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<a href="ModelFitter_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MODELFITTER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MODELFITTER_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FeaFiModule_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeaFiModule.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="ProductModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/ProductModel.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="IsotopeModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeModel.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ExtendedIsotopeModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/ExtendedIsotopeModel.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="LmaIsotopeModel_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaIsotopeModel.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="Fitter1D_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="AsymmetricStatistics_8h.html">OpenMS/MATH/STATISTICS/AsymmetricStatistics.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="StatisticFunctions_8h.html">OpenMS/MATH/STATISTICS/StatisticFunctions.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="Factory_8h.html">OpenMS/CONCEPT/Factory.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <boost/math/special_functions/fpclassify.hpp></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <numeric></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <cmath></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <set></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> {</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keyword">template</span> <<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType></div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html"> 77</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1ModelFitter.html">ModelFitter</a> :</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a><PeakType, FeatureType>,</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keyword">public</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  {</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf"> 84</a></span>  <span class="keyword">typedef</span> IndexSet::const_iterator <a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1"> 86</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1BaseFeature.html#a8ca1d75ff489493f4458fa7137186089">Feature::QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a75145a9f1f2689d0f54565ffbdb1f5d6"> 88</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Peak2D.html#a063d40a3528749f1a905ab04d76387e0">Feature::CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a75145a9f1f2689d0f54565ffbdb1f5d6">CoordinateType</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#adec9115bab6f7a59f89207e636875543"> 90</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Feature::IntensityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#adec9115bab6f7a59f89207e636875543">IntensityType</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a9f65527757d7146ea4eabbb506c9a646"> 92</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1BaseFeature.html#a87171116869a9f9511d7ce9ad7baf5d6">Feature::ChargeType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f65527757d7146ea4eabbb506c9a646">ChargeType</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a79ea228cdc8755284e64dd9f625170a3"> 94</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule<PeakType, FeatureType></a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a79ea228cdc8755284e64dd9f625170a3">Base</a>;</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a31ac7361125f91f71e3d07be39a76023"> 96</a></span>  <span class="keyword">typedef</span> std::vector<PeakType> <a class="code" href="classOpenMS_1_1ModelFitter.html#a31ac7361125f91f71e3d07be39a76023">RawDataArrayType</a>;</div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keyword">enum</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  {</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da"> 100</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a> = <a class="code" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">Peak2D::RT</a>,</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867"> 101</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a> = <a class="code" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">Peak2D::MZ</a></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  };</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a00b389ceb266aea7a8b43fb9a2d899e0"> 105</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a00b389ceb266aea7a8b43fb9a2d899e0">ModelFitter</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<PeakType></a> * map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<FeatureType></a> * features, <a class="code" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * ff) :</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html">Base</a>(map, features, ff),</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>(),</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401">mz_stat_</a>(),</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>(),</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd">monoisotopic_mz_</a>(0),</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> #ifdef <a class="code" href="EGHFitter1D_8h.html#a113411f16080334fa17209bc7a0175a7">DEBUG_FEATUREFINDER</a></div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  counter_(1),</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> #endif</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#abfeee1372fcfb6bea261621d9f553e3d">iso_stdev_first_</a>(0),</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a61031e41af78cf1ff1d097717b27faaa">iso_stdev_last_</a>(0),</div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a929a8e237da6180773aa965601894c60">iso_stdev_stepsize_</a>(0),</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a>(0),</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a>(0),</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#ad14e23949d04910624b46731e5268fb5">quality_rt_</a>(0),</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a>(0)</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  {</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a>(<span class="stringliteral">"ModelFitter"</span>);</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  this-><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">"fit_algorithm"</span>, <span class="stringliteral">"simple"</span>, <span class="stringliteral">"Fitting algorithm type (internal parameter)."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  std::vector<String> fit_opts;</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  fit_opts.push_back(<span class="stringliteral">"simple"</span>);</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  fit_opts.push_back(<span class="stringliteral">"simplest"</span>);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  fit_opts.push_back(<span class="stringliteral">"wavelet"</span>);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  this-><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">"fit_algorithm"</span>, fit_opts);</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  this-><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">"max_iteration"</span>, 500, <span class="stringliteral">"Maximum number of iterations for fitting with Levenberg-Marquardt algorithm."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  this-><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">"max_iteration"</span>, 1);</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  this-><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">"deltaAbsError"</span>, 0.0001, <span class="stringliteral">"Absolute error used by the Levenberg-Marquardt algorithm."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  this-><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">"deltaAbsError"</span>, 0.0);</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  this-><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">"deltaRelError"</span>, 0.0001, <span class="stringliteral">"Relative error used by the Levenberg-Marquardt algorithm."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  this-><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">"deltaRelError"</span>, 0.0);</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span> </div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  this-><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">"tolerance_stdev_bounding_box"</span>, 3.0f, <span class="stringliteral">"Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  this-><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">"tolerance_stdev_bounding_box"</span>, 0.0);</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  this-><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">"intensity_cutoff_factor"</span>, 0.05f, <span class="stringliteral">"Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model"</span>);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  this-><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">"intensity_cutoff_factor"</span>, 0.0);</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  this-><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">"intensity_cutoff_factor"</span>, 1.0);</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  this-><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">"feature_intensity_sum"</span>, 1, <span class="stringliteral">"Determines what is reported as feature intensity.\n1: the sum of peak intensities;\n0: the maximum intensity of all peaks"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  this-><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">"feature_intensity_sum"</span>, 0);</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a37de948351467fdccb9d12f601dc8205">setMaxInt</a>(<span class="stringliteral">"feature_intensity_sum"</span>, 1);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  this-><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">"min_num_peaks:final"</span>, 5, <span class="stringliteral">"Minimum number of peaks left after cutoff. If smaller, feature will be discarded."</span>);</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  this-><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">"min_num_peaks:final"</span>, 1);</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  this-><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">"min_num_peaks:extended"</span>, 10, <span class="stringliteral">"Minimum number of peaks after extension. If smaller, feature will be discarded."</span>);</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  this-><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">"min_num_peaks:extended"</span>, 1);</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  this-><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">"min_num_peaks"</span>, <span class="stringliteral">"Required number of peaks for a feature."</span>);</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  this-><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">"rt:interpolation_step"</span>, 0.2f, <span class="stringliteral">"Step size in seconds used to interpolate model for RT."</span>);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  this-><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">"rt:interpolation_step"</span>, 0.0);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  this-><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">"rt"</span>, <span class="stringliteral">"Model settings in RT dimension."</span>);</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  this-><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">"mz:interpolation_step"</span>, 0.03f, <span class="stringliteral">"Interpolation step size for m/z."</span>);</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  this-><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">"mz:interpolation_step"</span>, 0.001);</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  this-><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">"mz:model_type:first"</span>, 1, <span class="stringliteral">"Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian)."</span>);</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  this-><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">"mz:model_type:first"</span>, 0);</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  this-><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">"mz:model_type:last"</span>, 4, <span class="stringliteral">"Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian)."</span>);</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  this-><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">"mz:model_type:last"</span>, 0);</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  this-><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">"mz"</span>, <span class="stringliteral">"Model settings in m/z dimension."</span>);</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  this-><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">"quality:type"</span>, <span class="stringliteral">"Correlation"</span>, <span class="stringliteral">"Type of the quality measure used to assess the fit of model vs data."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  std::vector<String> quality_opts;</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  quality_opts.push_back(<span class="stringliteral">"Correlation"</span>);</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  quality_opts.push_back(<span class="stringliteral">"RankCorrelation"</span>);</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  this-><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">"quality:type"</span>, quality_opts);</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  this-><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">"quality:minimum"</span>, 0.65f, <span class="stringliteral">"Minimum quality of fit, features below this threshold are discarded."</span>);</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  this-><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">"quality:minimum"</span>, 0.0);</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  this-><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">"quality:minimum"</span>, 1.0);</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  this-><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">"quality"</span>, <span class="stringliteral">"Fitting quality settings."</span>);</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  this-><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">"isotope_model:stdev:first"</span>, 0.04f, <span class="stringliteral">"First standard deviation to be considered for isotope model."</span>);</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  this-><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">"isotope_model:stdev:first"</span>, 0.0);</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  this-><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">"isotope_model:stdev:last"</span>, 0.12f, <span class="stringliteral">"Last standard deviation to be considered for isotope model."</span>);</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  this-><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">"isotope_model:stdev:last"</span>, 0.0);</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  this-><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">"isotope_model:stdev:step"</span>, 0.04f, <span class="stringliteral">"Step size for standard deviations considered for isotope model."</span>);</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  this-><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">"isotope_model:stdev:step"</span>, 0.0);</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  this-><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">"isotope_model:stdev"</span>, <span class="stringliteral">"Instrument resolution settings for m/z dimension."