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<a href="FeatureFinder__impl_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
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<div class="line"><a name="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="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>
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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_FEATUREFINDER_IMPL_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_FEATUREFINDER_IMPL_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="Factory_8h.html">OpenMS/CONCEPT/Factory.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;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureFinderAlgorithm__impl_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm_impl.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;  <span class="comment">// This is documented in the declaration, see FeatureFinder.h</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</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="l00047"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c">   47</a></span>&#160;  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c">FeatureFinder::run</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; algorithm_name, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakType&gt;</a> &amp; input_map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;FeatureType&gt;</a> &amp; features, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; param, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;FeatureType&gt;</a> &amp; seeds)</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="comment">// Nothing to do if there is no data</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;    <span class="keywordflow">if</span> ((algorithm_name != <span class="stringliteral">&quot;mrm&quot;</span> &amp;&amp; input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>()) || (algorithm_name == <span class="stringliteral">&quot;mrm&quot;</span> &amp;&amp; input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">getChromatograms</a>().empty()))</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">   52</span>&#160;      features.<a class="code" href="classOpenMS_1_1FeatureMap.html#a7b5660c6199fa9d5fef65974c7e3e733">clear</a>(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;      <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    }</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;    <span class="comment">// check input</span></div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    {</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;      <span class="comment">// We need updated ranges =&gt; check number of peaks</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;      <span class="keywordflow">if</span> (algorithm_name != <span class="stringliteral">&quot;mrm&quot;</span> &amp;&amp; input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#aac09407a6369916d487f3a83527b8398">getSize</a>() == 0)</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;      {</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;FeatureFinder needs updated ranges on input map. Aborting.&quot;</span>);</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;      }</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;      <span class="comment">// We need MS1 data only =&gt; check levels</span></div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;      <span class="keywordflow">if</span> (algorithm_name != <span class="stringliteral">&quot;mrm&quot;</span> &amp;&amp; (input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#adbc1e31b95b2364ef4b3b1ba94b0aa8d">getMSLevels</a>().size() != 1 || input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#adbc1e31b95b2364ef4b3b1ba94b0aa8d">getMSLevels</a>()[0] != 1))</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;        <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;FeatureFinder can only operate on MS level 1 data. Please do not use MS/MS data. Aborting.&quot;</span>);</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;      }</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;      <span class="comment">//Check if the peaks are sorted according to m/z</span></div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;      <span class="keywordflow">if</span> (!input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a50d19782103ccc00edaabfba88dd2598">isSorted</a>(<span class="keyword">true</span>))</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">   73</span>&#160;        <a class="code" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a> &lt;&lt; <span class="stringliteral">&quot;Input map is not sorted by RT and m/z! This is done now, before applying the algorithm!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;        input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac518a80bea4f92fd700b235a12146658">sortSpectra</a>(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;        input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#aa679772c8c6b65183102bc220ebe7870">sortChromatograms</a>(<span class="keyword">true</span>);</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="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s &lt; input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++s)</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;        <span class="keywordflow">if</span> (input_map[s].empty())</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        <span class="keywordflow">if</span> (input_map[s][0].getMZ() &lt; 0)</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">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;FeatureFinder can only operate on spectra that contain peaks with positive m/z values. Filter the data accordingly beforehand! Aborting.&quot;</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">   86</span>&#160;    }</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;    <span class="comment">// initialize</span></div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <span class="keywordflow">if</span> (algorithm_name != <span class="stringliteral">&quot;mrm&quot;</span> &amp;&amp; algorithm_name != <span class="stringliteral">&quot;centroided&quot;</span>)</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    {</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <span class="comment">// Resize peak flag vector</span></div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinder.html#a9d6dd782a9b8b7ced5a44f7bc29f5ecc">flags_</a>.resize(input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</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;        <a class="code" href="classOpenMS_1_1FeatureFinder.html#a9d6dd782a9b8b7ced5a44f7bc29f5ecc">flags_</a>[i].assign(input_map[i].size(), <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">UNUSED</a>);</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      }</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    }</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;    <span class="comment">// do the work</span></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="keywordflow">if</span> (algorithm_name != <span class="stringliteral">&quot;none&quot;</span>)</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;    {</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;</a> * algorithm = <a class="code" href="classOpenMS_1_1Factory.html">Factory&lt;FeatureFinderAlgorithm&lt;PeakType, FeatureType&gt;</a> &gt;::create(algorithm_name);</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;      algorithm-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;      algorithm-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a7e594645b8460e600602bb64a8403537">setData</a>(input_map, features, *<span class="keyword">this</span>);</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;      algorithm-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">setSeeds</a>(seeds);</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;      algorithm-&gt;<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a18954417d3124a8095783ea13dc6d00b">run</a>();</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;      <span class="keyword">delete</span>(algorithm);</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="l00110"></a><span class="lineno">  110</span>&#160;    <span class="keywordflow">if</span> (algorithm_name != <span class="stringliteral">&quot;mrm&quot;</span>)   <span class="comment">// mrm  