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<li class="navelem"><a class="el" href="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_9f700962877a340cb515a8f4e78fa50c.html">TRANSFORMATIONS</a></li><li class="navelem"><a class="el" href="dir_37e9c1b52d0b253b62f883ccdf65930c.html">FEATUREFINDER</a></li> </ul>
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<div class="title">FeatureFinderAlgorithmSH.h</div> </div>
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<a href="FeatureFinderAlgorithmSH_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> <span class="comment">// --------------------------------------------------------------------------</span></div>
28
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
29
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
30
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
31
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
32
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
33
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
34
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
35
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
36
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
37
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
38
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
39
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
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<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
41
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
42
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
43
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
44
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
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<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
46
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
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<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <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="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
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<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
50
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
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<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
52
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
53
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
54
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
55
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
56
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
57
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Florian Zeller $</span></div>
58
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Florian Zeller $</span></div>
59
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
60
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
61
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMSH_H</span></div>
62
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMSH_H</span></div>
63
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
64
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="FeatureFinderAlgorithmSHCtrl_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmSHCtrl.h</a>></span></div>
65
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="FeatureFinderAlgorithm_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h</a>></span></div>
66
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div>
67
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include "boost/shared_ptr.hpp"</span></div>
68
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div>
69
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">namespace </span>OpenMS</div>
70
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div>
71
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keyword">template</span> <<span class="keyword">class</span> PeakType, <span class="keyword">class</span> FeatureType></div>
72
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html"> 102</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html">FeatureFinderAlgorithmSH</a> :</div>
73
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><PeakType, FeatureType>,</div>
74
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keyword">public</span> <a class="code" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></div>
75
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  {</div>
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<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
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<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> <span class="keyword">public</span>:</div>
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<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a2f89be2feec82f5414aedc09e488420b"> 108</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">FeatureFinderAlgorithm<PeakType, FeatureType>::MapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a2f89be2feec82f5414aedc09e488420b">MapType</a>; <span class="comment">// MSExperiment</span></div>
79
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#abb9911ee4d024e85861f29bbbd0a63ef"> 109</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureFinderAlgorithm<PeakType, FeatureType>::FeatureMapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#abb9911ee4d024e85861f29bbbd0a63ef">FeatureMapType</a>;</div>
80
<div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#ae4e0f0c176662a323a6a64d29ff986dd"> 110</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MapType::SpectrumType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a>;</div>
81
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
82
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::features_</a>;</div>
83
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
84
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a27120a1be410ba8c6fba4fc9fcbe57c2"> 114</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a27120a1be410ba8c6fba4fc9fcbe57c2">FeatureFinderAlgorithmSH</a>() :</div>
85
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><<a class="code" href="classOpenMS_1_1Peak2D.html">PeakType</a>, FeatureType>()</div>
86
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  {</div>
87
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
88
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  this-><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">"centroiding:active"</span>, <span class="stringliteral">"false"</span>, <span class="stringliteral">"MS1 data centroid data"</span>);</div>
89
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"centroiding:active"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
90
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
91
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  this-><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">"ms1:precursor_detection_scan_levels"</span>, <a class="code" href="classOpenMS_1_1IntList.html#ac244d9a257aab1a24c1a622ccacab745">IntList::create</a>(1), <span class="stringliteral">"Precursor detection scan levels"</span>);</div>
92
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
93
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  this-><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">"ms1:max_inter_scan_distance"</span>, 0, <span class="stringliteral">"MS1 max inter scan distance"</span>); <span class="comment">// was 0.1</span></div>
