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<a href="SpectraMerger_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: Chris Bielow $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Chris Bielow, Andreas Bertsch $</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> <span class="comment">//</span></div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FILTERING_TRANSFORMERS_SPECTRAMERGER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FILTERING_TRANSFORMERS_SPECTRAMERGER_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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="CompleteLinkage_8h.html">OpenMS/COMPARISON/CLUSTERING/CompleteLinkage.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="SingleLinkage_8h.html">OpenMS/COMPARISON/CLUSTERING/SingleLinkage.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="ClusterAnalyzer_8h.html">OpenMS/COMPARISON/CLUSTERING/ClusterAnalyzer.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ClusterHierarchical_8h.html">OpenMS/COMPARISON/CLUSTERING/ClusterHierarchical.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="SpectrumAlignment_8h.html">OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="StandardTypes_8h.html">OpenMS/KERNEL/StandardTypes.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <<a class="code" href="RangeUtils_8h.html">OpenMS/KERNEL/RangeUtils.h</a>></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <<a class="code" href="BaseFeature_8h.html">OpenMS/KERNEL/BaseFeature.h</a>></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <<a class="code" href="LogStream_8h.html">OpenMS/CONCEPT/LogStream.h</a>></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span> {</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger.html"> 61</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a> :</div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="comment">/* Determine distance between two spectra</span></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="comment"></span></div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="comment"> Distance is determined as</span></div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="comment"></span></div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="comment"> (d_rt/rt_max_ + d_mz/mz_max_) / 2</span></div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="comment"></span></div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00074"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html"> 74</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html">SpectraDistance_</a> :</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</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> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a3e1ce06a993fb34b6500bb445f679855"> 78</a></span>  <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a3e1ce06a993fb34b6500bb445f679855">SpectraDistance_</a>() :</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(<span class="stringliteral">"SpectraDistance"</span>)</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>  defaults_.setValue(<span class="stringliteral">"rt_tolerance"</span>, 10.0, <span class="stringliteral">"Maximal RT distance (in [s]) for two spectra's precursors."</span>);</div>
<div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  defaults_.setValue(<span class="stringliteral">"mz_tolerance"</span>, 1.0, <span class="stringliteral">"Maximal m/z distance (in Da) for two spectra's precursors."</span>);</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  defaultsToParam_();</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  }</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#aaf258e1a9846d9b238ee4b3005ad3ee9"> 86</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a>()</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  {</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  rt_max_ = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>) param_.getValue(<span class="stringliteral">"rt_tolerance"</span>);</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  mz_max_ = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>) param_.getValue(<span class="stringliteral">"mz_tolerance"</span>);</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>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  }</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a7fb55778db17a7d8a41e21f0828b962a"> 94</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a7fb55778db17a7d8a41e21f0828b962a">getSimilarity</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> d_rt, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> d_mz)<span class="keyword"> const</span></div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="comment">// 1 - distance</span></div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordflow">return</span> 1 - ((d_rt / rt_max_ + d_mz / mz_max_) / 2);</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  }</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="comment">// measure of SIMILARITY (not distance, i.e. 1-distance)!!</span></div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#aa8aa5be634ab501e385beae080dc4b0c"> 101</a></span>  <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#aa8aa5be634ab501e385beae080dc4b0c">operator()</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> & first, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> & second)<span class="keyword"> const</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// get RT distance:</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="classdouble.html">DoubleReal</a> d_rt = fabs(first.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>() - second.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>());</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <a class="code" href="classdouble.html">DoubleReal</a> d_mz = fabs(first.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() - second.<a class="code" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>());</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>  <span class="keywordflow">if</span> (d_rt > rt_max_ || d_mz > mz_max_) {<span class="keywordflow">return</span> 0; }</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>  <span class="comment">// calculate similarity (0-1):</span></div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="classdouble.html">DoubleReal</a> sim = getSimilarity(d_rt, d_mz);</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordflow">return</span> sim;</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> </div>
<div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#addd12cc59f1a0dcd6b23ecd7fb291dfd"> 116</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#addd12cc59f1a0dcd6b23ecd7fb291dfd">rt_max_</a>;</div>
