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<a href="OptimizePick_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<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>&#160;<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>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
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<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<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>&#160;<span class="comment">//    without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<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>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Eva Lange $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPICK_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPICK_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="PeakShape_8h.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakShape.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Peak1D_8h.html">OpenMS/KERNEL/Peak1D.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_vector.h&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_multifit_nlin.h&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_blas.h&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;iostream&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;fstream&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;{</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;  <span class="keyword">namespace </span>OptimizationFunctions</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;  {</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="namespaceOpenMS_1_1OptimizationFunctions.html#a1b5cab7fcfe8ad040fb7363dd14913f1">   59</a></span>&#160;    <span class="keyword">typedef</span> std::vector&lt;Peak1D&gt; <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a1b5cab7fcfe8ad040fb7363dd14913f1">RawDataVector</a>;</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">   61</a></span>&#160;    <span class="keyword">typedef</span> RawDataVector::iterator <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a>;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;</div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">   71</a></span>&#160;    <span class="keyword">struct </span>OPENMS_DLLAPI <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">PenaltyFactors</a></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    {</div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ab17f5ae37b7817df4c3479ebfa6f3f48">   73</a></span>&#160;      <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ab17f5ae37b7817df4c3479ebfa6f3f48">PenaltyFactors</a>() :</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;        pos(0), lWidth(0), rWidth(0) {}</div>
<div class="line"><a name="l00075"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ae2acb9d1e3e0cd8ac48b11e58974aca0">   75</a></span>&#160;      <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ae2acb9d1e3e0cd8ac48b11e58974aca0">PenaltyFactors</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">PenaltyFactors</a> &amp; p) :</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;        pos(p.pos), lWidth(p.lWidth), rWidth(p.rWidth) {}</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ad586941d523262bc710038ecb19af79e">   77</a></span>&#160;      <span class="keyword">inline</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">PenaltyFactors</a> &amp; <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ad586941d523262bc710038ecb19af79e">operator=</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">PenaltyFactors</a> &amp; p)</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      {</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;        pos = p.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">pos</a>;</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        lWidth = p.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">lWidth</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        rWidth = p.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">rWidth</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      }</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ae89675bc0b01641aeece694576987c77">   86</a></span>&#160;      <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ae89675bc0b01641aeece694576987c77">~PenaltyFactors</a>(){}</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">   89</a></span>&#160;      <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">pos</a>;</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">   91</a></span>&#160;      <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">lWidth</a>;</div>
<div class="line"><a name="l00093"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">   93</a></span>&#160;      <span class="keywordtype">double</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">rWidth</a>;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    };</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <span class="keywordtype">int</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a3d21e47729faa48b51b02169c9383902">residual</a>(<span class="keyword">const</span> gsl_vector * x, <span class="keywordtype">void</span> * params, gsl_vector * f);</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="keywordtype">int</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a906050fe19898e6bdaad3442b61c7199">jacobian</a>(<span class="keyword">const</span> gsl_vector * x, <span class="keywordtype">void</span> * params, gsl_matrix * J);</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;    <span class="keywordtype">int</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>(<span class="keyword">const</span> gsl_vector * x, <span class="keywordtype">void</span> * params, gsl_vector * f, gsl_matrix * J);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    <span class="keywordtype">void</span> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a1221d2aacdd4ec15f8604ec526e500a4">printSignal</a>(<span class="keyword">const</span> gsl_vector * x, <span class="keywordtype">void</span> * param, <span class="keywordtype">float</span> resolution = 0.25);</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;  }</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html">  116</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1OptimizePick.html">OptimizePick</a></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;  {</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizePick_1_1Data.html">  120</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html">Data</a></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    {</div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">  123</a></span>&#160;      std::vector&lt;double&gt; <a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">positions</a>;</div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">  124</a></span>&#160;      std::vector&lt;double&gt; <a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">signal</a>;</div>