</span>);</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  this-><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">"isotope_model:averagines:C"</span>, 0.04443989f, <span class="stringliteral">"Number of C atoms per Dalton of the mass."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  this-><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">"isotope_model:averagines:C"</span>, 0.0);</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  this-><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">"isotope_model:averagines:H"</span>, 0.06981572f, <span class="stringliteral">"Number of H atoms per Dalton of the mass."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  this-><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">"isotope_model:averagines:H"</span>, 0.0);</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  this-><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">"isotope_model:averagines:N"</span>, 0.01221773f, <span class="stringliteral">"Number of N atoms per Dalton of the mass."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  this-><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">"isotope_model:averagines:N"</span>, 0.0);</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  this-><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">"isotope_model:averagines:O"</span>, 0.01329399f, <span class="stringliteral">"Number of O atoms per Dalton of the mass."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  this-><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">"isotope_model:averagines:O"</span>, 0.0);</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  this-><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">"isotope_model:averagines:S"</span>, 0.00037525f, <span class="stringliteral">"Number of S atoms per Dalton of the mass."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  this-><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">"isotope_model:averagines:S"</span>, 0.0);</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  this-><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">"isotope_model:averagines"</span>, <span class="stringliteral">"Averagines are used to approximate the number of atoms (C,H,N,O,S) which a peptide of a given mass contains."</span>);</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  this-><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">"isotope_model:isotope:trim_right_cutoff"</span>, 0.001f, <span class="stringliteral">"Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  this-><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">"isotope_model:isotope:trim_right_cutoff"</span>, 0.0);</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  this-><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">"isotope_model:isotope:maximum"</span>, 100, <span class="stringliteral">"Maximum number of isotopes being used for the IsotopeModel."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  this-><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">"isotope_model:isotope:maximum"</span>, 1);</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  this-><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">"isotope_model:isotope:distance"</span>, 1.000495f, <span class="stringliteral">"Distance between consecutive isotopic peaks."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  this-><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">"isotope_model:isotope:distance"</span>, 0.0);</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  this-><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">"isotope_model"</span>, <span class="stringliteral">"Settings of the isotope model (m/z)."</span>);</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span> </div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>();</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span> </div>
<div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#af8b43fcf339870914680f9afe812cd85"> 209</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#af8b43fcf339870914680f9afe812cd85">~ModelFitter</a>()</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  {</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  }</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div>
<div class="line"><a name="l00215"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a4aeb5297e8e231a3cc8e6a4f599944b5"> 215</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#a4aeb5297e8e231a3cc8e6a4f599944b5">setMonoIsotopicMass</a>(<a class="code" href="classdouble.html">CoordinateType</a> mz)</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  {</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd">monoisotopic_mz_</a> = mz;</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  }</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span> </div>
<div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e"> 226</a></span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">fit</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">ChargedIndexSet</a> & index_set)</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  {</div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="comment">// Test the number of peaks (not enough peaks to fit)</span></div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  <span class="keywordflow">if</span> (index_set.size() < <a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>(this-><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">"min_num_peaks:extended"</span>)))</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  {</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> mess = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Skipping feature, IndexSet size too small: "</span>) + index_set.size();</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"UnableToFit-IndexSet"</span>, mess.c_str());</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  }</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="comment">// Calculate statistics for mz and rt</span></div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401">mz_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#a6068425aeb34eec009695897d0408453">update</a></div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  (</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html">Internal::IntensityIterator<ModelFitter></a>(index_set.begin(), <span class="keyword">this</span>),</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html">Internal::IntensityIterator<ModelFitter></a>(index_set.end(), <span class="keyword">this</span>),</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <a class="code" href="structOpenMS_1_1Internal_1_1MzIterator.html">Internal::MzIterator<ModelFitter></a>(index_set.begin(), <span class="keyword">this</span>)</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  );</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html#a74998f835798420ad045536c0c2a3106">update</a></div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  (</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html">Internal::IntensityIterator<ModelFitter></a>(index_set.begin(), <span class="keyword">this</span>),</div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <a class="code" href="structOpenMS_1_1Internal_1_1IntensityIterator.html">Internal::IntensityIterator<ModelFitter></a>(index_set.end(), <span class="keyword">this</span>),</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <a class="code" href="structOpenMS_1_1Internal_1_1RtIterator.html">Internal::RtIterator<ModelFitter></a>(index_set.begin(), <span class="keyword">this</span>)</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  );</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="comment">// set charge</span></div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordflow">if</span> (index_set.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a> != 0)</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  {</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a> = index_set.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a>;</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a> = index_set.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a>;</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  }</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span> </div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a> > <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a>) <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidParameter.html">Exception::InvalidParameter</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"ModelFitter::fit(): charge range tested is not valid; check \"model_type:first\" and \"model_type:last\" "</span>);</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="comment">// Check charge estimate if charge is not specified by user</span></div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> <span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Checking charge state from "</span> << <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a> << <span class="stringliteral">" to "</span> << <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a> << std::endl;</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="comment">// ** Projection</span></div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">doProjectionDim_</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>, index_set, <a class="code" href="classOpenMS_1_1ModelFitter.html#a100b9653d9495c862bc57cee3dcdbb3f">rt_input_data_</a>);</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">doProjectionDim_</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>, index_set, <a class="code" href="classOpenMS_1_1ModelFitter.html#ad1dd87342de3593f23630e645f995d1f">mz_input_data_</a>);</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">// Fit rt model</span></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * model_rt = 0;</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#ad14e23949d04910624b46731e5268fb5">quality_rt_</a> = <a class="code" href="classOpenMS_1_1ModelFitter.html#a5e69531f4b15948d57b30909fdba0cb4">fitRT_</a>(model_rt);</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a8cd14764d47842020930ef7023a2d912">setModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>, model_rt); <span class="comment">// Set model in 2D-model</span></div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> </div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<Feature></a> feature_collection;</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9f65527757d7146ea4eabbb506c9a646">ChargeType</a> charge = <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a>; charge <= <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a>; ++charge)</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  {</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> f;</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  {</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <span class="comment">// "reset" model2D!!</span></div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a6f73a9c8459a5cc55dada279e525437e">setScale</a>(1.);</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span> </div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="comment">// TODO: intensity scaling should use a more robust estimator (rather than comparing max of data vs. model)</span></div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span> </div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="comment">// Compute model with the best correlation</span></div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="comment">// result is in model2D_</span></div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> max_quality = <a class="code" href="classOpenMS_1_1ModelFitter.html#aa08948a609e0be02a55895209d3d77a9">fitMZLoop_</a>(index_set, charge);</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span> </div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="comment">// find peak with highest predicted intensity to use as cutoff</span></div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> model_max = 0;</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> </div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = index_set.begin(); it != index_set.end(); ++it)</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  {</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> model_int = <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#ac4534e8323ba5dc157bc4bba75096d50">getIntensity</a>(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it)));</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordflow">if</span> (model_int > model_max) model_max = model_int;</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  }</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1BaseModel.html#a464bd13b1e846ea0bc7bb0632f8e7256">setCutOff</a>(model_max * <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>(this-><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">"intensity_cutoff_factor"</span>)));</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="comment">// Cutoff low intensities wrt to model maximum -> cutoff independent of scaling</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">IndexSet</a> model_set;</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = index_set.begin(); it != index_set.end(); ++it)</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  {</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">isContained</a>(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this->getPeakRt(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it))))</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  {</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  model_set.insert(*it);</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  }</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  }</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> </div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="comment">// Print number of selected peaks after cutoff</span></div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span> <span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">" Selected "</span> << model_set.size() << <span class="stringliteral">" from "</span> << index_set.size() << <span class="stringliteral">" peaks.\n"</span>;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="comment">// Calculate intensity scaling</span></div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> model_sum = 0;</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="comment">//IntensityType data_sum = 0;</span></div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> data_max = 0;</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = model_set.begin(); it != model_set.end(); ++it)</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  {</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> model_int = <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#ac4534e8323ba5dc157bc4bba75096d50">getIntensity</a>(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it)));</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  model_sum += model_int;</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="comment">//data_sum += this->getPeakIntensity( *it );</span></div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keywordflow">if</span> (this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it) > data_max) data_max = this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it);</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  }</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">if</span> (model_sum == 0)</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  {</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"UnableToFit-ZeroSum"</span>, <span class="stringliteral">"Skipping feature, model_sum zero."