traces,</div>
<div class="line"><a name="l02082"></a><span class="lineno"> 2082</span>&#160;                              <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a>&amp; seed_mz, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a>&amp; min_feature_score,</div>
<div class="line"><a name="l02083"></a><span class="lineno"> 2083</span>&#160;                              <a class="code" href="classOpenMS_1_1String.html">String</a>&amp; error_msg, <a class="code" href="classdouble.html">DoubleReal</a>&amp; fit_score, <a class="code" href="classdouble.html">DoubleReal</a>&amp; correlation, <a class="code" href="classdouble.html">DoubleReal</a>&amp; final_score)</div>
<div class="line"><a name="l02084"></a><span class="lineno"> 2084</span>&#160;    {</div>
<div class="line"><a name="l02085"></a><span class="lineno"> 2085</span>&#160;      <span class="keywordtype">bool</span> feature_ok = <span class="keyword">true</span>;</div>
<div class="line"><a name="l02086"></a><span class="lineno"> 2086</span>&#160;</div>
<div class="line"><a name="l02087"></a><span class="lineno"> 2087</span>&#160;      <span class="comment">//check if the sigma fit was ok (if it is larger than &#39;max_rt_span&#39;)</span></div>
<div class="line"><a name="l02088"></a><span class="lineno"> 2088</span>&#160;      <span class="keywordflow">if</span> (feature_ok)</div>
<div class="line"><a name="l02089"></a><span class="lineno"> 2089</span>&#160;      {</div>
<div class="line"><a name="l02090"></a><span class="lineno"> 2090</span>&#160;        <span class="comment">// 5.0 * sigma &gt; max_rt_span_ * region_rt_span</span></div>
<div class="line"><a name="l02091"></a><span class="lineno"> 2091</span>&#160;        <span class="keywordflow">if</span> (fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#af72d2c9ae5ecbd8b8d4605fbbef613cc">checkMaximalRTSpan</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">max_rt_span_</a>))</div>
<div class="line"><a name="l02092"></a><span class="lineno"> 2092</span>&#160;        {</div>
<div class="line"><a name="l02093"></a><span class="lineno"> 2093</span>&#160;          feature_ok = <span class="keyword">false</span>;</div>
<div class="line"><a name="l02094"></a><span class="lineno"> 2094</span>&#160;          error_msg = <span class="stringliteral">&quot;Invalid fit: Fitted model is bigger than &#39;max_rt_span&#39;&quot;</span>;</div>
<div class="line"><a name="l02095"></a><span class="lineno"> 2095</span>&#160;        }</div>
<div class="line"><a name="l02096"></a><span class="lineno"> 2096</span>&#160;      }</div>
<div class="line"><a name="l02097"></a><span class="lineno"> 2097</span>&#160;</div>
<div class="line"><a name="l02098"></a><span class="lineno"> 2098</span>&#160;      <span class="comment">//check if the feature is valid</span></div>
<div class="line"><a name="l02099"></a><span class="lineno"> 2099</span>&#160;      <span class="keywordflow">if</span> (!feature_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a7e409d85407a4cfbc76fdc4aac06f185">isValid</a>(seed_mz, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a>))</div>
<div class="line"><a name="l02100"></a><span class="lineno"> 2100</span>&#160;      {</div>
<div class="line"><a name="l02101"></a><span class="lineno"> 2101</span>&#160;        feature_ok = <span class="keyword">false</span>;</div>
<div class="line"><a name="l02102"></a><span class="lineno"> 2102</span>&#160;        error_msg = <span class="stringliteral">&quot;Invalid feature after fit - too few traces or peaks left&quot;</span>;</div>
<div class="line"><a name="l02103"></a><span class="lineno"> 2103</span>&#160;      }</div>
<div class="line"><a name="l02104"></a><span class="lineno"> 2104</span>&#160;</div>
<div class="line"><a name="l02105"></a><span class="lineno"> 2105</span>&#160;      <span class="comment">//check if x0 is inside feature bounds</span></div>
<div class="line"><a name="l02106"></a><span class="lineno"> 2106</span>&#160;      <span class="keywordflow">if</span> (feature_ok)</div>
<div class="line"><a name="l02107"></a><span class="lineno"> 2107</span>&#160;      {</div>
<div class="line"><a name="l02108"></a><span class="lineno"> 2108</span>&#160;        std::pair&lt;DoubleReal, DoubleReal&gt; rt_bounds = feature_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#adee689cac2b64d7164dbfc3d48110d91">getRTBounds</a>();</div>
<div class="line"><a name="l02109"></a><span class="lineno"> 2109</span>&#160;        <span class="keywordflow">if</span> (fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>() &lt; rt_bounds.first || fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>() &gt; rt_bounds.second)</div>
<div class="line"><a name="l02110"></a><span class="lineno"> 2110</span>&#160;        {</div>
<div class="line"><a name="l02111"></a><span class="lineno"> 2111</span>&#160;          feature_ok = <span class="keyword">false</span>;</div>
<div class="line"><a name="l02112"></a><span class="lineno"> 2112</span>&#160;          error_msg = <span class="stringliteral">&quot;Invalid fit: Center outside of feature bounds&quot;</span>;</div>
<div class="line"><a name="l02113"></a><span class="lineno"> 2113</span>&#160;        }</div>
<div class="line"><a name="l02114"></a><span class="lineno"> 2114</span>&#160;      }</div>
<div class="line"><a name="l02115"></a><span class="lineno"> 2115</span>&#160;</div>
<div class="line"><a name="l02116"></a><span class="lineno"> 2116</span>&#160;      <span class="comment">//check if the remaining traces fill out at least &#39;min_rt_span&#39; of the RT span</span></div>
<div class="line"><a name="l02117"></a><span class="lineno"> 2117</span>&#160;      <span class="keywordflow">if</span> (feature_ok)</div>
<div class="line"><a name="l02118"></a><span class="lineno"> 2118</span>&#160;      {</div>
<div class="line"><a name="l02119"></a><span class="lineno"> 2119</span>&#160;        std::pair&lt;DoubleReal, DoubleReal&gt; rt_bounds = feature_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#adee689cac2b64d7164dbfc3d48110d91">getRTBounds</a>();</div>
<div class="line"><a name="l02120"></a><span class="lineno"> 2120</span>&#160;        <span class="keywordflow">if</span> (fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a2190523e8d48946faff97a41131fcf92">checkMinimalRTSpan</a>(rt_bounds, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">min_rt_span_</a>))</div>
<div class="line"><a name="l02121"></a><span class="lineno"> 2121</span>&#160;        {</div>
<div class="line"><a name="l02122"></a><span class="lineno"> 2122</span>&#160;          feature_ok = <span class="keyword">false</span>;</div>
<div class="line"><a name="l02123"></a><span class="lineno"> 2123</span>&#160;          error_msg = <span class="stringliteral">&quot;Invalid fit: Less than &#39;min_rt_span&#39; left after fit&quot;</span>;</div>
<div class="line"><a name="l02124"></a><span class="lineno"> 2124</span>&#160;        }</div>
<div class="line"><a name="l02125"></a><span class="lineno"> 2125</span>&#160;      }</div>
<div class="line"><a name="l02126"></a><span class="lineno"> 2126</span>&#160;</div>
<div class="line"><a name="l02127"></a><span class="lineno"> 2127</span>&#160;      <span class="comment">//check if feature quality is high enough (average relative deviation and correlation of the whole feature)</span></div>
<div class="line"><a name="l02128"></a><span class="lineno"> 2128</span>&#160;      <span class="keywordflow">if</span> (feature_ok)</div>
<div class="line"><a name="l02129"></a><span class="lineno"> 2129</span>&#160;      {</div>
<div class="line"><a name="l02130"></a><span class="lineno"> 2130</span>&#160;        std::vector&lt;DoubleReal&gt; v_theo, v_real;</div>
<div class="line"><a name="l02131"></a><span class="lineno"> 2131</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> deviation = 0.0;</div>
<div class="line"><a name="l02132"></a><span class="lineno"> 2132</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> t = 0; t &lt; feature_traces.size(); ++t)</div>
<div class="line"><a name="l02133"></a><span class="lineno"> 2133</span>&#160;        {</div>
<div class="line"><a name="l02134"></a><span class="lineno"> 2134</span>&#160;          <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">MassTrace</a>&amp; trace = feature_traces[t];</div>
<div class="line"><a name="l02135"></a><span class="lineno"> 2135</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; trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l02136"></a><span class="lineno"> 2136</span>&#160;          {</div>
<div class="line"><a name="l02137"></a><span class="lineno"> 2137</span>&#160;            <span class="comment">// was DoubleReal theo = new_traces.baseline + trace.theoretical_int *  height * exp(-0.5 * pow(trace.peaks[k].first - x0, 2) / pow(sigma, 2) );</span></div>
<div class="line"><a name="l02138"></a><span class="lineno"> 2138</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> theo = feature_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a> + fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">computeTheoretical</a>(trace, <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>);</div>
<div class="line"><a name="l02139"></a><span class="lineno"> 2139</span>&#160;            v_theo.push_back(theo);</div>
<div class="line"><a name="l02140"></a><span class="lineno"> 2140</span>&#160;            <a class="code" href="classdouble.html">DoubleReal</a> real = trace.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">peaks</a>[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].second-&gt;getIntensity();</div>
<div class="line"><a name="l02141"></a><span class="lineno"> 2141</span>&#160;            v_real.push_back(real);</div>
<div class="line"><a name="l02142"></a><span class="lineno"> 2142</span>&#160;            deviation += std::fabs(real - theo) / theo;</div>
<div class="line"><a name="l02143"></a><span class="lineno"> 2143</span>&#160;          }</div>
<div class="line"><a name="l02144"></a><span class="lineno"> 2144</span>&#160;        }</div>
<div class="line"><a name="l02145"></a><span class="lineno"> 2145</span>&#160;        fit_score = std::max(0.0, 1.0 - (deviation / feature_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">getPeakCount</a>()));</div>
<div class="line"><a name="l02146"></a><span class="lineno"> 2146</span>&#160;        correlation = std::max(0.0, <a class="code" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">Math::pearsonCorrelationCoefficient</a>(v_theo.begin(), v_theo.end(), v_real.begin(), v_real.end()));</div>
<div class="line"><a name="l02147"></a><span class="lineno"> 2147</span>&#160;        final_score = std::sqrt(correlation * fit_score);</div>
<div class="line"><a name="l02148"></a><span class="lineno"> 2148</span>&#160;</div>
<div class="line"><a name="l02149"></a><span class="lineno"> 2149</span>&#160;        <span class="keywordflow">if</span> (final_score &lt; min_feature_score)</div>
<div class="line"><a name="l02150"></a><span class="lineno"> 2150</span>&#160;        {</div>
<div class="line"><a name="l02151"></a><span class="lineno"> 2151</span>&#160;          feature_ok = <span class="keyword">false</span>;</div>
<div class="line"><a name="l02152"></a><span class="lineno"> 2152</span>&#160;          error_msg = <span class="stringliteral">&quot;Feature quality too low after fit&quot;</span>;</div>
<div class="line"><a name="l02153"></a><span class="lineno"> 2153</span>&#160;        }</div>
<div class="line"><a name="l02154"></a><span class="lineno"> 2154</span>&#160;</div>
<div class="line"><a name="l02155"></a><span class="lineno"> 2155</span>&#160;        <span class="comment">//quality output</span></div>
<div class="line"><a name="l02156"></a><span class="lineno"> 2156</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>)</div>
