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<a href="SimpleSeeder_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>
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<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">// $Maintainer: Clemens Groepl$</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">#include &lt;<a class="code" href="FeatureFinder_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h</a>&gt;</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;</div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SIMPLESEEDER_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SIMPLESEEDER_H</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.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="FeaFiModule_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeaFiModule.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SignalToNoiseEstimatorMedian_8h.html">OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.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;algorithm&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor">#include &lt;iostream&gt;</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;</div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;{</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</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="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html">   61</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1SimpleSeeder.html">SimpleSeeder</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a>&lt;PeakType, FeatureType&gt;,</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <span class="keyword">public</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</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;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#a79ea228cdc8755284e64dd9f625170a3">   66</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule&lt;PeakType, FeatureType&gt;</a> <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a79ea228cdc8755284e64dd9f625170a3">Base</a>;</div>
<div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#adf6f376e844058d129ce8ba868276643">   67</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_1SimpleSeeder.html#adf6f376e844058d129ce8ba868276643">MapType</a>;</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;</div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#a26be3e303b6eebf9cf1a0d2835fb4390">   70</a></span>&#160;    <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a26be3e303b6eebf9cf1a0d2835fb4390">SimpleSeeder</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakType&gt;</a> * map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;FeatureType&gt;</a> * features, <a class="code" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * ff) :</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;      <a class="code" href="classOpenMS_1_1FeaFiModule.html">Base</a>(map, features, ff),</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;      <a class="code" href="classOpenMS_1_1SimpleSeeder.html#aef7436a220692b5b863db4e9d8b870a3">initialized_</a>(false)</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    {</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a>(<span class="stringliteral">&quot;SimpleSeeder&quot;</span>);</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</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;min_intensity&quot;</span>, 0.0, <span class="stringliteral">&quot;Absolute value for the minimum intensity required for a seed.&quot;</span>);</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;min_intensity&quot;</span>, 0.0);</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</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;signal_to_noise&quot;</span>, 10.0, <span class="stringliteral">&quot;Minimal required SignalToNoise (S/N) ratio for a seed.&quot;</span>);</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">setMinFloat</a>(<span class="stringliteral">&quot;signal_to_noise&quot;</span>, 0.0);</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;      <span class="comment">//this-&gt;subsections_.push_back(&quot;SignalToNoiseEstimationParameter&quot;);</span></div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;      <a class="code" href="classOpenMS_1_1SignalToNoiseEstimatorMedian.html">SignalToNoiseEstimatorMedian&lt;typename MapType::SpectrumType&gt;</a> sne;              <span class="comment">// make sure this is the same as in pick()!</span></div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">insert</a>(<span class="stringliteral">&quot;SignalToNoiseEstimationParameter:&quot;</span>, sne.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a>());</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;      this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>();</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="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#aff93a5cc657a9ed140db72b42ec1d655">   89</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1SimpleSeeder.html#aff93a5cc657a9ed140db72b42ec1d655">~SimpleSeeder</a>()</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;    }</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">   94</a></span>&#160;    <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">nextSeed</a>()</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;      <span class="keywordflow">if</span> (!<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aef7436a220692b5b863db4e9d8b870a3">initialized_</a>)</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;        <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">initialize_</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;      <span class="comment">// while the current peak is either already used or in a feature jump to next peak...