<div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizePick_1_1Data.html#a94e1162876121fe33025ea03b5edb343">  126</a></span>&#160;      std::vector&lt;PeakShape&gt; <a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#a94e1162876121fe33025ea03b5edb343">peaks</a>;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;</div>
<div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="structOpenMS_1_1OptimizePick_1_1Data.html#a221f0a0f0ba583ad1920b8c7eb2dbed1">  128</a></span>&#160;      <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OptimizationFunctions::PenaltyFactors</a> <a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#a221f0a0f0ba583ad1920b8c7eb2dbed1">penalties</a>;</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    };</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a1b5cab7fcfe8ad040fb7363dd14913f1">  134</a></span>&#160;    <span class="keyword">typedef</span> std::vector&lt;Peak1D&gt; <a class="code" href="classOpenMS_1_1OptimizePick.html#a1b5cab7fcfe8ad040fb7363dd14913f1">RawDataVector</a>;</div>
<div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a335cff277df421bfa0ce8d2412f02134">  136</a></span>&#160;    <span class="keyword">typedef</span> RawDataVector::iterator <a class="code" href="classOpenMS_1_1OptimizePick.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a>;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a2dff86d91b30ee05eb547abc01ed5131">  140</a></span>&#160;    <a class="code" href="classOpenMS_1_1OptimizePick.html#a2dff86d91b30ee05eb547abc01ed5131">OptimizePick</a>() :</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;      max_iteration_(0),</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      eps_abs_(0),</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;      eps_rel_(0) {}</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    <a class="code" href="classOpenMS_1_1OptimizePick.html">OptimizePick</a>(<span class="keyword">const</span> <span class="keyword">struct</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OptimizationFunctions::PenaltyFactors</a> &amp; penalties_,</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;                 <span class="keyword">const</span> <span class="keywordtype">int</span> max_iteration_,</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;                 <span class="keyword">const</span> <span class="keywordtype">double</span> eps_abs_,</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;                 <span class="keyword">const</span> <span class="keywordtype">double</span> eps_rel_);</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;    ~<a class="code" href="classOpenMS_1_1OptimizePick.html">OptimizePick</a>();</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;</div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#ad26c4154078fd21612ab3f03033775cb">  155</a></span>&#160;    <span class="keyword">inline</span> <span class="keyword">const</span> <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OptimizationFunctions::PenaltyFactors</a> &amp; <a class="code" href="classOpenMS_1_1OptimizePick.html#ad26c4154078fd21612ab3f03033775cb">getPenalties</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> penalties_; }</div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a8ec8a1c17e038e537d08398eeb4314d7">  157</a></span>&#160;    <span class="keyword">inline</span> <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OptimizationFunctions::PenaltyFactors</a> &amp; <a class="code" href="classOpenMS_1_1OptimizePick.html#a8ec8a1c17e038e537d08398eeb4314d7">getPenalties</a>() { <span class="keywordflow">return</span> penalties_; }</div>
<div class="line"><a name="l00159"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a124c4f2b2da566cd87823238ca1101b7">  159</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#a124c4f2b2da566cd87823238ca1101b7">setPenalties</a>(<span class="keyword">const</span> <span class="keyword">struct</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OptimizationFunctions::PenaltyFactors</a> &amp; penalties) { penalties_ = penalties; }</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00162"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#ac6f52ecba2bb619fa215070e6486c77e">  162</a></span>&#160;    <span class="keyword">inline</span> <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1OptimizePick.html#ac6f52ecba2bb619fa215070e6486c77e">getNumberIterations</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> max_iteration_; }</div>
<div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a80531a446500090395d74f7a62f40cff">  164</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> &amp; <a class="code" href="classOpenMS_1_1OptimizePick.html#a80531a446500090395d74f7a62f40cff">getNumberIterations</a>() { <span class="keywordflow">return</span> max_iteration_; }</div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a0eda2287a69d416407ac20013ac5df63">  166</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#a0eda2287a69d416407ac20013ac5df63">setNumberIterations</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> max_iteration) { max_iteration_ = max_iteration; }</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;</div>