94
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"ms1:max_inter_scan_distance"</span>, 0); <span class="comment">// Markus needs to clarify this parameter</span></div>
95
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
96
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  this-><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">"ms1:tr_resolution"</span>, 0.01, <span class="stringliteral">"MS1 LC retention time resolution"</span>); <span class="comment">// seems to have no effect</span></div>
97
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  this-><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">"ms1:tr_resolution"</span>, 0);</div>
98
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
99
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  this-><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">"ms1:intensity_threshold"</span>, 1000.0, <span class="stringliteral">"FT peak detect MS1 intensity min threshold"</span>);</div>
100
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  this-><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">"ms1:intensity_threshold"</span>, 0);</div>
101
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
102
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  this-><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">"ms1:max_inter_scan_rt_distance"</span>, 0.1, <span class="stringliteral">"MS1 max inter scan distance"</span>); <span class="comment">// seems to have no effect</span></div>
103
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  this-><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">"ms1:max_inter_scan_rt_distance"</span>, 0);</div>
104
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
105
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  this-><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">"ms1:min_nb_cluster_members"</span>, 4, <span class="stringliteral">"FT peak detect MS1 min nb peak members"</span>);</div>
106
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"ms1:min_nb_cluster_members"</span>, 0);</div>
107
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
108
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  this-><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">"ms1:detectable_isotope_factor"</span>, 0.05, <span class="stringliteral">"Detectable isotope factor"</span>);</div>
109
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  this-><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">"ms1:detectable_isotope_factor"</span>, 0);</div>
110
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
111
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  this-><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">"ms1:intensity_cv"</span>, 0.9, <span class="stringliteral">"IntensityCV"</span>);</div>
112
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  this-><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">"ms1:intensity_cv"</span>, 0);</div>
113
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
114
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  this-><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">"centroiding:window_width"</span>, 5, <span class="stringliteral">"Centroid window width"</span>);</div>
115
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"centroiding:window_width"</span>, 1);</div>
116
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
117
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  this-><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">"centroiding:absolute_isotope_mass_precision"</span>, 0.01, <span class="stringliteral">"Absolute isotope mass precision (Da)"</span>);</div>
118
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  this-><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">"centroiding:absolute_isotope_mass_precision"</span>, 0.0);</div>
119
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
120
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  this-><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">"centroiding:relative_isotope_mass_precision"</span>, 10.0, <span class="stringliteral">"Relative isotope mass precision"</span>);</div>
121
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  this-><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">"centroiding:relative_isotope_mass_precision"</span>, 0.0);</div>
122
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
123
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  this-><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">"centroiding:minimal_peak_height"</span>, 0.0, <span class="stringliteral">"Minimal peak height"</span>);</div>
124
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  this-><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">"centroiding:minimal_peak_height"</span>, 0.0);</div>
125
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
126
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  this-><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">"centroiding:min_ms_signal_intensity"</span>, 50.0, <span class="stringliteral">"Minimal Centroid MS Signal Intensity"</span>);</div>
127
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  this-><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">"centroiding:min_ms_signal_intensity"</span>, 0.0);</div>
128
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
129
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  this-><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">"ms1:retention_time_tolerance"</span>, 0.5, <span class="stringliteral">"MS1 retention time tolerance (minutes)"</span>);</div>
130
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  this-><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">"ms1:retention_time_tolerance"</span>, 0.0);</div>
131
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
132
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  this-><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">"ms1:mz_tolerance"</span>, 0.0, <span class="stringliteral">"MS1 m/z tolerance (ppm)"</span>);</div>
133
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  this-><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">"ms1:mz_tolerance"</span>, 0.0);</div>
134
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
135
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  this-><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">"ms1_feature_merger:active"</span>, <span class="stringliteral">"true"</span>, <span class="stringliteral">"Activation of MS1 feature merging post processing"</span>);</div>
136
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">setValidStrings</a>(<span class="stringliteral">"ms1_feature_merger:active"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
137
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
138
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  this-><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">"ms1_feature_merger:tr_resolution"</span>, 0.01, <span class="stringliteral">"MS1 LC retention time resolution"</span>);</div>
139
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  this-><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">"ms1_feature_merger:tr_resolution"</span>, 0.0);</div>