</span>);</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  }</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="comment">//std::cout << "data_max: " << data_max << " model_max: " << model_max << " model2dscale: " << (data_max / model_max) << std::endl;</span></div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a6f73a9c8459a5cc55dada279e525437e">setScale</a>(data_max / model_max); <span class="comment">// use max quotient instead of sum quotient</span></div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span> </div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="comment">//std::cout << model2D_.getParameters() << std::endl;</span></div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="comment">// Build Feature</span></div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="comment">// The feature coordinate in rt dimension is given</span></div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="comment">// by the centroid of the rt model whereas the coordinate</span></div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="comment">// in mz dimension is equal to the monoisotopic peak.</span></div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#a59f31f35e2e4a45316651cebbb358a1d">setModelDescription</a>(<a class="code" href="classOpenMS_1_1ModelDescription.html">ModelDescription<2></a>(&<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>));</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">setOverallQuality</a>(max_quality);</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(static_cast<InterpolationModel *>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>))->getCenter());</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(static_cast<InterpolationModel *>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>))->getCenter());</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span> </div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="comment">// set and check convex hull whether m/z is contained or not</span></div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#ac641d17ba54cde66c331d17bdee355e8">addConvexHull</a>(model_set, f);</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordflow">if</span> (!f.<a class="code" href="classOpenMS_1_1Feature.html#a57c4a49592647cc2db0dc517ed9a1a02">encloses</a>(f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>(), f.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>())) f.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(f.<a class="code" href="classOpenMS_1_1Feature.html#ab071fe5bd7b2f969e4f9ed5d7467da1e">getConvexHull</a>().<a class="code" href="classOpenMS_1_1ConvexHull2D.html#a88c6186ce22fc5eae73df90899695229">getBoundingBox</a>().minY());</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span> </div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="comment">// feature charge ...</span></div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <span class="comment">// if we used a simple Gaussian model to fit the feature, we can't say anything about</span></div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="comment">// its charge state. The value 0 indicates that charge state is undetermined.</span></div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>)-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() == <span class="stringliteral">"LmaIsotopeModel"</span>)</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  {</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">setCharge</a>(static_cast<LmaIsotopeModel *>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>))->getCharge());</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  }</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>)-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() == <span class="stringliteral">"IsotopeModel"</span>)</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  {</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">setCharge</a>(static_cast<IsotopeModel *>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>))->getCharge());</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  }</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>)-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() == <span class="stringliteral">"ExtendedIsotopeModel"</span>)</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  {</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">setCharge</a>(static_cast<ExtendedIsotopeModel *>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">getModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>))->getCharge());</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  }</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  {</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">setCharge</a>(0);</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  }</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="comment">// feature intensity</span></div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <span class="keyword">const</span> intensity_choice = this-><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">"feature_intensity_sum"</span>);</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <a class="code" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> feature_intensity = 0.0;</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordflow">if</span> (intensity_choice == 1)</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  {</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="comment">// intensity of the feature is the sum of all included data points</span></div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = model_set.begin(); it != model_set.end(); ++it)</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  {</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  feature_intensity += this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it);</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  }</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  }</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  {</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="comment">// feature intensity is the maximum intensity of all peaks</span></div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = model_set.begin(); it != model_set.end(); ++it)</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  {</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">if</span> (this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it) > feature_intensity)</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  {</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  feature_intensity = this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it);</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  }</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  }</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  }</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span> </div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="comment">// set intensity</span></div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(feature_intensity);</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span> </div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="comment">// set quality (1D)</span></div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">setQuality</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>, <a class="code" href="classOpenMS_1_1ModelFitter.html#ad14e23949d04910624b46731e5268fb5">quality_rt_</a>);</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  f.<a class="code" href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">setQuality</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>, <a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a>);</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> </div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  <span class="comment">//std::cout << "QA: " << f.getOverallQuality() << " qMZ: " << f.getQuality(1) << " charge: " << f.getCharge() << " stdev: " << f.getModelDescription().getParam().getValue("MZ:isotope:stdev")<< std::endl;</span></div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span> </div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span> <span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span> <span class="preprocessor"></span> <span class="comment">// debug output</span></div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="keywordflow">if</span> (this-><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">"fit_algorithm"</span>) != <span class="stringliteral">"wavelet"</span>)</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  {</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  std::cout << <span class="stringliteral">"Feature "</span> << counter_ << <span class="stringliteral">": ("</span> << f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>() << <span class="stringliteral">","</span> << f.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() << <span class="stringliteral">") Qual.: "</span> << max_quality << std::endl;</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  }</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="comment">// Save meta data in feature for TOPPView</span></div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  f.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">setMetaValue</a>(3, <a class="code" href="classOpenMS_1_1String.html">String</a>(counter_));</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span> </div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  std::cout << <span class="stringliteral">"Feature charge: "</span> << f.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>() << std::endl;</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  std::cout << <span class="stringliteral">"Feature quality in mz: "</span> << f.<a class="code" href="classOpenMS_1_1Feature.html#a1ad0c0f264440b15c5d699f3845b8ad7">getQuality</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>) << std::endl;</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> </div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  <span class="comment">// write debug output</span></div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <a class="code" href="classdouble.html">CoordinateType</a> rt = f.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>();</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <a class="code" href="classdouble.html">CoordinateType</a> mz = f.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>();</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span> </div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="comment">// write feature model</span></div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> fname = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"model"</span>) + counter_ + <span class="stringliteral">"_"</span> + rt + <span class="stringliteral">"_"</span> + mz;</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  std::ofstream file(fname.c_str());</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = model_set.begin(); it != model_set.end(); ++it)</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  {</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a> pos = <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it));</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">isContained</a>(pos))</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  {</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  file << pos[<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>] << <span class="stringliteral">" "</span> << pos[<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>] << <span class="stringliteral">" "</span> << <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#ac4534e8323ba5dc157bc4bba75096d50">getIntensity</a>(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it))) << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  }</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  }</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  file.close();</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span> </div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="comment">// wrote peaks remaining after model fit</span></div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  fname = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"feature"</span>) + counter_ + <span class="stringliteral">"_"</span> + rt + <span class="stringliteral">"_"</span> + mz;</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  std::ofstream file2(fname.c_str());</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = model_set.begin(); it != model_set.end(); ++it)</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  {</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a> pos = <a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it));</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">isContained</a>(pos))</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  {</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  file2 << pos[<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">RT</a>] << <span class="stringliteral">" "</span> << pos[<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>] << <span class="stringliteral">" "</span> << this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it) << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  }</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  }</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  file2.close();</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span> </div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="comment">// Count features</span></div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  ++counter_;</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span> </div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  feature_collection.push_back(f);</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  } <span class="comment">// ! try</span></div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a> & <span class="comment">/*e*/</span>)</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  {</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  <span class="comment">//std::cout << "CAUGHT!! " << e.getName() << " " << e.getMessage() << std::endl;</span></div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  }</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  }</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span> </div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keywordflow">if</span> (feature_collection.empty())</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  {</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> mess = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Skipping feature, nothing in the feature collection."</span>);</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"UnableToFit-EmptyFeatureCollection"</span>, mess.c_str());</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  }</div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> best_quality = -std::numeric_limits<QualityType>::max();</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="comment">// find best feature</span></div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  std::size_t best_idx = 0;</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <span class="keywordflow">for</span> (std::size_t idx = 0; idx < feature_collection.size(); ++idx)</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  {</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordflow">if</span> (best_quality < feature_collection[idx].getOverallQuality())</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  {</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  best_quality = feature_collection[idx].getOverallQuality();</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  best_idx = idx;</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  }</div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  }</div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> best_feature = feature_collection[best_idx];</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="comment">// check some more conditions</span></div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="comment">// not enough peaks left for feature</span></div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span> </div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  <span class="comment">// fit has too low quality or fit was not possible i.e. because of zero stdev</span></div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="keywordflow">if</span> (best_feature.