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<a href="FeatureFinderAlgorithmIsotopeWavelet_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>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<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>
<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>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<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>
<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>
<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>
<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>
<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>
<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>
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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>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<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>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<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="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Rene Hussong $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMISOTOPEWAVELET_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMISOTOPEWAVELET_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="IsotopeWaveletTransform_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletTransform.h</a>></span></div>
<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>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="MzDataFile_8h.html">OpenMS/FORMAT/MzDataFile.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <time.h></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <algorithm></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#ifdef OPENMS_HAS_TBB</span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor"></span><span class="preprocessor">#include <<a class="code" href="IsotopeWaveletParallelFor_8h.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletParallelFor.h</a>></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <tbb/task_scheduler_init.h></span></div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include <tbb/pipeline.h></span></div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#include <tbb/parallel_for.h></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> {</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> PeakType, <span class="keyword">typename</span> FeatureType></div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html"> 76</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html">FeatureFinderAlgorithmIsotopeWavelet</a> :</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><PeakType, FeatureType></div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  {</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="preprocessor">#ifdef OPENMS_HAS_TBB</span></div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="preprocessor"></span> <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="classOpenMS_1_1IsotopeWaveletParallelFor.html">IsotopeWaveletParallelFor</a><PeakType, FeatureType>;</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a7837c64b8bc2ae095bf949d6ea9fe2d5"> 85</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType></a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a7837c64b8bc2ae095bf949d6ea9fe2d5">Base</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span> </div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3ee942662a8e6bbd9a705201a1896666"> 89</a></span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3ee942662a8e6bbd9a705201a1896666">FeatureFinderAlgorithmIsotopeWavelet</a>()</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  {</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</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">"max_charge"</span>, 3, <span class="stringliteral">"The maximal charge state to be considered."</span>);</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</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">"max_charge"</span>, 1);</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</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">"intensity_threshold"</span>, -1., <span class="stringliteral">"The final threshold t' is build upon the formula: t' = av+t*sd, "</span></div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="stringliteral">"where t is the intensity_threshold, av the average intensity within the wavelet transformed signal "</span></div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="stringliteral">"and sd the standard deviation of the transform. "</span></div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="stringliteral">"If you set intensity_threshold=-1, t' will be zero.\n"</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="stringliteral">"As the 'optimal' value for this parameter is highly data dependent, we would recommend to start "</span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="stringliteral">"with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one "</span></div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="stringliteral">"might increase the threshold to find an optimized trade-off between false positives and true positives. "</span></div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="stringliteral">"Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data "</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="stringliteral">"features even very high intensity values, t can also adopt values up to around 30. "</span></div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="stringliteral">"Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g."</span>);</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</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">"intensity_type"</span>, <span class="stringliteral">"ref"</span>, <span class="stringliteral">"Determines the intensity type returned for the identified features. 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</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">"intensity_type"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"ref,trans,corrected"</span>));</div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</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">"check_ppm"</span>, <span class="stringliteral">"false"</span>, <span class="stringliteral">"Enables/disables a ppm test vs. the averagine model, i.e. "</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="stringliteral">"potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</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">"check_ppm"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</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">"hr_data"</span>, <span class="stringliteral">"false"</span>, <span class="stringliteral">"Must be true in case of high-resolution data, i.e. "</span></div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="stringliteral">"for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check "</span></div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="stringliteral">"a single MS scan out of your recording, if you are unsure."</span>);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</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">"hr_data"</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"true,false"</span>));</div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="preprocessor">#if (defined(OPENMS_HAS_CUDA) || defined(OPENMS_HAS_TBB))</span></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span> <span class="preprocessor"></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">"parallel:use_gpus"</span>, <span class="stringliteral">"-1"</span>, <span class="stringliteral">"A comma-separated list of IDs corresponding to the GPU devices to use.\n"</span></div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="stringliteral">"'-1' disables parallelization (CUDA/TBB) at all.\n"</span>);</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> <span class="preprocessor"></span></div>
<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">"sweep_line:rt_votes_cutoff"</span>, 5, <span class="stringliteral">"Defines the minimum number of "</span></div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="stringliteral">"subsequent scans where a pattern must occur to be considered as a feature."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<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#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"sweep_line:rt_votes_cutoff"</span>, 0);</div>
<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#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"sweep_line:rt_interleave"</span>, 1, <span class="stringliteral">"Defines the maximum number of "</span></div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="stringliteral">"scans (w.r.t. rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value."</span>, <a class="code" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create</a>(<span class="stringliteral">"advanced"</span>));</div>
<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#a3a23089ec40eeed796efe7b69ecb02ac">setMinInt</a>(<span class="stringliteral">"sweep_line:rt_interleave"</span>, 0);</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  this-><a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a>();</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a522648bd9fecc67681ffdbf0a15b3139"> 132</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a522648bd9fecc67681ffdbf0a15b3139">~FeatureFinderAlgorithmIsotopeWavelet</a>()</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  {</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  }</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div>
