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<a href="MapAlignmentAlgorithmSpectrumAlignment_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>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<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>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Erhan Kenar $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Vipul Patel $</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_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_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="MapAlignmentAlgorithm_8h.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="PeakSpectrumCompareFunctor_8h.html">OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <gsl/gsl_errno.h></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <gsl/gsl_spline.h></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <gsl/gsl_fft_real.h></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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html"> 59</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> :</div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  {</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a>();</div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a>();</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="comment">//Docu in base class</span></div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> alignPeakMaps(std::vector<<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a> > &, std::vector<TransformationDescription> &);</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9584ec9238430832ac2c381039513247"> 73</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9584ec9238430832ac2c381039513247">create</a>()</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  {</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordflow">return</span> <span class="keyword">new</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a>();</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  }</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8d4600093afb26cff7d7db82a1837e9f"> 79</a></span>  <span class="keyword">static</span> <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8d4600093afb26cff7d7db82a1837e9f">getProductName</a>()</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  {</div>
<div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">return</span> <span class="stringliteral">"spectrum_alignment"</span>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  }</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> &);</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> &);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html"> 98</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html">Compare</a></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  {</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a8b3ab54ed3e81c69863d65e4e6c424a0"> 101</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a8b3ab54ed3e81c69863d65e4e6c424a0">flag</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a73903d9b2ec03887bcf011b913248c51"> 106</a></span>  <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a73903d9b2ec03887bcf011b913248c51">Compare</a>(<span class="keywordtype">bool</span> b = <span class="keyword">false</span>) :</div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  flag(b)</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  {</div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  }</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a4134b184bb1ace0daa488516a620fc8e"> 112</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a4134b184bb1ace0daa488516a620fc8e">operator()</a>(<span class="keyword">const</span> std::pair<std::pair<Int, Real>, <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> & c1, <span class="keyword">const</span> std::pair<std::pair<Int, Real>, <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> & c2)</div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  {</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  <span class="keywordflow">if</span> (!flag)</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="keywordflow">return</span> c1.second > c2.second;</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  }</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  {</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordflow">return</span> (c1.first).first < (c2.first).first;</div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  }</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  }</div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a41a09dd2e9375b9816c28893156bfd28"> 125</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a41a09dd2e9375b9816c28893156bfd28">operator()</a>(<span class="keyword">const</span> std::pair<Real, Real> & c1, <span class="keyword">const</span> std::pair<Real, Real> & c2)</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  {</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">if</span> (!flag)</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  {</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="keywordflow">return</span> c1.first > c2.first;</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  }</div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  {</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">return</span> c1.first < c2.first;</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"> 136</span> </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> </div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  <span class="keywordtype">void</span> prepareAlign_(<span class="keyword">const</span> std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & pattern, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a> & aligned, std::vector<TransformationDescription> & transformation);</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordtype">void</span> msFilter_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a> & peakmap, std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & spectrum_pointer_container);</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordtype">void</span> fourierActivation_(std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & spectrum_pointer_container);</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordtype">void</span> transform_(<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> & spec);</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordtype">bool</span> insideBand_(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m, <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> k_);</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> bestk_(<span class="keyword">const</span> std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & pattern, std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & aligned, std::map<<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::map<Size, Real> > & buffer, <span class="keywordtype">bool</span> column_row_orientation, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xbegin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xend, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ybegin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> yend);</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span> </div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> scoreCalculation_(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> patternbegin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> alignbegin, <span class="keyword">const</span> std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & pattern, std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & aligned, std::map<<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::map<Size, Real> > & buffer, <span class="keywordtype">bool</span> column_row_orientation);</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> scoring_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> & a, <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> & b);</div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordtype">void</span> affineGapalign_(<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xbegin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ybegin, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xend, <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> yend, <span