works on chromatograms; the next section is only for conventional data</span></div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    {</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      <span class="comment">//report RT apex spectrum index and native ID for each feature</span></div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; features.size(); ++i)</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      {</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;        <span class="comment">//index</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum_index = input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">RTBegin</a>(features[i].getRT()) - input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>();</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        features[i].setMetaValue(<span class="stringliteral">&quot;spectrum_index&quot;</span>, spectrum_index);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        <span class="comment">//native id</span></div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        <span class="keywordflow">if</span> (spectrum_index &lt; input_map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>())</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        {</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;          <a class="code" href="classOpenMS_1_1String.html">String</a> native_id = input_map[spectrum_index].getNativeID();</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;          features[i].setMetaValue(<span class="stringliteral">&quot;spectrum_native_id&quot;</span>, native_id);</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;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;        {</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;          std::cerr &lt;&lt; <span class="stringliteral">&quot;FeatureFinderAlgorithm_impl, line=&quot;</span> &lt;&lt; __LINE__ &lt;&lt; <span class="stringliteral">&quot;; FixMe this cannot be, but happens&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;        }</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="l00133"></a><span class="lineno">  133</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;<span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_IMPL_H</span></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_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">OpenMS::FeatureFinderDefs::UNUSED</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:63</div></div>
<div class="ttc" id="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"><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_1Factory_html"><div class="ttname"><a href="classOpenMS_1_1Factory.html">OpenMS::Factory</a></div><div class="ttdoc">Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...</div><div class="ttdef"><b>Definition:</b> Factory.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a2387033802383edbdc95f9bbb12a707e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">OpenMS::MSExperiment::begin</a></div><div class="ttdeci">Iterator begin()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac518a80bea4f92fd700b235a12146658"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac518a80bea4f92fd700b235a12146658">OpenMS::MSExperiment::sortSpectra</a></div><div class="ttdeci">void sortSpectra(bool sort_mz=true)</div><div class="ttdoc">Sorts the data points by retention time. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:575</div></div>
<div class="ttc" id="FeatureFinderAlgorithm__impl_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithm__impl_8h.html">FeatureFinderAlgorithm_impl.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &amp;param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="LogStream_8h_html_aea3f57d6dcc5b4ac957e2679e87dde27"><div class="ttname"><a href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a></div><div class="ttdeci">#define LOG_WARN</div><div class="ttdoc">Macro if a warning, a piece of information which should be read by the user, should be logged...</div><div class="ttdef"><b>Definition:</b> LogStream.h:451</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_adb2f0f3e10754ca4dc7be677f15689a3"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">OpenMS::MSExperiment::RTBegin</a></div><div class="ttdeci">ConstIterator RTBegin(CoordinateType rt) const </div><div class="ttdoc">Fast search for spectrum range begin. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:349</div></div>
<div class="ttc" id="Factory_8h_html"><div class="ttname"><a href="Factory_8h.html">Factory.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_aa679772c8c6b65183102bc220ebe7870"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aa679772c8c6b65183102bc220ebe7870">OpenMS::MSExperiment::sortChromatograms</a></div><div class="ttdeci">void sortChromatograms(bool sort_rt=true)</div><div class="ttdoc">Sorts the data points of the chromatograms by m/z. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:594</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_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="classOpenMS_1_1FeatureFinder_html_a001d4adf21652ff6cdd58efe56e4fb1c"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html#a001d4adf21652ff6cdd58efe56e4fb1c">OpenMS::FeatureFinder::run</a></div><div class="ttdeci">void run(const String &amp;algorithm_name, MSExperiment&lt; PeakType &gt; &amp;input_map, FeatureMap&lt; FeatureType &gt; &amp;features, const Param &amp;param, const FeatureMap&lt; FeatureType &gt; &amp;seeds)</div><div class="ttdoc">Executes the FeatureFinder using the given algorithm. </div><div class="ttdef"><b>Definition:</b> FeatureFinder_impl.h:47</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_1MSExperiment_html_adbc1e31b95b2364ef4b3b1ba94b0aa8d"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#adbc1e31b95b2364ef4b3b1ba94b0aa8d">OpenMS::MSExperiment::getMSLevels</a></div><div class="ttdeci">const std::vector&lt; UInt &gt; &amp; getMSLevels() const </div><div class="ttdoc">returns an array of MS levels </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:561</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="classOpenMS_1_1MSExperiment_html_a50d19782103ccc00edaabfba88dd2598"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a50d19782103ccc00edaabfba88dd2598">OpenMS::MSExperiment::isSorted</a></div><div class="ttdeci">bool isSorted(bool check_mz=true) const </div><div class="ttdoc">Checks if all spectra are sorted with respect to ascending RT. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:613</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="classOpenMS_1_1MSExperiment_html_aac09407a6369916d487f3a83527b8398"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aac09407a6369916d487f3a83527b8398">OpenMS::MSExperiment::getSize</a></div><div class="ttdeci">UInt64 getSize() const </div><div class="ttdoc">returns the total number of peaks </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:555</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="classOpenMS_1_1FeatureFinder_html_a9d6dd782a9b8b7ced5a44f7bc29f5ecc"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html#a9d6dd782a9b8b7ced5a44f7bc29f5ecc">OpenMS::FeatureFinder::flags_</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; Flag &gt; &gt; flags_</div><div class="ttdoc">Container for flags attached to input data. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac6e61de369e994009e36f344f99c15ad"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">OpenMS::MSExperiment::empty</a></div><div class="ttdeci">bool empty() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a7b5660c6199fa9d5fef65974c7e3e733"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a7b5660c6199fa9d5fef65974c7e3e733">OpenMS::FeatureMap::clear</a></div><div class="ttdeci">void clear(bool clear_meta_data=true)</div><div class="ttdoc">Clears all data and meta data. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:468</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>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a02fccfed86a20f8bd0f6b98c23fadb2e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a02fccfed86a20f8bd0f6b98c23fadb2e">OpenMS::MSExperiment::getChromatograms</a></div><div class="ttdeci">const std::vector&lt; MSChromatogram&lt; ChromatogramPeakType &gt; &gt; &amp; getChromatograms() const </div><div class="ttdoc">returns the chromatogram list </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:768</div></div>
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