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>() < (<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>) (this-><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">"quality:minimum"</span>)))</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  {</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> mess = <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Skipping feature, correlation too small: "</span>) + best_feature.<a class="code" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">getOverallQuality</a>();</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"UnableToFit-Correlation"</span>, mess.c_str());</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  }</div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span> </div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="comment">// free unused peaks for best feature</span></div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">IndexSet</a> model_set;</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  <a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html">ProductModel<2></a> * best_model = <span class="keyword">static_cast<</span><a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html">ProductModel<2></a> *<span class="keyword">></span>(best_feature.<a class="code" href="classOpenMS_1_1Feature.html#a94eabbe00bbab2a589688631c807005e">getModelDescription</a>().<a class="code" href="classOpenMS_1_1ModelDescription.html#a3f962855dbc9bbf8074f4306cb9c1a7b">createModel</a>());</div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">IndexSetIter</a> it = index_set.begin(); it != index_set.end(); ++it)</div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  {</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  <span class="keywordflow">if</span> (best_model-><a class="code" href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">isContained</a>(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this->getPeakRt(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it))))</div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  {</div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  model_set.insert(*it);</div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  }</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  {</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">getPeakFlag</a>(*it) = <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">UNUSED</a>;</div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  }</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  }</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <span class="keyword">delete</span> best_model;</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <span class="keywordflow">if</span> (model_set.size() < (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>) (this-><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">"min_num_peaks:final"</span>)))</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  {</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1UnableToFit.html">Exception::UnableToFit</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"UnableToFit-FinalSet"</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Skipping feature, IndexSet size after cutoff too small: "</span>) + model_set.size());</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  }</div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span> </div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="comment">// add all but the best feature to the suboptimal ones</span></div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  <span class="keywordflow">for</span> (std::size_t idx = 0; idx < feature_collection.size(); ++idx)</div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  {</div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <span class="keywordflow">if</span> (idx == best_idx) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  best_feature.<a class="code" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">getSubordinates</a>().push_back(feature_collection[idx]);</div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  }</div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span> </div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  <span class="comment">// return "best" feature</span></div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  <span class="keywordflow">return</span> best_feature;</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span> </div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  }</div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span> </div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span> </div>
<div class="line"><a name="l00517"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a776f7572fc4f466e9527ca233471920d"> 517</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  {</div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">algorithm_</a> = this-><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">"fit_algorithm"</span>);</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span> </div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a65156c6922b9524db057849c1d14cd56">max_iteration_</a> = this-><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">"max_iteration"</span>);</div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a29677fd7ae2cbf6f04964da70997b4d6">deltaAbsError_</a> = this-><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">"deltaAbsError"</span>);</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#aae802b51d6efd35a1378b228f4f40770">deltaRelError_</a> = this-><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">"deltaRelError"</span>);</div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span> </div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b">tolerance_stdev_box_</a> = this-><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">"tolerance_stdev_bounding_box"</span>);</div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#ae29ab2ec7ad095c17fd97d56d4501c1c">max_isotope_</a> = this-><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">"isotope_model:isotope:maximum"</span>);</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span> </div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5cf51152410c3773eeb23c45f288986c">interpolation_step_mz_</a> = this-><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">"mz:interpolation_step"</span>);</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#adf3e31ca2a7272a82a67175153f39f98">interpolation_step_rt_</a> = this-><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">"rt:interpolation_step"</span>);</div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span> </div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#abfeee1372fcfb6bea261621d9f553e3d">iso_stdev_first_</a> = this-><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">"isotope_model:stdev:first"</span>);</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a61031e41af78cf1ff1d097717b27faaa">iso_stdev_last_</a> = this-><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">"isotope_model:stdev:last"</span>);</div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a929a8e237da6180773aa965601894c60">iso_stdev_stepsize_</a> = this-><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">"isotope_model:stdev:step"</span>);</div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span> </div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a> = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>) this-><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">"mz:model_type:first"</span>);</div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a> = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>) this-><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">"mz:model_type:last"</span>);</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  }</div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span> </div>
<div class="line"><a name="l00540"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#aa08948a609e0be02a55895209d3d77a9"> 540</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#aa08948a609e0be02a55895209d3d77a9">fitMZLoop_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">ChargedIndexSet</a> & set, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f65527757d7146ea4eabbb506c9a646">ChargeType</a> & charge)</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  {</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span> </div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  <span class="comment">// Fit mz model ... test different charge states and stdevs</span></div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> max_quality_mz = -std::numeric_limits<QualityType>::max();</div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span> </div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * best_model_mz = 0;</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> stdev = <a class="code" href="classOpenMS_1_1ModelFitter.html#abfeee1372fcfb6bea261621d9f553e3d">iso_stdev_first_</a>; stdev <= <a class="code" href="classOpenMS_1_1ModelFitter.html#a61031e41af78cf1ff1d097717b27faaa">iso_stdev_last_</a>; stdev += <a class="code" href="classOpenMS_1_1ModelFitter.html#a929a8e237da6180773aa965601894c60">iso_stdev_stepsize_</a>)</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  {</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a141bcda36021c50ea1e95a234e9aacff">isotope_stdev_</a> = stdev;</div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span> </div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  <a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * model_mz = 0;</div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a> = <a class="code" href="classOpenMS_1_1ModelFitter.html#a4e1ed92e7c5c8f3b4db0378a122ef3b1">fitMZ_</a>(model_mz, charge);</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span> </div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span> </div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a> > max_quality_mz)</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  {</div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  max_quality_mz = <a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a>;</div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  <span class="keywordflow">if</span> (best_model_mz) <span class="keyword">delete</span> best_model_mz;</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  best_model_mz = model_mz;</div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  }</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  {</div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  <span class="keyword">delete</span> model_mz;</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  }</div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  }</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span> </div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#a8cd14764d47842020930ef7023a2d912">setModel</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>, best_model_mz); <span class="comment">// Set model in 2D-model</span></div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span> </div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a> = max_quality_mz;</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span> </div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  <span class="comment">// return overall quality</span></div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#a520ad36c37273100004a5dca3c2a6c24">evaluate_</a>(set);</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  }</div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span> </div>
<div class="line"><a name="l00576"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a520ad36c37273100004a5dca3c2a6c24"> 576</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a520ad36c37273100004a5dca3c2a6c24">evaluate_</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">IndexSet</a> & set)<span class="keyword"> const</span></div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> quality = 0.0;</div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span> </div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="comment">// Calculate the pearson correlation coefficient for the values in [begin_a, end_a) and [begin_b, end_b)</span></div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">algorithm_</a> != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  {</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  std::vector<Real> real_data;</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  real_data.reserve(set.size());</div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  std::vector<Real> model_data;</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  model_data.reserve(set.size());</div>
<div class="line"><a name="l00587"></a><span class="lineno"> 587</span> </div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="keywordflow">for</span> (IndexSet::const_iterator it = set.begin(); it != set.end(); ++it)</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  {</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  real_data.push_back(this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it));</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  model_data.push_back(<a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>.<a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html#ac4534e8323ba5dc157bc4bba75096d50">getIntensity</a>(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<2></a>(this->getPeakRt(*it), this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it))));</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  }</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span> </div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  <span class="keywordflow">if</span> (this-><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">"quality:type"</span>) == <span class="stringliteral">"RankCorrelation"</span>)</div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  {</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  quality = <a class="code" href="group__MathFunctionsStatistics.html#ga67443c0e3d0ee860daf4f6f1e371ce2c">Math::rankCorrelationCoefficient</a>(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());</div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  }</div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  <span class="keywordflow">else</span> quality = <a class="code" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">Math::pearsonCorrelationCoefficient</a>(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());</div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  }</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span> </div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  <span class="keywordflow">if</span> (boost::math::isnan(quality)) quality = -1.0;</div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span> </div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <span class="keywordflow">return</span> quality;</div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  }</div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span> </div>