140
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
141
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  this-><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">"ms1_feature_merger:initial_apex_tr_tolerance"</span>, 5.0, <span class="stringliteral">"Initial Apex Tr tolerance"</span>);</div>
142
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  this-><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">"ms1_feature_merger:initial_apex_tr_tolerance"</span>, 0.0);</div>
143
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
144
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  this-><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">"ms1_feature_merger:feature_merging_tr_tolerance"</span>, 1.0, <span class="stringliteral">"MS1 feature Tr merging tolerance"</span>);</div>
145
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  this-><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">"ms1_feature_merger:feature_merging_tr_tolerance"</span>, 0.0);</div>
146
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
147
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  this-><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">"ms1_feature_merger:intensity_variation_percentage"</span>, 25.0, <span class="stringliteral">"Percentage of intensity variation between LC border peaks"</span>);</div>
148
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  this-><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">"ms1_feature_merger:intensity_variation_percentage"</span>, 0.0);</div>
149
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">setMaxFloat</a>(<span class="stringliteral">"ms1_feature_merger:intensity_variation_percentage"</span>, 100.0);</div>
150
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
151
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  this-><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">"ms1_feature_merger:ppm_tolerance_for_mz_clustering"</span>, 10.0, <span class="stringliteral">"PPM value for the m/z clustering of merging candidates"</span>);</div>
152
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  this-><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">"ms1_feature_merger:ppm_tolerance_for_mz_clustering"</span>, 0.0);</div>
153
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
154
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
155
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  this-><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">"ms1_feature_selection_options:start_elution_window"</span>, 0.0, <span class="stringliteral">"start elution window (minutes)"</span>);</div>
156
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  this-><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">"ms1_feature_selection_options:start_elution_window"</span>, 0.0);</div>
157
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
158
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  this-><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">"ms1_feature_selection_options:end_elution_window"</span>, 180.0, <span class="stringliteral">"end elution window (minutes)"</span>);</div>
159
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  this-><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">"ms1_feature_selection_options:end_elution_window"</span>, 0.0);</div>
160
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
161
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  this-><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">"ms1_feature_selection_options:mz_range_min"</span>, 0.0, <span class="stringliteral">"MS1 feature mz range min"</span>);</div>
162
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  this-><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">"ms1_feature_selection_options:mz_range_min"</span>, 0.0);</div>
163
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
164
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  this-><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">"ms1_feature_selection_options:mz_range_max"</span>, 2000.0, <span class="stringliteral">"MS1 feature mz range max"</span>);</div>
165
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  this-><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">"ms1_feature_selection_options:mz_range_max"</span>, 0.0);</div>
166
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
167
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  this-><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">"ms1_feature_selection_options:chrg_range_min"</span>, 1, <span class="stringliteral">"MS1 feature CHRG range min"</span>);</div>
168
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"ms1_feature_selection_options:chrg_range_min"</span>, 0);</div>
169
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="comment">// ----------------------------------------------------------------------------------------------------</span></div>
170
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  this-><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">"ms1_feature_selection_options:chrg_range_max"</span>, 5, <span class="stringliteral">"MS1 feature CHRG range max"</span>);</div>
171
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"ms1_feature_selection_options:chrg_range_max"</span>, 0);</div>
172
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div>
173
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a> = <span class="keyword">false</span>;</div>
174
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  }</div>
175
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div>
176
<div class="line"><a name="l00206"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aaac70aafcb9fa245ca59256e26a12b88"> 206</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aaac70aafcb9fa245ca59256e26a12b88">getNativeScanId</a>(<a class="code" href="classOpenMS_1_1String.html">String</a> native_id)</div>
177
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  {</div>
178
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div>
179
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start_idx = 0;</div>
180
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordflow">while</span> (!isdigit(native_id[start_idx]) && start_idx < native_id.length())</div>
181
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  {</div>
182
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  ++start_idx;</div>
183
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  }</div>
184
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">if</span> (start_idx == native_id.length())</div>
185
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  {</div>
186
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  std::cout << <span class="stringliteral">"Native id could not be determined: "</span> << native_id;</div>
187
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1InvalidParameter.html">Exception::InvalidParameter</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"Cannot convert native id to unsigned integer"</span>);</div>
188
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  }</div>
189
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span> </div>
190
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> end_idx = start_idx;</div>
191
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordflow">while</span> (isdigit(native_id[end_idx]))</div>