<div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a512f34fae6d03198dea390c33e52e75d"> 136</a></span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html">IsotopeWaveletTransform<PeakType>::TransSpectrum</a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a512f34fae6d03198dea390c33e52e75d">prepareHRDataCuda</a>(<span class="keyword">const</span> <a class="code" href="classunsigned_01int.html">UInt</a> i, <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html">IsotopeWaveletTransform<PeakType></a> * iwt)</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  {</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> * new_spec(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33">createHRData</a>(i));</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html">IsotopeWaveletTransform<PeakType>::TransSpectrum</a> * c_trans = <span class="keyword">new</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html">IsotopeWaveletTransform<PeakType>::TransSpectrum</a>(new_spec);</div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  iwt->initializeScanCuda(*new_spec);</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">return</span> c_trans;</div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  }</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33"> 145</a></span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33">createHRData</a>(<span class="keyword">const</span> <a class="code" href="classunsigned_01int.html">UInt</a> i)</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  {</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> spec((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]);</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> & specr((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]);</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> j = 0; j < spec.size() - 1; ++j)</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  {</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  spec[j].setMZ(-1 * (specr[j + 1].getMZ() - specr[j].getMZ()));</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  spec[j].setIntensity((specr[j].getIntensity() + specr[j + 1].getIntensity()));</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  }</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  spec[spec.size() - 1].setMZ(-1); spec[spec.size() - 1].setIntensity(-1);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <a class="code" href="classOpenMS_1_1ConstRefVector.html">ConstRefVector<MSSpectrum<PeakType></a> > c_sorted_spec(spec.begin(), spec.end());</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="comment">//Sort in ascending order according to the intensities present in the transform</span></div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  c_sorted_spec.<a class="code" href="classOpenMS_1_1ConstRefVector.html#a86f7b200260209865e730a2e4fcaa628">sortByPosition</a>();</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> <span class="preprocessor"></span> std::ofstream ofilex(<span class="stringliteral">"spacings.trans"</span>);</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> j = 0; j < spec.size() - 1; ++j)</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  {</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  ofilex << ::std::setprecision(12) << std::fixed << spec[j].getMZ() << <span class="stringliteral">"\t"</span> << spec[j].getIntensity() << std::endl;</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  }</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  ofilex.close();</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <a class="code" href="classunsigned_01int.html">UInt</a> pos = 0;</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  <span class="keywordflow">while</span> (c_sorted_spec[pos].getIntensity() <= 0)</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  {</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordflow">if</span> (++pos >= c_sorted_spec.size())</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  {</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  std::cout << <span class="stringliteral">"Detected empty scan or a scan that cannot be interpolated with zeros in HR mode. "</span> << std::endl;</div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  std::cout << <span class="stringliteral">"Please check scan # "</span> << i << <span class="stringliteral">" of your data set."</span> << std::endl;</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  exit(-1);</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  }</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  }</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <a class="code" href="classdouble.html">DoubleReal</a> bound = -1 * c_sorted_spec[pos].getMZ();</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordflow">if</span> (bound > (1. / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>) / 2.)</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  {</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="comment">//that might be case for simulated spectra,</span></div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="comment">//which might show a very artificial spacing</span></div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  bound = (1. / <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>) / 2. / 4.;</div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  }</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> * new_spec = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  new_spec->reserve(200000);</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  new_spec-><a class="code" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">setRT</a>(((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]).getRT());</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  PeakType p; p.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(specr[0].getMZ()); p.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(specr[0].getIntensity());</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  new_spec->push_back(p);</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <a class="code" href="classunsigned_01int.html">UInt</a> count;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> j = 0; j < spec.size() - 1; ++j)</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  {</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  count = 0;</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keywordflow">while</span> (-spec[j].getMZ() - count * bound > bound)</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  {</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  ++count;</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  p.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(specr[j].getMZ() + count * bound); p.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(0);</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  new_spec->push_back(p);</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  }</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  p.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(specr[j + 1].getMZ()); p.<a class="code" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">setIntensity</a>(specr[j + 1].getIntensity());</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  new_spec->push_back(p);</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  }</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> <span class="preprocessor"></span> std::ofstream ofiley(<span class="stringliteral">"new_spec.trans"</span>);</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> j = 0; j < new_spec->size(); ++j)</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  {</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  ofiley << ::std::setprecision(12) << std::fixed << (*new_spec)[j].getMZ() << <span class="stringliteral">"\t"</span> << (*new_spec)[j].getIntensity() << std::endl;</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  }</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  ofiley.close();</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordflow">return</span> new_spec;</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  }</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1"> 223</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">run</a>()</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  {</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  <a class="code" href="classdouble.html">DoubleReal</a> max_mz = this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1RangeManager.html#ab54df5a3894df5cebc88022e8684ff65">getMax</a>()[1];</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  <a class="code" href="classdouble.html">DoubleReal</a> min_mz = this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1RangeManager.html#ad7e9497afbc70b1bd40dba2874802954">getMin</a>()[1];</div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_size = 0;</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> <span class="preprocessor">#ifdef OPENMS_HAS_CUDA</span></div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a>) <span class="comment">//some preprocessing necessary for the GPU computation</span></div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  {</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> i = 0; i < this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  {</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  max_size = std::max(max_size, (*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i].size());</div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  }</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  }</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="comment">//Check for useless RT_votes_cutoff_ parameter</span></div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">RT_votes_cutoff_</a> > this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>())</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  {</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a> = 0;</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  }</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  {</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a> = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">RT_votes_cutoff_</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  }</div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a>(<a class="code" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">ProgressLogger::CMD</a>);</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a> = 