<div class="line"><a name="l00117"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a928fb61988283ac1482ad929f7491ba6"> 117</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a928fb61988283ac1482ad929f7491ba6">mz_max_</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  }; <span class="comment">// end of SpectraDistance</span></div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span> </div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger.html#a3efb73bac53473f68d223255eaa465cc"> 124</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1Map.html">Map<Size, std::vector<Size></a> > <a class="code" href="classOpenMS_1_1SpectraMerger.html#a3efb73bac53473f68d223255eaa465cc">MergeBlocks</a>;</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">// @name Constructors and Destructors</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="comment">// @{</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="comment"></span> <a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a>();</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a> & source);</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span> </div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a>();</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="comment">// @}</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>  <span class="comment">// @name Operators</span></div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">// @{</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="comment"></span> <a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SpectraMerger.html">SpectraMerger</a> & source);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="comment">// @}</span></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>  <span class="comment">// @name Merging functions</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="comment">// @{</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment"></span> <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger.html#aeaf496592f0320a1c46ed50236cc154d"> 148</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpectraMerger.html#aeaf496592f0320a1c46ed50236cc154d">mergeSpectraBlockWise</a>(MapType & exp)</div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  {</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> ms_levels = (<a class="code" href="classOpenMS_1_1IntList.html">IntList</a>) (param_.getValue(<span class="stringliteral">"block_method:ms_levels"</span>));</div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> rt_block_size(param_.getValue(<span class="stringliteral">"block_method:rt_block_size"</span>));</div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <a class="code" href="classdouble.html">DoubleReal</a> rt_max_length = (param_.getValue(<span class="stringliteral">"block_method:rt_max_length"</span>));</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> </div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordflow">if</span> (rt_max_length == 0) <span class="comment">// no rt restriction set?</span></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>  rt_max_length = (std::numeric_limits<DoubleReal>::max)(); <span class="comment">// set max rt span to very large value</span></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> </div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordflow">for</span> (IntList::iterator it_mslevel = ms_levels.begin(); it_mslevel < ms_levels.end(); ++it_mslevel)</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  {</div>
<div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <a class="code" href="classOpenMS_1_1Map.html">MergeBlocks</a> spectra_to_merge;</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> idx_block(0);</div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> block_size_count(rt_block_size + 1);</div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> idx_spectrum(0);</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> MapType::const_iterator it1 = exp.begin(); it1 != exp.end(); ++it1)</div>
<div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  {</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <span class="keywordflow">if</span> (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(it1->getMSLevel()) == *it_mslevel)</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  {</div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="comment">// block full if it contains a maximum number of scans or if maximum rt length spanned</span></div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">if</span> (++block_size_count >= rt_block_size ||</div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  exp[idx_spectrum].getRT() - exp[idx_block].getRT() > rt_max_length)</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  {</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  block_size_count = 0;</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  idx_block = idx_spectrum;</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>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  {</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  spectra_to_merge[idx_block].push_back(idx_spectrum);</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> </div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  ++idx_spectrum;</div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  }</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="comment">// check if last block had sacrifice spectra</span></div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordflow">if</span> (block_size_count == 0) <span class="comment">//block just got initialized</span></div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  {</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  spectra_to_merge[idx_block] = std::vector<Size>();</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>  <span class="comment">// merge spectra, remove all old MS spectra and add new consensus spectra</span></div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  mergeSpectra_(exp, spectra_to_merge, *it_mslevel);</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> </div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  exp.sortSpectra();</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>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  }</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00201"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger.html#a600d56293a3a35b7ef362d788c35eb99"> 201</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpectraMerger.html#a600d56293a3a35b7ef362d788c35eb99">mergeSpectraPrecursors</a>(MapType & exp)</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  {</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> </div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="comment">// convert spectra's precursors to clusterizable data</span></div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> data_size;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  std::vector<BinaryTreeNode> tree;</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <a class="code" href="classOpenMS_1_1Map.html">Map<Size, Size></a> index_mapping;</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="comment">// local scope to save memory - we do not need the clustering stuff later</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>  std::vector<BaseFeature> data;</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> </div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp.size(); ++i)</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>  <span class="keywordflow">if</span> (exp[i].getMSLevel() != 2) <span class="keywordflow">continue</span>;</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>  <span class="comment">// remember which index in distance data ==> experiment index</span></div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  index_mapping[data.size()] = i;</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="comment">// make cluster element</span></div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> bf;</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  bf.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(exp[i].getRT());</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  std::vector<Precursor> pcs = exp[i].getPrecursors();</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="keywordflow">if</span> (pcs.empty()) <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1MissingInformation.html">Exception::MissingInformation</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Scan #"</span>) + <a class="code" href="classOpenMS_1_1String.html">String</a>(i) + <span class="stringliteral">" does not contain any precursor information! Unable to cluster!"</span>);</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">if</span> (pcs.size() > 1) <a class="code" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a> << <span class="stringliteral">"More than one precursor found. Using first one!"</span> << std::endl;</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  bf.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(pcs[0].getMZ());</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  data.push_back(bf);</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>  data_size = data.size();</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span> </div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html">SpectraDistance_</a> llc;</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  llc.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(param_.copy(<span class="stringliteral">"precursor_method:"</span>, <span class="keyword">true</span>));</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <a class="code" href="classOpenMS_1_1SingleLinkage.html">SingleLinkage</a> sl;</div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <a class="code" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix<Real></a> dist; <span class="comment">// will be filled</span></div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <a class="code" href="classOpenMS_1_1ClusterHierarchical.html">ClusterHierarchical</a> ch;</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>  <span class="comment">//ch.setThreshold(0.99);</span></div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="comment">// clustering ; threshold is implicitly at 1.0, i.e. distances of 1.0 (== similiarity 0) will not be clustered</span></div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  ch.<a class="code" href="classOpenMS_1_1ClusterHierarchical.html#ae2f71a927933400ed5ce71513352e9ae">cluster</a><<a class="code" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a>, <a class="code" href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html">SpectraDistance_</a>>(data, llc, sl, tree, dist);</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  }</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> </div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="comment">// extract the clusters</span></div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <a class="code" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> ca;</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  std::vector<std::vector<Size> > clusters;</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="comment">// count number of real tree nodes (not the -1 ones):</span></div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> node_count = 0;</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ii = 0; ii < tree.size(); ++ii)</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>  <span class="keywordflow">if</span> (tree[ii].distance >= 1) tree[ii].distance = -1; <span class="comment">// manually set to disconnect, as SingleLinkage does not support it</span></div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordflow">if</span> (tree[ii].distance != -1) ++node_count;</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  }</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  ca.<a class="code" href="classOpenMS_1_1ClusterAnalyzer.html#a1ddae30375fef566e4a1f53fb43baba9">cut</a>(data_size - node_count, tree, clusters);</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="comment">//std::cerr << "Treesize: " << (tree.size()+1) << " #clusters: " << clusters.size() << std::endl;</span></div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="comment">//std::cerr << "tree:\n" << ca.newickTree(tree, true) << "\n";</span></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>  <span class="comment">// convert to blocks</span></div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <a class="code" href="classOpenMS_1_1Map.html">MergeBlocks</a> spectra_to_merge;</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span> </div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i_outer = 0; i_outer < clusters.size(); ++i_outer)</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  {</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keywordflow">if</span> (clusters[i_outer].size() <= 1) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <span class="comment">// init block with first cluster element</span></div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cl_index0 = clusters[i_outer][0];</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  spectra_to_merge[index_mapping[cl_index0]] = std::vector<Size>();</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <span class="comment">// add all other elements</span></div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i_inner = 1; i_inner < clusters[i_outer].size(); ++i_inner)</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  {</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cl_index = clusters[i_outer][i_inner];</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  spectra_to_merge[index_mapping[cl_index0]].push_back(index_mapping[cl_index]);</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  }</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  }</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span> </div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="comment">// do it</span></div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  mergeSpectra_(exp, spectra_to_merge, 2);</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span> </div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  exp.sortSpectra();</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="keywordflow">return</span>;</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  }</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span> </div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="comment">// @}</span></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="keyword">protected</span>:</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00296"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectraMerger.html#abe04755c7518a6ee530902afccc9c2e6"> 296</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpectraMerger.html#abe04755c7518a6ee530902afccc9c2e6">mergeSpectra_</a>(MapType & exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Map.html">MergeBlocks</a> & spectra_to_merge, <span class="keyword">const</span> <a class="code" href="classunsigned_01int.html">UInt</a> ms_level)</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  {</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz_binning_width(param_.getValue(<span class="stringliteral">"mz_binning_width"</span>));</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> mz_binning_unit(param_.getValue(<span class="stringliteral">"mz_binning_width_unit"</span>));</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span> </div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="comment">// merge spectra</span></div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  MapType merged_spectra;</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span> </div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <a class="code" href="classOpenMS_1_1Map.html">Map<Size, Size></a> cluster_sizes;</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  std::set<Size> merged_indices;</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span> </div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="comment">// set up alignment</span></div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a> sas;</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <a class="code" href="classOpenMS_1_1Param.html">Param</a> p;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  p.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"tolerance"</span>, mz_binning_width);</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">if</span> (!(mz_binning_unit == <span class="stringliteral">"Da"</span> || mz_binning_unit == <span class="stringliteral">"ppm"</span>)) <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalSelfOperation.html">Exception::IllegalSelfOperation</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__); <span class="comment">// sanity check</span></div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="comment">// TODO : SpectrumAlignment does not implement is_relative_tolerance</span></div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  p.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">"is_relative_tolerance"</span>, mz_binning_unit == <span class="stringliteral">"Da"</span> ? <span class="stringliteral">"false"</span> : <span class="stringliteral">"true"</span>);</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  sas.<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a>(p);</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  std::vector<std::pair<Size, Size> > alignment;</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> count_peaks_aligned(0);</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> count_peaks_overall(0);</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span> </div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="comment">// each BLOCK</span></div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1Map.html">Map</a><<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::vector<Size> >::ConstIterator it = spectra_to_merge.begin(); it != spectra_to_merge.end(); ++it)</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  {</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  ++cluster_sizes[it->second.size() + 1]; <span class="comment">// for stats</span></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span> </div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keyword">typename</span> MapType::SpectrumType consensus_spec = exp[it->first];</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  consensus_spec.setMSLevel(ms_level);</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="comment">//consensus_spec.unify(exp[it->first]); // append meta info</span></div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  merged_indices.insert(it->first);</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span> </div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="comment">//typename MapType::SpectrumType all_peaks = exp[it->first];</span></div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <a class="code" href="classdouble.html">DoubleReal</a> rt_average = consensus_spec.getRT();</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <a class="code" href="classdouble.html">DoubleReal</a> precursor_mz_average = 0.0;</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_count(0);</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keywordflow">if</span> (!consensus_spec.getPrecursors().empty())</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>  precursor_mz_average = consensus_spec.getPrecursors()[0].getMZ();</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  ++precursor_count;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  }</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> </div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  count_peaks_overall += consensus_spec.size();</div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="comment">// block