192
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  {</div>
193
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  ++end_idx;</div>
194
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  }</div>
195
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div>
196
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <span class="keywordflow">return</span> native_id.<a class="code" href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">substr</a>(start_idx, end_idx - start_idx).<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
197
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  }</div>
198
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span> </div>
199
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb"> 229</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">run</a>()</div>
200
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  {</div>
201
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  std::cout << <span class="stringliteral">"SuperHirn feature extraction...\n"</span>;</div>
202
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div>
203
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a> = *(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType>::map_</a>);</div>
204
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
205
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <a class="code" href="group__FeatureFinder.html#ga69e18760fc6f819a5a7d5bec62f1c44e">MyMap</a> dummyMap;</div>
206
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <a class="code" href="namespaceOpenMS.html#afc24cc74414bcf1d9129d3e8d4eb1a7f">Vec</a> datavec;</div>
207
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  datavec.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">resize</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
208
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> scanId = 0;</div>
209
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> </div>
210
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="comment">// Ordering by native IDs order by scan numbers</span></div>
211
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="comment">// To achieve the exact same results as the original</span></div>
212
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="comment">// superhirn does, this is necessary.</span></div>
213
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="comment">// However, its is very experimental and will work</span></div>
214
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="comment">// for all data since its based on string comparison.</span></div>
215
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <span class="keywordtype">bool</span> orderByNativeIds = <span class="keyword">false</span>;</div>
216
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> </div>
217
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="comment">// go through map, extract data and store it in a vector of RawData objects</span></div>
218
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> s = 0; s < <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); s++)</div>
219
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  {</div>
220
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a> & spectrum = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>[s];</div>
221
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <span class="keywordtype">double</span> rt = spectrum.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>();</div>
222
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div>
223
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keywordflow">if</span> (orderByNativeIds)</div>
224
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  {</div>
225
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  scanId = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aaac70aafcb9fa245ca59256e26a12b88">getNativeScanId</a>(spectrum.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>());</div>
226
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">if</span> (scanId == 0)</div>
227
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  {</div>
228
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  std::cout << <span class="stringliteral">"Order by native ids not working, turning it off.\n"</span>;</div>
229
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  orderByNativeIds = <span class="keyword">false</span>;</div>
230
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  scanId = 1;</div>
231
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  }</div>
232
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  }</div>
233
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keywordflow">else</span></div>
234
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  {</div>
235
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  scanId++;</div>
236
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  }</div>
237
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span> </div>
238
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  std::vector<double> vmzvals;</div>
239
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  std::vector<double> vintvals;</div>
240
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> </div>
241
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p < spectrum.size(); ++p)</div>
242
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  {</div>
243
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  vmzvals.push_back(spectrum[p].getMZ());</div>
244
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  vintvals.push_back(spectrum[p].getIntensity());</div>
245
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  }</div>
246
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span> </div>
247
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="comment">//RawData* data = new RawData(vmzvals, vintvals);</span></div>
248
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  boost::shared_ptr<RawData> data_ptr(<span class="keyword">new</span> <a class="code" href="classOpenMS_1_1RawData.html">RawData</a>(vmzvals, vintvals));</div>
249
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div>
250
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <a class="code" href="group__FeatureFinder.html#ga69e18760fc6f819a5a7d5bec62f1c44e">MyMap</a> map_ptr(rt / 60, data_ptr);</div>
251
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span> <span class="comment">// m[rt/60.0] = data;</span></div>
252
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> scanIndex = scanId - 1;</div>
253
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  datavec[scanIndex] = map_ptr;</div>
254
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  }</div>
255
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div>
256
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="comment">// apply the SuperHirn FeatureFinder algorithm</span></div>
257
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl.html">FeatureFinderAlgorithmSHCtrl</a> ctrl;</div>
258
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  ctrl.<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl.html#aa8f1a5d0b36919f45750fc2a15089f77">initParams</a>(this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>);</div>
259