</span></div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      <span class="keywordflow">while</span> (<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a> != <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.end() &amp;&amp; this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">getPeakFlag</a>(*<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a>) == <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c">USED</a>)</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;      {</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        ++<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a>;</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;      }</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;      <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a> == <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.end())</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;        <span class="comment">// if no seed was found:</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.empty()) <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">NoSuccessor</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a>());</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">NoSuccessor</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, *(<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a> - 1));</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      }</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a> - <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.begin());</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;      <span class="comment">// set flag</span></div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">getPeakFlag</a>(*<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a>) = <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c">USED</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;      <span class="keywordflow">return</span> *(<a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a>++);</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    }         <span class="comment">// nextSeed</span></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;<span class="keyword">protected</span>:</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"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">  124</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">initialize_</a>()</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;    {</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;      <span class="comment">// determine mininum intensity and signal-to-noise parameter for last seed</span></div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;      <span class="keyword">typename</span> FeatureType::IntensityType noise_threshold  = 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;min_intensity&quot;</span>);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;      <span class="keyword">typename</span> FeatureType::IntensityType sn  = 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;signal_to_noise&quot;</span>);</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;<span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;<span class="preprocessor"></span>      std::cout &lt;&lt; <span class="stringliteral">&quot;Intensity threshold: &quot;</span> &lt;&lt; noise_threshold &lt;&lt; std::endl;</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;      std::cout &lt;&lt; <span class="stringliteral">&quot;S/N: &quot;</span> &lt;&lt; sn &lt;&lt; std::endl;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      <span class="comment">// fill indices_ for peaks above noise threshold and S/N</span></div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;      <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a> tmp = std::make_pair(0, 0);</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;      <span class="keywordflow">if</span> (sn == 0)</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;      {</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;        <span class="keywordflow">while</span> (tmp.first &lt; (*this-&gt;map_).size())</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;        {</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;          tmp.second = 0;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;          <span class="keywordflow">while</span> (tmp.second &lt; (*this-&gt;map_)[tmp.first].size())</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;          {</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;            <span class="keywordflow">if</span> (this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(tmp) &gt; noise_threshold)</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;            {</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;              <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.push_back(tmp);</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;            }</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;            ++tmp.second;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;          }</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;          ++tmp.first;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;        }</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;      }</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;      {</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;        <a class="code" href="classOpenMS_1_1SignalToNoiseEstimatorMedian.html">SignalToNoiseEstimatorMedian&lt;typename MapType::SpectrumType&gt;</a> estimator;</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;        <a class="code" href="classOpenMS_1_1Param.html">Param</a> param(this-&gt;<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">copy</a>(<span class="stringliteral">&quot;SignalToNoiseEstimationParameter:&quot;</span>, <span class="keyword">true</span>));</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;        estimator.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param);</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;        <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MapType::ConstIterator</a> it = (*this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>).begin(); it != (*this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a>).end(); ++it)</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;        {</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;          estimator.