0;</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, 2 * this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>, <span class="stringliteral">"analyzing spectra"</span>);</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span> <span class="preprocessor">#if defined(OPENMS_HAS_TBB) && defined(OPENMS_HAS_CUDA)</span></div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a>)</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  {</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <a class="code" href="classunsigned_01int.html">UInt</a> num_gpus = this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>.size();</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  tbb::task_scheduler_init init(num_gpus);</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  std::vector<IsotopeWaveletTransform<PeakType> *> iwts(num_gpus);</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span> </div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> t = 0; t < num_gpus; ++t)</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  {</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  iwts[t] = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html">IsotopeWaveletTransform<PeakType></a>(min_mz, max_mz, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>, max_size, <span class="keyword">true</span>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af082d2d0e78145cb7e949f3e6a4d92a7">hr_data_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a17a0a86ea1bf9a231c53429ea99e086b">intensity_type_</a>);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  }</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="keyword">static</span> tbb::affinity_partitioner ap;</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="comment">//The parallel execution over all available GPU devices</span></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  tbb::parallel_for(tbb::blocked_range<size_t>(0, num_gpus, 1), <a class="code" href="classOpenMS_1_1IsotopeWaveletParallelFor.html">IsotopeWaveletParallelFor<PeakType, FeatureType></a>(iwts, <span class="keyword">this</span>), ap);</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span> </div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Merging."</span>; std::cout.flush();</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> t = 1; t < num_gpus; ++t)</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  {</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  iwts[0]->mergeFeatures(iwts[t], <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">RT_interleave_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">RT_votes_cutoff_</a>);</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  }</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> </div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Final mapping."</span>; std::cout.flush();</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span> <span class="preprocessor"></span> *this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a> = iwts[0]->mapSeeds2Features(*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a>);</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span> </div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> t = 0; t < num_gpus; ++t)</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  {</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keyword">delete</span> (iwts[t]);</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  }</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  }</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a>)</div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  {</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  std::cerr << <span class="stringliteral">"Error: You requested computation via TBB, but OpenMS has not been configured for TBB usage."</span> << std::endl;</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  std::cerr << <span class="stringliteral">"Error: You need to rebuild OpenMS using the configure flag \"--enable-tbb-release\" or \"--enable-tbb-debug\"."</span> << std::endl;</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  std::cerr << <span class="stringliteral">"Error: Please note that the multithreaded FeatureFinder needs necessarily the CUDA library, which must be enabled with \"--enable-cuda\"."</span> << std::endl;</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  }</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordflow">if</span> (!<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a>)</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  {</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html">IsotopeWaveletTransform<PeakType></a> * iwt = <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html">IsotopeWaveletTransform<PeakType></a>(min_mz, max_mz, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>, max_size, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af082d2d0e78145cb7e949f3e6a4d92a7">hr_data_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a17a0a86ea1bf9a231c53429ea99e086b">intensity_type_</a>);</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span> <span class="preprocessor">#ifdef OPENMS_HAS_CUDA</span></div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (use_cuda_)</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  {</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  cudaSetDevice(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>[0]);</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  std::cout << <span class="stringliteral">"Using device with ID: "</span> << <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>[0] << std::endl;</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  cudaDeviceProp props;</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  cudaGetDeviceProperties(&props, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>[0]);</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  std::cout << <span class="stringliteral">"This device is named: "</span> << props.name << std::endl;</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  }</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> i = 0; i < this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  {</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> & c_ref((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]);</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span> </div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span> <span class="preprocessor"></span> std::cout << ::std::fixed << ::std::setprecision(6) << <span class="stringliteral">"Spectrum "</span> << i + 1 << <span class="stringliteral">" ("</span> << (*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i].getRT() << <span class="stringliteral">") of "</span> << this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>-><a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() << <span class="stringliteral">" ... "</span>;</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  std::cout.flush();</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="keywordflow">if</span> (c_ref.size() <= 1) <span class="comment">//unable to do transform anything</span></div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  {</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"scan empty or consisting of a single data point. Skipping."</span> << std::endl;</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a> += 2);</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  }</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keywordflow">if</span> (!use_cuda_)</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  {</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">if</span> (!hr_data_) <span class="comment">//Lowres data</span></div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  {</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ab99b362c90b6915c337cc919b73b599f">initializeScan</a>((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]);</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> < <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>)</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  {</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> c_trans(c_ref);</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span> </div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#a54c204f5b2d6a44874df21661e992224">getTransform</a>(c_trans, c_ref, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span> </div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> <span class="preprocessor"></span> std::stringstream stream;</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  stream << <span class="stringliteral">"cpu_lowres_"</span> << c_ref.