elements</span></div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordflow">for</span> (std::vector<Size>::const_iterator sit = it->second.begin(); sit != it->second.end(); ++sit)</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  {</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  consensus_spec.unify(exp[*sit]); <span class="comment">// append meta info</span></div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  merged_indices.insert(*sit);</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span> </div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  rt_average += exp[*sit].getRT();</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keywordflow">if</span> (ms_level >= 2 && exp[*sit].getPrecursors().size() > 0)</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  {</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  precursor_mz_average += exp[*sit].getPrecursors()[0].getMZ();</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  ++precursor_count;</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> </div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="comment">// merge data points</span></div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  sas.<a class="code" href="classOpenMS_1_1SpectrumAlignment.html#a1e695a5349c395939217edc717effe84">getSpectrumAlignment</a>(alignment, consensus_spec, exp[*sit]);</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  <span class="comment">//std::cerr << "alignment of " << it->first << " with " << *sit << " yielded " << alignment.size() << " common peaks!\n";</span></div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  count_peaks_aligned += alignment.size();</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  count_peaks_overall += exp[*sit].size();</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>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> align_index(0);</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_b_index(0);</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>  <span class="comment">// sanity check for number of peaks</span></div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec_a = consensus_spec.size(), spec_b = exp[*sit].size(), align_size = alignment.size();</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordflow">for</span> (<span class="keyword">typename</span> MapType::SpectrumType::ConstIterator pit = exp[*sit].begin(); pit != exp[*sit].end(); ++pit)</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  {</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="comment">// either add aligned peak height to existing peak</span></div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keywordflow">if</span> (alignment.size() > 0 && alignment[align_index].second == spec_b_index)</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>  consensus_spec[alignment[align_index].first].setIntensity(consensus_spec[alignment[align_index].first].getIntensity() +</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  pit->getIntensity());</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  ++align_index; <span class="comment">// this aligned peak was explained, wait for next aligned peak ...</span></div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordflow">if</span> (align_index == alignment.size()) alignment.clear(); <span class="comment">// end reached -> avoid going into this block again</span></div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  }</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="keywordflow">else</span> <span class="comment">// ... or add unaligned peak</span></div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  {</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  consensus_spec.push_back(*pit);</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  }</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  ++spec_b_index;</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  }</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  consensus_spec.sortByPosition(); <span class="comment">// sort, otherwise next alignment will fail</span></div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  <span class="keywordflow">if</span> (spec_a + spec_b - align_size != consensus_spec.size()) std::cerr << <span class="stringliteral">"\n\n ERRROR \n\n"</span>;</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  }</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  rt_average /= it->second.size() + 1;</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  consensus_spec.setRT(rt_average);</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span> </div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="keywordflow">if</span> (ms_level >= 2)</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  {</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <span class="keywordflow">if</span> (precursor_count) precursor_mz_average /= precursor_count;</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  std::vector<Precursor> pcs = consensus_spec.getPrecursors();</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="comment">//if (pcs.size()>1) LOG_WARN << "Removing excessive precursors - leaving only one per MS2 spectrum.\n";</span></div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  pcs.resize(1);</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  pcs[0].setMZ(precursor_mz_average);</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  consensus_spec.setPrecursors(pcs);</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  }</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>  <span class="keywordflow">if</span> (consensus_spec.empty()) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="keywordflow">else</span> merged_spectra.addSpectrum(consensus_spec);</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</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>  <a class="code" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a> << <span class="stringliteral">"Cluster sizes:\n"</span>;</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="keywordflow">for</span> (<a class="code" href="classOpenMS_1_1Map.html">Map<Size, Size>::const_iterator</a> it = cluster_sizes.begin(); it != cluster_sizes.end(); ++it)</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  {</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  <a class="code" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a> << <span class="stringliteral">" size "</span> << it->first << <span class="stringliteral">": "</span> << it->second << <span class="stringliteral">"x\n"</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> </div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordtype">char</span> buffer[200];</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  