<a class="code" href="classOpenMS_1_1SignalToNoiseEstimator.html#a2fba92bbe2385c5e632a4a802b7e49ae">init</a>(it-&gt;begin(), it-&gt;end());</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;          tmp.second = 0;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;          <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MapType::SpectrumType::ConstIterator</a> spec = it-&gt;begin(); spec != it-&gt;end(); ++spec)</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;          {</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;            <span class="keywordflow">if</span> (estimator.<a class="code" href="classOpenMS_1_1SignalToNoiseEstimator.html#a504423b06b9d69e88d2ff68c9050889a">getSignalToNoise</a>(spec) &gt; sn &amp;&amp; this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a>(tmp) &gt; noise_threshold)</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;            {</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;              <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.push_back(tmp);</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;            }</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            ++tmp.second;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;          }</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;          ++tmp.first;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;        }</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;      }</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;<span class="preprocessor">#ifdef DEBUG_FEATUREFINDER</span></div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;<span class="preprocessor"></span>      std::cout &lt;&lt; <span class="stringliteral">&quot;Number of peaks above threshold (&quot;</span> &lt;&lt; noise_threshold   &lt;&lt; <span class="stringliteral">&quot;) and S/N (&quot;</span> &lt;&lt; sn &lt;&lt; <span class="stringliteral">&quot;): &quot;</span> &lt;&lt; <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.size() &lt;&lt; std::endl;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;      <span class="comment">// sort index vector by intensity of peaks (highest first)</span></div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;      sort(<a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.begin(), <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.end(),</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;           <a class="code" href="namespaceOpenMS.html#a74e80d32be63268d8a46039297e18cc6">reverseComparator</a>(<a class="code" href="structOpenMS_1_1Internal_1_1IntensityLess.html">Internal::IntensityLess&lt;Base&gt;</a>(*<span class="keyword">this</span>))</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;           );</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;      <span class="comment">// progress logger</span></div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;      this-&gt;<a class="code" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-&gt;<a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.size(), <span class="stringliteral">&quot;FeatureFinder&quot;</span>);</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      <a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a> = <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>.begin();</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      <a class="code" href="classOpenMS_1_1SimpleSeeder.html#aef7436a220692b5b863db4e9d8b870a3">initialized_</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;    }</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;</div>
<div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">  193</a></span>&#160;    std::vector&lt;IndexPair&gt; <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">indices_</a>;</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;</div>
<div class="line"><a name="l00196"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">  196</a></span>&#160;    std::vector&lt;IndexPair&gt;::const_iterator <a class="code" href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">current_peak_</a>;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;</div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SimpleSeeder.html#aef7436a220692b5b863db4e9d8b870a3">  199</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1SimpleSeeder.html#aef7436a220692b5b863db4e9d8b870a3">initialized_</a>;</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a10182f992ebcabc30c6381a0ca717b0f">SimpleSeeder</a>();</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    <a class="code" href="classOpenMS_1_1SimpleSeeder.html">SimpleSeeder</a> &amp; <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a423e81ab59850dc5bfc289f6194c166d">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SimpleSeeder.html">SimpleSeeder</a> &amp;);</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;    <a class="code" href="classOpenMS_1_1SimpleSeeder.html#a10182f992ebcabc30c6381a0ca717b0f">SimpleSeeder</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SimpleSeeder.html">SimpleSeeder</a> &amp;);</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">// class SimpleSeeder</span></div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;} <span class="comment">// namespace OpenMS</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;<span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SIMPLESEEDER_H</span></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseEstimator_html_a504423b06b9d69e88d2ff68c9050889a"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimator.html#a504423b06b9d69e88d2ff68c9050889a">OpenMS::SignalToNoiseEstimator::getSignalToNoise</a></div><div class="ttdeci">virtual double getSignalToNoise(const PeakIterator &amp;data_point)</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimator.h:130</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html">OpenMS::FeaFiModule</a></div><div class="ttdoc">Implements a module of the FeatureFinder algorithm. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a6aca068dd3cf1a6c7e78091c9bdae961"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">OpenMS::SimpleSeeder::initialize_</a></div><div class="ttdeci">void initialize_()</div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:124</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_aaee0bfd850887fdc58115cead9e9b8b9"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">OpenMS::FeatureFinderDefs::IndexPair</a></div><div class="ttdeci">IsotopeCluster::IndexPair IndexPair</div><div class="ttdoc">Index to peak consisting of two UInts (scan index / peak index) </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:54</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html_a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c">OpenMS::FeatureFinderDefs::USED</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:63</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_1DefaultParamHandler_html_a02f02fa9832ca3e8d47c575a39803a2a"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">OpenMS::DefaultParamHandler::getDefaults</a></div><div class="ttdeci">const Param &amp; getDefaults() const </div><div class="ttdoc">Non-mutable access to the default parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a79ea228cdc8755284e64dd9f625170a3"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a79ea228cdc8755284e64dd9f625170a3">OpenMS::SimpleSeeder::Base</a></div><div class="ttdeci">FeaFiModule&lt; PeakType, FeatureType &gt; Base</div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_ad2dc775a73f96e91dd97c61c39e4e7b8"><div class="ttname"><a href="classOpenMS_1_1Param.html#ad2dc775a73f96e91dd97c61c39e4e7b8">OpenMS::Param::insert</a></div><div class="ttdeci">void insert(const String &amp;prefix, const Param &amp;param)</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a4698fa90bfbdd5729e0e25c62345ff0d"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">OpenMS::FeaFiModule::getPeakIntensity</a></div><div class="ttdeci">IntensityType getPeakIntensity(const FeatureFinderDefs::IndexPair &amp;index) const </div><div class="ttdoc">Returns the intensity of a peak. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:190</div></div>
<div class="ttc" id="classOpenMS_1_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="FeaFiModule_8h_html"><div class="ttname"><a href="FeaFiModule_8h.html">FeaFiModule.h</a></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_1SimpleSeeder_html_adf6f376e844058d129ce8ba868276643"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#adf6f376e844058d129ce8ba868276643">OpenMS::SimpleSeeder::MapType</a></div><div class="ttdeci">MSExperiment&lt; PeakType &gt; MapType</div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:67</div></div>
<div class="ttc" id="namespaceOpenMS_html_a74e80d32be63268d8a46039297e18cc6"><div class="ttname"><a href="namespaceOpenMS.html#a74e80d32be63268d8a46039297e18cc6">OpenMS::reverseComparator</a></div><div class="ttdeci">ReverseComparator&lt; Cmp &gt; reverseComparator(Cmp const &amp;cmp)</div><div class="ttdoc">Make-function to create a ReverseComparator from another comparator without the need to specify the t...</div><div class="ttdef"><b>Definition:</b> ComparatorUtils.h:261</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a9101eb2633f34b26a1436b3d8e1e7522"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">OpenMS::SimpleSeeder::nextSeed</a></div><div class="ttdeci">IndexPair nextSeed()</div><div class="ttdoc">return the next seed </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:94</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="classOpenMS_1_1FeaFiModule_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeaFiModule::ff_</a></div><div class="ttdeci">FeatureFinder * ff_</div><div class="ttdoc">Pointer to the calling FeatureFinder that is used to access the feature flags and report progress...</div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:415</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderDefs_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderDefs.html">OpenMS::FeatureFinderDefs</a></div><div class="ttdoc">The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...</div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1FeaFiModule_html_a365c5cf67d48519199fe00cb5688d628"><div class="ttname"><a href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">OpenMS::FeaFiModule::map_</a></div><div class="ttdeci">const MapType * map_</div><div class="ttdoc">Input data pointer. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:411</div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a423e81ab59850dc5bfc289f6194c166d"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a423e81ab59850dc5bfc289f6194c166d">OpenMS::SimpleSeeder::operator=</a></div><div class="ttdeci">SimpleSeeder &amp; operator=(const SimpleSeeder &amp;)</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_aa14c9407cdca7351284985b4ceddc466"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#aa14c9407cdca7351284985b4ceddc466">OpenMS::SimpleSeeder::current_peak_</a></div><div class="ttdeci">std::vector&lt; IndexPair &gt;::const_iterator current_peak_</div><div class="ttdoc">Points to the next peak in the peak vector. </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:196</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a25319a96118d2373efc5af9c8679b98b"><div class="ttname"><a href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">OpenMS::Param::copy</a></div><div class="ttdeci">Param copy(const String &amp;prefix, bool remove_prefix=false) const </div><div class="ttdoc">Returns a new Param object containing all entries that start with prefix. </div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a10182f992ebcabc30c6381a0ca717b0f"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a10182f992ebcabc30c6381a0ca717b0f">OpenMS::SimpleSeeder::SimpleSeeder</a></div><div class="ttdeci">SimpleSeeder()</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseEstimator_html_a2fba92bbe2385c5e632a4a802b7e49ae"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimator.html#a2fba92bbe2385c5e632a4a802b7e49ae">OpenMS::SignalToNoiseEstimator::init</a></div><div class="ttdeci">virtual void init(const PeakIterator &amp;it_begin, const PeakIterator &amp;it_end)</div><div class="ttdoc">Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimat...</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimator.h:111</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_1SimpleSeeder_html_aff93a5cc657a9ed140db72b42ec1d655"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#aff93a5cc657a9ed140db72b42ec1d655">OpenMS::SimpleSeeder::~SimpleSeeder</a></div><div class="ttdeci">virtual ~SimpleSeeder()</div><div class="ttdoc">destructor </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:89</div></div>