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() << <span class="stringliteral">"_"</span> << <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> + 1 << <span class="stringliteral">".trans\0"</span>;</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  std::ofstream ofile(stream.str().c_str());</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < c_ref.size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  {</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  ofile << ::std::setprecision(8) << std::fixed << c_trans[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getMZ() << <span class="stringliteral">"\t"</span> << c_trans[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getIntensity() << <span class="stringliteral">"\t"</span> << c_ref[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getIntensity() << std::endl;</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  }</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  ofile.close();</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"transform O.K. ... "</span>; std::cout.flush();</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span> </div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ad7b38b52b1b16ca069e80ff8b8618295">identifyCharge</a>(c_trans, c_ref, i, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a>);</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> </div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"charge recognition O.K. ... "</span>; std::cout.flush();</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  }</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  }</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="keywordflow">else</span> <span class="comment">//Highres data</span></div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  {</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> * new_spec(<a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>);</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> < <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>)</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  {</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  new_spec = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33">createHRData</a>(i);</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ab99b362c90b6915c337cc919b73b599f">initializeScan</a>(*new_spec, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> c_trans(*new_spec);</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span> </div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ad9ced5a5293256ab54096986d28d693f">getTransformHighRes</a>(c_trans, *new_spec, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span> </div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span> <span class="preprocessor"></span> std::stringstream stream;</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  stream << <span class="stringliteral">"cpu_highres_"</span> << new_spec-><a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() << <span class="stringliteral">"_"</span> << <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> + 1 << <span class="stringliteral">".trans\0"</span>;</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  std::ofstream ofile(stream.str().c_str());</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < new_spec->size(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  {</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  ofile << ::std::setprecision(8) << std::fixed << c_trans[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getMZ() << <span class="stringliteral">"\t"</span> << c_trans[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getIntensity() << <span class="stringliteral">"\t"</span> << (*new_spec)[<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>].getIntensity() << std::endl;</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  }</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  ofile.close();</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"transform O.K. ... "</span>; std::cout.flush();</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span> </div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ad7b38b52b1b16ca069e80ff8b8618295">identifyCharge</a>(c_trans, *new_spec, i, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a>);</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span> </div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"charge recognition O.K. ... "</span>; std::cout.flush();</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span> </div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="keyword">delete</span> (new_spec); new_spec = <a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>;</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  }</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  }</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  }</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <span class="keywordflow">else</span> <span class="comment">//use CUDA but not TBB</span></div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  {</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span> <span class="preprocessor">#ifdef OPENMS_HAS_CUDA</span></div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span> <span class="preprocessor"></span> <span class="keywordtype">bool</span> success = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html">IsotopeWaveletTransform<PeakType>::TransSpectrum</a> * c_trans(<a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>); <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> * new_spec(<a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>);</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  <span class="keywordflow">if</span> (!hr_data_) <span class="comment">//LowRes data</span></div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  {</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  c_trans = <span class="keyword">new</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html">IsotopeWaveletTransform<PeakType>::TransSpectrum</a>(&(*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]);</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  success = iwt->initializeScanCuda((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]) == <a class="code" href="namespaceOpenMS_1_1Constants.html#a53aae8780a5fb5cca0b69ece3f1c226c">Constants::CUDA_INIT_SUCCESS</a>;</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span> </div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <span class="keywordflow">if</span> (success)</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  {</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> < <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>)</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  {</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  iwt->getTransformCuda(*c_trans, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span> </div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span> <span class="preprocessor"></span> std::stringstream stream;</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  stream << <span class="stringliteral">"gpu_lowres_"</span> << ((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]).getRT() << <span class="stringliteral">"_"</span> << <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> + 1 << <span class="stringliteral">".trans\0"</span>;</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  std::ofstream ofile(stream.str().c_str());</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  {</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  ofile << ::std::setprecision(8) << std::fixed << c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a9c10530886aa26b8dc86fd13846907e1">getMZ</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << <span class="stringliteral">"\t"</span> << c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a420f9a11eb02b46c5bb50b13b857ca95">getTransIntensity</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << <span class="stringliteral">"\t"</span> << c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a5891967609c1abd65616dcd4456e41da">getRefIntensity</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << std::endl;</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  }</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  ofile.close();</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"cuda transform for charge "</span> << <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> + 1 << <span class="stringliteral">" O.K. ... "</span>; std::cout.flush();</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> </div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  iwt->identifyChargeCuda(*c_trans, i, c, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a>);</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> </div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"cuda charge recognition for charge "</span> << c + 1 << <span class="stringliteral">" O.K."</span> << std::endl;</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  }</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  iwt->finalizeScanCuda();</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  }</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  {</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  std::cout << <span class="stringliteral">"Warning/Error generated at scan "</span> << i << <span class="stringliteral">" ("</span> << ((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]).getRT() << <span class="stringliteral">")."</span> << std::endl;</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  }</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  }</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  <span class="keywordflow">else</span> <span class="comment">//HighRes data</span></div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  {</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  c_trans = <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a512f34fae6d03198dea390c33e52e75d">prepareHRDataCuda</a>(i, iwt);</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> < <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>)</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  {</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  iwt->getTransformCuda(*c_trans, <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>);</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span> </div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span> <span class="preprocessor"></span> std::stringstream stream;</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  stream << <span class="stringliteral">"gpu_highres_"</span> << ((*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>)[i]).getRT() << <span class="stringliteral">"_"</span> << <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> + 1 << <span class="stringliteral">".trans\0"</span>;</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  std::ofstream ofile(stream.str().c_str());</div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  {</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  ofile << ::std::setprecision(8) << std::fixed << c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a9c10530886aa26b8dc86fd13846907e1">getMZ</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << <span class="stringliteral">"\t"</span> << c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a420f9a11eb02b46c5bb50b13b857ca95">getTransIntensity</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << <span class="stringliteral">"\t"</span> << c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a5891967609c1abd65616dcd4456e41da">getRefIntensity</a>(<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << std::endl;</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  }</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  ofile.close();</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"cuda transform for charge "</span> << <a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a> + 1 << <span class="stringliteral">" O.K. ... "</span>; std::cout.flush();</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span> </div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  iwt->identifyChargeCuda(*c_trans, i, c, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a>);</div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span> </div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"cuda charge recognition for charge "</span> << c + 1 << <span class="stringliteral">" O.K."