<div class="line"><a name="l02157"></a><span class="lineno"> 2157</span>&#160;        {</div>
<div class="line"><a name="l02158"></a><span class="lineno"> 2158</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot;Quality estimation:&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l02159"></a><span class="lineno"> 2159</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - relative deviation: &quot;</span> &lt;&lt; fit_score &lt;&lt; std::endl;</div>
<div class="line"><a name="l02160"></a><span class="lineno"> 2160</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; - correlation: &quot;</span> &lt;&lt; correlation &lt;&lt; std::endl;</div>
<div class="line"><a name="l02161"></a><span class="lineno"> 2161</span>&#160;          <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a> &lt;&lt; <span class="stringliteral">&quot; =&gt; final score: &quot;</span> &lt;&lt; final_score &lt;&lt; std::endl;</div>
<div class="line"><a name="l02162"></a><span class="lineno"> 2162</span>&#160;        }</div>
<div class="line"><a name="l02163"></a><span class="lineno"> 2163</span>&#160;      }</div>
<div class="line"><a name="l02164"></a><span class="lineno"> 2164</span>&#160;</div>
<div class="line"><a name="l02165"></a><span class="lineno"> 2165</span>&#160;      <span class="keywordflow">return</span> feature_ok;</div>
<div class="line"><a name="l02166"></a><span class="lineno"> 2166</span>&#160;    }</div>
<div class="line"><a name="l02167"></a><span class="lineno"> 2167</span>&#160;</div>
<div class="line"><a name="l02181"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4"> 2181</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4">writeFeatureDebugInfo_</a>(<a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter&lt;PeakType&gt;</a>* fitter,</div>
<div class="line"><a name="l02182"></a><span class="lineno"> 2182</span>&#160;                                <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a>&amp; traces,</div>
<div class="line"><a name="l02183"></a><span class="lineno"> 2183</span>&#160;                                <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">MassTraces</a>&amp; new_traces,</div>
<div class="line"><a name="l02184"></a><span class="lineno"> 2184</span>&#160;                                <span class="keywordtype">bool</span> feature_ok, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> error_msg, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> final_score, <span class="keyword">const</span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> plot_nr, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>&amp; peak,</div>
<div class="line"><a name="l02185"></a><span class="lineno"> 2185</span>&#160;                                <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> path  = <span class="stringliteral">&quot;debug/features/&quot;</span>)</div>
<div class="line"><a name="l02186"></a><span class="lineno"> 2186</span>&#160;    {</div>
<div class="line"><a name="l02187"></a><span class="lineno"> 2187</span>&#160;</div>
<div class="line"><a name="l02188"></a><span class="lineno"> 2188</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> pseudo_rt_shift = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;debug:pseudo_rt_shift&quot;</span>);</div>
<div class="line"><a name="l02189"></a><span class="lineno"> 2189</span>&#160;      <a class="code" href="classOpenMS_1_1TextFile.html">TextFile</a> tf;</div>
<div class="line"><a name="l02190"></a><span class="lineno"> 2190</span>&#160;      <span class="comment">//gnuplot script</span></div>
<div class="line"><a name="l02191"></a><span class="lineno"> 2191</span>&#160;      <a class="code" href="classOpenMS_1_1String.html">String</a> script = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">&quot;plot \&quot;&quot;</span>) + path + plot_nr + <span class="stringliteral">&quot;.dta\&quot; title &#39;before fit (RT: &quot;</span> +  <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>(), 2) + <span class="stringliteral">&quot; m/z: &quot;</span> +  <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(peak.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>(), 4) + <span class="stringliteral">&quot;)&#39; with points 1&quot;</span>;</div>
<div class="line"><a name="l02192"></a><span class="lineno"> 2192</span>&#160;      <span class="comment">//feature before fit</span></div>
<div class="line"><a name="l02193"></a><span class="lineno"> 2193</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; traces.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l02194"></a><span class="lineno"> 2194</span>&#160;      {</div>
<div class="line"><a name="l02195"></a><span class="lineno"> 2195</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].peaks.size(); ++j)</div>
<div class="line"><a name="l02196"></a><span class="lineno"> 2196</span>&#160;        {</div>
<div class="line"><a name="l02197"></a><span class="lineno"> 2197</span>&#160;          tf.push_back(<a class="code" href="classOpenMS_1_1String.html">String</a>(pseudo_rt_shift * <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> + traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].peaks[j].first) + <span class="stringliteral">&quot;\t&quot;</span> + traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].peaks[j].second-&gt;getIntensity());</div>
<div class="line"><a name="l02198"></a><span class="lineno"> 2198</span>&#160;        }</div>
<div class="line"><a name="l02199"></a><span class="lineno"> 2199</span>&#160;      }</div>
<div class="line"><a name="l02200"></a><span class="lineno"> 2200</span>&#160;      tf.<a class="code" href="classOpenMS_1_1TextFile.html#a4fb93f999151e70a0f506c4c36f63fd7">store</a>(path + plot_nr + <span class="stringliteral">&quot;.dta&quot;</span>);</div>
<div class="line"><a name="l02201"></a><span class="lineno"> 2201</span>&#160;      <span class="comment">//fitted feature</span></div>
<div class="line"><a name="l02202"></a><span class="lineno"> 2202</span>&#160;      <span class="keywordflow">if</span> (new_traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">getPeakCount</a>() != 0)</div>
<div class="line"><a name="l02203"></a><span class="lineno"> 2203</span>&#160;      {</div>
<div class="line"><a name="l02204"></a><span class="lineno"> 2204</span>&#160;        tf.clear();</div>
<div class="line"><a name="l02205"></a><span class="lineno"> 2205</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; new_traces.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l02206"></a><span class="lineno"> 2206</span>&#160;        {</div>
<div class="line"><a name="l02207"></a><span class="lineno"> 2207</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt; new_traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].peaks.size(); ++j)</div>
<div class="line"><a name="l02208"></a><span class="lineno"> 2208</span>&#160;          {</div>
<div class="line"><a name="l02209"></a><span class="lineno"> 2209</span>&#160;            tf.push_back(<a class="code" href="classOpenMS_1_1String.html">String</a>(pseudo_rt_shift * <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> + new_traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].peaks[j].first) + <span class="stringliteral">&quot;\t&quot;</span> + new_traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].peaks[j].second-&gt;getIntensity());</div>
<div class="line"><a name="l02210"></a><span class="lineno"> 2210</span>&#160;          }</div>
<div class="line"><a name="l02211"></a><span class="lineno"> 2211</span>&#160;        }</div>
<div class="line"><a name="l02212"></a><span class="lineno"> 2212</span>&#160;</div>
<div class="line"><a name="l02213"></a><span class="lineno"> 2213</span>&#160;        tf.<a class="code" href="classOpenMS_1_1TextFile.html#a4fb93f999151e70a0f506c4c36f63fd7">store</a>(path + plot_nr + <span class="stringliteral">&quot;_cropped.dta&quot;</span>);</div>
<div class="line"><a name="l02214"></a><span class="lineno"> 2214</span>&#160;        script = script + <span class="stringliteral">&quot;, \&quot;&quot;</span> + path + plot_nr + <span class="stringliteral">&quot;_cropped.dta\&quot; title &#39;feature &quot;</span>;</div>
<div class="line"><a name="l02215"></a><span class="lineno"> 2215</span>&#160;</div>
<div class="line"><a name="l02216"></a><span class="lineno"> 2216</span>&#160;        <span class="keywordflow">if</span> (!feature_ok)</div>
<div class="line"><a name="l02217"></a><span class="lineno"> 2217</span>&#160;        {</div>
<div class="line"><a name="l02218"></a><span class="lineno"> 2218</span>&#160;          script = script + <span class="stringliteral">&quot; - &quot;</span> + error_msg;</div>
<div class="line"><a name="l02219"></a><span class="lineno"> 2219</span>&#160;        }</div>
<div class="line"><a name="l02220"></a><span class="lineno"> 2220</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l02221"></a><span class="lineno"> 2221</span>&#160;        {</div>
<div class="line"><a name="l02222"></a><span class="lineno"> 2222</span>&#160;          script = script + (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>-&gt;size() + 1) + <span class="stringliteral">&quot; (score: &quot;</span> +  <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(final_score, 3) + <span class="stringliteral">&quot;)&quot;</span>;</div>
<div class="line"><a name="l02223"></a><span class="lineno"> 2223</span>&#160;        }</div>
<div class="line"><a name="l02224"></a><span class="lineno"> 2224</span>&#160;        script = script + <span class="stringliteral">&quot;&#39; with points 3&quot;</span>;</div>
<div class="line"><a name="l02225"></a><span class="lineno"> 2225</span>&#160;      }</div>
<div class="line"><a name="l02226"></a><span class="lineno"> 2226</span>&#160;      <span class="comment">//fitted functions</span></div>
<div class="line"><a name="l02227"></a><span class="lineno"> 2227</span>&#160;      tf.clear();</div>
<div class="line"><a name="l02228"></a><span class="lineno"> 2228</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; traces.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l02229"></a><span class="lineno"> 2229</span>&#160;      {</div>
<div class="line"><a name="l02230"></a><span class="lineno"> 2230</span>&#160;        <span class="keywordtype">char</span> fun = <span class="charliteral">&#39;f&#39;</span>;</div>
<div class="line"><a name="l02231"></a><span class="lineno"> 2231</span>&#160;        fun += (char)<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>;</div>
<div class="line"><a name="l02232"></a><span class="lineno"> 2232</span>&#160;        tf.push_back(fitter-&gt;<a class="code" href="classOpenMS_1_1TraceFitter.html#ab67d38bd9a15db565531cc729df77924">getGnuplotFormula</a>(traces[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>], fun, traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">baseline</a>, pseudo_rt_shift * k));</div>
<div class="line"><a name="l02233"></a><span class="lineno"> 2233</span>&#160;        <span class="comment">//tf.push_back(String(fun)+&quot;(x)= &quot; + traces.baseline + &quot; + &quot; + fitter-&gt;getGnuplotFormula(traces[k], pseudo_rt_shift * k));</span></div>
<div class="line"><a name="l02234"></a><span class="lineno"> 2234</span>&#160;        script =  script + <span class="stringliteral">&quot;, &quot;</span> + fun + <span class="stringliteral">&quot;(x) title &#39;Trace &quot;</span> + k + <span class="stringliteral">&quot; (m/z: &quot;</span> + <a class="code" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number</a>(traces[k].getAvgMZ(), 4) + <span class="stringliteral">&quot;)&#39;&quot;</span>;</div>
<div class="line"><a name="l02235"></a><span class="lineno"> 2235</span>&#160;      }</div>
<div class="line"><a name="l02236"></a><span class="lineno"> 2236</span>&#160;</div>