<div class="line"><a name="l00169"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a8e66c4bb9601b0c87307512a044930b8">  169</a></span>&#160;    <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1OptimizePick.html#a8e66c4bb9601b0c87307512a044930b8">getMaxAbsError</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> eps_abs_; }</div>
<div class="line"><a name="l00171"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#aa744c79773126814b3f2df53b02e6c03">  171</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">double</span> &amp; <a class="code" href="classOpenMS_1_1OptimizePick.html#aa744c79773126814b3f2df53b02e6c03">getMaxAbsError</a>() { <span class="keywordflow">return</span> eps_abs_; }</div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a9d6ce3c6884623b4bcf7acf1fc3f212f">  173</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#a9d6ce3c6884623b4bcf7acf1fc3f212f">setMaxAbsError</a>(<span class="keywordtype">double</span> eps_abs) { eps_abs_ = eps_abs; }</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;</div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#ac061845432fbff0f67d3212a815ebac9">  176</a></span>&#160;    <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1OptimizePick.html#ac061845432fbff0f67d3212a815ebac9">getMaxRelError</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> eps_rel_; }</div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a4a8cecafd3b1609f089186f57eb58d7f">  178</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">double</span> &amp; <a class="code" href="classOpenMS_1_1OptimizePick.html#a4a8cecafd3b1609f089186f57eb58d7f">getMaxRelError</a>() { <span class="keywordflow">return</span> eps_rel_; }</div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a6d72f377d140f4725e7abf59e64f933f">  180</a></span>&#160;    <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#a6d72f377d140f4725e7abf59e64f933f">setMaxRelError</a>(<span class="keywordtype">double</span> eps_rel) { eps_rel_ = eps_rel; }</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    <span class="keywordtype">void</span> optimize(std::vector&lt;PeakShape&gt; &amp; peaks, Data &amp; data);</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00188"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#af7df305bd35b7978a9c0cd0f838de3d9">  188</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OptimizationFunctions::PenaltyFactors</a> penalties_;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;</div>
<div class="line"><a name="l00191"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#a5d82df812f95e4524ebe5c2bc8fb9d6c">  191</a></span>&#160;    <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#a5d82df812f95e4524ebe5c2bc8fb9d6c">max_iteration_</a>;</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;</div>
<div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#ad1856398408be678d1d922b96896577f">  194</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#ad1856398408be678d1d922b96896577f">eps_abs_</a>;</div>
<div class="line"><a name="l00195"></a><span class="lineno"><a class="line" href="classOpenMS_1_1OptimizePick.html#ae697d70a93e0ca1c77d18a255dee8505">  195</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1OptimizePick.html#ae697d70a93e0ca1c77d18a255dee8505">eps_rel_</a>;</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;<span class="comment">//       /** @brief Returns the squared pearson coefficient.</span></div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;<span class="comment">//         Computes the correlation of the peak and the original data given by the peak enpoints.</span></div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;<span class="comment">//         If the value is near 1, the fitted peakshape and the raw data are expected to be very similar.</span></div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;<span class="comment">//     */</span></div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;<span class="comment">//     double correlate_(const PeakShape&amp; peak,</span></div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;<span class="comment">//                                          double left_endpoint,</span></div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;<span class="comment">//                                          double right_endpoint,Data&amp; data);</span></div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;  };</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;}</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html_a649cc300c964845ccc272fd2229b6ed4"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">OpenMS::OptimizePick::Data::positions</a></div><div class="ttdeci">std::vector&lt; double &gt; positions</div><div class="ttdoc">Positions and intensity values of the raw data. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:123</div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a5d82df812f95e4524ebe5c2bc8fb9d6c"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a5d82df812f95e4524ebe5c2bc8fb9d6c">OpenMS::OptimizePick::max_iteration_</a></div><div class="ttdeci">unsigned int max_iteration_</div><div class="ttdoc">Maximum number of iterations during optimization. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:191</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html">OpenMS::OptimizePick::Data</a></div><div class="ttdef"><b>Definition:</b> OptimizePick.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a6d72f377d140f4725e7abf59e64f933f"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a6d72f377d140f4725e7abf59e64f933f">OpenMS::OptimizePick::setMaxRelError</a></div><div class="ttdeci">void setMaxRelError(double eps_rel)</div><div class="ttdoc">Mutable access to the maximum relative error. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:180</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a9d6ce3c6884623b4bcf7acf1fc3f212f"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a9d6ce3c6884623b4bcf7acf1fc3f212f">OpenMS::OptimizePick::setMaxAbsError</a></div><div class="ttdeci">void setMaxAbsError(double eps_abs)</div><div class="ttdoc">Mutable access to the maximum absolute error. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:173</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a0eda2287a69d416407ac20013ac5df63"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a0eda2287a69d416407ac20013ac5df63">OpenMS::OptimizePick::setNumberIterations</a></div><div class="ttdeci">void setNumberIterations(const int max_iteration)</div><div class="ttdoc">Mutable access to the number of iterations. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:166</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a2dff86d91b30ee05eb547abc01ed5131"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a2dff86d91b30ee05eb547abc01ed5131">OpenMS::OptimizePick::OptimizePick</a></div><div class="ttdeci">OptimizePick()</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:140</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_ae89675bc0b01641aeece694576987c77"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ae89675bc0b01641aeece694576987c77">OpenMS::OptimizationFunctions::PenaltyFactors::~PenaltyFactors</a></div><div class="ttdeci">~PenaltyFactors()</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a8e66c4bb9601b0c87307512a044930b8"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a8e66c4bb9601b0c87307512a044930b8">OpenMS::OptimizePick::getMaxAbsError</a></div><div class="ttdeci">DoubleReal getMaxAbsError() const </div><div class="ttdoc">Non-mutable access to the maximum absolute error. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:169</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_ad586941d523262bc710038ecb19af79e"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ad586941d523262bc710038ecb19af79e">OpenMS::OptimizationFunctions::PenaltyFactors::operator=</a></div><div class="ttdeci">PenaltyFactors &amp; operator=(const PenaltyFactors &amp;p)</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_ad26c4154078fd21612ab3f03033775cb"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#ad26c4154078fd21612ab3f03033775cb">OpenMS::OptimizePick::getPenalties</a></div><div class="ttdeci">struct OptimizationFunctions::PenaltyFactors &amp; getPenalties() const </div><div class="ttdoc">Non-mutable access to the penalty factors. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:155</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html_a221f0a0f0ba583ad1920b8c7eb2dbed1"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html#a221f0a0f0ba583ad1920b8c7eb2dbed1">OpenMS::OptimizePick::Data::penalties</a></div><div class="ttdeci">OptimizationFunctions::PenaltyFactors penalties</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:128</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_ae2acb9d1e3e0cd8ac48b11e58974aca0"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ae2acb9d1e3e0cd8ac48b11e58974aca0">OpenMS::OptimizationFunctions::PenaltyFactors::PenaltyFactors</a></div><div class="ttdeci">PenaltyFactors(const PenaltyFactors &amp;p)</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:75</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_a1b5cab7fcfe8ad040fb7363dd14913f1"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#a1b5cab7fcfe8ad040fb7363dd14913f1">OpenMS::OptimizationFunctions::RawDataVector</a></div><div class="ttdeci">std::vector&lt; Peak1D &gt; RawDataVector</div><div class="ttdoc">Raw data vector type. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:59</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_abb10592f0ea83f824c0a14f4afa95be4"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">OpenMS::OptimizationFunctions::PenaltyFactors::lWidth</a></div><div class="ttdeci">double lWidth</div><div class="ttdoc">Penalty factor for the peak shape&amp;#39;s left width parameter. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_ac061845432fbff0f67d3212a815ebac9"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#ac061845432fbff0f67d3212a815ebac9">OpenMS::OptimizePick::getMaxRelError</a></div><div class="ttdeci">DoubleReal getMaxRelError() const </div><div class="ttdoc">Non-mutable access to the maximum relative error. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:176</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_a335cff277df421bfa0ce8d2412f02134"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">OpenMS::OptimizationFunctions::PeakIterator</a></div><div class="ttdeci">RawDataVector::iterator PeakIterator</div><div class="ttdoc">Raw data iterator type. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:61</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html_a94e1162876121fe33025ea03b5edb343"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html#a94e1162876121fe33025ea03b5edb343">OpenMS::OptimizePick::Data::peaks</a></div><div class="ttdeci">std::vector&lt; PeakShape &gt; peaks</div><div class="ttdoc">This container contains the peak shapes to be optimized. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:126</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_aacf12ce6c8657d87174c792d19c318bf"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">OpenMS::OptimizationFunctions::evaluate</a></div><div class="ttdeci">int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)</div><div class="ttdoc">Driver function for the evaluation of function and jacobian. </div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a4a8cecafd3b1609f089186f57eb58d7f"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a4a8cecafd3b1609f089186f57eb58d7f">OpenMS::OptimizePick::getMaxRelError</a></div><div class="ttdeci">double &amp; getMaxRelError()</div><div class="ttdoc">Mutable access to the maximum relative error. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:178</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_ad1856398408be678d1d922b96896577f"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#ad1856398408be678d1d922b96896577f">OpenMS::OptimizePick::eps_abs_</a></div><div class="ttdeci">double eps_abs_</div><div class="ttdoc">Maximum absolute and relative error used in the optimization. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:194</div></div>