</span> << std::endl;</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span> <span class="preprocessor"></span> this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(++<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>);</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  }</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  c_trans-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#aed2d208f4d304cc6def0a15b73f115bf">destroy</a>();</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  iwt->finalizeScanCuda();</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  }</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span> </div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  <span class="keyword">delete</span> (new_spec); new_spec = <a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>;</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  <span class="keyword">delete</span> (c_trans); c_trans = <a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>;</div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span> </div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span> <span class="preprocessor"></span> std::cerr << <span class="stringliteral">"Error: You requested computation on GPU, but OpenMS has not been configured for CUDA usage."</span> << std::endl;</div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  std::cerr << <span class="stringliteral">"Error: You need to rebuild OpenMS using the configure flag \"--enable-cuda\"."</span> << std::endl;</div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span> <span class="preprocessor"></span> }</div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span> </div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ac0b48539bdee44dbe1368bcfd412f33f">updateBoxStates</a>(*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, i, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">RT_interleave_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a>);</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"updated box states."</span> << std::endl;</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  std::cout.flush();</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  }</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span> </div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a>-><a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span> </div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  <span class="comment">//Forces to empty OpenBoxes_ and to synchronize ClosedBoxes_</span></div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#ac0b48539bdee44dbe1368bcfd412f33f">updateBoxStates</a>(*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, INT_MAX, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">RT_interleave_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a>);</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span> </div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span> <span class="preprocessor">#ifdef OPENMS_DEBUG_ISOTOPE_WAVELET</span></div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Final mapping."</span>; std::cout.flush();</div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span> <span class="preprocessor"></span> *this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a> = iwt-><a class="code" href="classOpenMS_1_1IsotopeWaveletTransform.html#a12db861a7fd5db1a8aea9e6c4a403a89">mapSeeds2Features</a>(*this-><a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a>);</div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span> </div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  <span class="keyword">delete</span> (iwt);</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  }</div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  {</div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span> <span class="preprocessor">#ifndef OPENMS_HAS_TBB</span></div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span> <span class="preprocessor"></span> std::cerr << <span class="stringliteral">"Error: You requested multi-threaded computation via threading building blocks, but OpenMS has not been configured for TBB usage."</span> << std::endl;</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  std::cerr << <span class="stringliteral">"Error: You need to rebuild OpenMS with -DENABLE_TBB=ON."</span> << std::endl;</div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span> <span class="preprocessor"></span> }</div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  }</div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span> </div>
<div class="line"><a name="l00520"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af73fd15708e50e77665070023a09cc87"> 520</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_1FeatureFinderAlgorithmIsotopeWavelet.html#af73fd15708e50e77665070023a09cc87">getProductName</a>()</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  {</div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <span class="keywordflow">return</span> <span class="stringliteral">"isotope_wavelet"</span>;</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  }</div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span> </div>
<div class="line"><a name="l00525"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a81483ea6deb5aa7b6e11d0c3c871f532"> 525</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm<PeakType, FeatureType></a> * <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a81483ea6deb5aa7b6e11d0c3c871f532">create</a>()</div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  {</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3ee942662a8e6bbd9a705201a1896666">FeatureFinderAlgorithmIsotopeWavelet</a>();</div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  }</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span> </div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span> </div>
<div class="line"><a name="l00533"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html"> 533</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html">BoxElement</a></div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  {</div>
<div class="line"><a name="l00535"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#ae7800b5f37aa029e53c6776f1952cdc7"> 535</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#ae7800b5f37aa029e53c6776f1952cdc7">mz</a>;</div>
<div class="line"><a name="l00536"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#a6d47e4bb5a579f9dd390c2a4f07a3cd3"> 536</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#a6d47e4bb5a579f9dd390c2a4f07a3cd3">c</a>; </div>
<div class="line"><a name="l00537"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#aa2ac7da25c2023e7cf03863e5b907fd9"> 537</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#aa2ac7da25c2023e7cf03863e5b907fd9">score</a>;</div>
<div class="line"><a name="l00538"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#a991a665a859b92931ef2ddccea7d98c5"> 538</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#a991a665a859b92931ef2ddccea7d98c5">intens</a>;</div>
<div class="line"><a name="l00539"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#afc4478a0397a76fef003746ff45fc201"> 539</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#afc4478a0397a76fef003746ff45fc201">RT</a>; </div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  };</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span> </div>
<div class="line"><a name="l00542"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae0878340ed972926f2d75b7196ac65c9"> 542</a></span>  <span class="keyword">typedef</span> std::map<UInt, BoxElement> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae0878340ed972926f2d75b7196ac65c9">Box</a>; </div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span> </div>
<div class="line"><a name="l00544"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972"> 544</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>; </div>
<div class="line"><a name="l00545"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b"> 545</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a>; </div>
<div class="line"><a name="l00546"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803"> 546</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">RT_votes_cutoff_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">RT_interleave_</a>; </div>
<div class="line"><a name="l00547"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a"> 547</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a">use_gpus_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a17a0a86ea1bf9a231c53429ea99e086b">intensity_type_</a>;</div>
<div class="line"><a name="l00548"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41"> 548</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a>, <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af082d2d0e78145cb7e949f3e6a4d92a7">hr_data_</a>;</div>
