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<a href="FeatureFinderAlgorithm_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>
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<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>
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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: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</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_FEATUREFINDERALGORITHM_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_FEATUREFINDERALGORITHM_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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.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="FeatureFinder_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="keyword">namespace </span>OpenMS</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;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;  <span class="comment">// forward declaration</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;  <span class="keyword">class </span>FeatureFinder;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;</div>
<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html">   50</a></span>&#160;  <span class="keyword">struct </span>OPENMS_DLLAPI <a class="code" href="structOpenMS_1_1Summary.html">Summary</a></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;  {</div>
<div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">   52</a></span>&#160;    std::map&lt;String, UInt&gt; <a class="code" href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">exception</a>;    <span class="comment">//count exceptions</span></div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#ac68ce663c906bb967bc90b60c355d009">   53</a></span>&#160;    <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="structOpenMS_1_1Summary.html#ac68ce663c906bb967bc90b60c355d009">no_exceptions</a>;</div>
<div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">   54</a></span>&#160;    std::map&lt;String, UInt&gt; <a class="code" href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">mz_model</a>;    <span class="comment">//count used mz models</span></div>
<div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">   55</a></span>&#160;    std::map&lt;float, UInt&gt; <a class="code" href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">mz_stdev</a>;    <span class="comment">//count used mz standard deviations</span></div>
<div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">   56</a></span>&#160;    std::vector&lt;UInt&gt; <a class="code" href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">charge</a>;     <span class="comment">//count used charges</span></div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">   57</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> corr_mean, corr_max, <a class="code" href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">corr_min</a>;       <span class="comment">//boxplot for correlation</span></div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="structOpenMS_1_1Summary.html#aefa4763f220277411c5ad31d828d05f4">   60</a></span>&#160;    <a class="code" href="structOpenMS_1_1Summary.html#aefa4763f220277411c5ad31d828d05f4">Summary</a>() :</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;      no_exceptions(0),</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;      corr_mean(0),</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;      corr_max(0),</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;      corr_min(1)</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;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;  };</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType&gt;</div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html">   74</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a> :</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;  {</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">   79</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakType&gt;</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a>;</div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ae6ccfa631b2715c7d67fb491ebb6c422">   81</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classdouble.html">MapType::CoordinateType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ae6ccfa631b2715c7d67fb491ebb6c422">CoordinateType</a>;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ad697cf4c925820f74c876c10d0cb5570">   83</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#a221361082f641c3fccc58e9bc66aeee1">MapType::IntensityType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ad697cf4c925820f74c876c10d0cb5570">IntensityType</a>;</div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">   85</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;FeatureType&gt;</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ab3f8cbcd66e98d658af1c794192988a8">   88</a></span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ab3f8cbcd66e98d658af1c794192988a8">FeatureFinderAlgorithm</a>() :</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(<span class="stringliteral">&quot;FeatureFinderAlgorithm&quot;</span>),</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>(0),</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>(0),</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>(0)</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;    }</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"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a636289874783c1efc7df5cb0359007d5">   97</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a636289874783c1efc7df5cb0359007d5">~FeatureFinderAlgorithm</a>()</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    {</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    }</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a0619c54ebc0b33a02eb71f942bb00111">registerChildren</a>();</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</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_1FeatureFinderAlgorithm.html#a18954417d3124a8095783ea13dc6d00b">run</a>() = 