<div class="ttc" id="structOpenMS_1_1Internal_1_1IntensityLess_html"><div class="ttname"><a href="structOpenMS_1_1Internal_1_1IntensityLess.html">OpenMS::Internal::IntensityLess</a></div><div class="ttdoc">Comparator that allows to compare the indices of two peaks by their intensity. </div><div class="ttdef"><b>Definition:</b> FeaFiModule.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html">OpenMS::FeatureFinderDefs::NoSuccessor</a></div><div class="ttdoc">Exception that is thrown if a method an invalid IndexPair is given. </div><div class="ttdef"><b>Definition:</b> FeatureFinderDefs.h:66</div></div>
<div class="ttc" id="SignalToNoiseEstimatorMedian_8h_html"><div class="ttname"><a href="SignalToNoiseEstimatorMedian_8h.html">SignalToNoiseEstimatorMedian.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_aef7436a220692b5b863db4e9d8b870a3"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#aef7436a220692b5b863db4e9d8b870a3">OpenMS::SimpleSeeder::initialized_</a></div><div class="ttdeci">bool initialized_</div><div class="ttdoc">Flag that indicates of the indices are initialized. </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:199</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_1SignalToNoiseEstimatorMedian_html"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimatorMedian.html">OpenMS::SignalToNoiseEstimatorMedian</a></div><div class="ttdoc">Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram ba...</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimatorMedian.h:71</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_1SimpleSeeder_html_a26be3e303b6eebf9cf1a0d2835fb4390"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a26be3e303b6eebf9cf1a0d2835fb4390">OpenMS::SimpleSeeder::SimpleSeeder</a></div><div class="ttdeci">SimpleSeeder(const MSExperiment&lt; PeakType &gt; *map, FeatureMap&lt; FeatureType &gt; *features, FeatureFinder *ff)</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_aee0a1a68d0fab63eefa6e14010b4a7f0"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">OpenMS::MSExperiment::ConstIterator</a></div><div class="ttdeci">std::vector&lt; SpectrumType &gt;::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af1c45ecd71b5041b70319249e8e73591"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">OpenMS::ProgressLogger::startProgress</a></div><div class="ttdeci">void startProgress(SignedSize begin, SignedSize end, const String &amp;label) const </div><div class="ttdoc">Initializes the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a8852277abd03220cc7b80d6c1bed6fed"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">OpenMS::ProgressLogger::setProgress</a></div><div class="ttdeci">void setProgress(SignedSize value) const </div><div class="ttdoc">Sets the current progress. </div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html_a706b87b86a3e85488364af294e5a31fa"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html#a706b87b86a3e85488364af294e5a31fa">OpenMS::SimpleSeeder::indices_</a></div><div class="ttdeci">std::vector&lt; IndexPair &gt; indices_</div><div class="ttdoc">contains the indizes </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:193</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html">OpenMS::FeatureFinder</a></div><div class="ttdoc">The main feature finder class. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a77d37f2e1c12e8bd33ea0e660a89e927"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">OpenMS::DefaultParamHandler::setName</a></div><div class="ttdeci">void setName(const String &amp;name)</div><div class="ttdoc">Mutable access to the name. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinder_html_a91adbb58dfeb79d2b5d78c1047f406c9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinder.html#a91adbb58dfeb79d2b5d78c1047f406c9">OpenMS::FeatureFinder::getPeakFlag</a></div><div class="ttdeci">const Flag &amp; getPeakFlag(const IndexPair &amp;index) const </div><div class="ttdoc">Returns a non-mutable reference to a peak flag. </div><div class="ttdef"><b>Definition:</b> FeatureFinder.h:91</div></div>
<div class="ttc" id="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SimpleSeeder_html"><div class="ttname"><a href="classOpenMS_1_1SimpleSeeder.html">OpenMS::SimpleSeeder</a></div><div class="ttdoc">Simple seeding class that uses the strongest peak as next seed. </div><div class="ttdef"><b>Definition:</b> SimpleSeeder.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_aadc7a8536eb15f8c6fa05eefca0e25be"><div class="ttname"><a href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">OpenMS::Param::setMinFloat</a></div><div class="ttdeci">void setMinFloat(const String &amp;key, DoubleReal min)</div><div class="ttdoc">Sets the minimum value for the floating point or floating point list parameter key. </div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a2802c591e6d7fd3fd9cc35f5e875d0ba"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">OpenMS::DefaultParamHandler::defaultsToParam_</a></div><div class="ttdeci">void defaultsToParam_()</div><div class="ttdoc">Updates the parameters after the defaults have been set in the constructor. </div></div>
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