<div class="line"><a name="l00549"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213"> 549</a></span>  std::vector<UInt> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>; </div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span> </div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span> <span class="preprocessor">#if defined(OPENMS_HAS_TBB) && defined(OPENMS_HAS_CUDA)</span></div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span> <span class="preprocessor"></span> tbb::atomic<int> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>;</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> device_num_, gpu_to_exclude_;</div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00555"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c"> 555</a></span> <span class="preprocessor"></span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">progress_counter_</a>;</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00558"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9"> 558</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a>()</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  {</div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a> = this-><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">"max_charge"</span>);</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a> = this-><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">"intensity_threshold"</span>);</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">RT_votes_cutoff_</a> = this-><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">"sweep_line:rt_votes_cutoff"</span>);</div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">RT_interleave_</a> = this-><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">"sweep_line:rt_interleave"</span>);</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  <a class="code" href="classOpenMS_1_1IsotopeWavelet.html#aa18cf670f680c9c2eb6930d640e65b22">IsotopeWavelet::setMaxCharge</a>(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a>);</div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a> = ((<a class="code" href="classOpenMS_1_1String.html">String</a>)(this-><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">"check_ppm"</span>)) == <span class="stringliteral">"true"</span>);</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af082d2d0e78145cb7e949f3e6a4d92a7">hr_data_</a> = ((<a class="code" href="classOpenMS_1_1String.html">String</a>)(this-><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">"hr_data"</span>)) == <span class="stringliteral">"true"</span>);</div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a17a0a86ea1bf9a231c53429ea99e086b">intensity_type_</a> = ((<a class="code" href="classOpenMS_1_1String.html">String</a>)(this-><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">"intensity_type"</span>)));</div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span> <span class="preprocessor">#if defined(OPENMS_HAS_CUDA) || defined(OPENMS_HAS_TBB)</span></div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span> <span class="preprocessor"></span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a">use_gpus_</a> = this-><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">"parallel:use_gpus"</span>);</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  std::vector<String> tokens;</div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  <span class="keywordflow">if</span> (!<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a">use_gpus_</a>.<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">','</span>, tokens))</div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  {</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  tokens.push_back(<a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a">use_gpus_</a>);</div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  }</div>
<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  <span class="comment">//Attention: updateMembers_ can be called several times!</span></div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>.clear();</div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  <span class="keywordflow">if</span> (tokens[0].trim().toInt() == -1) <span class="comment">//no parallelization</span></div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  {</div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  }</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>.push_back(tokens[0].trim().toInt());</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> i = 1; i < tokens.size(); ++i)</div>
<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  {</div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="keywordflow">if</span> (tokens[i].trim().toInt() == (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>) <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>[i - 1])</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  {</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  }</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a>.push_back(tokens[i].trim().toInt());</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a> = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  }</div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span> <span class="preprocessor">#else</span></div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span> <span class="preprocessor"></span> <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <a class="code" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span> <span class="preprocessor"></span> }</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span> </div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  };</div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span> </div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span> } <span class="comment">//namespace</span></div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span> </div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a53aae8780a5fb5cca0b69ece3f1c226c"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a53aae8780a5fb5cca0b69ece3f1c226c">OpenMS::Constants::CUDA_INIT_SUCCESS</a></div><div class="ttdeci">const int CUDA_INIT_SUCCESS</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletConstants.h:92</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a93a8dc068053ec44ee7e45864ef969f7"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a></div><div class="ttdeci">const double k</div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html_a12db861a7fd5db1a8aea9e6c4a403a89"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html#a12db861a7fd5db1a8aea9e6c4a403a89">OpenMS::IsotopeWaveletTransform::mapSeeds2Features</a></div><div class="ttdeci">FeatureMap< Feature > mapSeeds2Features(const MSExperiment< PeakType > &map, const UInt RT_votes_cutoff)</div><div class="ttdoc">Filters the candidates further more and maps the internally used data structures to the OpenMS framew...</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:2313</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html_a54c204f5b2d6a44874df21661e992224"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html#a54c204f5b2d6a44874df21661e992224">OpenMS::IsotopeWaveletTransform::getTransform</a></div><div class="ttdeci">virtual void getTransform(MSSpectrum< PeakType > &c_trans, const MSSpectrum< PeakType > &c_ref, const UInt c)</div><div class="ttdoc">Computes the isotope wavelet transform of charge state c. </div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:693</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a5f09052343ef99616ad653897841ce3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">OpenMS::FeatureFinderAlgorithm::features_</a></div><div class="ttdeci">FeatureMapType * features_</div><div class="ttdoc">Output data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a761b1937850c141d0c6fff0e4d633a04"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">OpenMS::DefaultParamHandler::defaults_</a></div><div class="ttdeci">Param defaults_</div><div class="ttdoc">Container for default parameters. This member should be filled in the constructor of derived classes!...</div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:155</div></div>
<div class="ttc" id="classOpenMS_1_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>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum_html_aed2d208f4d304cc6def0a15b73f115bf"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#aed2d208f4d304cc6def0a15b73f115bf">OpenMS::IsotopeWaveletTransform::TransSpectrum::destroy</a></div><div class="ttdeci">virtual void destroy()</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:137</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_adf68cb378c76b322b2cc4dbb2c145a3e"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">OpenMS::FeatureFinderAlgorithm::ff_</a></div><div class="ttdeci">FeatureFinder * ff_</div><div class="ttdoc">Pointer to the calling FeatureFinder that is used to access the feature flags. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:147</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a2694f0775c46d9076355cb85d9815425"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">OpenMS::Peak2D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a3de08d2b695a532ae39b30bd7c46e68a"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::use_gpus_</a></div><div class="ttdeci">String use_gpus_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:547</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="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a40b4eaf0409b4d2ffff61e83e35aba41"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::use_tbb_</a></div><div class="ttdeci">bool use_tbb_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:548</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html_a365c5cf67d48519199fe00cb5688d628"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">OpenMS::FeatureFinderAlgorithm::map_</a></div><div class="ttdeci">const MapType * map_</div><div class="ttdoc">Input data pointer. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a7837c64b8bc2ae095bf949d6ea9fe2d5"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a7837c64b8bc2ae095bf949d6ea9fe2d5">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::Base</a></div><div class="ttdeci">FeatureFinderAlgorithm< PeakType, FeatureType > Base</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:85</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWavelet_html_aa18cf670f680c9c2eb6930d640e65b22"><div class="ttname"><a href="classOpenMS_1_1IsotopeWavelet.html#aa18cf670f680c9c2eb6930d640e65b22">OpenMS::IsotopeWavelet::setMaxCharge</a></div><div class="ttdeci">static void setMaxCharge(const UInt max_charge)</div><div class="ttdoc">Sets the max_charge parameter. </div><div class="ttdef"><b>Definition:</b> IsotopeWavelet.h:116</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement_html_aa2ac7da25c2023e7cf03863e5b907fd9"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#aa2ac7da25c2023e7cf03863e5b907fd9">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::score</a></div><div class="ttdeci">DoubleReal score</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:537</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="IsotopeWaveletParallelFor_8h_html_a070d2ce7b6bb7e5c05602aa8c308d0c4"><div class="ttname"><a href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a></div><div class="ttdeci">#define NULL</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletParallelFor.h:41</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_ae0878340ed972926f2d75b7196ac65c9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae0878340ed972926f2d75b7196ac65c9">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::Box</a></div><div class="ttdeci">std::map< UInt, BoxElement > Box</div><div class="ttdoc">Key: RT (index), value: BoxElement. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:542</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithm.html">OpenMS::FeatureFinderAlgorithm</a></div><div class="ttdoc">Abstract base class for FeatureFinder algorithms. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithm.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a0864e2810fe75ef5519f320c957efb1b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::RT_interleave_</a></div><div class="ttdeci">UInt RT_interleave_</div><div class="ttdoc">The number of subsequent scans a pattern must cover in order to be considered as signal. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:546</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_af73fd15708e50e77665070023a09cc87"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af73fd15708e50e77665070023a09cc87">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::getProductName</a></div><div class="ttdeci">static const String getProductName()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:520</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement_html_a6d47e4bb5a579f9dd390c2a4f07a3cd3"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#a6d47e4bb5a579f9dd390c2a4f07a3cd3">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::c</a></div><div class="ttdeci">UInt c</div><div class="ttdoc">Note, this is not the charge (it is charge-1!!!) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:536</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement_html_ae7800b5f37aa029e53c6776f1952cdc7"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#ae7800b5f37aa029e53c6776f1952cdc7">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::mz</a></div><div class="ttdeci">DoubleReal mz</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:535</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a8fc6defe4e499b1b9b9c275689e44352"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">OpenMS::Constants::c</a></div><div class="ttdeci">const double c</div></div>
<div class="ttc" id="classOpenMS_1_1RangeManager_html_ab54df5a3894df5cebc88022e8684ff65"><div class="ttname"><a href="classOpenMS_1_1RangeManager.html#ab54df5a3894df5cebc88022e8684ff65">OpenMS::RangeManager::getMax</a></div><div class="ttdeci">const PositionType & getMax() const </div><div class="ttdoc">Returns the maximum position. </div><div class="ttdef"><b>Definition:</b> RangeManager.h:115</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement_html_a991a665a859b92931ef2ddccea7d98c5"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#a991a665a859b92931ef2ddccea7d98c5">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::intens</a></div><div class="ttdeci">DoubleReal intens</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:538</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html">OpenMS::IsotopeWaveletTransform::TransSpectrum</a></div><div class="ttdoc">Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU...</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:112</div></div>
<div class="ttc" id="MzDataFile_8h_html"><div class="ttname"><a href="MzDataFile_8h.html">MzDataFile.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab875c2479c6cd2a0189e4684bfa4f97d"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">OpenMS::Peak2D::setIntensity</a></div><div class="ttdeci">void setIntensity(IntensityType intensity)</div><div class="ttdoc">Non-mutable access to the data point intensity (height) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:167</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html_ad9ced5a5293256ab54096986d28d693f"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html#ad9ced5a5293256ab54096986d28d693f">OpenMS::IsotopeWaveletTransform::getTransformHighRes</a></div><div class="ttdeci">virtual void getTransformHighRes(MSSpectrum< PeakType > &c_trans, const MSSpectrum< PeakType > &c_ref, const UInt c)</div><div class="ttdoc">Computes the isotope wavelet transform of charge state c. </div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:736</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement_html"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement</a></div><div class="ttdoc">Internally used data structure for the sweep line algorithm. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:533</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum_html_a9c10530886aa26b8dc86fd13846907e1"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a9c10530886aa26b8dc86fd13846907e1">OpenMS::IsotopeWaveletTransform::TransSpectrum::getMZ</a></div><div class="ttdeci">DoubleReal getMZ(const UInt i) const </div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:152</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a1cc1012b0cdaea97f58d571af1ff45de"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">OpenMS::ProgressLogger::endProgress</a></div><div class="ttdeci">void endProgress() const </div><div class="ttdoc">Ends the progress display. </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 & getValue(const String &key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a522648bd9fecc67681ffdbf0a15b3139"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a522648bd9fecc67681ffdbf0a15b3139">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::~FeatureFinderAlgorithmIsotopeWavelet</a></div><div class="ttdeci">virtual ~FeatureFinderAlgorithmIsotopeWavelet()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_ae8f10b1319ef92b7f0ed3a31aaab93a9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::use_cuda_</a></div><div class="ttdeci">bool use_cuda_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:548</div></div>
<div class="ttc" id="IsotopeWaveletParallelFor_8h_html"><div class="ttname"><a href="IsotopeWaveletParallelFor_8h.html">IsotopeWaveletParallelFor.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html_ab99b362c90b6915c337cc919b73b599f"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html#ab99b362c90b6915c337cc919b73b599f">OpenMS::IsotopeWaveletTransform::initializeScan</a></div><div class="ttdeci">virtual void initializeScan(const MSSpectrum< PeakType > &c_ref, const UInt c=0)</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:774</div></div>
<div class="ttc" id="classOpenMS_1_1RangeManager_html_ad7e9497afbc70b1bd40dba2874802954"><div class="ttname"><a href="classOpenMS_1_1RangeManager.html#ad7e9497afbc70b1bd40dba2874802954">OpenMS::RangeManager::getMin</a></div><div class="ttdeci">const PositionType & getMin() const </div><div class="ttdoc">Returns the minimum position. </div><div class="ttdef"><b>Definition:</b> RangeManager.h:109</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html">OpenMS::IsotopeWaveletTransform</a></div><div class="ttdoc">A class implementing the isotope wavelet transform. If you just want to find features using the isoto...</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:87</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a792fce9b5d6d0fe62dfd0303b33e557b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::intensity_threshold_</a></div><div class="ttdeci">DoubleReal intensity_threshold_</div><div class="ttdoc">The only parameter of the isotope wavelet. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:545</div></div>
<div class="ttc" id="IsotopeWaveletTransform_8h_html"><div class="ttname"><a href="IsotopeWaveletTransform_8h.html">IsotopeWaveletTransform.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html">OpenMS::FeatureFinderAlgorithmIsotopeWavelet</a></div><div class="ttdoc">Implements the isotope wavelet feature finder. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1StringList_html_a5f86b59b547048311dd50df5fb6d3bb5"><div class="ttname"><a href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">OpenMS::StringList::create</a></div><div class="ttdeci">static StringList create(const String &list, const char splitter= ',')</div><div class="ttdoc">Returns a list that is created by splitting the given (comma-separated) string (String are not trimme...</div></div>