<div class="line"><a name="l00607"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a5e69531f4b15948d57b30909fdba0cb4"> 607</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a5e69531f4b15948d57b30909fdba0cb4">fitRT_</a>(<a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * & model)<span class="keyword"> const</span></div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> quality;</div>
<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> param;</div>
<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  <a class="code" href="classOpenMS_1_1Fitter1D.html">Fitter1D</a> * fitter;</div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span> </div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">algorithm_</a> == <span class="stringliteral">"simplest"</span>) <span class="comment">// Fit with BiGauss</span></div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  {</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"tolerance_stdev_bounding_box"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b">tolerance_stdev_box_</a>);</div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:mean"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#af6efe0afdae7cbb85a5ac3bed200c048">mean</a>());</div>
<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:variance"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#a620e83f1ef3e206cacdacb1293677e05">variance</a>());</div>
<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:variance1"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html#ad7008a00da75aa4248c4f6076f1dc58c">variance1</a>());</div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:variance2"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html#af5dad3b7af1fd39433b75414fed36f2c">variance2</a>());</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"interpolation_step"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#adf3e31ca2a7272a82a67175153f39f98">interpolation_step_rt_</a>);</div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span> </div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  fitter = <a class="code" href="classOpenMS_1_1Factory.html#a4cfac1ac1b4ac63d3b169291ac8019ed">Factory<Fitter1D>::create</a>(<span class="stringliteral">"BiGaussFitter1D"</span>);</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  }</div>
<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  <span class="keywordflow">else</span> <span class="comment">// Fit with EMG (LM optimization)</span></div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  {</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"tolerance_stdev_bounding_box"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b">tolerance_stdev_box_</a>);</div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:mean"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#af6efe0afdae7cbb85a5ac3bed200c048">mean</a>());</div>
<div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:variance"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#a620e83f1ef3e206cacdacb1293677e05">variance</a>());</div>
<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"interpolation_step"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#adf3e31ca2a7272a82a67175153f39f98">interpolation_step_rt_</a>);</div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"max_iteration"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a65156c6922b9524db057849c1d14cd56">max_iteration_</a>);</div>
<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"deltaAbsError"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a29677fd7ae2cbf6f04964da70997b4d6">deltaAbsError_</a>);</div>
<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"deltaRelError"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#aae802b51d6efd35a1378b228f4f40770">deltaRelError_</a>);</div>
<div class="line"><a name="l00633"></a><span class="lineno"> 633</span> </div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  fitter = <a class="code" href="classOpenMS_1_1Factory.html#a4cfac1ac1b4ac63d3b169291ac8019ed">Factory<Fitter1D>::create</a>(<span class="stringliteral">"EmgFitter1D"</span>);</div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  }</div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span> </div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  <span class="comment">// Set parameter for fitter</span></div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  fitter-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param);</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span> </div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  <span class="comment">// Construct model for rt</span></div>
<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  quality = fitter-><a class="code" href="classOpenMS_1_1Fitter1D.html#a78595664bcabdc63cf91fd338883d309">fit1d</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#a100b9653d9495c862bc57cee3dcdbb3f">rt_input_data_</a>, model);</div>
<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  <span class="comment">// Check quality</span></div>
<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  <span class="keywordflow">if</span> (boost::math::isnan(quality)) quality = -1.0;</div>
<div class="line"><a name="l00644"></a><span class="lineno"> 644</span> </div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  <span class="keyword">delete</span>(fitter);</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span> </div>
<div class="line"><a name="l00647"></a><span class="lineno"> 647</span>  <span class="keywordflow">return</span> quality;</div>
<div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  }</div>
<div class="line"><a name="l00649"></a><span class="lineno"> 649</span> </div>
<div class="line"><a name="l00651"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a4e1ed92e7c5c8f3b4db0378a122ef3b1"> 651</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a4e1ed92e7c5c8f3b4db0378a122ef3b1">fitMZ_</a>(<a class="code" href="classOpenMS_1_1InterpolationModel.html">InterpolationModel</a> * & model, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f65527757d7146ea4eabbb506c9a646">ChargeType</a> & charge)<span class="keyword"> const</span></div>
<div class="line"><a name="l00652"></a><span class="lineno"> 652</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> quality;</div>
<div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> param;</div>
<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  <a class="code" href="classOpenMS_1_1Fitter1D.html">Fitter1D</a> * fitter;</div>
<div class="line"><a name="l00656"></a><span class="lineno"> 656</span> </div>
<div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"tolerance_stdev_bounding_box"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b">tolerance_stdev_box_</a>);</div>
<div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:mean"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401">mz_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#af6efe0afdae7cbb85a5ac3bed200c048">mean</a>());</div>
<div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:variance"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401">mz_stat_</a>.<a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html#a620e83f1ef3e206cacdacb1293677e05">variance</a>());</div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"interpolation_step"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a5cf51152410c3773eeb23c45f288986c">interpolation_step_mz_</a>);</div>
<div class="line"><a name="l00661"></a><span class="lineno"> 661</span> </div>
<div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd">monoisotopic_mz_</a> != 0) <span class="comment">// monoisotopic mz is known</span></div>
<div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  {</div>
<div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"statistics:mean"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd">monoisotopic_mz_</a>);</div>
<div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  }</div>
<div class="line"><a name="l00666"></a><span class="lineno"> 666</span> </div>
<div class="line"><a name="l00667"></a><span class="lineno"> 667</span>  <span class="keywordflow">if</span> (charge != 0) <span class="comment">// charge is not zero</span></div>
<div class="line"><a name="l00668"></a><span class="lineno"> 668</span>  {</div>
<div class="line"><a name="l00669"></a><span class="lineno"> 669</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"charge"</span>, charge);</div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"isotope:stdev"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a141bcda36021c50ea1e95a234e9aacff">isotope_stdev_</a>);</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"isotope:maximum"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#ae29ab2ec7ad095c17fd97d56d4501c1c">max_isotope_</a>);</div>
<div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  fitter = <a class="code" href="classOpenMS_1_1Factory.html#a4cfac1ac1b4ac63d3b169291ac8019ed">Factory<Fitter1D>::create</a>(<span class="stringliteral">"IsotopeFitter1D"</span>);</div>
<div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  }</div>
<div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  <span class="keywordflow">else</span> <span class="comment">// charge is zero</span></div>
<div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  {</div>
<div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">algorithm_</a> == <span class="stringliteral">"simplest"</span>) <span class="comment">// Fit with GaussModel</span></div>
<div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  {</div>
<div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"charge"</span>, charge);</div>
<div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"isotope:stdev"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a141bcda36021c50ea1e95a234e9aacff">isotope_stdev_</a>);</div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"isotope:maximum"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#ae29ab2ec7ad095c17fd97d56d4501c1c">max_isotope_</a>);</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  fitter = <a class="code" href="classOpenMS_1_1Factory.html#a4cfac1ac1b4ac63d3b169291ac8019ed">Factory<Fitter1D>::create</a>(<span class="stringliteral">"IsotopeFitter1D"</span>);</div>
<div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  }</div>
<div class="line"><a name="l00683"></a><span class="lineno"> 683</span>  <span class="keywordflow">else</span> <span class="comment">// Fit with LmaGaussModel</span></div>
<div class="line"><a name="l00684"></a><span class="lineno"> 684</span>  {</div>
<div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"max_iteration"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a65156c6922b9524db057849c1d14cd56">max_iteration_</a>);</div>
<div class="line"><a name="l00686"></a><span class="lineno"> 686</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"deltaAbsError"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#a29677fd7ae2cbf6f04964da70997b4d6">deltaAbsError_</a>);</div>
<div class="line"><a name="l00687"></a><span class="lineno"> 687</span>  param.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"deltaRelError"</span>, <a class="code" href="classOpenMS_1_1ModelFitter.html#aae802b51d6efd35a1378b228f4f40770">deltaRelError_</a>);</div>
<div class="line"><a name="l00688"></a><span class="lineno"> 688</span>  fitter = <a class="code" href="classOpenMS_1_1Factory.html#a4cfac1ac1b4ac63d3b169291ac8019ed">Factory<Fitter1D>::create</a>(<span class="stringliteral">"LmaGaussFitter1D"</span>);</div>
<div class="line"><a name="l00689"></a><span class="lineno"> 689</span>  }</div>
<div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  }</div>
<div class="line"><a name="l00691"></a><span class="lineno"> 691</span> </div>
<div class="line"><a name="l00692"></a><span class="lineno"> 692</span>  <span class="comment">// Set parameter for fitter</span></div>
<div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  fitter-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param);</div>
<div class="line"><a name="l00694"></a><span class="lineno"> 694</span> </div>
<div class="line"><a name="l00695"></a><span class="lineno"> 695</span>  <span class="comment">// Construct model for mz</span></div>
<div class="line"><a name="l00696"></a><span class="lineno"> 696</span>  quality = fitter-><a class="code" href="classOpenMS_1_1Fitter1D.html#a78595664bcabdc63cf91fd338883d309">fit1d</a>(<a class="code" href="classOpenMS_1_1ModelFitter.html#ad1dd87342de3593f23630e645f995d1f">mz_input_data_</a>, model);</div>
<div class="line"><a name="l00697"></a><span class="lineno"> 697</span> </div>
<div class="line"><a name="l00698"></a><span class="lineno"> 698</span>  <span class="comment">//std::cout << "model after fitting: " << model->getParameters() << std::endl << std::endl;</span></div>
<div class="line"><a name="l00699"></a><span class="lineno"> 699</span> </div>
<div class="line"><a name="l00700"></a><span class="lineno"> 700</span>  <span class="comment">// Check quality</span></div>
<div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  <span class="keywordflow">if</span> (boost::math::isnan(quality)) quality = -1.0;</div>
<div class="line"><a name="l00702"></a><span class="lineno"> 702</span> </div>
<div class="line"><a name="l00703"></a><span class="lineno"> 703</span>  <span class="keyword">delete</span>(fitter);</div>
<div class="line"><a name="l00704"></a><span class="lineno"> 704</span> </div>
<div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  <span class="keywordflow">return</span> quality;</div>
<div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  }</div>
<div class="line"><a name="l00707"></a><span class="lineno"> 707</span> </div>
<div class="line"><a name="l00709"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d"> 709</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">doProjectionDim_</a>(<span class="keyword">const</span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> dim, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">ChargedIndexSet</a> & index_set, <a class="code" href="classOpenMS_1_1ModelFitter.html#a31ac7361125f91f71e3d07be39a76023">RawDataArrayType</a> & set)<span class="keyword"> const</span></div>
<div class="line"><a name="l00710"></a><span class="lineno"> 710</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00711"></a><span class="lineno"> 711</span> </div>
<div class="line"><a name="l00712"></a><span class="lineno"> 712</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">algorithm_</a> != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00713"></a><span class="lineno"> 713</span>  {</div>
<div class="line"><a name="l00714"></a><span class="lineno"> 714</span>  std::map<CoordinateType, CoordinateType> data_map;</div>
<div class="line"><a name="l00715"></a><span class="lineno"> 715</span> </div>
<div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  <span class="keywordflow">if</span> (dim == <a class="code" href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">MZ</a>)</div>
<div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  {</div>
<div class="line"><a name="l00718"></a><span class="lineno"> 718</span>  <span class="keywordflow">for</span> (IndexSet::const_iterator it = index_set.begin(); it != index_set.end(); ++it)</div>
<div class="line"><a name="l00719"></a><span class="lineno"> 719</span>  {</div>
<div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  data_map[this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a>(*it)] += this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it);</div>
<div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  }</div>
<div class="line"><a name="l00722"></a><span class="lineno"> 722</span>  }</div>
<div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00724"></a><span class="lineno"> 724</span>  {</div>
<div class="line"><a name="l00725"></a><span class="lineno"> 725</span>  <span class="keywordflow">for</span> (IndexSet::const_iterator it = index_set.begin(); it != index_set.end(); ++it)</div>