<div class="line"><a name="l02237"></a><span class="lineno"> 2237</span>&#160;      <span class="comment">//output</span></div>
<div class="line"><a name="l02238"></a><span class="lineno"> 2238</span>&#160;      tf.push_back(<span class="stringliteral">&quot;set xlabel \&quot;pseudo RT (mass traces side-by-side)\&quot;&quot;</span>);</div>
<div class="line"><a name="l02239"></a><span class="lineno"> 2239</span>&#160;      tf.push_back(<span class="stringliteral">&quot;set ylabel \&quot;intensity\&quot;&quot;</span>);</div>
<div class="line"><a name="l02240"></a><span class="lineno"> 2240</span>&#160;      tf.push_back(<span class="stringliteral">&quot;set samples 1000&quot;</span>);</div>
<div class="line"><a name="l02241"></a><span class="lineno"> 2241</span>&#160;      tf.push_back(script);</div>
<div class="line"><a name="l02242"></a><span class="lineno"> 2242</span>&#160;      tf.push_back(<span class="stringliteral">&quot;pause -1&quot;</span>);</div>
<div class="line"><a name="l02243"></a><span class="lineno"> 2243</span>&#160;      tf.<a class="code" href="classOpenMS_1_1TextFile.html#a4fb93f999151e70a0f506c4c36f63fd7">store</a>(path + plot_nr + <span class="stringliteral">&quot;.plot&quot;</span>);</div>
<div class="line"><a name="l02244"></a><span class="lineno"> 2244</span>&#160;    }</div>
<div class="line"><a name="l02245"></a><span class="lineno"> 2245</span>&#160;</div>
<div class="line"><a name="l02247"></a><span class="lineno"> 2247</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l02248"></a><span class="lineno"> 2248</span>&#160;</div>
<div class="line"><a name="l02250"></a><span class="lineno"> 2250</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a>&amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ab76605572e7deccf4898a4398aa30d91">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a>&amp;);</div>
<div class="line"><a name="l02252"></a><span class="lineno"> 2252</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">FeatureFinderAlgorithmPicked</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a>&amp;);</div>
<div class="line"><a name="l02253"></a><span class="lineno"> 2253</span>&#160;  };</div>
<div class="line"><a name="l02254"></a><span class="lineno"> 2254</span>&#160;</div>
<div class="line"><a name="l02255"></a><span class="lineno"> 2255</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l02256"></a><span class="lineno"> 2256</span>&#160;</div>
<div class="line"><a name="l02257"></a><span class="lineno"> 2257</span>&#160;<span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_H</span></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a604ce6f3380b18acbebda3c1ed14e70c"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a604ce6f3380b18acbebda3c1ed14e70c">OpenMS::FeatureMap::sortByMZ</a></div><div class="ttdeci">void sortByMZ()</div><div class="ttdoc">Sort features by m/z position. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:322</div></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="classOpenMS_1_1DBoundingBox_html_ac55b302033b5b9d7c78a223db8cfaffb"><div class="ttname"><a href="classOpenMS_1_1DBoundingBox.html#ac55b302033b5b9d7c78a223db8cfaffb">OpenMS::DBoundingBox::encloses</a></div><div class="ttdeci">bool encloses(const PositionType &amp;position) const </div><div class="ttdoc">Checks whether this range contains a certain point. </div><div class="ttdef"><b>Definition:</b> DBoundingBox.h:159</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a7678e0cd827e8669246943be392bd8d0"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">OpenMS::FeatureFinderAlgorithmPicked::intensity_thresholds_</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; DoubleReal &gt; &gt; &gt; intensity_thresholds_</div><div class="ttdoc">Precalculated intensity 20-quantiles (binned) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1154</div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_afa3f4fa08a8a3b675e2dab06e29412a1"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">OpenMS::FeatureFinderAlgorithmPicked::debug_</a></div><div class="ttdeci">bool debug_</div><div class="ttdoc">debug flag </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1119</div></div>
<div class="ttc" id="group__MathFunctionsMisc_html_gadaeb3f406822442307da5b2b94c40885"><div class="ttname"><a href="group__MathFunctionsMisc.html#gadaeb3f406822442307da5b2b94c40885">OpenMS::Math::isOdd</a></div><div class="ttdeci">bool isOdd(UInt x)</div><div class="ttdoc">Returns true if the given interger is odd. </div><div class="ttdef"><b>Definition:</b> MathFunctions.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_a135a7e818125b31198a8a65d9ac7a3d1"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">OpenMS::MetaInfoInterface::setMetaValue</a></div><div class="ttdeci">void setMetaValue(const String &amp;name, const DataValue &amp;value)</div><div class="ttdoc">sets the DataValue corresponding to a name </div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a642bbbd0de05e84147e701bfeaf188a2"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">OpenMS::TraceFitter::getFeatureIntensityContribution</a></div><div class="ttdeci">virtual DoubleReal getFeatureIntensityContribution()=0</div></div>
<div class="ttc" id="MathFunctions_8h_html"><div class="ttname"><a href="MathFunctions_8h.html">MathFunctions.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ae4e0f0c176662a323a6a64d29ff986dd"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">OpenMS::FeatureFinderAlgorithmPicked::SpectrumType</a></div><div class="ttdeci">MapType::SpectrumType SpectrumType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_ac80a487ac41c375532f8bff16871ae15"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">OpenMS::BaseFeature::getCharge</a></div><div class="ttdeci">const ChargeType &amp; getCharge() const </div><div class="ttdoc">Non-mutable access to charge state. </div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::IsotopeDistribution::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdoc">returns the size of the distribtion which is the number of isotopes in the distribution ...</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_ab67d38bd9a15db565531cc729df77924"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#ab67d38bd9a15db565531cc729df77924">OpenMS::TraceFitter::getGnuplotFormula</a></div><div class="ttdeci">virtual String getGnuplotFormula(FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt; PeakType &gt; const &amp;trace, const char function_name, const DoubleReal baseline, const DoubleReal rt_shift)=0</div></div>
<div class="ttc" id="FeatureXMLFile_8h_html"><div class="ttname"><a href="FeatureXMLFile_8h.html">FeatureXMLFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_a6d64276a665c3c0dca8fb4ade3c8b477"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#a6d64276a665c3c0dca8fb4ade3c8b477">OpenMS::IsotopeDistribution::Iterator</a></div><div class="ttdeci">ContainerType::iterator Iterator</div><div class="ttdef"><b>Definition:</b> IsotopeDistribution.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a5f09052343ef99616ad653897841ce3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">OpenMS::FeatureFinderAlgorithm::features_</a></div><div class="ttdeci">FeatureMapType * features_</div><div class="ttdoc">Output data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:144</div></div>
<div class="ttc" id="group__Concept_html_gab685845059e8a2c92743427d9a698c70"><div class="ttname"><a href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">OpenMS::Real</a></div><div class="ttdeci">float Real</div><div class="ttdoc">Real type. </div><div class="ttdef"><b>Definition:</b> Types.h:109</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a761b1937850c141d0c6fff0e4d633a04"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">OpenMS::DefaultParamHandler::defaults_</a></div><div class="ttdeci">Param defaults_</div><div class="ttdoc">Container for default parameters. This member should be filled in the constructor of derived classes!...</div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a37daff803c85d8fa7e2ba173b3138d60"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">OpenMS::FeatureFinderAlgorithmPicked::positionScore_</a></div><div class="ttdeci">DoubleReal positionScore_(DoubleReal pos1, DoubleReal pos2, DoubleReal allowed_deviation) const </div><div class="ttdoc">Calculates a score between 0 and 1 for the m/z deviation of two peaks. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1723</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_acc97fb931afc9e8f86fe9e40683a5a6c"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#acc97fb931afc9e8f86fe9e40683a5a6c">OpenMS::FeatureFinderAlgorithmPicked::intersection_</a></div><div class="ttdeci">DoubleReal intersection_(const Feature &amp;f1, const Feature &amp;f2) const </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1193</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a432099944e11263aa20aaf8ea1389790"><div class="ttname"><a href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">OpenMS::Param::setValue</a></div><div class="ttdeci">void setValue(const String &amp;key, const DataValue &amp;value, const String &amp;description=&quot;&quot;, const StringList &amp;tags=StringList())</div><div class="ttdoc">Sets a value. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ad832d6128e519d1c6a7fefd89158c37e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad832d6128e519d1c6a7fefd89158c37e">OpenMS::FeatureFinderAlgorithmPicked::chooseTraceFitter_</a></div><div class="ttdeci">TraceFitter&lt; PeakType &gt; * chooseTraceFitter_(double &amp;tau)</div><div class="ttdoc">Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1914</div></div>
<div class="ttc" id="ElementDB_8h_html"><div class="ttname"><a href="ElementDB_8h.html">ElementDB.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_aa2835fd8d8621a7ff9effbf85801917d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">OpenMS::FeatureFinderAlgorithmPicked::intensity_percentage_</a></div><div class="ttdeci">DoubleReal intensity_percentage_</div><div class="ttdoc">Isotope pattern intensity contribution of required peaks. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1134</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a5ae84d207afd136419c46d9ec811bb97"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">OpenMS::FeatureFinderAlgorithmPicked::intensityScore_</a></div><div class="ttdeci">DoubleReal intensityScore_(Size spectrum, Size peak) const </div><div class="ttdoc">Compute the intensity score for the peak peak in spectrum spectrum. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1840</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed_html_ae90f6d024629703c9ba0dbd5eb5ef4b2"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum</a></div><div class="ttdeci">Size spectrum</div><div class="ttdoc">Spectrum index. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a99b8e7ca327a789a40e0b03d4a280ca5"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">OpenMS::FeatureFinderAlgorithmPicked::min_isotope_fit_</a></div><div class="ttdeci">DoubleReal min_isotope_fit_</div><div class="ttdoc">Mimimum isotope pattern fit for a feature. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1139</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeatureFinderAlgorithm::ff_</a></div><div class="ttdeci">FeatureFinder * ff_</div><div class="ttdoc">Pointer to the calling FeatureFinder that is used to access the feature flags. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html">OpenMS::Peak2D</a></div><div class="ttdoc">A 2-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a2694f0775c46d9076355cb85d9815425"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">OpenMS::Peak2D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">OpenMS::FeatureFinderAlgorithmPicked</a></div><div class="ttdoc">FeatureFinderAlgorithm for picked peaks. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a0adf747960bee685e34bfbbe57a7089b"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">OpenMS::Feature::getOverallQuality</a></div><div class="ttdeci">QualityType getOverallQuality() const </div><div class="ttdoc">Non-mutable access to the overall quality. </div></div>