sprintf(buffer, <span class="stringliteral">"%d/%d (%.2f %%) of blocked spectra"</span>, (<span class="keywordtype">int</span>)count_peaks_aligned,</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  (<span class="keywordtype">int</span>)count_peaks_overall, <span class="keywordtype">float</span>(count_peaks_aligned) / <span class="keywordtype">float</span>(count_peaks_overall) * 100.);</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <a class="code" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a> << <span class="stringliteral">"Number of merged peaks: "</span> << <a class="code" href="classOpenMS_1_1String.html">String</a>(buffer) << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span> </div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="comment">// remove all spectra that were within a cluster</span></div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keyword">typename</span> MapType::SpectrumType empty_spec;</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  MapType exp_tmp;</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < exp.size(); ++i)</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  {</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordflow">if</span> (merged_indices.count(i) == 0) <span class="comment">// save unclustered ones</span></div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  {</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  exp_tmp.addSpectrum(exp[i]);</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  exp[i] = empty_spec;</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  }</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> </div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="comment">//typedef std::vector<typename MapType::SpectrumType> Base;</span></div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="comment">//exp.Base::operator=(exp_tmp);</span></div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  exp.clear(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  exp.getSpectra().insert(exp.end(), exp_tmp.begin(), exp_tmp.end());</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span> </div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="comment">// exp.erase(remove_if(exp.begin(), exp.end(), InMSLevelRange<typename MapType::SpectrumType>(IntList::create(String(ms_level)), false)), exp.end());</span></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>  <span class="comment">// ... and add consensus spectra</span></div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  exp.getSpectra().insert(exp.end(), merged_spectra.begin(), merged_spectra.end());</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span> </div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  }</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span> </div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  };</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> }</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span> <span class="preprocessor">#endif //OPENMS_FILTERING_TRANSFORMERS_SPECTRAMERGER_H</span></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="StandardTypes_8h_html"><div class="ttname"><a href="StandardTypes_8h.html">StandardTypes.h</a></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_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="SingleLinkage_8h_html"><div class="ttname"><a href="SingleLinkage_8h.html">SingleLinkage.h</a></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="LogStream_8h_html_aeb4f36db01bd128c7afeac5889dac311"><div class="ttname"><a href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a></div><div class="ttdeci">#define LOG_INFO</div><div class="ttdoc">Macro if a information, e.g. a status should be reported. </div><div class="ttdef"><b>Definition:</b> LogStream.h:455</div></div>
<div class="ttc" id="classOpenMS_1_1ClusterAnalyzer_html"><div class="ttname"><a href="classOpenMS_1_1ClusterAnalyzer.html">OpenMS::ClusterAnalyzer</a></div><div class="ttdoc">Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode&#39;s) </div><div class="ttdef"><b>Definition:</b> ClusterAnalyzer.h:58</div></div>
<div class="ttc" id="RangeUtils_8h_html"><div class="ttname"><a href="RangeUtils_8h.html">RangeUtils.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_html_abe04755c7518a6ee530902afccc9c2e6"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger.html#abe04755c7518a6ee530902afccc9c2e6">OpenMS::SpectraMerger::mergeSpectra_</a></div><div class="ttdeci">void mergeSpectra_(MapType &exp, const MergeBlocks &spectra_to_merge, const UInt ms_level)</div><div class="ttdoc">merges blocks of spectra of a certain level </div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:296</div></div>
<div class="ttc" id="classOpenMS_1_1DistanceMatrix_html"><div class="ttname"><a href="classOpenMS_1_1DistanceMatrix.html">OpenMS::DistanceMatrix</a></div><div class="ttdoc">A two-dimensional distance matrix, similar to OpenMS::Matrix. </div><div class="ttdef"><b>Definition:</b> DistanceMatrix.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_html_aeaf496592f0320a1c46ed50236cc154d"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger.html#aeaf496592f0320a1c46ed50236cc154d">OpenMS::SpectraMerger::mergeSpectraBlockWise</a></div><div class="ttdeci">void mergeSpectraBlockWise(MapType &exp)</div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_html"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger.html">OpenMS::SpectraMerger</a></div><div class="ttdoc">Merges blocks of MS or MS2 spectra. </div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:61</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="group__Concept_html_gae113cb41304c6692c7bf5d0624dc6f0f"><div class="ttname"><a href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">OpenMS::SignedSize</a></div><div class="ttdeci">ptrdiff_t SignedSize</div><div class="ttdoc">Signed Size type e.g. used as pointer difference. </div><div class="ttdef"><b>Definition:</b> Types.h:151</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_ab4e0f356f837ce58e57695da114adce3"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">OpenMS::Peak2D::getRT</a></div><div class="ttdeci">CoordinateType getRT() const </div><div class="ttdoc">Returns the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:203</div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_abc8067511cfc949ae942ea2b08588f81"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">OpenMS::DefaultParamHandler::setParameters</a></div><div class="ttdeci">void setParameters(const Param &param)</div><div class="ttdoc">Sets the parameters. </div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_1_1SpectraDistance___html_a3e1ce06a993fb34b6500bb445f679855"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a3e1ce06a993fb34b6500bb445f679855">OpenMS::SpectraMerger::SpectraDistance_::SpectraDistance_</a></div><div class="ttdeci">SpectraDistance_()</div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html">OpenMS::BaseFeature</a></div><div class="ttdoc">A basic LC-MS feature. </div><div class="ttdef"><b>Definition:</b> BaseFeature.h:55</div></div>