<div class="line"><a name="l00726"></a><span class="lineno"> 726</span>  {</div>
<div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  data_map[this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a>(*it)] += this-><a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(*it);</div>
<div class="line"><a name="l00728"></a><span class="lineno"> 728</span>  }</div>
<div class="line"><a name="l00729"></a><span class="lineno"> 729</span>  }</div>
<div class="line"><a name="l00730"></a><span class="lineno"> 730</span> </div>
<div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  <span class="comment">// Copy the raw data into set</span></div>
<div class="line"><a name="l00732"></a><span class="lineno"> 732</span>  set.resize(data_map.size());</div>
<div class="line"><a name="l00733"></a><span class="lineno"> 733</span>  std::map<CoordinateType, CoordinateType>::iterator it;</div>
<div class="line"><a name="l00734"></a><span class="lineno"> 734</span>  <a class="code" href="classunsigned_01int.html">UInt</a> i = 0;</div>
<div class="line"><a name="l00735"></a><span class="lineno"> 735</span>  <span class="keywordflow">for</span> (it = data_map.begin(); it != data_map.end(); ++it, ++i)</div>
<div class="line"><a name="l00736"></a><span class="lineno"> 736</span>  {</div>
<div class="line"><a name="l00737"></a><span class="lineno"> 737</span>  set[i].setPosition((*it).first);</div>
<div class="line"><a name="l00738"></a><span class="lineno"> 738</span>  set[i].setIntensity((*it).second);</div>
<div class="line"><a name="l00739"></a><span class="lineno"> 739</span>  }</div>
<div class="line"><a name="l00740"></a><span class="lineno"> 740</span> </div>
<div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  }</div>
<div class="line"><a name="l00742"></a><span class="lineno"> 742</span> </div>
<div class="line"><a name="l00743"></a><span class="lineno"> 743</span>  }</div>
<div class="line"><a name="l00744"></a><span class="lineno"> 744</span> </div>
<div class="line"><a name="l00746"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574"> 746</a></span>  <a class="code" href="classOpenMS_1_1ProductModel_3_012_01_4.html">ProductModel<2></a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">model2D_</a>;</div>
<div class="line"><a name="l00748"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401"> 748</a></span>  <a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html">Math::BasicStatistics<></a> <a class="code" href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401">mz_stat_</a>;</div>
<div class="line"><a name="l00750"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa"> 750</a></span>  <a class="code" href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html">Math::AsymmetricStatistics<></a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">rt_stat_</a>;</div>
<div class="line"><a name="l00752"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#ad1dd87342de3593f23630e645f995d1f"> 752</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a31ac7361125f91f71e3d07be39a76023">RawDataArrayType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#ad1dd87342de3593f23630e645f995d1f">mz_input_data_</a>;</div>
<div class="line"><a name="l00754"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a100b9653d9495c862bc57cee3dcdbb3f"> 754</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a31ac7361125f91f71e3d07be39a76023">RawDataArrayType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a100b9653d9495c862bc57cee3dcdbb3f">rt_input_data_</a>;</div>
<div class="line"><a name="l00756"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b"> 756</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b">tolerance_stdev_box_</a>;</div>
<div class="line"><a name="l00758"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd"> 758</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd">monoisotopic_mz_</a>;</div>
<div class="line"><a name="l00759"></a><span class="lineno"> 759</span> <span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00760"></a><span class="lineno"> 760</span> <span class="preprocessor"></span> <a class="code" href="classunsigned_01int.html">UInt</a> counter_;</div>
<div class="line"><a name="l00762"></a><span class="lineno"> 762</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00763"></a><span class="lineno"> 763</span> <span class="preprocessor"></span> <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a5cf51152410c3773eeb23c45f288986c">interpolation_step_mz_</a>;</div>
<div class="line"><a name="l00766"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#adf3e31ca2a7272a82a67175153f39f98"> 766</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#adf3e31ca2a7272a82a67175153f39f98">interpolation_step_rt_</a>;</div>
<div class="line"><a name="l00768"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#ae29ab2ec7ad095c17fd97d56d4501c1c"> 768</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#ae29ab2ec7ad095c17fd97d56d4501c1c">max_isotope_</a>;</div>
<div class="line"><a name="l00770"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#abfeee1372fcfb6bea261621d9f553e3d"> 770</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#abfeee1372fcfb6bea261621d9f553e3d">iso_stdev_first_</a>;</div>
<div class="line"><a name="l00772"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a61031e41af78cf1ff1d097717b27faaa"> 772</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a61031e41af78cf1ff1d097717b27faaa">iso_stdev_last_</a>;</div>
<div class="line"><a name="l00774"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a929a8e237da6180773aa965601894c60"> 774</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a929a8e237da6180773aa965601894c60">iso_stdev_stepsize_</a>;</div>
<div class="line"><a name="l00776"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae"> 776</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">first_mz_model_</a>;</div>
<div class="line"><a name="l00778"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519"> 778</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">last_mz_model_</a>;</div>
<div class="line"><a name="l00780"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a141bcda36021c50ea1e95a234e9aacff"> 780</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a141bcda36021c50ea1e95a234e9aacff">isotope_stdev_</a>;</div>
<div class="line"><a name="l00782"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb"> 782</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">algorithm_</a>;</div>
<div class="line"><a name="l00784"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#a65156c6922b9524db057849c1d14cd56"> 784</a></span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a65156c6922b9524db057849c1d14cd56">max_iteration_</a>;</div>
<div class="line"><a name="l00786"></a><span class="lineno"> 786</span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#a29677fd7ae2cbf6f04964da70997b4d6">deltaAbsError_</a>;</div>
<div class="line"><a name="l00789"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#aae802b51d6efd35a1378b228f4f40770"> 789</a></span>  <a class="code" href="classdouble.html">CoordinateType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#aae802b51d6efd35a1378b228f4f40770">deltaRelError_</a>;</div>
<div class="line"><a name="l00791"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#abbc8755ed3bfc1ce70b9a6e01b46bafd"> 791</a></span>  <a class="code" href="classOpenMS_1_1Math_1_1BasicStatistics.html">Math::BasicStatistics<></a> <a class="code" href="classOpenMS_1_1ModelFitter.html#abbc8755ed3bfc1ce70b9a6e01b46bafd">basic_stat_</a>;</div>
<div class="line"><a name="l00793"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#ad14e23949d04910624b46731e5268fb5"> 793</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#ad14e23949d04910624b46731e5268fb5">quality_rt_</a>;</div>
<div class="line"><a name="l00795"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b"> 795</a></span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">QualityType</a> <a class="code" href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">quality_mz_</a>;</div>
<div class="line"><a name="l00796"></a><span class="lineno"> 796</span> </div>
<div class="line"><a name="l00797"></a><span class="lineno"> 797</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00798"></a><span class="lineno"> 798</span> </div>
<div class="line"><a name="l00800"></a><span class="lineno"> 800</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a1fe4d38b96532c05c6931436ed5bc4db">ModelFitter</a>();</div>
<div class="line"><a name="l00802"></a><span class="lineno"> 802</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html">ModelFitter</a> & <a class="code" href="classOpenMS_1_1ModelFitter.html#a713ca6314eab4ecca52be610f61e76a1">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModelFitter.html">ModelFitter</a> &);</div>
<div class="line"><a name="l00804"></a><span class="lineno"> 804</span>  <a class="code" href="classOpenMS_1_1ModelFitter.html#a1fe4d38b96532c05c6931436ed5bc4db">ModelFitter</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ModelFitter.html">ModelFitter</a> &);</div>
<div class="line"><a name="l00805"></a><span class="lineno"> 805</span> </div>
<div class="line"><a name="l00806"></a><span class="lineno"> 806</span>  };</div>
<div class="line"><a name="l00807"></a><span class="lineno"> 807</span> </div>
<div class="line"><a name="l00808"></a><span class="lineno"> 808</span> }</div>
<div class="line"><a name="l00809"></a><span class="lineno"> 809</span> </div>
<div class="line"><a name="l00810"></a><span class="lineno"> 810</span> <span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_MODELFITTER_H</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="ProductModel_8h_html"><div class="ttname"><a href="ProductModel_8h.html">ProductModel.h</a></div></div>
<div class="ttc" id="ExtendedIsotopeModel_8h_html"><div class="ttname"><a href="ExtendedIsotopeModel_8h.html">ExtendedIsotopeModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html_a8cd14764d47842020930ef7023a2d912"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html#a8cd14764d47842020930ef7023a2d912">OpenMS::ProductModel< 2 >::setModel</a></div><div class="ttdeci">ProductModel & setModel(UInt dim, BaseModel< 1 > *dist)</div><div class="ttdoc">set model dist for dimension dim </div><div class="ttdef"><b>Definition:</b> ProductModel.h:184</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 &name, const DataValue &value)</div><div class="ttdoc">sets the DataValue corresponding to a name </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 & getCharge() const </div><div class="ttdoc">Non-mutable access to charge state. </div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1AsymmetricStatistics_html_a74998f835798420ad045536c0c2a3106"><div class="ttname"><a href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html#a74998f835798420ad045536c0c2a3106">OpenMS::Math::AsymmetricStatistics::update</a></div><div class="ttdeci">void update(ProbabilityIterator const probability_begin, ProbabilityIterator const probability_end, CoordinateIterator const coordinate_begin)</div><div class="ttdoc">You can call this as often as you like, using different input vectors. </div><div class="ttdef"><b>Definition:</b> AsymmetricStatistics.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html">OpenMS::FeaFiModule</a></div><div class="ttdoc">Implements a module of the FeatureFinder algorithm. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a9f3a5a09e281e06e938ab4ba54154aae"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a9f3a5a09e281e06e938ab4ba54154aae">OpenMS::ModelFitter::first_mz_model_</a></div><div class="ttdeci">Int first_mz_model_</div><div class="ttdoc">first mz model (0=Gaussian, 1....n = charge ) </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:776</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a550aafc7c40f4722708edca5488f5b6b"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a550aafc7c40f4722708edca5488f5b6b">OpenMS::ModelFitter::tolerance_stdev_box_</a></div><div class="ttdeci">CoordinateType tolerance_stdev_box_</div><div class="ttdoc">tolerance used for bounding box </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:756</div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1AsymmetricStatistics_html_af5dad3b7af1fd39433b75414fed36f2c"><div class="ttname"><a href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html#af5dad3b7af1fd39433b75414fed36f2c">OpenMS::Math::AsymmetricStatistics::variance2</a></div><div class="ttdeci">RealType variance2() const </div><div class="ttdoc">&quot;variance to the right hand side&quot; </div><div class="ttdef"><b>Definition:</b> AsymmetricStatistics.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a063d40a3528749f1a905ab04d76387e0"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a063d40a3528749f1a905ab04d76387e0">OpenMS::Peak2D::CoordinateType</a></div><div class="ttdeci">DoubleReal CoordinateType</div><div class="ttdoc">Coordinate type (of the position) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaaf388fcb6d444ef59841ef549ca6ee0da">OpenMS::ModelFitter::RT</a></div><div class="ttdef"><b>Definition:</b> ModelFitter.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a4a8c5b2adc05e9ff96a007385bfe9b47"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">OpenMS::Peak2D::IntensityType</a></div><div class="ttdeci">Real IntensityType</div><div class="ttdoc">Intensity type. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:63</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a1fe4d38b96532c05c6931436ed5bc4db"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a1fe4d38b96532c05c6931436ed5bc4db">OpenMS::ModelFitter::ModelFitter</a></div><div class="ttdeci">ModelFitter()</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_ad1dd87342de3593f23630e645f995d1f"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#ad1dd87342de3593f23630e645f995d1f">OpenMS::ModelFitter::mz_input_data_</a></div><div class="ttdeci">RawDataArrayType mz_input_data_</div><div class="ttdoc">mz raw data </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:752</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_1ModelFitter_html_a9f65527757d7146ea4eabbb506c9a646"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a9f65527757d7146ea4eabbb506c9a646">OpenMS::ModelFitter::ChargeType</a></div><div class="ttdeci">Feature::ChargeType ChargeType</div><div class="ttdoc">Isotope charge. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a929a8e237da6180773aa965601894c60"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a929a8e237da6180773aa965601894c60">OpenMS::ModelFitter::iso_stdev_stepsize_</a></div><div class="ttdeci">CoordinateType iso_stdev_stepsize_</div><div class="ttdoc">step size </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:774</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 &key, const DataValue &value, const String &description="", const StringList &tags=StringList())</div><div class="ttdoc">Sets a value. </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_1Feature_html_a94eabbe00bbab2a589688631c807005e"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a94eabbe00bbab2a589688631c807005e">OpenMS::Feature::getModelDescription</a></div><div class="ttdeci">const ModelDescription< 2 > & getModelDescription() const </div><div class="ttdoc">Non-mutable access to the model description. </div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a8e5564d7b686645a7d7d6f5aed8cd494"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">OpenMS::FeaFiModule::getPeakRt</a></div><div class="ttdeci">CoordinateType getPeakRt(const FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">Returns the retention time of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:210</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a29677fd7ae2cbf6f04964da70997b4d6"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a29677fd7ae2cbf6f04964da70997b4d6">OpenMS::ModelFitter::deltaAbsError_</a></div><div class="ttdeci">CoordinateType deltaAbsError_</div><div class="ttdoc">Absolute error. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:787</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_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="classOpenMS_1_1FeaFiModule_html_a4698fa90bfbdd5729e0e25c62345ff0d"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">OpenMS::FeaFiModule::getPeakIntensity</a></div><div class="ttdeci">IntensityType getPeakIntensity(const FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">Returns the intensity of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:190</div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html_ac4534e8323ba5dc157bc4bba75096d50"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html#ac4534e8323ba5dc157bc4bba75096d50">OpenMS::ProductModel< 2 >::getIntensity</a></div><div class="ttdeci">IntensityType getIntensity(const PositionType &pos) const </div><div class="ttdoc">intensity equals product of intensities in each dimension </div><div class="ttdef"><b>Definition:</b> ProductModel.h:151</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="classOpenMS_1_1BaseFeature_html_a87171116869a9f9511d7ce9ad7baf5d6"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#a87171116869a9f9511d7ce9ad7baf5d6">OpenMS::BaseFeature::ChargeType</a></div><div class="ttdeci">Int ChargeType</div><div class="ttdoc">Type of charge values. </div><div class="ttdef"><b>Definition:</b> BaseFeature.h:64</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">OpenMS::FeatureFinderDefs::UNUSED</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:63</div></div>