0;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#abe2fce5095efeecbcd815817430058e0">  112</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#abe2fce5095efeecbcd815817430058e0">getDefaultParameters</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      <span class="keywordflow">return</span> this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;    }</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;</div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a7e594645b8460e600602bb64a8403537">  118</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a7e594645b8460e600602bb64a8403537">setData</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a> &amp; map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapType</a> &amp; features, <a class="code" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> &amp; ff)</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">  120</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a> = &amp;map;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a> = &amp;features;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a> = &amp;ff;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;    }</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">  130</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">setSeeds</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapType</a> &amp; seeds)</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;    {</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      <span class="keywordflow">if</span> (seeds.size() != 0)</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;      {</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;The used feature detection algorithm does not support user-specified seed lists!&quot;</span>);</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      }</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;    }</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;</div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">  141</a></span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">  144</a></span>&#160;    <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMapType</a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">  147</a></span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;<span class="keyword">private</span>:</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_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a> &amp; <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ad1421d0b78da35a1d0802a3394af0868">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a> &amp;);</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">  155</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ab3f8cbcd66e98d658af1c794192988a8">FeatureFinderAlgorithm</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a> &amp;);</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;  };</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;}</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;<span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHM_H</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_ac68ce663c906bb967bc90b60c355d009"><div class="ttname"><a href="structOpenMS_1_1Summary.html#ac68ce663c906bb967bc90b60c355d009">OpenMS::Summary::no_exceptions</a></div><div class="ttdeci">UInt no_exceptions</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a5f09052343ef99616ad653897841ce3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">OpenMS::FeatureFinderAlgorithm::features_</a></div><div class="ttdeci">FeatureMapType * features_</div><div class="ttdoc">Output data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:144</div></div>
<div class="ttc" id="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_1FeatureFinderAlgorithm_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeatureFinderAlgorithm::ff_</a></div><div class="ttdeci">FeatureFinder * ff_</div><div class="ttdoc">Pointer to the calling FeatureFinder that is used to access the feature flags. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_ae6ccfa631b2715c7d67fb491ebb6c422"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#ae6ccfa631b2715c7d67fb491ebb6c422">OpenMS::FeatureFinderAlgorithm::CoordinateType</a></div><div class="ttdeci">MapType::CoordinateType CoordinateType</div><div class="ttdoc">Coordinate/Position type of peaks. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:81</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a365c5cf67d48519199fe00cb5688d628"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">OpenMS::FeatureFinderAlgorithm::map_</a></div><div class="ttdeci">const MapType * map_</div><div class="ttdoc">Input data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:141</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_ab0eab2f15ba67b518f5f559aed34f033"><div class="ttname"><a href="structOpenMS_1_1Summary.html#ab0eab2f15ba67b518f5f559aed34f033">OpenMS::Summary::mz_model</a></div><div class="ttdeci">std::map&lt; String, UInt &gt; mz_model</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:54</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_ab3f8cbcd66e98d658af1c794192988a8"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#ab3f8cbcd66e98d658af1c794192988a8">OpenMS::FeatureFinderAlgorithm::FeatureFinderAlgorithm</a></div><div class="ttdeci">FeatureFinderAlgorithm()</div><div class="ttdoc">default constructor </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:88</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html">OpenMS::FeatureFinderAlgorithm</a></div><div class="ttdoc">Abstract base class for FeatureFinder algorithms. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_adf6f376e844058d129ce8ba868276643"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">OpenMS::FeatureFinderAlgorithm::MapType</a></div><div class="ttdeci">MSExperiment&lt; PeakType &gt; MapType</div><div class="ttdoc">Input map type. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:79</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_abe2fce5095efeecbcd815817430058e0"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#abe2fce5095efeecbcd815817430058e0">OpenMS::FeatureFinderAlgorithm::getDefaultParameters</a></div><div class="ttdeci">virtual Param getDefaultParameters() const </div><div class="ttdoc">Returns the default parameters. Reimplment. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:112</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a221361082f641c3fccc58e9bc66aeee1"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a221361082f641c3fccc58e9bc66aeee1">OpenMS::MSExperiment::IntensityType</a></div><div class="ttdeci">PeakType::IntensityType IntensityType</div><div class="ttdoc">Intenstiy type of peaks. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_ad1421d0b78da35a1d0802a3394af0868"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#ad1421d0b78da35a1d0802a3394af0868">OpenMS::FeatureFinderAlgorithm::operator=</a></div><div class="ttdeci">FeatureFinderAlgorithm &amp; operator=(const FeatureFinderAlgorithm &amp;)</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a0e61382ce2ca1e403a6cf0a540a205af"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a0e61382ce2ca1e403a6cf0a540a205af">OpenMS::Summary::mz_stdev</a></div><div class="ttdeci">std::map&lt; float, UInt &gt; mz_stdev</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:55</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="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalArgument_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalArgument.html">OpenMS::Exception::IllegalArgument</a></div><div class="ttdoc">A method or algorithm argument contains illegal values. </div><div class="ttdef"><b>Definition:</b> Exception.h:634</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a21ea3968c35235b6b3cd78a2190280d9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">OpenMS::FeatureFinderAlgorithm::FeatureMapType</a></div><div class="ttdeci">FeatureMap&lt; FeatureType &gt; FeatureMapType</div><div class="ttdoc">Output feature type. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:85</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a08ed2a5eb5d54783930d2b81ec1a54f3"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a08ed2a5eb5d54783930d2b81ec1a54f3">OpenMS::Summary::exception</a></div><div class="ttdeci">std::map&lt; String, UInt &gt; exception</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a18954417d3124a8095783ea13dc6d00b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a18954417d3124a8095783ea13dc6d00b">OpenMS::FeatureFinderAlgorithm::run</a></div><div class="ttdeci">virtual void run()=0</div><div class="ttdoc">Main method that implements the actual algorithm. </div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a9b56db69bb4951352b93c88462ff1ebf"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a9b56db69bb4951352b93c88462ff1ebf">OpenMS::Summary::charge</a></div><div class="ttdeci">std::vector&lt; UInt &gt; charge</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:56</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html"><div class="ttname"><a href="structOpenMS_1_1Summary.html">OpenMS::Summary</a></div><div class="ttdoc">Summary of fitting results. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a0619c54ebc0b33a02eb71f942bb00111"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a0619c54ebc0b33a02eb71f942bb00111">OpenMS::FeatureFinderAlgorithm::registerChildren</a></div><div class="ttdeci">static void registerChildren()</div><div class="ttdoc">register all derived classes here (see FeatureFinderAlgorithm_impl.h) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm_impl.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a683154793bbb12ab5d16db81209606b0"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">OpenMS::FeatureFinderAlgorithm::setSeeds</a></div><div class="ttdeci">virtual void setSeeds(const FeatureMapType &amp;seeds)</div><div class="ttdoc">Sets a reference to the calling FeatureFinder. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:130</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="FeatureFinder_8h_html"><div class="ttname"><a href="FeatureFinder_8h.html">FeatureFinder.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_a71cb946fce0c9a14ad9c16ce9b12478d"><div class="ttname"><a href="structOpenMS_1_1Summary.html#a71cb946fce0c9a14ad9c16ce9b12478d">OpenMS::Summary::corr_min</a></div><div class="ttdeci">DoubleReal corr_min</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a636289874783c1efc7df5cb0359007d5"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a636289874783c1efc7df5cb0359007d5">OpenMS::FeatureFinderAlgorithm::~FeatureFinderAlgorithm</a></div><div class="ttdeci">virtual ~FeatureFinderAlgorithm()</div><div class="ttdoc">destructor </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_ad697cf4c925820f74c876c10d0cb5570"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#ad697cf4c925820f74c876c10d0cb5570">OpenMS::FeatureFinderAlgorithm::IntensityType</a></div><div class="ttdeci">MapType::IntensityType IntensityType</div><div class="ttdoc">Intensity type of peaks. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html">OpenMS::FeatureFinder</a></div><div class="ttdoc">The main feature finder class. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:57</div></div>
<div class="ttc" id="structOpenMS_1_1Summary_html_aefa4763f220277411c5ad31d828d05f4"><div class="ttname"><a href="structOpenMS_1_1Summary.html#aefa4763f220277411c5ad31d828d05f4">OpenMS::Summary::Summary</a></div><div class="ttdeci">Summary()</div><div class="ttdoc">Initial values. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:60</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="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a7e594645b8460e600602bb64a8403537"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a7e594645b8460e600602bb64a8403537">OpenMS::FeatureFinderAlgorithm::setData</a></div><div class="ttdeci">void setData(const MapType &amp;map, FeatureMapType &amp;features, FeatureFinder &amp;ff)</div><div class="ttdoc">Sets a reference to the calling FeatureFinder. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:118</div></div>
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