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  std::vector<Feature> thefeatures = ctrl.<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl.html#a67c83639cb3ab4285b8bd6bce6a688e5">extractPeaks</a>(datavec);</div>
260
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span> </div>
261
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < thefeatures.size(); ++i)</div>
262
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a>->push_back(thefeatures[i]);</div>
263
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  }</div>
264
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span> </div>
265
<div class="line"><a name="l00295"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aba691daad70f85242bed281fbcd0eca5"> 295</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<Peak1D, Feature></a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aba691daad70f85242bed281fbcd0eca5">create</a>()</div>
266
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  {</div>
267
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a27120a1be410ba8c6fba4fc9fcbe57c2">FeatureFinderAlgorithmSH</a>();</div>
268
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  }</div>
269
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span> </div>
270
<div class="line"><a name="l00300"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#af73fd15708e50e77665070023a09cc87"> 300</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
271
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  {</div>
272
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordflow">return</span> <span class="stringliteral">"superhirn"</span>;</div>
273
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  }</div>
274
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span> </div>
275
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span> <span class="keyword">protected</span>:</div>
276
<div class="line"><a name="l00306"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab"> 306</a></span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MapType</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a>;</div>
277
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span> </div>
278
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  };</div>
279
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> </div>
280
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> }</div>
281
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div>
282
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span> <span class="preprocessor">#endif</span></div>
283
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl_html_a67c83639cb3ab4285b8bd6bce6a688e5"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl.html#a67c83639cb3ab4285b8bd6bce6a688e5">OpenMS::FeatureFinderAlgorithmSHCtrl::extractPeaks</a></div><div class="ttdeci">std::vector< Feature > extractPeaks(Vec datavec)</div></div>
284
<div class="ttc" id="group__FeatureFinder_html_ga69e18760fc6f819a5a7d5bec62f1c44e"><div class="ttname"><a href="group__FeatureFinder.html#ga69e18760fc6f819a5a7d5bec62f1c44e">OpenMS::MyMap</a></div><div class="ttdeci">std::pair< double, boost::shared_ptr< RawData > > MyMap</div><div class="ttdoc">A facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSHCtrl.h:52</div></div>
285
<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>
286
<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>
287
<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 &key, const DataValue &value, const String &description="", const StringList &tags=StringList())</div><div class="ttdoc">Sets a value. </div></div>
288
<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>
289
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_a72fcb26a14f6beb1c3fbace9ab3e7dbb"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">OpenMS::FeatureFinderAlgorithmSH::run</a></div><div class="ttdeci">virtual void run()</div><div class="ttdoc">Main method that implements the actual algorithm. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:229</div></div>
290
<div class="ttc" id="classOpenMS_1_1Peak2D_html"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html">OpenMS::Peak2D</a></div><div class="ttdoc">A 2-dimensional raw data point or peak. </div><div class="ttdef"><b>Definition:</b> Peak2D.h:55</div></div>
291
<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>
292
<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>
293
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl_html_aa8f1a5d0b36919f45750fc2a15089f77"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl.html#aa8f1a5d0b36919f45750fc2a15089f77">OpenMS::FeatureFinderAlgorithmSHCtrl::initParams</a></div><div class="ttdeci">void initParams(Param param)</div></div>
294
<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>
295
<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>
296
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac2bc824d6ff2633ec34793c9e918d479"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">OpenMS::MSExperiment::resize</a></div><div class="ttdeci">void resize(Size s)</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:122</div></div>
297
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_abb9911ee4d024e85861f29bbbd0a63ef"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#abb9911ee4d024e85861f29bbbd0a63ef">OpenMS::FeatureFinderAlgorithmSH::FeatureMapType</a></div><div class="ttdeci">FeatureFinderAlgorithm< PeakType, FeatureType >::FeatureMapType FeatureMapType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:109</div></div>
298
<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>
299
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_ae4e0f0c176662a323a6a64d29ff986dd"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#ae4e0f0c176662a323a6a64d29ff986dd">OpenMS::FeatureFinderAlgorithmSH::SpectrumType</a></div><div class="ttdeci">MapType::SpectrumType SpectrumType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:110</div></div>
300
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_aaac70aafcb9fa245ca59256e26a12b88"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aaac70aafcb9fa245ca59256e26a12b88">OpenMS::FeatureFinderAlgorithmSH::getNativeScanId</a></div><div class="ttdeci">unsigned int getNativeScanId(String native_id)</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:206</div></div>
301
<div class="ttc" id="FeatureFinderAlgorithmSHCtrl_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithmSHCtrl_8h.html">FeatureFinderAlgorithmSHCtrl.h</a></div></div>
302
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_a0b28abb9db6a809eec07048c69fdfaab"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a0b28abb9db6a809eec07048c69fdfaab">OpenMS::FeatureFinderAlgorithmSH::map_</a></div><div class="ttdeci">MapType map_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:306</div></div>
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<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
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<div class="ttc" id="classOpenMS_1_1String_html_a28f849a39a6e1a02a891d9e7e7f6eb79"><div class="ttname"><a href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">OpenMS::String::toInt</a></div><div class="ttdeci">Int toInt() const </div><div class="ttdoc">Conversion to int. </div></div>