<div class="ttc" id="LogStream_8h_html_aeb4f36db01bd128c7afeac5889dac311"><div class="ttname"><a href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a></div><div class="ttdeci">#define LOG_INFO</div><div class="ttdoc">Macro if a information, e.g. a status should be reported. </div><div class="ttdef"><b>Definition:</b> LogStream.h:455</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a1f44db8f9a5426ed4be51833385f5d6a"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">OpenMS::FeatureFinderAlgorithmPicked::cropFeature_</a></div><div class="ttdeci">void cropFeature_(TraceFitter&lt; PeakType &gt; *fitter, const MassTraces &amp;traces, MassTraces &amp;new_traces)</div><div class="ttdoc">Creates new mass traces new_traces based on the fitting result and the original traces traces...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1979</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_ac71f27c40d35a3658e5753647c3e63ca"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::max_trace</a></div><div class="ttdeci">Size max_trace</div><div class="ttdoc">Maximum intensity trace. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:269</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a830e58a22131827d85007a70e3069a5f"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a830e58a22131827d85007a70e3069a5f">OpenMS::MSSpectrum::findNearest</a></div><div class="ttdeci">Size findNearest(CoordinateType mz) const </div><div class="ttdoc">Binary search for the peak nearest to a specific m/z. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:476</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a00f443c46b1d9f3485ef02d844b2433d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">OpenMS::FeatureFinderAlgorithmPicked::extendMassTraces_</a></div><div class="ttdeci">void extendMassTraces_(const IsotopePattern &amp;pattern, MassTraces &amp;traces, Size meta_index_overall) const </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1367</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::DefaultParamHandler::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">Container for current parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:148</div></div>
<div class="ttc" id="FeatureFinderAlgorithmPickedHelperStructs_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithmPickedHelperStructs_8h.html">FeatureFinderAlgorithmPickedHelperStructs.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ab071fe5bd7b2f969e4f9ed5d7467da1e"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ab071fe5bd7b2f969e4f9ed5d7467da1e">OpenMS::Feature::getConvexHull</a></div><div class="ttdeci">ConvexHull2D &amp; getConvexHull() const </div><div class="ttdoc">Returns the overall convex hull of the feature (calculated from the convex hulls of the mass traces) ...</div></div>
<div class="ttc" id="StatisticFunctions_8h_html"><div class="ttname"><a href="StatisticFunctions_8h.html">StatisticFunctions.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a48c8332d7771967946379f577ca3d973"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">OpenMS::FeatureFinderAlgorithmPicked::findIsotope_</a></div><div class="ttdeci">void findIsotope_(DoubleReal pos, Size spectrum_index, IsotopePattern &amp;pattern, Size pattern_index, Size &amp;peak_index) const </div><div class="ttdoc">Searches for an isotopic peak in the current spectrum and the adjacent spectra. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1642</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a09903c7965f8ece31f2c1e07b41ae6dd"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">OpenMS::Peak2D::getIntensity</a></div><div class="ttdeci">IntensityType getIntensity() const </div><div class="ttdef"><b>Definition:</b> Peak2D.h:161</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ac58a0fa7d6013c1855f905dbaa13c22f"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">OpenMS::FeatureFinderAlgorithmPicked::mass_window_width_</a></div><div class="ttdeci">DoubleReal mass_window_width_</div><div class="ttdoc">Width of the isotope pattern mass bins. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1137</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a></div><div class="ttdoc">Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:153</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a1fd714af1f19177741eb0b4f6eb43e35"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">OpenMS::FeatureFinderAlgorithmPicked::log_</a></div><div class="ttdeci">std::ofstream log_</div><div class="ttdoc">Output stream for log/debug info. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1117</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ae8eb5ec37d3582ac0963d06ea624ab48"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">OpenMS::FeatureFinderAlgorithmPicked::pattern_tolerance_</a></div><div class="ttdeci">DoubleReal pattern_tolerance_</div><div class="ttdoc">Stores mass_trace:mz_tolerance. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1129</div></div>
<div class="ttc" id="TraceFitter_8h_html"><div class="ttname"><a href="TraceFitter_8h.html">TraceFitter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html_ae05e70281bd2c24b9cfa431200669858"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">OpenMS::FeatureXMLFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const FeatureMap&lt;&gt; &amp;feature_map)</div><div class="ttdoc">stores the map feature_map in file with name filename. </div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html">OpenMS::TraceFitter</a></div><div class="ttdoc">Abstract fitter for RT profile fitting. </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_abe26e024e3bac78f99e2a6d487cfe007"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">OpenMS::FeatureFinderAlgorithmPicked::min_rt_span_</a></div><div class="ttdeci">DoubleReal min_rt_span_</div><div class="ttdoc">Minimum RT range that has to be left after the fit. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1141</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_a7e409d85407a4cfbc76fdc4aac06f185"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a7e409d85407a4cfbc76fdc4aac06f185">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::isValid</a></div><div class="ttdeci">bool isValid(DoubleReal seed_mz, DoubleReal trace_tolerance)</div><div class="ttdoc">Checks if still valid (seed still contained and enough traces) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:174</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_ab45dae688fc5d8983727abffa4389003"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#ab45dae688fc5d8983727abffa4389003">OpenMS::IsotopeDistribution::end</a></div><div class="ttdeci">Iterator end()</div><div class="ttdef"><b>Definition:</b> IsotopeDistribution.h:187</div></div>
<div class="ttc" id="group__Conditions_html_gad781993fbeead99f7a76a5b0c67b70e1"><div class="ttname"><a href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</a></div><div class="ttdeci">#define OPENMS_POSTCONDITION(condition, message)</div><div class="ttdoc">Postcondition macro. </div><div class="ttdef"><b>Definition:</b> Macros.h:114</div></div>
<div class="ttc" id="group__Concept_html_gaba0996d26f7be2572973245b51852757"><div class="ttname"><a href="group__Concept.html#gaba0996d26f7be2572973245b51852757">OpenMS::UInt</a></div><div class="ttdeci">unsigned int UInt</div><div class="ttdoc">Unsigned integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a2190523e8d48946faff97a41131fcf92"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a2190523e8d48946faff97a41131fcf92">OpenMS::TraceFitter::checkMinimalRTSpan</a></div><div class="ttdeci">virtual bool checkMinimalRTSpan(const std::pair&lt; DoubleReal, DoubleReal &gt; &amp;rt_bounds, const DoubleReal min_rt_span)=0</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html_af2e76e2f5a4b1549e43a4dac9a3c35c2"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#af2e76e2f5a4b1549e43a4dac9a3c35c2">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::optional_begin</a></div><div class="ttdeci">Size optional_begin</div><div class="ttdoc">Number of optional peaks at the beginning of the pattern. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:282</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern</a></div><div class="ttdoc">Helper structure for a theoretical isotope pattern used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:277</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html">OpenMS::FeatureFinderAlgorithm</a></div><div class="ttdoc">Abstract base class for FeatureFinder algorithms. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a9227a818c19cefa0d29f2940d87de2c6"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">OpenMS::FeatureFinderAlgorithmPicked::getIsotopeDistribution_</a></div><div class="ttdeci">const TheoreticalIsotopePattern &amp; getIsotopeDistribution_(DoubleReal mass) const </div><div class="ttdoc">Returns the isotope distribution for a certain mass window. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1249</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html_a4671707ce0fc9ba23aa8319f67afa141"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::mz_score</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; mz_score</div><div class="ttdoc">m/z score of peak (0 if peak index is -1 or -2) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:309</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1AreaIterator_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1AreaIterator.html">OpenMS::Internal::AreaIterator</a></div><div class="ttdoc">Forward iterator for an area of peaks in an experiment. </div><div class="ttdef"><b>Definition:</b> AreaIterator.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html">OpenMS::IsotopeDistribution</a></div><div class="ttdoc">Isotope distribution class. </div><div class="ttdef"><b>Definition:</b> IsotopeDistribution.h:61</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdoc">Returns the size. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:290</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a290ced0989c9db9d895a6a3435360f47"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">OpenMS::FeatureFinderAlgorithmPicked::abort_reasons_</a></div><div class="ttdeci">std::map&lt; Seed, String &gt; abort_reasons_</div><div class="ttdoc">Array of abort reasons. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1123</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_abb9911ee4d024e85861f29bbbd0a63ef"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abb9911ee4d024e85861f29bbbd0a63ef">OpenMS::FeatureFinderAlgorithmPicked::FeatureMapType</a></div><div class="ttdeci">FeatureFinderAlgorithm&lt; PeakType, FeatureType &gt;::FeatureMapType FeatureMapType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a57c4a49592647cc2db0dc517ed9a1a02"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a57c4a49592647cc2db0dc517ed9a1a02">OpenMS::Feature::encloses</a></div><div class="ttdeci">bool encloses(DoubleReal rt, DoubleReal mz) const </div><div class="ttdoc">Returns if the mass trace convex hulls of the feature enclose the position specified by rt and mz...</div></div>