<div class="ttc" id="FeaFiModule_8h_html"><div class="ttname"><a href="FeaFiModule_8h.html">FeaFiModule.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 & 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_1Math_1_1BasicStatistics_html_a620e83f1ef3e206cacdacb1293677e05"><div class="ttname"><a href="classOpenMS_1_1Math_1_1BasicStatistics.html#a620e83f1ef3e206cacdacb1293677e05">OpenMS::Math::BasicStatistics::variance</a></div><div class="ttdeci">RealType variance() const </div><div class="ttdoc">Returns the variance. </div><div class="ttdef"><b>Definition:</b> BasicStatistics.h:175</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">OpenMS::Peak2D::RT</a></div><div class="ttdoc">Retention time dimension id (0 if used as a const int) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a221361082f641c3fccc58e9bc66aeee1"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">OpenMS::FeaFiModule::IntensityType</a></div><div class="ttdeci">PeakType::IntensityType IntensityType</div><div class="ttdoc">Input intensity type. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:168</div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1BasicStatistics_html_af6efe0afdae7cbb85a5ac3bed200c048"><div class="ttname"><a href="classOpenMS_1_1Math_1_1BasicStatistics.html#af6efe0afdae7cbb85a5ac3bed200c048">OpenMS::Math::BasicStatistics::mean</a></div><div class="ttdeci">RealType mean() const </div><div class="ttdoc">Returns the mean. </div><div class="ttdef"><b>Definition:</b> BasicStatistics.h:171</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_1Fitter1D_html_a78595664bcabdc63cf91fd338883d309"><div class="ttname"><a href="classOpenMS_1_1Fitter1D.html#a78595664bcabdc63cf91fd338883d309">OpenMS::Fitter1D::fit1d</a></div><div class="ttdeci">virtual QualityType fit1d(const RawDataArrayType &, InterpolationModel *&)</div><div class="ttdoc">return interpolation model </div><div class="ttdef"><b>Definition:</b> Fitter1D.h:95</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_1ModelFitter_html_a5226d265fd03c7b41e9945248d241af1"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a5226d265fd03c7b41e9945248d241af1">OpenMS::ModelFitter::QualityType</a></div><div class="ttdeci">Feature::QualityType QualityType</div><div class="ttdoc">Quality of a feature. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a31ac7361125f91f71e3d07be39a76023"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a31ac7361125f91f71e3d07be39a76023">OpenMS::ModelFitter::RawDataArrayType</a></div><div class="ttdeci">std::vector< PeakType > RawDataArrayType</div><div class="ttdoc">Raw data container type using for the temporary storage of the input data. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:96</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_aae802b51d6efd35a1378b228f4f40770"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#aae802b51d6efd35a1378b228f4f40770">OpenMS::ModelFitter::deltaRelError_</a></div><div class="ttdeci">CoordinateType deltaRelError_</div><div class="ttdoc">Relative error. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:789</div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1BasicStatistics_html_a6068425aeb34eec009695897d0408453"><div class="ttname"><a href="classOpenMS_1_1Math_1_1BasicStatistics.html#a6068425aeb34eec009695897d0408453">OpenMS::Math::BasicStatistics::update</a></div><div class="ttdeci">void update(ProbabilityIterator probability_begin, ProbabilityIterator const probability_end)</div><div class="ttdoc">This does the actual calculation. </div><div class="ttdef"><b>Definition:</b> BasicStatistics.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1AsymmetricStatistics_html"><div class="ttname"><a href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html">OpenMS::Math::AsymmetricStatistics</a></div><div class="ttdoc">Internal class for asymmetric distributions. </div><div class="ttdef"><b>Definition:</b> AsymmetricStatistics.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a9e7780ed6d3446aebf9ba5ccf1bb9574"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a9e7780ed6d3446aebf9ba5ccf1bb9574">OpenMS::ModelFitter::model2D_</a></div><div class="ttdeci">ProductModel< 2 > model2D_</div><div class="ttdoc">2D model </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:746</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a79ea228cdc8755284e64dd9f625170a3"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a79ea228cdc8755284e64dd9f625170a3">OpenMS::ModelFitter::Base</a></div><div class="ttdeci">FeaFiModule< PeakType, FeatureType > Base</div><div class="ttdoc">FeaFiModule. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:94</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_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 &key, const String &description)</div><div class="ttdoc">Sets a description for an existing section. </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_1ModelFitter_html_a4aeb5297e8e231a3cc8e6a4f599944b5"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a4aeb5297e8e231a3cc8e6a4f599944b5">OpenMS::ModelFitter::setMonoIsotopicMass</a></div><div class="ttdeci">void setMonoIsotopicMass(CoordinateType mz)</div><div class="ttdoc">Sets or fixed the monoisotopic m/z at a specific position. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">OpenMS::Peak2D::MZ</a></div><div class="ttdoc">Mass-to-charge dimension id (1 if used as a const int) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a59f31f35e2e4a45316651cebbb358a1d"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a59f31f35e2e4a45316651cebbb358a1d">OpenMS::Feature::setModelDescription</a></div><div class="ttdeci">void setModelDescription(const ModelDescription< 2 > &q)</div><div class="ttdoc">Set the model description. </div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab4e0f356f837ce58e57695da114adce3"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">OpenMS::Peak2D::getRT</a></div><div class="ttdeci">CoordinateType getRT() const </div><div class="ttdoc">Returns the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:203</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_adc75bbd0ca620523daf2e796efdd1cdf"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#adc75bbd0ca620523daf2e796efdd1cdf">OpenMS::ModelFitter::IndexSetIter</a></div><div class="ttdeci">IndexSet::const_iterator IndexSetIter</div><div class="ttdoc">IndexSet iterator. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html">OpenMS::ProductModel< 2 ></a></div><div class="ttdoc">The class template is only implemented for D=2 because we use Peak2D here. </div><div class="ttdef"><b>Definition:</b> ProductModel.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1BasicStatistics_html"><div class="ttname"><a href="classOpenMS_1_1Math_1_1BasicStatistics.html">OpenMS::Math::BasicStatistics</a></div><div class="ttdoc">Calculates some basic statistical parameters of a distribution: sum, mean, variance, and provides the normal approximation. </div><div class="ttdef"><b>Definition:</b> BasicStatistics.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a65156c6922b9524db057849c1d14cd56"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a65156c6922b9524db057849c1d14cd56">OpenMS::ModelFitter::max_iteration_</a></div><div class="ttdeci">Int max_iteration_</div><div class="ttdoc">Maximum number of iterations. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:784</div></div>
<div class="ttc" id="classOpenMS_1_1Factory_html_a4cfac1ac1b4ac63d3b169291ac8019ed"><div class="ttname"><a href="classOpenMS_1_1Factory.html#a4cfac1ac1b4ac63d3b169291ac8019ed">OpenMS::Factory::create</a></div><div class="ttdeci">static FactoryProduct * create(const String &name)</div><div class="ttdoc">return FactoryProduct according to unique identifier name </div><div class="ttdef"><b>Definition:</b> Factory.h:113</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 &param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeaFiModule::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 and report progress...</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:415</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_1ModelFitter_html_a75145a9f1f2689d0f54565ffbdb1f5d6"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a75145a9f1f2689d0f54565ffbdb1f5d6">OpenMS::ModelFitter::CoordinateType</a></div><div class="ttdeci">Feature::CoordinateType CoordinateType</div><div class="ttdoc">Single coordinate. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:88</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_1ModelFitter_html_ad14e23949d04910624b46731e5268fb5"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#ad14e23949d04910624b46731e5268fb5">OpenMS::ModelFitter::quality_rt_</a></div><div class="ttdeci">QualityType quality_rt_</div><div class="ttdoc">fit quality in RT dimension </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:793</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a37de948351467fdccb9d12f601dc8205"><div class="ttname"><a href="classOpenMS_1_1Param.html#a37de948351467fdccb9d12f601dc8205">OpenMS::Param::setMaxInt</a></div><div class="ttdeci">void setMaxInt(const String &key, Int max)</div><div class="ttdoc">Sets the maximum value for the integer or integer list parameter key. </div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_aa08948a609e0be02a55895209d3d77a9"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#aa08948a609e0be02a55895209d3d77a9">OpenMS::ModelFitter::fitMZLoop_</a></div><div class="ttdeci">QualityType fitMZLoop_(const ChargedIndexSet &set, const ChargeType &charge)</div><div class="ttdoc">main fit loop </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:540</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a100b9653d9495c862bc57cee3dcdbb3f"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a100b9653d9495c862bc57cee3dcdbb3f">OpenMS::ModelFitter::rt_input_data_</a></div><div class="ttdeci">RawDataArrayType rt_input_data_</div><div class="ttdoc">rt raw data </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:754</div></div>
<div class="ttc" id="Factory_8h_html"><div class="ttname"><a href="Factory_8h.html">Factory.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1InterpolationModel_html"><div class="ttname"><a href="classOpenMS_1_1InterpolationModel.html">OpenMS::InterpolationModel</a></div><div class="ttdoc">Abstract class for 1D-models that are approximated using linear interpolation. </div><div class="ttdef"><b>Definition:</b> InterpolationModel.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1ModelDescription_html_a3f962855dbc9bbf8074f4306cb9c1a7b"><div class="ttname"><a href="classOpenMS_1_1ModelDescription.html#a3f962855dbc9bbf8074f4306cb9c1a7b">OpenMS::ModelDescription::createModel</a></div><div class="ttdeci">BaseModel< D > * createModel()</div><div class="ttdef"><b>Definition:</b> ModelDescription.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a5e69531f4b15948d57b30909fdba0cb4"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a5e69531f4b15948d57b30909fdba0cb4">OpenMS::ModelFitter::fitRT_</a></div><div class="ttdeci">QualityType fitRT_(InterpolationModel *&model) const </div><div class="ttdoc">1d fit in RT </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:607</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_adf3e31ca2a7272a82a67175153f39f98"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#adf3e31ca2a7272a82a67175153f39f98">OpenMS::ModelFitter::interpolation_step_rt_</a></div><div class="ttdeci">CoordinateType interpolation_step_rt_</div><div class="ttdoc">interpolation step size (in retention time) </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:766</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a606049d47faacd506705556d333849a2"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">OpenMS::FeaFiModule::getPeakMz</a></div><div class="ttdeci">CoordinateType getPeakMz(const FeatureFinderDefs::IndexPair &index) const </div><div class="ttdoc">Returns the m/z of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:200</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 & getValue(const String &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="classOpenMS_1_1ModelFitter_html_a776f7572fc4f466e9527ca233471920d"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a776f7572fc4f466e9527ca233471920d">OpenMS::ModelFitter::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> ModelFitter.h:517</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::DefaultParamHandler::getName</a></div><div class="ttdeci">const String & getName() const </div><div class="ttdoc">Non-mutable access to the name. </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_1ModelFitter_html_abbc8755ed3bfc1ce70b9a6e01b46bafd"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#abbc8755ed3bfc1ce70b9a6e01b46bafd">OpenMS::ModelFitter::basic_stat_</a></div><div class="ttdeci">Math::BasicStatistics basic_stat_</div><div class="ttdoc">statistics </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:791</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a5cf51152410c3773eeb23c45f288986c"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a5cf51152410c3773eeb23c45f288986c">OpenMS::ModelFitter::interpolation_step_mz_</a></div><div class="ttdeci">CoordinateType interpolation_step_mz_</div><div class="ttdoc">interpolation step size (in m/z) </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:764</div></div>