<div class="ttc" id="PeakShape_8h_html"><div class="ttname"><a href="PeakShape_8h.html">PeakShape.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_aa744c79773126814b3f2df53b02e6c03"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#aa744c79773126814b3f2df53b02e6c03">OpenMS::OptimizePick::getMaxAbsError</a></div><div class="ttdeci">double &amp; getMaxAbsError()</div><div class="ttdoc">Mutable access to the maximum absolute error. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:171</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_a3d21e47729faa48b51b02169c9383902"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#a3d21e47729faa48b51b02169c9383902">OpenMS::OptimizationFunctions::residual</a></div><div class="ttdeci">int residual(const gsl_vector *x, void *params, gsl_vector *f)</div><div class="ttdoc">Evaluation of the target function for nonlinear optimization. </div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_a5e9dd75fc35bca3ebe4981821077aebe"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">OpenMS::OptimizationFunctions::PenaltyFactors::pos</a></div><div class="ttdeci">double pos</div><div class="ttdoc">Penalty factor for the peak shape&amp;#39;s position. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:89</div></div>
<div class="ttc" id="Peak1D_8h_html"><div class="ttname"><a href="Peak1D_8h.html">Peak1D.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a80531a446500090395d74f7a62f40cff"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a80531a446500090395d74f7a62f40cff">OpenMS::OptimizePick::getNumberIterations</a></div><div class="ttdeci">unsigned int &amp; getNumberIterations()</div><div class="ttdoc">Mutable access to the number of iterations. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:164</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_a478a632c0b5a363e215061428eee1a1c"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">OpenMS::OptimizationFunctions::PenaltyFactors::rWidth</a></div><div class="ttdeci">double rWidth</div><div class="ttdoc">Penalty factor for the peak shape&amp;#39;s right width parameter. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:93</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_a906050fe19898e6bdaad3442b61c7199"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#a906050fe19898e6bdaad3442b61c7199">OpenMS::OptimizationFunctions::jacobian</a></div><div class="ttdeci">int jacobian(const gsl_vector *x, void *params, gsl_matrix *J)</div><div class="ttdoc">Compute the Jacobian of the residual, where each row of the matrix corresponds to a point in the data...</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OpenMS::OptimizationFunctions::PenaltyFactors</a></div><div class="ttdoc">Class for the penalty factors used during the optimization. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:71</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_ac6f52ecba2bb619fa215070e6486c77e"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#ac6f52ecba2bb619fa215070e6486c77e">OpenMS::OptimizePick::getNumberIterations</a></div><div class="ttdeci">UInt getNumberIterations() const </div><div class="ttdoc">Non-mutable access to the number of iterations. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:162</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html_afc5753d32dfc3c8659038a3e1ac68c86"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">OpenMS::OptimizePick::Data::signal</a></div><div class="ttdeci">std::vector&lt; double &gt; signal</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a335cff277df421bfa0ce8d2412f02134"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a335cff277df421bfa0ce8d2412f02134">OpenMS::OptimizePick::PeakIterator</a></div><div class="ttdeci">RawDataVector::iterator PeakIterator</div><div class="ttdoc">Raw data iterator type. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:136</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_ae697d70a93e0ca1c77d18a255dee8505"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#ae697d70a93e0ca1c77d18a255dee8505">OpenMS::OptimizePick::eps_rel_</a></div><div class="ttdeci">double eps_rel_</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:195</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_a1221d2aacdd4ec15f8604ec526e500a4"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#a1221d2aacdd4ec15f8604ec526e500a4">OpenMS::OptimizationFunctions::printSignal</a></div><div class="ttdeci">void printSignal(const gsl_vector *x, void *param, float resolution=0.25)</div><div class="ttdoc">Print all peak shapes. </div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html">OpenMS::OptimizePick</a></div><div class="ttdoc">This class provides the non-linear optimization of the peak parameters. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a8ec8a1c17e038e537d08398eeb4314d7"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a8ec8a1c17e038e537d08398eeb4314d7">OpenMS::OptimizePick::getPenalties</a></div><div class="ttdeci">struct OptimizationFunctions::PenaltyFactors &amp; getPenalties()</div><div class="ttdoc">Mutable access to the penalty factors. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a124c4f2b2da566cd87823238ca1101b7"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a124c4f2b2da566cd87823238ca1101b7">OpenMS::OptimizePick::setPenalties</a></div><div class="ttdeci">void setPenalties(const struct OptimizationFunctions::PenaltyFactors &amp;penalties)</div><div class="ttdoc">Mutable access to the penalty factors. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:159</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_ab17f5ae37b7817df4c3479ebfa6f3f48"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#ab17f5ae37b7817df4c3479ebfa6f3f48">OpenMS::OptimizationFunctions::PenaltyFactors::PenaltyFactors</a></div><div class="ttdeci">PenaltyFactors()</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_a1b5cab7fcfe8ad040fb7363dd14913f1"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#a1b5cab7fcfe8ad040fb7363dd14913f1">OpenMS::OptimizePick::RawDataVector</a></div><div class="ttdeci">std::vector&lt; Peak1D &gt; RawDataVector</div><div class="ttdoc">Raw data vector type. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:134</div></div>
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