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<a href="TraceFitter_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>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<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>&#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>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<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>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<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">// $Maintainer: Stephan Aiche$</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Stephan Aiche, Marc Sturm $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_TRACEFITTER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_TRACEFITTER_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="LogStream_8h.html">OpenMS/CONCEPT/LogStream.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureFinderAlgorithmPickedHelperStructs_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_rng.h&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_vector.h&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_multifit_nlin.h&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_blas.h&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="l00051"></a><span class="lineno">   51</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakType&gt;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html">   62</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> :</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;  {</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#a113c8da1eadad990ed5c5c3fbfd5c2df">   68</a></span>&#160;    <a class="code" href="classOpenMS_1_1TraceFitter.html#a113c8da1eadad990ed5c5c3fbfd5c2df">TraceFitter</a>() :</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(<span class="stringliteral">&quot;TraceFitter&quot;</span>)</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    {</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;max_iteration&quot;</span>, 500, <span class="stringliteral">&quot;Maximum number of iterations using by Levenberg-Marquardt algorithm.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;epsilon_abs&quot;</span>, 0.0001, <span class="stringliteral">&quot;Absolute error used by the Levenberg-Marquardt algorithm.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;epsilon_rel&quot;</span>, 0.0001, <span class="stringliteral">&quot;Relative error used by the Levenberg-Marquardt algorithm.&quot;</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">&quot;advanced&quot;</span>));</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    }</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#abdd45634136f9a86f16cf14743c903e0">   77</a></span>&#160;    <a class="code" href="classOpenMS_1_1TraceFitter.html#abdd45634136f9a86f16cf14743c903e0">TraceFitter</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> &amp; source) :</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(source),</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a>(source.<a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a>),</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a>(source.<a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a>),</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a>(source.<a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</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;    }</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">   86</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> &amp; <a class="code" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> &amp; source)</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    {</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">DefaultParamHandler::operator=</a>(source);</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a> = source.<a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a>  = source.<a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a>;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a> = source.<a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>();</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      <span class="keywordflow">return</span> *<span class="keyword">this</span>;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    }</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#a73cdd08b53019fc20c8b8a0119222988">   98</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#a73cdd08b53019fc20c8b8a0119222988">~TraceFitter</a>()</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    {</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    }</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">fit</a>(<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt;PeakType&gt;</a> &amp; traces) = 0;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a10ddb3b8cc795c598f76db017b9ca322">getLowerRTBound</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a0ab9bd668829f0fc9608bd56560ac1ae">getUpperRTBound</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">getHeight</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#aa1e7b6cd685312da3c92644d8fe71aac">getFWHM</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">computeTheoretical</a>(<span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt;PeakType&gt;</a> &amp; trace, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) = 0;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#a2190523e8d48946faff97a41131fcf92">checkMinimalRTSpan</a>(<span class="keyword">const</span> std::pair&lt;DoubleReal, DoubleReal&gt; &amp; rt_bounds, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> min_rt_span) = 0;</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#af72d2c9ae5ecbd8b8d4605fbbef613cc">checkMaximalRTSpan</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> max_rt_span) = 0;</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">getFeatureIntensityContribution</a>() = 