<div class="ttc" id="classOpenMS_1_1UniqueIdInterface_html_a9c908a735f82adb8f66a326547a9acf8"><div class="ttname"><a href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">OpenMS::UniqueIdInterface::setUniqueId</a></div><div class="ttdeci">Size setUniqueId()</div><div class="ttdoc">Assigns a new, valid unique id. Always returns 1. </div><div class="ttdef"><b>Definition:</b> UniqueIdInterface.h:150</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a5fe4516f447b7b646e39003f6c753ad5"><div class="ttname"><a href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">OpenMS::String::number</a></div><div class="ttdeci">static String number(DoubleReal d, UInt n)</div><div class="ttdoc">returns a string for d with exactly n decimal places </div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a10ddb3b8cc795c598f76db017b9ca322"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a10ddb3b8cc795c598f76db017b9ca322">OpenMS::TraceFitter::getLowerRTBound</a></div><div class="ttdeci">virtual DoubleReal getLowerRTBound() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a7dae78ea20f5b33125f50c6ee27b1a60"><div class="ttname"><a href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">OpenMS::Param::setSectionDescription</a></div><div class="ttdeci">void setSectionDescription(const String &amp;key, const String &amp;description)</div><div class="ttdoc">Sets a description for an existing section. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ae464adecb765a4c2b9c35b374620454e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">OpenMS::FeatureFinderAlgorithmPicked::reported_mz_</a></div><div class="ttdeci">String reported_mz_</div><div class="ttdoc">The mass type that is reported for features. &amp;#39;maximum&amp;#39; returns the m/z value of the highest mass trac...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1144</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_1FeatureFinderAlgorithmPicked_html_a41848085aa61f5c00fc88e683945adf7"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">OpenMS::FeatureFinderAlgorithmPicked::trace_tolerance_</a></div><div class="ttdeci">DoubleReal trace_tolerance_</div><div class="ttdoc">Stores isotopic_pattern:mz_tolerance. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1130</div></div>
<div class="ttc" id="group__Concept_html_gae113cb41304c6692c7bf5d0624dc6f0f"><div class="ttname"><a href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">OpenMS::SignedSize</a></div><div class="ttdeci">ptrdiff_t SignedSize</div><div class="ttdoc">Signed Size type e.g. used as pointer difference. </div><div class="ttdef"><b>Definition:</b> Types.h:151</div></div>
<div class="ttc" id="classOpenMS_1_1DBoundingBox_html_af99d7503ed85cda7c0ccc2217f36cee1"><div class="ttname"><a href="classOpenMS_1_1DBoundingBox.html#af99d7503ed85cda7c0ccc2217f36cee1">OpenMS::DBoundingBox::intersects</a></div><div class="ttdeci">bool intersects(const DBoundingBox &amp;bounding_box) const </div><div class="ttdef"><b>Definition:</b> DBoundingBox.h:180</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html_ac102a03577b6512164d6e4ff3cf78df0"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::intensity</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; intensity</div><div class="ttdoc">Peak intensity (0 if peak index is -1 or -2) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:307</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_a34c827b6d53a8c171b233332bfe4d634"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::getPeakCount</a></div><div class="ttdeci">Size getPeakCount() const </div><div class="ttdoc">Returns the peak count of all traces. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:163</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac2bc824d6ff2633ec34793c9e918d479"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">OpenMS::MSExperiment::resize</a></div><div class="ttdeci">void resize(Size s)</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:122</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a65120f4f127d69944775cd5aae06709f"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">OpenMS::TraceFitter::computeTheoretical</a></div><div class="ttdeci">virtual DoubleReal computeTheoretical(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt; PeakType &gt; &amp;trace, Size k)=0</div></div>
<div class="ttc" id="OpenSwathChromatogramExtractor_8C_html_ad1b6cd7c1daf3c44f94b28a904153b46"><div class="ttname"><a href="OpenSwathChromatogramExtractor_8C.html#ad1b6cd7c1daf3c44f94b28a904153b46">IF_MASTERTHREAD</a></div><div class="ttdeci">#define IF_MASTERTHREAD</div><div class="ttdef"><b>Definition:</b> OpenSwathChromatogramExtractor.C:48</div></div>
<div class="ttc" id="classOpenMS_1_1Element_html_af005f66c79814a28924d954f0150ec44"><div class="ttname"><a href="classOpenMS_1_1Element.html#af005f66c79814a28924d954f0150ec44">OpenMS::Element::setIsotopeDistribution</a></div><div class="ttdeci">void setIsotopeDistribution(const IsotopeDistribution &amp;isotopes)</div><div class="ttdoc">sets the isotope distribution of the element </div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a87d8ffa067f5ee283997ac69b197234f"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a87d8ffa067f5ee283997ac69b197234f">OpenMS::MSExperiment::getMaxMZ</a></div><div class="ttdeci">CoordinateType getMaxMZ() const </div><div class="ttdoc">returns the maximal m/z value </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:527</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a8fc6defe4e499b1b9b9c275689e44352"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">OpenMS::Constants::c</a></div><div class="ttdeci">const double c</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html_a7d03330cd21316709f10c3e9ca55f95c"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a7d03330cd21316709f10c3e9ca55f95c">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_mz</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; theoretical_mz</div><div class="ttdoc">Theoretical m/z value of the isotope peak. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:311</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="IsotopeDistribution_8h_html"><div class="ttname"><a href="IsotopeDistribution_8h.html">IsotopeDistribution.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ac3ad3885811bdd008ebad6dc58424303"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">OpenMS::FeatureFinderAlgorithmPicked::intensity_rt_step_</a></div><div class="ttdeci">DoubleReal intensity_rt_step_</div><div class="ttdoc">RT bin width. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1150</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a5f9d4faff212e67330d60f958f0ce4bc"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a5f9d4faff212e67330d60f958f0ce4bc">OpenMS::MSExperiment::areaEndConst</a></div><div class="ttdeci">ConstAreaIterator areaEndConst() const </div><div class="ttdoc">Returns an non-mutable invalid area iterator marking the end of an area. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:337</div></div>
<div class="ttc" id="LogStream_8h_html_a6ff63e8955665c4a58b1598f2b07c51a"><div class="ttname"><a href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a></div><div class="ttdeci">#define LOG_DEBUG</div><div class="ttdoc">Macro for general debugging information. </div><div class="ttdef"><b>Definition:</b> LogStream.h:459</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html">OpenMS::FeatureFinderDefs</a></div><div class="ttdoc">The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d8aab759e082ef93475344071fb7809"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d8aab759e082ef93475344071fb7809">OpenMS::MSExperiment::getMinMZ</a></div><div class="ttdeci">CoordinateType getMinMZ() const </div><div class="ttdoc">returns the minimal m/z value </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:521</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a4097a067534171488208ac7b101b5c0c"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">OpenMS::FeatureFinderAlgorithmPicked::FloatDataArrays</a></div><div class="ttdeci">SpectrumType::FloatDataArrays FloatDataArrays</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9244f3b9aefde24a9b246a8396c3bb84"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9244f3b9aefde24a9b246a8396c3bb84">OpenMS::MSExperiment::getMinRT</a></div><div class="ttdeci">CoordinateType getMinRT() const </div><div class="ttdoc">returns the minimal retention time value </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:533</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a7a25c5ed4c5f83b23ded7014aef42ad4"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">OpenMS::Constants::PROTON_MASS_U</a></div><div class="ttdeci">const double PROTON_MASS_U</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak2D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Non-mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:167</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_ae2fc906f686ab141e88c57655afd1774"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#ae2fc906f686ab141e88c57655afd1774">OpenMS::MSSpectrum&lt; PeakType &gt;::FloatDataArrays</a></div><div class="ttdeci">std::vector&lt; FloatDataArray &gt; FloatDataArrays</div><div class="ttdoc">Float data array vector type. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:113</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html_a5dbfbed553b8cf7f9ef1bcb2c4ac94ca"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern</a></div><div class="ttdeci">TheoreticalIsotopePattern theoretical_pattern</div><div class="ttdoc">Theoretical isotope pattern. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:313</div></div>
<div class="ttc" id="classOpenMS_1_1TextFile_html_a4fb93f999151e70a0f506c4c36f63fd7"><div class="ttname"><a href="classOpenMS_1_1TextFile.html#a4fb93f999151e70a0f506c4c36f63fd7">OpenMS::TextFile::store</a></div><div class="ttdeci">void store(const String &amp;filename)</div><div class="ttdoc">Writes the data to a file. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af73fd15708e50e77665070023a09cc87">OpenMS::FeatureFinderAlgorithmPicked::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1108</div></div>
<div class="ttc" id="classOpenMS_1_1GaussTraceFitter_html"><div class="ttname"><a href="classOpenMS_1_1GaussTraceFitter.html">OpenMS::GaussTraceFitter</a></div><div class="ttdoc">Fitter for RT profiles using a gaussian background model. </div><div class="ttdef"><b>Definition:</b> GaussTraceFitter.h:53</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html_a5ffc5efccefcdddcb7606303d72fa148"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum</a></div><div class="ttdeci">std::vector&lt; Size &gt; spectrum</div><div class="ttdoc">Spectrum index (undefined if peak index is -1 or -2) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:305</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a5c38e77e9286e4faf58e56afce913ee2"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5c38e77e9286e4faf58e56afce913ee2">OpenMS::FeatureFinderAlgorithmPicked::nearest_</a></div><div class="ttdeci">Size nearest_(DoubleReal pos, const SpectrumType &amp;spec, Size start) const </div><div class="ttdoc">Returns the index of the peak nearest to m/z pos in spectrum spec (linear search starting from index ...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1612</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace_html_aac1b70a2ed67ead038c4d3f5ac4d8a81"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#aac1b70a2ed67ead038c4d3f5ac4d8a81">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace::isValid</a></div><div class="ttdeci">bool isValid() const </div><div class="ttdoc">Checks if this Trace is valid (has more than 2 points) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:142</div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html">OpenMS::MzMLFile</a></div><div class="ttdoc">File adapter for MzML files. </div><div class="ttdef"><b>Definition:</b> MzMLFile.