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<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_a2f89be2feec82f5414aedc09e488420b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a2f89be2feec82f5414aedc09e488420b">OpenMS::FeatureFinderAlgorithmSH::MapType</a></div><div class="ttdeci">FeatureFinderAlgorithm< PeakType, FeatureType >::MapType MapType</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:108</div></div>
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<div class="ttc" id="classOpenMS_1_1StringList_html_a5f86b59b547048311dd50df5fb6d3bb5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">OpenMS::StringList::create</a></div><div class="ttdeci">static StringList create(const String &list, const char splitter= ',')</div><div class="ttdoc">Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...</div></div>
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<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html">OpenMS::FeatureFinderAlgorithmSH</a></div><div class="ttdoc">The Superhirn FeatureFinderAlgorithm. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:102</div></div>
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<div class="ttc" id="FeatureFinderAlgorithm_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithm_8h.html">FeatureFinderAlgorithm.h</a></div></div>
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<div class="ttc" id="classOpenMS_1_1Exception_1_1InvalidParameter_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1InvalidParameter.html">OpenMS::Exception::InvalidParameter</a></div><div class="ttdoc">Exception indicating that an invalid parameter was handed over to an algorithm. </div><div class="ttdef"><b>Definition:</b> Exception.h:348</div></div>
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<div class="ttc" id="classOpenMS_1_1Param_html_a10933782584a46cded91c40574027ee2"><div class="ttname"><a href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">OpenMS::Param::setValidStrings</a></div><div class="ttdeci">void setValidStrings(const String &key, const std::vector< String > &strings)</div><div class="ttdoc">Sets the valid strings for the parameter key. </div></div>
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<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>
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<div class="ttc" id="classOpenMS_1_1RawData_html"><div class="ttname"><a href="classOpenMS_1_1RawData.html">OpenMS::RawData</a></div><div class="ttdef"><b>Definition:</b> RawData.h:58</div></div>
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<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_aba691daad70f85242bed281fbcd0eca5"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#aba691daad70f85242bed281fbcd0eca5">OpenMS::FeatureFinderAlgorithmSH::create</a></div><div class="ttdeci">static FeatureFinderAlgorithm< Peak1D, Feature > * create()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:295</div></div>
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<div class="ttc" id="classOpenMS_1_1Param_html_a3a23089ec40eeed796efe7b69ecb02ac"><div class="ttname"><a href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">OpenMS::Param::setMinInt</a></div><div class="ttdeci">void setMinInt(const String &key, Int min)</div><div class="ttdoc">Sets the minimum value for the integer or integer list parameter key. </div></div>
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<div class="ttc" id="namespaceOpenMS_html_afc24cc74414bcf1d9129d3e8d4eb1a7f"><div class="ttname"><a href="namespaceOpenMS.html#afc24cc74414bcf1d9129d3e8d4eb1a7f">OpenMS::Vec</a></div><div class="ttdeci">std::vector< MyMap > Vec</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSHCtrl.h:53</div></div>
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<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>
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<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a7c3b265b697a57615da5cd3274780efd"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">OpenMS::DefaultParamHandler::check_defaults_</a></div><div class="ttdeci">bool check_defaults_</div><div class="ttdoc">If this member is set to false no checking if parameters in done;. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:174</div></div>
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<div class="ttc" id="classOpenMS_1_1String_html_a226b41d565aa586bd45aa7d046608511"><div class="ttname"><a href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">OpenMS::String::substr</a></div><div class="ttdeci">String substr(size_t pos=0, size_t n=npos) const </div><div class="ttdoc">Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...</div></div>
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<div class="ttc" id="classOpenMS_1_1IntList_html_ac244d9a257aab1a24c1a622ccacab745"><div class="ttname"><a href="classOpenMS_1_1IntList.html#ac244d9a257aab1a24c1a622ccacab745">OpenMS::IntList::create</a></div><div class="ttdeci">static IntList create(const String &list)</div><div class="ttdoc">Returns a list that is created by splitting the given comma-separated string (String are not trimmed!...</div></div>
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<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSHCtrl.html">OpenMS::FeatureFinderAlgorithmSHCtrl</a></div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSHCtrl.h:55</div></div>
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<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_a27120a1be410ba8c6fba4fc9fcbe57c2"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#a27120a1be410ba8c6fba4fc9fcbe57c2">OpenMS::FeatureFinderAlgorithmSH::FeatureFinderAlgorithmSH</a></div><div class="ttdeci">FeatureFinderAlgorithmSH()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:114</div></div>
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<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</div></div>
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<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ad368341c22d3447e324134c47adff081"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">OpenMS::SpectrumSettings::getNativeID</a></div><div class="ttdeci">const String & getNativeID() const </div><div class="ttdoc">returns the native identifier for the spectrum, used by the acquisition software. ...</div></div>
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<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 &key, DoubleReal min)</div><div class="ttdoc">Sets the minimum value for the floating point or floating point list parameter key. </div></div>
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<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmSH_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmSH.html#af73fd15708e50e77665070023a09cc87">OpenMS::FeatureFinderAlgorithmSH::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmSH.h:300</div></div>
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<div class="ttc" id="classOpenMS_1_1Param_html_a6b40506fffbae670045d065c354bb9b8"><div class="ttname"><a href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">OpenMS::Param::setMaxFloat</a></div><div class="ttdeci">void setMaxFloat(const String &key, DoubleReal max)</div><div class="ttdoc">Sets the maximum value for the floating point or floating point list parameter key. </div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:13 using doxygen 1.8.5</font></TD>
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