<div class="ttc" id="classOpenMS_1_1ProductModel_3_012_01_4_html_a5a40666cbd449e6dab1270ef7153f490"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html#a5a40666cbd449e6dab1270ef7153f490">OpenMS::ProductModel< 2 >::getModel</a></div><div class="ttdeci">BaseModel< 1 > * getModel(UInt dim) const </div><div class="ttdef"><b>Definition:</b> ProductModel.h:204</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< Feature > & getSubordinates() const </div><div class="ttdoc">immutable access to subordinate features </div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a1ad0c0f264440b15c5d699f3845b8ad7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a1ad0c0f264440b15c5d699f3845b8ad7">OpenMS::Feature::getQuality</a></div><div class="ttdeci">QualityType getQuality(Size index) const </div><div class="ttdoc">Non-mutable access to the quality in dimension c. </div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a00b389ceb266aea7a8b43fb9a2d899e0"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a00b389ceb266aea7a8b43fb9a2d899e0">OpenMS::ModelFitter::ModelFitter</a></div><div class="ttdeci">ModelFitter(const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_a93cd3fc199fc903768e3b8d7fafaeb95"><div class="ttname"><a href="classOpenMS_1_1Feature.html#a93cd3fc199fc903768e3b8d7fafaeb95">OpenMS::Feature::setQuality</a></div><div class="ttdeci">void setQuality(Size index, QualityType q)</div><div class="ttdoc">Set the quality in dimension c. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_af7439235b89a75354a2e87350e36834f"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">OpenMS::FeatureFinderDefs::IndexSet</a></div><div class="ttdeci">IsotopeCluster::IndexSet IndexSet</div><div class="ttdoc">A set of peak indices. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_ac641d17ba54cde66c331d17bdee355e8"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#ac641d17ba54cde66c331d17bdee355e8">OpenMS::FeaFiModule::addConvexHull</a></div><div class="ttdeci">void addConvexHull(const FeatureFinderDefs::IndexSet &set, Feature &feature) const </div><div class="ttdoc">Calculates the convex hull of a index set and adds it to the feature. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:393</div></div>
<div class="ttc" id="AsymmetricStatistics_8h_html"><div class="ttname"><a href="AsymmetricStatistics_8h.html">AsymmetricStatistics.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1RtIterator_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1RtIterator.html">OpenMS::Internal::RtIterator</a></div><div class="ttdoc">Retention time iterator for a FeatureFinderDefs::IndexSet. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a141bcda36021c50ea1e95a234e9aacff"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a141bcda36021c50ea1e95a234e9aacff">OpenMS::ModelFitter::isotope_stdev_</a></div><div class="ttdeci">CoordinateType isotope_stdev_</div><div class="ttdoc">isotope stdev </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:780</div></div>
<div class="ttc" id="LmaIsotopeModel_8h_html"><div class="ttname"><a href="LmaIsotopeModel_8h.html">LmaIsotopeModel.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a26fe6c8385c2f47cc989960b4826c0bd"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a26fe6c8385c2f47cc989960b4826c0bd">OpenMS::ModelFitter::monoisotopic_mz_</a></div><div class="ttdeci">CoordinateType monoisotopic_mz_</div><div class="ttdoc">monoistopic mass </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:758</div></div>
<div class="ttc" id="classOpenMS_1_1Math_1_1AsymmetricStatistics_html_ad7008a00da75aa4248c4f6076f1dc58c"><div class="ttname"><a href="classOpenMS_1_1Math_1_1AsymmetricStatistics.html#ad7008a00da75aa4248c4f6076f1dc58c">OpenMS::Math::AsymmetricStatistics::variance1</a></div><div class="ttdeci">RealType variance1() const </div><div class="ttdoc">&quot;variance to the left hand side&quot; </div><div class="ttdef"><b>Definition:</b> AsymmetricStatistics.h:81</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 &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_1ModelFitter_html"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html">OpenMS::ModelFitter</a></div><div class="ttdoc">Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model...</div><div class="ttdef"><b>Definition:</b> ModelFitter.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_ac230d1bc572fc770f8e254d4f06088cb"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#ac230d1bc572fc770f8e254d4f06088cb">OpenMS::ModelFitter::algorithm_</a></div><div class="ttdeci">String algorithm_</div><div class="ttdoc">algorithm </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:782</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_a8ca1d75ff489493f4458fa7137186089"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#a8ca1d75ff489493f4458fa7137186089">OpenMS::BaseFeature::QualityType</a></div><div class="ttdeci">Real QualityType</div><div class="ttdoc">Type of quality values. </div><div class="ttdef"><b>Definition:</b> BaseFeature.h:62</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< 2 > getBoundingBox() const </div><div class="ttdoc">returns the bounding box of the feature hull points </div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1InvalidParameter_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1InvalidParameter.html">OpenMS::Exception::InvalidParameter</a></div><div class="ttdoc">Exception indicating that an invalid parameter was handed over to an algorithm. </div><div class="ttdef"><b>Definition:</b> Exception.h:348</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a520ad36c37273100004a5dca3c2a6c24"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a520ad36c37273100004a5dca3c2a6c24">OpenMS::ModelFitter::evaluate_</a></div><div class="ttdeci">QualityType evaluate_(const IndexSet &set) const </div><div class="ttdoc">evaluate 2d-model </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:576</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_1ProductModel_3_012_01_4_html_a6f73a9c8459a5cc55dada279e525437e"><div class="ttname"><a href="classOpenMS_1_1ProductModel_3_012_01_4.html#a6f73a9c8459a5cc55dada279e525437e">OpenMS::ProductModel< 2 >::setScale</a></div><div class="ttdeci">void setScale(IntensityType scale)</div><div class="ttdoc">set the intensity scaling factor </div><div class="ttdef"><b>Definition:</b> ProductModel.h:217</div></div>
<div class="ttc" id="group__MathFunctionsStatistics_html_ga67443c0e3d0ee860daf4f6f1e371ce2c"><div class="ttname"><a href="group__MathFunctionsStatistics.html#ga67443c0e3d0ee860daf4f6f1e371ce2c">OpenMS::Math::rankCorrelationCoefficient</a></div><div class="ttdeci">static DoubleReal rankCorrelationCoefficient(IteratorType1 begin_a, IteratorType1 end_a, IteratorType2 begin_b, IteratorType2 end_b)</div><div class="ttdoc">calculates the rank correlation coefficient for the values in [begin_a, end_a) and [begin_b...</div><div class="ttdef"><b>Definition:</b> StatisticFunctions.h:379</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_ae29ab2ec7ad095c17fd97d56d4501c1c"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#ae29ab2ec7ad095c17fd97d56d4501c1c">OpenMS::ModelFitter::max_isotope_</a></div><div class="ttdeci">Int max_isotope_</div><div class="ttdoc">maximum isotopic rank to be considered </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:768</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 &key, const std::vector< String > &strings)</div><div class="ttdoc">Sets the valid strings for the parameter key. </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_1ModelFitter_html_a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a6b7b47dd702d9e331586d485013fd1eaa35008b046ec2687e53152082281d0867">OpenMS::ModelFitter::MZ</a></div><div class="ttdef"><b>Definition:</b> ModelFitter.h:101</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="structOpenMS_1_1Internal_1_1MzIterator_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1MzIterator.html">OpenMS::Internal::MzIterator</a></div><div class="ttdoc">m/z iterator for a FeatureFinderDefs::IndexSet </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:110</div></div>
<div class="ttc" id="classOpenMS_1_1ModelDescription_html"><div class="ttname"><a href="classOpenMS_1_1ModelDescription.html">OpenMS::ModelDescription< 2 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a4e1ed92e7c5c8f3b4db0378a122ef3b1"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a4e1ed92e7c5c8f3b4db0378a122ef3b1">OpenMS::ModelFitter::fitMZ_</a></div><div class="ttdeci">QualityType fitMZ_(InterpolationModel *&model, const ChargeType &charge) const </div><div class="ttdoc">1d fit in MZ </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:651</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_afe69329d6075fc44aba749ead1fe6a8b"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#afe69329d6075fc44aba749ead1fe6a8b">OpenMS::ModelFitter::quality_mz_</a></div><div class="ttdeci">QualityType quality_mz_</div><div class="ttdoc">fit quality in MZ dimension </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:795</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityIterator_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityIterator.html">OpenMS::Internal::IntensityIterator</a></div><div class="ttdoc">Intensity iterator for a FeatureFinderDefs::IndexSet. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:88</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_1ModelFitter_html_a966741575418441aef18050ea04b8519"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a966741575418441aef18050ea04b8519">OpenMS::ModelFitter::last_mz_model_</a></div><div class="ttdeci">Int last_mz_model_</div><div class="ttdoc">last mz model </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:778</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a9e49d9564896fee1216a006f907d139d"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">OpenMS::ModelFitter::doProjectionDim_</a></div><div class="ttdeci">void doProjectionDim_(const Int dim, const ChargedIndexSet &index_set, RawDataArrayType &set) const </div><div class="ttdoc">Project the raw data into 1-dim array. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:709</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1UnableToFit_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1UnableToFit.html">OpenMS::Exception::UnableToFit</a></div><div class="ttdoc">Exception used if an error occurred while fitting a model to a given dataset. </div><div class="ttdef"><b>Definition:</b> Exception.h:662</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 &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="classOpenMS_1_1BaseModel_html_aca183c4ace75384f91bc04579eada9bc"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">OpenMS::BaseModel::isContained</a></div><div class="ttdeci">virtual bool isContained(const PositionType &pos) const </div><div class="ttdoc">check if position pos is part of the model regarding the models cut-off. </div><div class="ttdef"><b>Definition:</b> BaseModel.h:101</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet_html"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">OpenMS::IsotopeCluster::ChargedIndexSet</a></div><div class="ttdoc">index set with associated charge estimate </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1Fitter1D_html"><div class="ttname"><a href="classOpenMS_1_1Fitter1D.html">OpenMS::Fitter1D</a></div><div class="ttdoc">Abstract base class for all 1D-dimensional model fitter. </div><div class="ttdef"><b>Definition:</b> Fitter1D.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a61031e41af78cf1ff1d097717b27faaa"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a61031e41af78cf1ff1d097717b27faaa">OpenMS::ModelFitter::iso_stdev_last_</a></div><div class="ttdeci">CoordinateType iso_stdev_last_</div><div class="ttdoc">last stdev </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:772</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 &ch)</div><div class="ttdoc">Set charge state. </div></div>
<div class="ttc" id="EGHFitter1D_8h_html_a113411f16080334fa17209bc7a0175a7"><div class="ttname"><a href="EGHFitter1D_8h.html#a113411f16080334fa17209bc7a0175a7">DEBUG_FEATUREFINDER</a></div><div class="ttdeci">#define DEBUG_FEATUREFINDER</div><div class="ttdef"><b>Definition:</b> EGHFitter1D.h:38</div></div>
<div class="ttc" id="IsotopeModel_8h_html"><div class="ttname"><a href="IsotopeModel_8h.html">IsotopeModel.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet_html_a8253a7962ca1c79b71e6af96589b7720"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">OpenMS::IsotopeCluster::ChargedIndexSet::charge</a></div><div class="ttdeci">Int charge</div><div class="ttdoc">charge estimate (convention: zero means &quot;no charge estimate&quot;) </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html">OpenMS::FeatureFinder</a></div><div class="ttdoc">The main feature finder class. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a77d37f2e1c12e8bd33ea0e660a89e927"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">OpenMS::DefaultParamHandler::setName</a></div><div class="ttdeci">void setName(const String &name)</div><div class="ttdoc">Mutable access to the name. </div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a3c4dee13554dda34293916d83f811aaa"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a3c4dee13554dda34293916d83f811aaa">OpenMS::ModelFitter::rt_stat_</a></div><div class="ttdeci">Math::AsymmetricStatistics rt_stat_</div><div class="ttdoc">statistics for rt </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:750</div></div>
<div class="ttc" id="Fitter1D_8h_html"><div class="ttname"><a href="Fitter1D_8h.html">Fitter1D.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_af8b43fcf339870914680f9afe812cd85"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#af8b43fcf339870914680f9afe812cd85">OpenMS::ModelFitter::~ModelFitter</a></div><div class="ttdeci">virtual ~ModelFitter()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:209</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html_a91adbb58dfeb79d2b5d78c1047f406c9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">OpenMS::FeatureFinder::getPeakFlag</a></div><div class="ttdeci">const Flag & getPeakFlag(const IndexPair &index) const </div><div class="ttdoc">Returns a non-mutable reference to a peak flag. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_ab30d394914362ab0b7a8918133eec401"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#ab30d394914362ab0b7a8918133eec401">OpenMS::ModelFitter::mz_stat_</a></div><div class="ttdeci">Math::BasicStatistics mz_stat_</div><div class="ttdoc">statistics for mz </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:748</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_adec9115bab6f7a59f89207e636875543"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#adec9115bab6f7a59f89207e636875543">OpenMS::ModelFitter::IntensityType</a></div><div class="ttdeci">Feature::IntensityType IntensityType</div><div class="ttdoc">Single intensity. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:90</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_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 &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_1ModelFitter_html_a9a599157dfa0c832cf50f5596342c73e"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">OpenMS::ModelFitter::fit</a></div><div class="ttdeci">Feature fit(const ChargedIndexSet &index_set)</div><div class="ttdoc">Return next feature. </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:226</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a464bd13b1e846ea0bc7bb0632f8e7256"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a464bd13b1e846ea0bc7bb0632f8e7256">OpenMS::BaseModel::setCutOff</a></div><div class="ttdeci">virtual void setCutOff(IntensityType cut_off)</div><div class="ttdoc">set cutoff value </div><div class="ttdef"><b>Definition:</b> BaseModel.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1ModelFitter_html_a713ca6314eab4ecca52be610f61e76a1"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#a713ca6314eab4ecca52be610f61e76a1">OpenMS::ModelFitter::operator=</a></div><div class="ttdeci">ModelFitter & operator=(const ModelFitter &)</div><div class="ttdoc">Not implemented. </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="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 &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="classOpenMS_1_1ModelFitter_html_abfeee1372fcfb6bea261621d9f553e3d"><div class="ttname"><a href="classOpenMS_1_1ModelFitter.html#abfeee1372fcfb6bea261621d9f553e3d">OpenMS::ModelFitter::iso_stdev_first_</a></div><div class="ttdeci">CoordinateType iso_stdev_first_</div><div class="ttdoc">first stdev </div><div class="ttdef"><b>Definition:</b> ModelFitter.h:770</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 11:19:17 using doxygen 1.8.5</font></TD>
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