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1Element_html"><div class="ttname"><a href="classOpenMS_1_1Element.html">OpenMS::Element</a></div><div class="ttdoc">Representation of an element. </div><div class="ttdef"><b>Definition:</b> Element.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt; PeakType &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a1b9ec9e0082be83ffb6db38de5d6a59e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">OpenMS::FeatureFinderAlgorithmPicked::intensity_bins_</a></div><div class="ttdeci">UInt intensity_bins_</div><div class="ttdoc">Number of bins (in RT and MZ) for intensity significance estimation. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1138</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a301b8bd9f8b8404ffd2bf375b1f0cf2b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">OpenMS::FeatureFinderAlgorithmPicked::max_rt_span_</a></div><div class="ttdeci">DoubleReal max_rt_span_</div><div class="ttdoc">Maximum RT range the model is allowed to span. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1142</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ad608d4f3d2a370fe2c1672c7818146b4"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4">OpenMS::FeatureFinderAlgorithmPicked::writeFeatureDebugInfo_</a></div><div class="ttdeci">void writeFeatureDebugInfo_(TraceFitter&lt; PeakType &gt; *fitter, const MassTraces &amp;traces, const MassTraces &amp;new_traces, bool feature_ok, const String error_msg, const DoubleReal final_score, const Int plot_nr, const PeakType &amp;peak, const String path=&quot;debug/features/&quot;)</div><div class="ttdoc">Creates several files containing plots and viewable data of the fitted mass trace. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:2181</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a1cc1012b0cdaea97f58d571af1ff45de"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">OpenMS::ProgressLogger::endProgress</a></div><div class="ttdeci">void endProgress() const </div><div class="ttdoc">Ends the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a3e0a91daf1d288f768c9683e317488f4"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">OpenMS::FeatureFinderAlgorithmPicked::IsotopePattern</a></div><div class="ttdeci">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern IsotopePattern</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:107</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a1d3473af083e9dd668d782424aa2da05"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a1d3473af083e9dd668d782424aa2da05">OpenMS::Internal::DIntervalBase::width</a></div><div class="ttdeci">CoordinateType width() const </div><div class="ttdoc">Returns the width of the area i.e. the difference of dimension zero (X). </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:292</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue &amp; getValue(const String &amp;key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a396c5ebcac2e70f9b9a478bb2456985b"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">OpenMS::Peak2D::setRT</a></div><div class="ttdeci">void setRT(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:209</div></div>
<div class="ttc" id="group__MathFunctionsStatistics_html_gac7a454e1847d508ba6635d47f49fbe8c"><div class="ttname"><a href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">OpenMS::Math::pearsonCorrelationCoefficient</a></div><div class="ttdeci">static DoubleReal pearsonCorrelationCoefficient(IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)</div><div class="ttdoc">Calculates the Pearson correlation coefficient for the values in [begin_a, end_a) and [begin_b...</div><div class="ttdef"><b>Definition:</b> StatisticFunctions.h:285</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_aa23ed32415e6667bd2737377c24c16fb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aa23ed32415e6667bd2737377c24c16fb">OpenMS::MSExperiment::areaBeginConst</a></div><div class="ttdeci">ConstAreaIterator areaBeginConst(CoordinateType min_rt, CoordinateType max_rt, CoordinateType min_mz, CoordinateType max_mz) const </div><div class="ttdoc">Returns a non-mutable area iterator for area. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:327</div></div>
<div class="ttc" id="Constants_8h_html"><div class="ttname"><a href="Constants_8h.html">Constants.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace_html_a7db81fa54d4743c867872ac5b0938247"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a7db81fa54d4743c867872ac5b0938247">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace::theoretical_int</a></div><div class="ttdeci">DoubleReal theoretical_int</div><div class="ttdoc">Theoretical intensity value (scaled to [0,1]) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_aaa5e4ac166de2cd5d3e38ccb4157bd77"><div class="ttname"><a href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">OpenMS::Feature::getSubordinates</a></div><div class="ttdeci">const std::vector&lt; Feature &gt; &amp; getSubordinates() const </div><div class="ttdoc">immutable access to subordinate features </div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_a261a831dc055b354545a8c0e48f57cad"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#a261a831dc055b354545a8c0e48f57cad">OpenMS::IsotopeDistribution::setMaxIsotope</a></div><div class="ttdeci">void setMaxIsotope(Size max_isotope)</div><div class="ttdoc">sets the maximal isotope with max_isotope </div></div>
<div class="ttc" id="classOpenMS_1_1ElementDB_html_a62508929fb2f7f12cfbd486272f1b480"><div class="ttname"><a href="classOpenMS_1_1ElementDB.html#a62508929fb2f7f12cfbd486272f1b480">OpenMS::ElementDB::getElement</a></div><div class="ttdeci">const Element * getElement(const String &amp;name) const </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_aea2bb0ee05df783538f89be9649dc3a6"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">OpenMS::FeatureFinderAlgorithmPicked::FeatureFinderAlgorithmPicked</a></div><div class="ttdeci">FeatureFinderAlgorithmPicked()</div><div class="ttdoc">default constructor </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a26002e622e0cb7f544d7d364be7c274a"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">OpenMS::FeatureFinderAlgorithmPicked::optional_fit_improvement_</a></div><div class="ttdeci">DoubleReal optional_fit_improvement_</div><div class="ttdoc">Minimal imrovment for leaving out optional isotope. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1136</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_1TraceFitter_html_af72d2c9ae5ecbd8b8d4605fbbef613cc"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#af72d2c9ae5ecbd8b8d4605fbbef613cc">OpenMS::TraceFitter::checkMaximalRTSpan</a></div><div class="ttdeci">virtual bool checkMaximalRTSpan(const DoubleReal max_rt_span)=0</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_aef59aef1baf90c9ea2376d677c9bf79d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">OpenMS::FeatureFinderAlgorithmPicked::checkFeatureQuality_</a></div><div class="ttdeci">bool checkFeatureQuality_(TraceFitter&lt; PeakType &gt; *fitter, MassTraces &amp;feature_traces, const DoubleReal &amp;seed_mz, const DoubleReal &amp;min_feature_score, String &amp;error_msg, DoubleReal &amp;fit_score, DoubleReal &amp;correlation, DoubleReal &amp;final_score)</div><div class="ttdoc">Checks the feature based on different score thresholds and model constraints. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:2080</div></div>
<div class="ttc" id="GaussTraceFitter_8h_html"><div class="ttname"><a href="GaussTraceFitter_8h.html">GaussTraceFitter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_a2387033802383edbdc95f9bbb12a707e"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#a2387033802383edbdc95f9bbb12a707e">OpenMS::IsotopeDistribution::begin</a></div><div class="ttdeci">Iterator begin()</div><div class="ttdef"><b>Definition:</b> IsotopeDistribution.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a0eac57e7b543d5084b9cdbb940fd031c"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">OpenMS::TraceFitter::getHeight</a></div><div class="ttdeci">virtual DoubleReal getHeight() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_aa1e7b6cd685312da3c92644d8fe71aac"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#aa1e7b6cd685312da3c92644d8fe71aac">OpenMS::TraceFitter::getFWHM</a></div><div class="ttdeci">virtual DoubleReal getFWHM() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1MzMLFile_html_adb795d215478320be7c6130ff7ddf853"><div class="ttname"><a href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">OpenMS::MzMLFile::store</a></div><div class="ttdeci">void store(const String &amp;filename, const MapType &amp;map) const </div><div class="ttdoc">Stores a map in a MzML file. </div><div class="ttdef"><b>Definition:</b> MzMLFile.h:126</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_adf5dffb508ec1b791c73f990ff92a3dd"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#adf5dffb508ec1b791c73f990ff92a3dd">OpenMS::IsotopeDistribution::trimLeft</a></div><div class="ttdeci">void trimLeft(DoubleReal cutoff)</div><div class="ttdoc">Trims the left side of the isotope distribution to isotopes with a significant contribution. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ac7db097c6fa88dec6877edd3b7638b00"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">OpenMS::FeatureFinderAlgorithmPicked::max_feature_intersection_</a></div><div class="ttdeci">DoubleReal max_feature_intersection_</div><div class="ttdoc">Maximum allowed feature intersection (if larger, that one of the feature is removed) ...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1143</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ae9d0a125b344c7315dd63aed9b6871fc"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">OpenMS::FeatureFinderAlgorithmPicked::min_trace_score_</a></div><div class="ttdeci">DoubleReal min_trace_score_</div><div class="ttdoc">Minimum quality of a traces. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1140</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a0ab9bd668829f0fc9608bd56560ac1ae"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a0ab9bd668829f0fc9608bd56560ac1ae">OpenMS::TraceFitter::getUpperRTBound</a></div><div class="ttdeci">virtual DoubleReal getUpperRTBound() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_a5f86b59b547048311dd50df5fb6d3bb5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">OpenMS::StringList::create</a></div><div class="ttdeci">static StringList create(const String &amp;list, const char splitter= ',')</div><div class="ttdoc">Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_a2a548700db35cba3fec126772ef27c72"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#a2a548700db35cba3fec126772ef27c72">OpenMS::IsotopeDistribution::estimateFromPeptideWeight</a></div><div class="ttdeci">void estimateFromPeptideWeight(double average_weight)</div><div class="ttdoc">Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported...</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_a055e732ad7e3eed9cce0d279ae7af3a6"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#a055e732ad7e3eed9cce0d279ae7af3a6">OpenMS::IsotopeDistribution::trimRight</a></div><div class="ttdeci">void trimRight(DoubleReal cutoff)</div><div class="ttdoc">Trims the right side of the isotope distribution to isotopes with a significant contribution. </div></div>