0;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#ab67d38bd9a15db565531cc729df77924">getGnuplotFormula</a>(<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt;PeakType&gt;</a> <span class="keyword">const</span> &amp; trace, <span class="keyword">const</span> <span class="keywordtype">char</span> function_name, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> baseline, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> rt_shift) = 0;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#aa392ac4217e565f35cfe6ec42edd4e19">printState_</a>(<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> iter, gsl_multifit_fdfsolver * s) = 0;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">  182</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    {</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a> = this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;max_iteration&quot;</span>);</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a> = this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;epsilon_abs&quot;</span>);</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a> = this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;epsilon_rel&quot;</span>);</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;    }</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#a6ce8e085d31fd86c925b6e8805f2facd">getOptimizedParameters_</a>(gsl_multifit_fdfsolver * s) = 0;</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;</div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">  199</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">optimize_</a>(<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt;PeakType&gt;</a> &amp; traces, <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_params, <span class="keywordtype">double</span> x_init[],</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;                   <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> (* <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="l00201"></a><span class="lineno">  201</span>&#160;                   <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> (* <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="l00202"></a><span class="lineno">  202</span>&#160;                   <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> (* <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="l00203"></a><span class="lineno">  203</span>&#160;    {</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;      <span class="keyword">const</span> gsl_multifit_fdfsolver_type * T;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;      gsl_multifit_fdfsolver * s;</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;      <span class="keyword">const</span> <span class="keywordtype">size_t</span> data_count = traces.<a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">getPeakCount</a>();</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="comment">// gsl always expects N&gt;=p or default gsl error handler invoked,</span></div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;      <span class="comment">// cause Jacobian be rectangular M x N with M&gt;=N</span></div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;      <span class="keywordflow">if</span> (data_count &lt; num_params) <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">&quot;UnableToFit-FinalSet&quot;</span>, <span class="stringliteral">&quot;Skipping feature, gsl always expects N&gt;=p&quot;</span>);</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;      gsl_multifit_function_fdf func;</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;      gsl_vector_view x = gsl_vector_view_array(x_init, num_params);</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;      gsl_rng_env_setup();</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;      func.f = (<a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a3d21e47729faa48b51b02169c9383902">residual</a>);</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;      func.df = (<a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a906050fe19898e6bdaad3442b61c7199">jacobian</a>);</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;      func.fdf = (<a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>);</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;      func.n = data_count;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      func.p = num_params;</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;      func.params = &amp;traces;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      T = gsl_multifit_fdfsolver_lmsder;</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;      s = gsl_multifit_fdfsolver_alloc(T, data_count, num_params);</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;      gsl_multifit_fdfsolver_set(s, &amp;func, &amp;x.vector);</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> iter = 0;</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;      <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> gsl_status_;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;      <span class="keywordflow">do</span></div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;      {</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;        iter++;</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;        gsl_status_ = gsl_multifit_fdfsolver_iterate(s);</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;        <a class="code" href="classOpenMS_1_1TraceFitter.html#aa392ac4217e565f35cfe6ec42edd4e19">printState_</a>(iter, s);</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;        <span class="keywordflow">if</span> (gsl_status_) <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;        gsl_status_ = gsl_multifit_test_delta(s-&gt;dx, s-&gt;x, <a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a>, <a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a>);</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;      }</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;      <span class="keywordflow">while</span> (gsl_status_ == GSL_CONTINUE &amp;&amp; iter &lt; <a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a>);</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;      <span class="comment">// get the parameters out of the fdfsolver</span></div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;      <a class="code" href="classOpenMS_1_1TraceFitter.html#a6ce8e085d31fd86c925b6e8805f2facd">getOptimizedParameters_</a>(s);</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;      gsl_multifit_fdfsolver_free(s);</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;    }</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">  247</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a>;</div>