<div class="ttc" id="FeatureFinderAlgorithm_8h_html"><div class="ttname"><a href="FeatureFinderAlgorithm_8h.html">FeatureFinderAlgorithm.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement_html_afc4478a0397a76fef003746ff45fc201"><div class="ttname"><a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html#afc4478a0397a76fef003746ff45fc201">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::RT</a></div><div class="ttdeci">DoubleReal RT</div><div class="ttdoc">The elution time (not the scan index) </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:539</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html_ac0b48539bdee44dbe1368bcfd412f33f"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html#ac0b48539bdee44dbe1368bcfd412f33f">OpenMS::IsotopeWaveletTransform::updateBoxStates</a></div><div class="ttdeci">void updateBoxStates(const MSExperiment< PeakType > &map, const Size scan_index, const UInt RT_interleave, const UInt RT_votes_cutoff, const Int front_bound=-1, const Int end_bound=-1)</div><div class="ttdoc">A function keeping track of currently open and closed sweep line boxes. This function is used by the ...</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:2029</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a80a937e9a0dd8e9426bd2e0051ecaa33"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::createHRData</a></div><div class="ttdeci">MSSpectrum< PeakType > * createHRData(const UInt i)</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:145</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_aaf258e1a9846d9b238ee4b3005ad3ee9"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::updateMembers_</a></div><div class="ttdeci">void updateMembers_()</div><div class="ttdoc">This method is used to update extra member variables at the end of the setParameters() method...</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:558</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_html_ad7b38b52b1b16ca069e80ff8b8618295"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform.html#ad7b38b52b1b16ca069e80ff8b8618295">OpenMS::IsotopeWaveletTransform::identifyCharge</a></div><div class="ttdeci">virtual void identifyCharge(const MSSpectrum< PeakType > &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const DoubleReal ampl_cutoff, const bool check_PPMs)</div><div class="ttdoc">Given an isotope wavelet transformed spectrum candidates, this function assigns to every significant ...</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:1180</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a17a0a86ea1bf9a231c53429ea99e086b"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a17a0a86ea1bf9a231c53429ea99e086b">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::intensity_type_</a></div><div class="ttdeci">String intensity_type_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:547</div></div>
<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>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum_html_a420f9a11eb02b46c5bb50b13b857ca95"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a420f9a11eb02b46c5bb50b13b857ca95">OpenMS::IsotopeWaveletTransform::TransSpectrum::getTransIntensity</a></div><div class="ttdeci">DoubleReal getTransIntensity(const UInt i) const </div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:164</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a512f34fae6d03198dea390c33e52e75d"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a512f34fae6d03198dea390c33e52e75d">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::prepareHRDataCuda</a></div><div class="ttdeci">IsotopeWaveletTransform< PeakType >::TransSpectrum * prepareHRDataCuda(const UInt i, IsotopeWaveletTransform< PeakType > *iwt)</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:136</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">OpenMS::ProgressLogger::CMD</a></div><div class="ttdoc">Command line progress. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:68</div></div>
<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>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_aac8c50f318154e9e5b7b01aee806e17f"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">OpenMS::MSSpectrum::setRT</a></div><div class="ttdeci">void setRT(DoubleReal rt)</div><div class="ttdoc">Sets the absolute retention time (is seconds) </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:221</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_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 &label) const </div><div class="ttdoc">Initializes the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_af082d2d0e78145cb7e949f3e6a4d92a7"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af082d2d0e78145cb7e949f3e6a4d92a7">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::hr_data_</a></div><div class="ttdeci">bool hr_data_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:548</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletParallelFor_html"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletParallelFor.html">OpenMS::IsotopeWaveletParallelFor</a></div><div class="ttdoc">A class for distributing the data over several GPUs using Intel Threading Building Blocks...</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletParallelFor.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a10c429e143b68ec85d225b005e0d752c"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a10c429e143b68ec85d225b005e0d752c">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::progress_counter_</a></div><div class="ttdeci">Int progress_counter_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:555</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a32280019a7d0e19a07e0c3fd44aee972"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::max_charge_</a></div><div class="ttdeci">UInt max_charge_</div><div class="ttdoc">The maximal charge state we will consider. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:544</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_1IsotopeWaveletTransform_1_1TransSpectrum_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::IsotopeWaveletTransform::TransSpectrum::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:176</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a3ee942662a8e6bbd9a705201a1896666"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3ee942662a8e6bbd9a705201a1896666">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::FeatureFinderAlgorithmIsotopeWavelet</a></div><div class="ttdeci">FeatureFinderAlgorithmIsotopeWavelet()</div><div class="ttdoc">Default Constructor. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:89</div></div>
<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>
<div class="ttc" id="classOpenMS_1_1ConstRefVector_html"><div class="ttname"><a href="classOpenMS_1_1ConstRefVector.html">OpenMS::ConstRefVector</a></div><div class="ttdoc">This vector holds pointer to the elements of another container. </div><div class="ttdef"><b>Definition:</b> ConstRefVector.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum_html_a5891967609c1abd65616dcd4456e41da"><div class="ttname"><a href="classOpenMS_1_1IsotopeWaveletTransform_1_1TransSpectrum.html#a5891967609c1abd65616dcd4456e41da">OpenMS::IsotopeWaveletTransform::TransSpectrum::getRefIntensity</a></div><div class="ttdeci">DoubleReal getRefIntensity(const UInt i) const </div><div class="ttdef"><b>Definition:</b> IsotopeWaveletTransform.h:158</div></div>
<div class="ttc" id="classOpenMS_1_1ConstRefVector_html_a86f7b200260209865e730a2e4fcaa628"><div class="ttname"><a href="classOpenMS_1_1ConstRefVector.html#a86f7b200260209865e730a2e4fcaa628">OpenMS::ConstRefVector::sortByPosition</a></div><div class="ttdeci">void sortByPosition()</div><div class="ttdoc">Lexicographically sorts the elements by their position. </div><div class="ttdef"><b>Definition:</b> ConstRefVector.h:766</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a3fd609fd7b023618f7f2c5c64e8ed803"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::RT_votes_cutoff_</a></div><div class="ttdeci">UInt RT_votes_cutoff_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:546</div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ae580d960e12c7f0ebc5c95931cf39ad5"><div class="ttname"><a href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">OpenMS::String::split</a></div><div class="ttdeci">bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const </div><div class="ttdoc">Splits a string into substrings using splitter as delimiter. </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a81483ea6deb5aa7b6e11d0c3c871f532"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a81483ea6deb5aa7b6e11d0c3c871f532">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::create</a></div><div class="ttdeci">static FeatureFinderAlgorithm< PeakType, FeatureType > * create()</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:525</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_a13a43e6d814de94978c515cb084873b1"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::run</a></div><div class="ttdeci">void run()</div><div class="ttdoc">The working horse of this class. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:223</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_acc3538c5284777d8702ccaefeb61e74c"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">OpenMS::ProgressLogger::setLogType</a></div><div class="ttdeci">void setLogType(LogType type) const </div><div class="ttdoc">Sets the progress log that should be used. The default type is NONE! </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>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_ac0914e52b60b67388b6ca7648922b447"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::check_PPMs_</a></div><div class="ttdeci">bool check_PPMs_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:548</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_ab9444d66ec037a0f90523b6ac87c9087"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::real_RT_votes_cutoff_</a></div><div class="ttdeci">UInt real_RT_votes_cutoff_</div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:546</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_html_af8edb64f6f222069d7e8d143d4034213"><div class="ttname"><a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">OpenMS::FeatureFinderAlgorithmIsotopeWavelet::gpu_ids_</a></div><div class="ttdeci">std::vector< UInt > gpu_ids_</div><div class="ttdoc">A list of all GPU devices that can be used. </div><div class="ttdef"><b>Definition:</b> FeatureFinderAlgorithmIsotopeWavelet.h:549</div></div>
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