<div class="ttc" id="FeatureFinderAlgorithm_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithm_8h.html">FeatureFinderAlgorithm.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ConvexHull2D_html_a88c6186ce22fc5eae73df90899695229"><div class="ttname"><a href="classOpenMS_1_1ConvexHull2D.html#a88c6186ce22fc5eae73df90899695229">OpenMS::ConvexHull2D::getBoundingBox</a></div><div class="ttdeci">DBoundingBox&lt; 2 &gt; getBoundingBox() const </div><div class="ttdoc">returns the bounding box of the feature hull points </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ad47e8e2093326bd3a2476713d538dd9e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">OpenMS::FeatureFinderAlgorithmPicked::findBestIsotopeFit_</a></div><div class="ttdeci">DoubleReal findBestIsotopeFit_(const Seed &amp;center, UInt charge, IsotopePattern &amp;best_pattern) const </div><div class="ttdoc">Finds the best fitting position of the isotopic pattern estimate defined by center. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1270</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_acb405e09b194cb848140c99da3d6c34b"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::baseline</a></div><div class="ttdeci">DoubleReal baseline</div><div class="ttdoc">Estimated baseline in the region of the feature (used for the fit) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:271</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_1FeatureFinderAlgorithmPicked_html_a2f89be2feec82f5414aedc09e488420b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f89be2feec82f5414aedc09e488420b">OpenMS::FeatureFinderAlgorithmPicked::MapType</a></div><div class="ttdeci">FeatureFinderAlgorithm&lt; PeakType, FeatureType &gt;::MapType MapType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:91</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern</a></div><div class="ttdoc">Helper structure for a found isotope pattern used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:300</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ac02da3d017367d854cb162983679aadc"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">OpenMS::FeatureFinderAlgorithmPicked::Seed</a></div><div class="ttdeci">FeatureFinderAlgorithmPickedHelperStructs::Seed Seed</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_a908f7d0328c34d70706d48af082d4751"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#a908f7d0328c34d70706d48af082d4751">OpenMS::BaseFeature::setWidth</a></div><div class="ttdeci">void setWidth(WidthType fwhm)</div><div class="ttdoc">Set the width of the feature (FWHM) </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a55abad1b592c5e19bfaddfc9f9c4a43e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">OpenMS::FeatureFinderAlgorithmPicked::isotopeScore_</a></div><div class="ttdeci">DoubleReal isotopeScore_(const TheoreticalIsotopePattern &amp;isotopes, IsotopePattern &amp;pattern, bool consider_mz_distances) const </div><div class="ttdoc">Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1738</div></div>
<div class="ttc" id="EGHTraceFitter_8h_html"><div class="ttname"><a href="EGHTraceFitter_8h.html">EGHTraceFitter.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a10933782584a46cded91c40574027ee2"><div class="ttname"><a href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">OpenMS::Param::setValidStrings</a></div><div class="ttdeci">void setValidStrings(const String &amp;key, const std::vector&lt; String &gt; &amp;strings)</div><div class="ttdoc">Sets the valid strings for the parameter key. </div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a7b2aeb3c8d1a4fd03c5843af07474735"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">OpenMS::TraceFitter::fit</a></div><div class="ttdeci">virtual void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt; PeakType &gt; &amp;traces)=0</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a72fcb26a14f6beb1c3fbace9ab3e7dbb"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">OpenMS::FeatureFinderAlgorithmPicked::run</a></div><div class="ttdeci">virtual void run()</div><div class="ttdoc">Main method for actual FeatureFinder. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:218</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak2D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Returns the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:191</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1InvalidValue_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1InvalidValue.html">OpenMS::Exception::InvalidValue</a></div><div class="ttdoc">Invalid value exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:336</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_afea7a0615504af04bc1b922416f702f7"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">OpenMS::FeatureFinderAlgorithmPicked::intensity_percentage_optional_</a></div><div class="ttdeci">DoubleReal intensity_percentage_optional_</div><div class="ttdoc">Isotope pattern intensity contribution of optional peaks. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1135</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a3554cb60a93215ed6c61b257a67efcc3"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a3554cb60a93215ed6c61b257a67efcc3">OpenMS::FeatureMap::swapFeaturesOnly</a></div><div class="ttdeci">void swapFeaturesOnly(FeatureMap &amp;from)</div><div class="ttdoc">Swaps the feature content (plus its range information) of this map with the content of from...</div><div class="ttdef"><b>Definition:</b> FeatureMap.h:377</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a4c3291ae9ef170e82168ccf10eaece4b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">OpenMS::FeatureFinderAlgorithmPicked::max_missing_trace_peaks_</a></div><div class="ttdeci">UInt max_missing_trace_peaks_</div><div class="ttdoc">Stores mass_trace:max_missing. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1132</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_afebc8acd9f3b44ba2936d842469f47e4"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">OpenMS::FeatureFinderAlgorithmPicked::aborts_</a></div><div class="ttdeci">std::map&lt; String, UInt &gt; aborts_</div><div class="ttdoc">Array of abort reasons. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1121</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a6b1ec7d53602252d1f4d7cd0331fc917"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">OpenMS::FeatureFinderAlgorithmPicked::slope_bound_</a></div><div class="ttdeci">DoubleReal slope_bound_</div><div class="ttdoc">Max slope of mass trace intensities. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1133</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a84873a73e9e222a574dccff3bc2d860e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">OpenMS::Internal::DIntervalBase::minPosition</a></div><div class="ttdeci">PositionType const &amp; minPosition() const </div><div class="ttdoc">Accessor to minimum position. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:121</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_af8a4ff323b3f9b72d77f56f9974d5aff"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">OpenMS::FeatureFinderAlgorithmPicked::MassTraces</a></div><div class="ttdeci">FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt; PeakType &gt; MassTraces</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1FeatureXMLFile.html">OpenMS::FeatureXMLFile</a></div><div class="ttdoc">This class provides Input/Output functionality for feature maps. </div><div class="ttdef"><b>Definition:</b> FeatureXMLFile.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_aeba0cded976431f70fbea5499218ce18"><div class="ttname"><a href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">OpenMS::Feature::setOverallQuality</a></div><div class="ttdeci">void setOverallQuality(QualityType q)</div><div class="ttdoc">Set the overall quality. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_afd3d2147a4dba98319002b876781f9ee"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">OpenMS::FeatureFinderAlgorithmPicked::isotope_distributions_</a></div><div class="ttdeci">std::vector&lt; TheoreticalIsotopePattern &gt; isotope_distributions_</div><div class="ttdoc">Vector of precalculated isotope distributions for several mass windows. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1158</div></div>
<div class="ttc" id="classOpenMS_1_1ElementDB_html_ae141930c87ab8851ec484bc1fd0ccb90"><div class="ttname"><a href="classOpenMS_1_1ElementDB.html#ae141930c87ab8851ec484bc1fd0ccb90">OpenMS::ElementDB::getInstance</a></div><div class="ttdeci">static const ElementDB * getInstance()</div><div class="ttdoc">returns a pointer to the singleton instance of the element db </div><div class="ttdef"><b>Definition:</b> ElementDB.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_af67f955c87166e64d9361815dc3760b5"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#af67f955c87166e64d9361815dc3760b5">OpenMS::MSExperiment::getMaxRT</a></div><div class="ttdeci">CoordinateType getMaxRT() const </div><div class="ttdoc">returns the maximal retention time value </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:539</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a3a23089ec40eeed796efe7b69ecb02ac"><div class="ttname"><a href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">OpenMS::Param::setMinInt</a></div><div class="ttdeci">void setMinInt(const String &amp;key, Int min)</div><div class="ttdoc">Sets the minimum value for the integer or integer list parameter key. </div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace_html_a45696e11061da82e7cfd8a0ee88f5d8e"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace::peaks</a></div><div class="ttdeci">std::vector&lt; std::pair&lt; DoubleReal, const PeakType * &gt; &gt; peaks</div><div class="ttdoc">Contained peaks (pair of RT and pointer to peak) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a5fcb56e069842a53246cb6f063e99f22"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">OpenMS::FeatureFinderAlgorithmPicked::min_spectra_</a></div><div class="ttdeci">UInt min_spectra_</div><div class="ttdoc">Number of spectra that have to show the same mass (for finding a mass trace) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1131</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html_a511873304a043cc9222285de3a2c2913"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a511873304a043cc9222285de3a2c2913">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::optional_end</a></div><div class="ttdeci">Size optional_end</div><div class="ttdoc">Number of optional peaks at the end of the pattern. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:284</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a3430a3cac3d46d0420ab99024264359f"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3430a3cac3d46d0420ab99024264359f">OpenMS::FeatureFinderAlgorithmPicked::intensityScore_</a></div><div class="ttdeci">DoubleReal intensityScore_(Size rt_bin, Size mz_bin, DoubleReal intensity) const </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1930</div></div>