class="keyword">const</span> std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & pattern, std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & aligned, std::vector<int> & xcoordinate, std::vector<Real> & ycoordinate, std::vector<int> & xcoordinatepattern);</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span> </div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="keywordtype">void</span> bucketFilter_(<span class="keyword">const</span> std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & pattern, std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & aligned, std::vector<Int> & xcoordinate, std::vector<Real> & ycoordinate, std::vector<Int> & xcoordinatepattern);</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> </div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <span class="keywordtype">void</span> debugFileCreator_(<span class="keyword">const</span> std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & pattern, std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & aligned);</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keywordtype">void</span> eraseFloatDataArrayEntry_(std::vector<<a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a> *> & spectrum_pointer_container);</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span> </div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <span class="keywordtype">void</span> debugscoreDistributionCalculation_(<a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> score);</div>
<div class="line"><a name="l00300"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0bfda7af52aef129dd99f8664efd3da8"> 300</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0bfda7af52aef129dd99f8664efd3da8">gap_</a>;</div>
<div class="line"><a name="l00302"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a5f4343fd568e4980066be6af2eef3351"> 302</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a5f4343fd568e4980066be6af2eef3351">e_</a>;</div>
<div class="line"><a name="l00304"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab890c00034eaf606dcd4438319dac090"> 304</a></span>  <a class="code" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a> * <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab890c00034eaf606dcd4438319dac090">c1_</a>;</div>
<div class="line"><a name="l00306"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab194d52a2d0143fcdb17c626ebaaf588"> 306</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab194d52a2d0143fcdb17c626ebaaf588">cutoffScore_</a>;</div>
<div class="line"><a name="l00308"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a23c2cf21022e3e7bf4e9b82919dba1b8"> 308</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a23c2cf21022e3e7bf4e9b82919dba1b8">bucketsize_</a>;</div>
<div class="line"><a name="l00310"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4e8ad8a7db1b7e3ee65134b631931a1a"> 310</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4e8ad8a7db1b7e3ee65134b631931a1a">anchorPoints_</a>;</div>
<div class="line"><a name="l00312"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#afa3f4fa08a8a3b675e2dab06e29412a1"> 312</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a>;</div>
<div class="line"><a name="l00314"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af300c42aaa79482d8acadf3470835ab8"> 314</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af300c42aaa79482d8acadf3470835ab8">mismatchscore_</a>;</div>
<div class="line"><a name="l00316"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9b1cc0d5756927db86ca7ef37148b812"> 316</a></span>  <a class="code" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9b1cc0d5756927db86ca7ef37148b812">threshold_</a>;</div>
<div class="line"><a name="l00318"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0a9eefab469443f2ac99f95d3ffa167f"> 318</a></span>  std::vector<std::vector<Real> > <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0a9eefab469443f2ac99f95d3ffa167f">debugmatrix_</a>;</div>
<div class="line"><a name="l00320"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3d66c4ad95892c40bce2188850fb36d8"> 320</a></span>  std::vector<std::vector<Real> > <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3d66c4ad95892c40bce2188850fb36d8">debugscorematrix_</a>;</div>
<div class="line"><a name="l00322"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac7c42fdddecd7a8212baa9bfa43ff958"> 322</a></span>  std::vector<std::pair<Real, Real> > <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac7c42fdddecd7a8212baa9bfa43ff958">debugtraceback_</a>;</div>
<div class="line"><a name="l00324"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8e7a8926f87a4a4709278d537577e4f8"> 324</a></span>  std::vector<Real> <a class="code" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8e7a8926f87a4a4709278d537577e4f8">scoredistribution_</a>; <span class="comment">//save the cell i, j , matchscore, insertscore, traceback</span></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="comment">//docu in base class</span></div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordtype">void</span> updateMembers_();</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> </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="comment">// namespace OpenMS</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> <span class="preprocessor">#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H</span></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_ac7c42fdddecd7a8212baa9bfa43ff958"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac7c42fdddecd7a8212baa9bfa43ff958">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::debugtraceback_</a></div><div class="ttdeci">std::vector< std::pair< Real, Real > > debugtraceback_</div><div class="ttdoc">Container holding the path of the traceback. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:322</div></div>
<div class="ttc" id="group__Concept_html_gab685845059e8a2c92743427d9a698c70"><div class="ttname"><a href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">OpenMS::Real</a></div><div class="ttdeci">float Real</div><div class="ttdoc">Real type. </div><div class="ttdef"><b>Definition:</b> Types.h:109</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_1MapAlignmentAlgorithmSpectrumAlignment_html_a0bfda7af52aef129dd99f8664efd3da8"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0bfda7af52aef129dd99f8664efd3da8">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::gap_</a></div><div class="ttdeci">Real gap_</div><div class="ttdoc">Represent the gap cost for opening o closing a gap in the alignment. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:300</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a4e8ad8a7db1b7e3ee65134b631931a1a"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4e8ad8a7db1b7e3ee65134b631931a1a">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::anchorPoints_</a></div><div class="ttdeci">Size anchorPoints_</div><div class="ttdoc">Defines the amount of ankerpoints which are selected within one bucket. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:310</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a3d66c4ad95892c40bce2188850fb36d8"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3d66c4ad95892c40bce2188850fb36d8">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::debugscorematrix_</a></div><div class="ttdeci">std::vector< std::vector< Real > > debugscorematrix_</div><div class="ttdoc">Container holding the only the score of Spectrums. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:320</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a9b1cc0d5756927db86ca7ef37148b812"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9b1cc0d5756927db86ca7ef37148b812">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::threshold_</a></div><div class="ttdeci">Real threshold_</div><div class="ttdoc">This is the minimum score for counting as a match(1-cutoffScore_) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:316</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_afa3f4fa08a8a3b675e2dab06e29412a1"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#afa3f4fa08a8a3b675e2dab06e29412a1">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::debug_</a></div><div class="ttdeci">bool debug_</div><div class="ttdoc">Debug mode flag default: False. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:312</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare_html_a4134b184bb1ace0daa488516a620fc8e"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a4134b184bb1ace0daa488516a620fc8e">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::Compare::operator()</a></div><div class="ttdeci">bool operator()(const std::pair< std::pair< Int, Real >, Real > &c1, const std::pair< std::pair< Int, Real >, Real > &c2)</div><div class="ttdoc">overloaded operator() for comparing maps of maps std::pair&lt;std::pair&lt;Int,Real&gt;,Real&gt;. If flag is false the second argument of the outer map is selected. The output is an ascending order. If the order flag is true, the first argument of the inner class is selected to get a descending oder. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:112</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithm_html"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithm.html">OpenMS::MapAlignmentAlgorithm</a></div><div class="ttdoc">Base class for all map-alignment algorithms. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithm.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare_html_a41a09dd2e9375b9816c28893156bfd28"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a41a09dd2e9375b9816c28893156bfd28">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::Compare::operator()</a></div><div class="ttdeci">bool operator()(const std::pair< Real, Real > &c1, const std::pair< Real, Real > &c2)</div><div class="ttdoc">overloaded operator() for comparing pairs of Real, Real std::pair&lt;Real,Real&gt;. If the order flag is fa...</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_ab890c00034eaf606dcd4438319dac090"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab890c00034eaf606dcd4438319dac090">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::c1_</a></div><div class="ttdeci">PeakSpectrumCompareFunctor * c1_</div><div class="ttdoc">Pointer holds the scoringfunction, which can be selected. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:304</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare_html_a8b3ab54ed3e81c69863d65e4e6c424a0"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a8b3ab54ed3e81c69863d65e4e6c424a0">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::Compare::flag</a></div><div class="ttdeci">bool flag</div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a23c2cf21022e3e7bf4e9b82919dba1b8"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a23c2cf21022e3e7bf4e9b82919dba1b8">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::bucketsize_</a></div><div class="ttdeci">Size bucketsize_</div><div class="ttdoc">Defines the size of one bucket. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:308</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare_html_a73903d9b2ec03887bcf011b913248c51"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#a73903d9b2ec03887bcf011b913248c51">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::Compare::Compare</a></div><div class="ttdeci">Compare(bool b=false)</div><div class="ttdoc">Default constructor with an order flag. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:106</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum<></a></div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare_html"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::Compare</a></div><div class="ttdoc">innerclass necessary for using the sort algo. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:98</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a0a9eefab469443f2ac99f95d3ffa167f"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0a9eefab469443f2ac99f95d3ffa167f">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::debugmatrix_</a></div><div class="ttdeci">std::vector< std::vector< Real > > debugmatrix_</div><div class="ttdoc">Container holding the score of the matchmatrix and also the insertmatrix. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:318</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">OpenMS::MapAlignmentAlgorithmSpectrumAlignment</a></div><div class="ttdoc">A map alignment algorithm based on spectrum similarity (dynamic programming). </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a8e7a8926f87a4a4709278d537577e4f8"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8e7a8926f87a4a4709278d537577e4f8">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::scoredistribution_</a></div><div class="ttdeci">std::vector< Real > scoredistribution_</div><div class="ttdoc">Container holding the score of each cell(matchmatrix,insertmatrix, traceback) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:324</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a8d4600093afb26cff7d7db82a1837e9f"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8d4600093afb26cff7d7db82a1837e9f">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::getProductName</a></div><div class="ttdeci">static String getProductName()</div><div class="ttdoc">Returns the product name (for the Factory) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_af300c42aaa79482d8acadf3470835ab8"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af300c42aaa79482d8acadf3470835ab8">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::mismatchscore_</a></div><div class="ttdeci">Real mismatchscore_</div><div class="ttdoc">Represent the cost of a mismath in the alignment. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:314</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_ab194d52a2d0143fcdb17c626ebaaf588"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab194d52a2d0143fcdb17c626ebaaf588">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::cutoffScore_</a></div><div class="ttdeci">Real cutoffScore_</div><div class="ttdoc">This is the minimal score to be count as a mismatch(range 0.0 - 1.0) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:306</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a9584ec9238430832ac2c381039513247"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9584ec9238430832ac2c381039513247">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::create</a></div><div class="ttdeci">static MapAlignmentAlgorithm * create()</div><div class="ttdoc">Creates a new instance of this class (for Factory) </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_html_a5f4343fd568e4980066be6af2eef3351"><div class="ttname"><a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a5f4343fd568e4980066be6af2eef3351">OpenMS::MapAlignmentAlgorithmSpectrumAlignment::e_</a></div><div class="ttdeci">Real e_</div><div class="ttdoc">Extension cost after a gap ist open. </div><div class="ttdef"><b>Definition:</b> MapAlignmentAlgorithmSpectrumAlignment.h:302</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_1PeakSpectrumCompareFunctor_html"><div class="ttname"><a href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">OpenMS::PeakSpectrumCompareFunctor</a></div><div class="ttdoc">Base class for compare functors of spectra, that return a similiarity value for two spectra...</div><div class="ttdef"><b>Definition:</b> PeakSpectrumCompareFunctor.h:53</div></div>
<div class="ttc" id="PeakSpectrumCompareFunctor_8h_html"><div class="ttname"><a href="PeakSpectrumCompareFunctor_8h.html">PeakSpectrumCompareFunctor.h</a></div></div>
<div class="ttc" id="MapAlignmentAlgorithm_8h_html"><div class="ttname"><a href="MapAlignmentAlgorithm_8h.html">MapAlignmentAlgorithm.h</a></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="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
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