<div class="line"><a name="l00249"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">  249</a></span>&#160;    <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> <a class="code" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a>;</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;  };</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;}</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;<span class="preprocessor">#endif // #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_RTFITTING_H</span></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a93a8dc068053ec44ee7e45864ef969f7"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a></div><div class="ttdeci">const double k</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a642bbbd0de05e84147e701bfeaf188a2"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">OpenMS::TraceFitter::getFeatureIntensityContribution</a></div><div class="ttdeci">virtual DoubleReal getFeatureIntensityContribution()=0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_ab67d38bd9a15db565531cc729df77924"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#ab67d38bd9a15db565531cc729df77924">OpenMS::TraceFitter::getGnuplotFormula</a></div><div class="ttdeci">virtual String getGnuplotFormula(FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt; PeakType &gt; const &amp;trace, const char function_name, const DoubleReal baseline, const DoubleReal rt_shift)=0</div></div>
<div class="ttc" id="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_1Param_html_a432099944e11263aa20aaf8ea1389790"><div class="ttname"><a href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">OpenMS::Param::setValue</a></div><div class="ttdeci">void setValue(const String &amp;key, const DataValue &amp;value, const String &amp;description=&quot;&quot;, const StringList &amp;tags=StringList())</div><div class="ttdoc">Sets a value. </div></div>
<div class="ttc" id="classOpenMS_1_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_1TraceFitter_html_a5430cfbbe8dd77a2709a1442ca25a9db"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">OpenMS::TraceFitter::epsilon_rel_</a></div><div class="ttdeci">DoubleReal epsilon_rel_</div><div class="ttdoc">Relative error. </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a69d24e3ee5021aebcec9f61015fb5313"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">OpenMS::TraceFitter::optimize_</a></div><div class="ttdeci">void optimize_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt; PeakType &gt; &amp;traces, const Size num_params, double x_init[], Int(*residual)(const gsl_vector *x, void *params, gsl_vector *f), Int(*jacobian)(const gsl_vector *x, void *params, gsl_matrix *J), Int(*evaluate)(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J))</div><div class="ttdef"><b>Definition:</b> TraceFitter.h:199</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a776f7572fc4f466e9527ca233471920d"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">OpenMS::TraceFitter::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> TraceFitter.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::DefaultParamHandler::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">Container for current parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:148</div></div>
<div class="ttc" id="FeatureFinderAlgorithmPickedHelperStructs_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithmPickedHelperStructs_8h.html">FeatureFinderAlgorithmPickedHelperStructs.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a></div><div class="ttdoc">Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:153</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html">OpenMS::TraceFitter</a></div><div class="ttdoc">Abstract fitter for RT profile fitting. </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a2190523e8d48946faff97a41131fcf92"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a2190523e8d48946faff97a41131fcf92">OpenMS::TraceFitter::checkMinimalRTSpan</a></div><div class="ttdeci">virtual bool checkMinimalRTSpan(const std::pair&lt; DoubleReal, DoubleReal &gt; &amp;rt_bounds, const DoubleReal min_rt_span)=0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a10ddb3b8cc795c598f76db017b9ca322"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a10ddb3b8cc795c598f76db017b9ca322">OpenMS::TraceFitter::getLowerRTBound</a></div><div class="ttdeci">virtual DoubleReal getLowerRTBound() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a6ce8e085d31fd86c925b6e8805f2facd"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a6ce8e085d31fd86c925b6e8805f2facd">OpenMS::TraceFitter::getOptimizedParameters_</a></div><div class="ttdeci">virtual void getOptimizedParameters_(gsl_multifit_fdfsolver *s)=0</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="group__Concept_html_gae113cb41304c6692c7bf5d0624dc6f0f"><div class="ttname"><a href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">OpenMS::SignedSize</a></div><div class="ttdeci">ptrdiff_t SignedSize</div><div class="ttdoc">Signed Size type e.g. used as pointer difference. </div><div class="ttdef"><b>Definition:</b> Types.h:151</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces_html_a34c827b6d53a8c171b233332bfe4d634"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces::getPeakCount</a></div><div class="ttdeci">Size getPeakCount() const </div><div class="ttdoc">Returns the peak count of all traces. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:163</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a65120f4f127d69944775cd5aae06709f"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">OpenMS::TraceFitter::computeTheoretical</a></div><div class="ttdeci">virtual DoubleReal computeTheoretical(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace&lt; PeakType &gt; &amp;trace, Size k)=0</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></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_1TraceFitter_html_ac9fed0a961481c6439dfc3b32422d89c"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">OpenMS::TraceFitter::operator=</a></div><div class="ttdeci">virtual TraceFitter &amp; operator=(const TraceFitter &amp;source)</div><div class="ttdoc">assignment operator </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue &amp; getValue(const String &amp;key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_abdd45634136f9a86f16cf14743c903e0"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#abdd45634136f9a86f16cf14743c903e0">OpenMS::TraceFitter::TraceFitter</a></div><div class="ttdeci">TraceFitter(const TraceFitter &amp;source)</div><div class="ttdoc">copy constructor </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_af72d2c9ae5ecbd8b8d4605fbbef613cc"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#af72d2c9ae5ecbd8b8d4605fbbef613cc">OpenMS::TraceFitter::checkMaximalRTSpan</a></div><div class="ttdeci">virtual bool checkMaximalRTSpan(const DoubleReal max_rt_span)=0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a0eac57e7b543d5084b9cdbb940fd031c"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">OpenMS::TraceFitter::getHeight</a></div><div class="ttdeci">virtual DoubleReal getHeight() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_ae81a426a24a2be1e601bb7e8a946d6a6"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">OpenMS::TraceFitter::max_iterations_</a></div><div class="ttdeci">SignedSize max_iterations_</div><div class="ttdoc">Maximum number of iterations. </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:249</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_aa1e7b6cd685312da3c92644d8fe71aac"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#aa1e7b6cd685312da3c92644d8fe71aac">OpenMS::TraceFitter::getFWHM</a></div><div class="ttdeci">virtual DoubleReal getFWHM() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a0ab9bd668829f0fc9608bd56560ac1ae"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a0ab9bd668829f0fc9608bd56560ac1ae">OpenMS::TraceFitter::getUpperRTBound</a></div><div class="ttdeci">virtual DoubleReal getUpperRTBound() const =0</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_a5f86b59b547048311dd50df5fb6d3bb5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">OpenMS::StringList::create</a></div><div class="ttdeci">static StringList create(const String &amp;list, const char splitter= ',')</div><div class="ttdoc">Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a113c8da1eadad990ed5c5c3fbfd5c2df"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a113c8da1eadad990ed5c5c3fbfd5c2df">OpenMS::TraceFitter::TraceFitter</a></div><div class="ttdeci">TraceFitter()</div><div class="ttdoc">default constructor. </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:68</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="classOpenMS_1_1TraceFitter_html_a7b2aeb3c8d1a4fd03c5843af07474735"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">OpenMS::TraceFitter::fit</a></div><div class="ttdeci">virtual void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces&lt; PeakType &gt; &amp;traces)=0</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_a73cdd08b53019fc20c8b8a0119222988"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a73cdd08b53019fc20c8b8a0119222988">OpenMS::TraceFitter::~TraceFitter</a></div><div class="ttdeci">virtual ~TraceFitter()</div><div class="ttdoc">destructor </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:98</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_aa392ac4217e565f35cfe6ec42edd4e19"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#aa392ac4217e565f35cfe6ec42edd4e19">OpenMS::TraceFitter::printState_</a></div><div class="ttdeci">virtual void printState_(SignedSize iter, gsl_multifit_fdfsolver *s)=0</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="LogStream_8h_html"><div class="ttname"><a href="LogStream_8h.html">LogStream.h</a></div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="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="classOpenMS_1_1TraceFitter_html_a7914deb9fb6c8400f80b3532aa2e7b73"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">OpenMS::TraceFitter::epsilon_abs_</a></div><div class="ttdeci">DoubleReal epsilon_abs_</div><div class="ttdoc">Absolute error. </div><div class="ttdef"><b>Definition:</b> TraceFitter.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_ae6b6d68036a573a44f6609460ba2dfb6"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">OpenMS::DefaultParamHandler::operator=</a></div><div class="ttdeci">virtual DefaultParamHandler &amp; operator=(const DefaultParamHandler &amp;rhs)</div><div class="ttdoc">Assignment operator. </div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1TraceFitter_html_ae740893fa17f26ea27e6f2383d72cb40"><div class="ttname"><a href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">OpenMS::TraceFitter::getCenter</a></div><div class="ttdeci">virtual DoubleReal getCenter() const =0</div></div>
<div class="ttc" id="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="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a></div><div class="ttdoc">Helper struct for mass traces used in FeatureFinderAlgorithmPicked. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmPickedHelperStructs.h:83</div></div>
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