<div class="ttc" id="TextFile_8h_html"><div class="ttname"><a href="TextFile_8h.html">TextFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af1c45ecd71b5041b70319249e8e73591"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">OpenMS::ProgressLogger::startProgress</a></div><div class="ttdeci">void startProgress(SignedSize begin, SignedSize end, const String &amp;label) const </div><div class="ttdoc">Initializes the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac6e61de369e994009e36f344f99c15ad"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">OpenMS::MSExperiment::empty</a></div><div class="ttdeci">bool empty() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_aa839121d4666e45d2b5b6d6eab010c5f"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">OpenMS::FeatureFinderAlgorithmPicked::extendMassTrace_</a></div><div class="ttdeci">void extendMassTrace_(MassTrace &amp;trace, SignedSize spectrum_index, DoubleReal mz, bool increase_rt, Size meta_index_overall, DoubleReal min_rt=0.0, DoubleReal max_rt=0.0) const </div><div class="ttdoc">Extends a single mass trace in one RT direction. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1510</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a0b28abb9db6a809eec07048c69fdfaab"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">OpenMS::FeatureFinderAlgorithmPicked::map_</a></div><div class="ttdeci">MapType map_</div><div class="ttdoc">editable copy of the map </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1115</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_ab595724fe9b9eb5d37011f07d90b9e0b"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">OpenMS::BaseFeature::setCharge</a></div><div class="ttdeci">void setCharge(const ChargeType &amp;ch)</div><div class="ttdoc">Set charge state. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html_abe90dc4ba735b87228bfe913b490f9f2"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#abe90dc4ba735b87228bfe913b490f9f2">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::trimmed_left</a></div><div class="ttdeci">Size trimmed_left</div><div class="ttdoc">The number of isotopes trimmed on the left side. This is needed to reconstruct the monoisotopic peak...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:288</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_aa6c9b584cfcb710d0fce1c647086faaa"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">OpenMS::FeatureFinderAlgorithmPicked::MassTrace</a></div><div class="ttdeci">FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt; PeakType &gt; MassTrace</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:104</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a8852277abd03220cc7b80d6c1bed6fed"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">OpenMS::ProgressLogger::setProgress</a></div><div class="ttdeci">void setProgress(SignedSize value) const </div><div class="ttdoc">Sets the current progress. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_ac093fc547d9a49aef9950f6cd92b5588"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">OpenMS::Internal::DIntervalBase::maxPosition</a></div><div class="ttdeci">PositionType const &amp; maxPosition() const </div><div class="ttdoc">Accessor to maximum position. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:127</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_abd839e76d16452338866dd6bf6290c72"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#abd839e76d16452338866dd6bf6290c72">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::getTheoreticalmaxPosition</a></div><div class="ttdeci">Size getTheoreticalmaxPosition() const </div><div class="ttdoc">Returns the theoretical maximum trace index. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:195</div></div>
<div class="ttc" id="classOpenMS_1_1EGHTraceFitter_html"><div class="ttname"><a href="classOpenMS_1_1EGHTraceFitter.html">OpenMS::EGHTraceFitter</a></div><div class="ttdoc">A RT Profile fitter using an Exponential Gaussian Hybrid background model. </div><div class="ttdef"><b>Definition:</b> EGHTraceFitter.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a776f7572fc4f466e9527ca233471920d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">OpenMS::FeatureFinderAlgorithmPicked::updateMembers_</a></div><div class="ttdeci">virtual void updateMembers_()</div><div class="ttdoc">This method is used to update extra member variables at the end of the setParameters() method...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1161</div></div>
<div class="ttc" id="classOpenMS_1_1DBoundingBox_html"><div class="ttname"><a href="classOpenMS_1_1DBoundingBox.html">OpenMS::DBoundingBox</a></div><div class="ttdoc">A D-dimensional bounding box. </div><div class="ttdef"><b>Definition:</b> DBoundingBox.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a2f4fb91382abc4c1b9f767630d978f4d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">OpenMS::FeatureFinderAlgorithmPicked::seeds_</a></div><div class="ttdeci">FeatureMapType seeds_</div><div class="ttdoc">User-specified seed list. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1125</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_ac342b58a6d6d5e6fae39d3300c37178d"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac342b58a6d6d5e6fae39d3300c37178d">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::updateBaseline</a></div><div class="ttdeci">void updateBaseline()</div><div class="ttdoc">Sets the baseline to the lowest contained peak of the trace. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:216</div></div>
<div class="ttc" id="Element_8h_html"><div class="ttname"><a href="Element_8h.html">Element.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_ae740893fa17f26ea27e6f2383d72cb40"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">OpenMS::TraceFitter::getCenter</a></div><div class="ttdeci">virtual DoubleReal getCenter() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a5bce00011821a31f9344547c20c91e89"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">OpenMS::FeatureFinderAlgorithmPicked::intensity_mz_step_</a></div><div class="ttdeci">DoubleReal intensity_mz_step_</div><div class="ttdoc">m/z bin width </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1152</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeDistribution_html_ad66e45f6a7c4a7224810862a41545b1b"><div class="ttname"><a href="classOpenMS_1_1IsotopeDistribution.html#ad66e45f6a7c4a7224810862a41545b1b">OpenMS::IsotopeDistribution::set</a></div><div class="ttdeci">void set(const ContainerType &amp;distribution)</div><div class="ttdoc">overwrites the container which holds the distribution using distribution </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_aadc7a8536eb15f8c6fa05eefca0e25be"><div class="ttname"><a href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">OpenMS::Param::setMinFloat</a></div><div class="ttdeci">void setMinFloat(const String &amp;key, DoubleReal min)</div><div class="ttdoc">Sets the minimum value for the floating point or floating point list parameter key. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a81483ea6deb5aa7b6e11d0c3c871f532"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a81483ea6deb5aa7b6e11d0c3c871f532">OpenMS::FeatureFinderAlgorithmPicked::create</a></div><div class="ttdeci">static FeatureFinderAlgorithm&lt; PeakType, FeatureType &gt; * create()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1103</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a683154793bbb12ab5d16db81209606b0"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a683154793bbb12ab5d16db81209606b0">OpenMS::FeatureFinderAlgorithmPicked::setSeeds</a></div><div class="ttdeci">virtual void setSeeds(const FeatureMapType &amp;seeds)</div><div class="ttdoc">Sets a reference to the calling FeatureFinder. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:212</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern_html_ac102a03577b6512164d6e4ff3cf78df0"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity</a></div><div class="ttdeci">std::vector&lt; DoubleReal &gt; intensity</div><div class="ttdoc">Vector of intensity contributions. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:280</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_a5eeb26578a9f2313c4fff108fb2d9d7b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">OpenMS::FeatureFinderAlgorithmPicked::abort_</a></div><div class="ttdeci">void abort_(const Seed &amp;seed, const String &amp;reason)</div><div class="ttdoc">Writes the abort reason to the log file and counts occurrences for each reason. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:1182</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a93f1c9f620403aec160d98e83e125502"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a93f1c9f620403aec160d98e83e125502">OpenMS::FeatureMap::sortByIntensity</a></div><div class="ttdeci">void sortByIntensity(bool reverse=false)</div><div class="ttdoc">Sorts the peaks according to ascending intensity. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:297</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_adee689cac2b64d7164dbfc3d48110d91"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#adee689cac2b64d7164dbfc3d48110d91">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::getRTBounds</a></div><div class="ttdeci">std::pair&lt; DoubleReal, DoubleReal &gt; getRTBounds() const </div><div class="ttdoc">Returns the RT boundaries of the mass traces. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:246</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed_html_af40104dc784144260a2345e53e5f0305"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::Seed::peak</a></div><div class="ttdeci">Size peak</div><div class="ttdoc">Peak index. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:67</div></div>
<div class="ttc" id="MzMLFile_8h_html"><div class="ttname"><a href="MzMLFile_8h.html">MzMLFile.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern_html_aec70588359757e4c6f30670fc74d2ebe"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak</a></div><div class="ttdeci">std::vector&lt; SignedSize &gt; peak</div><div class="ttdoc">Peak index (-1 if peak was not found, -2 if it was removed to improve the isotope fit) ...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:303</div></div>
<div class="ttc" id="classOpenMS_1_1TextFile_html"><div class="ttname"><a href="classOpenMS_1_1TextFile.html">OpenMS::TextFile</a></div><div class="ttdoc">This class provides some basic file handling methods for text files. </div><div class="ttdef"><b>Definition:</b> TextFile.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_adb93f7d18f3a19b45d1a05e7c29dbeaa"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">OpenMS::FeatureFinderAlgorithmPicked::TheoreticalIsotopePattern</a></div><div class="ttdeci">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern TheoreticalIsotopePattern</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPicked.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a2802c591e6d7fd3fd9cc35f5e875d0ba"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">OpenMS::DefaultParamHandler::defaultsToParam_</a></div><div class="ttdeci">void defaultsToParam_()</div><div class="ttdoc">Updates the parameters after the defaults have been set in the constructor. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed_html_a2bf8eeb17dafb3d8ed1b08810fba2440"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#a2bf8eeb17dafb3d8ed1b08810fba2440">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::Seed::intensity</a></div><div class="ttdeci">Real intensity</div><div class="ttdoc">Intensity. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmPicked_html_ab76605572e7deccf4898a4398aa30d91"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ab76605572e7deccf4898a4398aa30d91">OpenMS::FeatureFinderAlgorithmPicked::operator=</a></div><div class="ttdeci">FeatureFinderAlgorithmPicked &amp; operator=(const FeatureFinderAlgorithmPicked &amp;)</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a6b40506fffbae670045d065c354bb9b8"><div class="ttname"><a href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">OpenMS::Param::setMaxFloat</a></div><div class="ttdeci">void setMaxFloat(const String &amp;key, DoubleReal max)</div><div class="ttdoc">Sets the maximum value for the floating point or floating point list parameter key. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a></div><div class="ttdoc">Helper struct for mass traces used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:83</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::Seed</a></div><div class="ttdoc">Helper structure for seeds used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:62</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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<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 11:19:13 using doxygen 1.8.5</font></TD>
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