<div class="ttc" id="LogStream_8h_html_aea3f57d6dcc5b4ac957e2679e87dde27"><div class="ttname"><a href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a></div><div class="ttdeci">#define LOG_WARN</div><div class="ttdoc">Macro if a warning, a piece of information which should be read by the user, should be logged...</div><div class="ttdef"><b>Definition:</b> LogStream.h:451</div></div>
<div class="ttc" id="ClusterAnalyzer_8h_html"><div class="ttname"><a href="ClusterAnalyzer_8h.html">ClusterAnalyzer.h</a></div></div>
<div class="ttc" id="ClusterHierarchical_8h_html"><div class="ttname"><a href="ClusterHierarchical_8h.html">ClusterHierarchical.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a396c5ebcac2e70f9b9a478bb2456985b"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">OpenMS::Peak2D::setRT</a></div><div class="ttdeci">void setRT(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:209</div></div>
<div class="ttc" id="CompleteLinkage_8h_html"><div class="ttname"><a href="CompleteLinkage_8h.html">CompleteLinkage.h</a></div></div>
<div class="ttc" id="BaseFeature_8h_html"><div class="ttname"><a href="BaseFeature_8h.html">BaseFeature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_1_1SpectraDistance___html"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html">OpenMS::SpectraMerger::SpectraDistance_</a></div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumAlignment_html"><div class="ttname"><a href="classOpenMS_1_1SpectrumAlignment.html">OpenMS::SpectrumAlignment</a></div><div class="ttdoc">Aligns the peaks of two spectra. </div><div class="ttdef"><b>Definition:</b> SpectrumAlignment.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html"><div class="ttname"><a href="classOpenMS_1_1Param.html">OpenMS::Param</a></div><div class="ttdoc">Management and storage of parameters / INI files. </div><div class="ttdef"><b>Definition:</b> Param.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_html_a3efb73bac53473f68d223255eaa465cc"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger.html#a3efb73bac53473f68d223255eaa465cc">OpenMS::SpectraMerger::MergeBlocks</a></div><div class="ttdeci">Map< Size, std::vector< Size > > MergeBlocks</div><div class="ttdoc">blocks of spectra (master-spectrum index to sacrifice-spectra(the ones being merged into the master-s...</div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak2D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Returns the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:191</div></div>
<div class="ttc" id="classOpenMS_1_1SingleLinkage_html"><div class="ttname"><a href="classOpenMS_1_1SingleLinkage.html">OpenMS::SingleLinkage</a></div><div class="ttdoc">SingleLinkage ClusterMethod. </div><div class="ttdef"><b>Definition:</b> SingleLinkage.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalSelfOperation_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalSelfOperation.html">OpenMS::Exception::IllegalSelfOperation</a></div><div class="ttdoc">Illegal self operation exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:379</div></div>
<div class="ttc" id="LogStream_8h_html"><div class="ttname"><a href="LogStream_8h.html">LogStream.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_1_1SpectraDistance___html_aa8aa5be634ab501e385beae080dc4b0c"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#aa8aa5be634ab501e385beae080dc4b0c">OpenMS::SpectraMerger::SpectraDistance_::operator()</a></div><div class="ttdeci">double operator()(const BaseFeature &first, const BaseFeature &second) const </div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:101</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_1SpectraMerger_1_1SpectraDistance___html_a928fb61988283ac1482ad929f7491ba6"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a928fb61988283ac1482ad929f7491ba6">OpenMS::SpectraMerger::SpectraDistance_::mz_max_</a></div><div class="ttdeci">DoubleReal mz_max_</div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:117</div></div>
<div class="ttc" id="SpectrumAlignment_8h_html"><div class="ttname"><a href="SpectrumAlignment_8h.html">SpectrumAlignment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_1_1SpectraDistance___html_a7fb55778db17a7d8a41e21f0828b962a"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#a7fb55778db17a7d8a41e21f0828b962a">OpenMS::SpectraMerger::SpectraDistance_::getSimilarity</a></div><div class="ttdeci">double getSimilarity(const DoubleReal d_rt, const DoubleReal d_mz) const </div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1ClusterAnalyzer_html_a1ddae30375fef566e4a1f53fb43baba9"><div class="ttname"><a href="classOpenMS_1_1ClusterAnalyzer.html#a1ddae30375fef566e4a1f53fb43baba9">OpenMS::ClusterAnalyzer::cut</a></div><div class="ttdeci">void cut(const Size cluster_quantity, const std::vector< BinaryTreeNode > &tree, std::vector< std::vector< Size > > &clusters)</div><div class="ttdoc">Method to calculate a partition resulting from a certain step in clustering given by the number of cl...</div></div>
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html_ae2f71a927933400ed5ce71513352e9ae"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html#ae2f71a927933400ed5ce71513352e9ae">OpenMS::ClusterHierarchical::cluster</a></div><div class="ttdeci">void cluster(std::vector< Data > &data, const SimilarityComparator &comparator, const ClusterFunctor &clusterer, std::vector< BinaryTreeNode > &cluster_tree, DistanceMatrix< Real > &original_distance)</div><div class="ttdoc">Clustering function. </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_html_a600d56293a3a35b7ef362d788c35eb99"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger.html#a600d56293a3a35b7ef362d788c35eb99">OpenMS::SpectraMerger::mergeSpectraPrecursors</a></div><div class="ttdeci">void mergeSpectraPrecursors(MapType &exp)</div><div class="ttdoc">merges spectra with similar precursors (must have MS2 level) </div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:201</div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_1_1SpectraDistance___html_addd12cc59f1a0dcd6b23ecd7fb291dfd"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#addd12cc59f1a0dcd6b23ecd7fb291dfd">OpenMS::SpectraMerger::SpectraDistance_::rt_max_</a></div><div class="ttdeci">DoubleReal rt_max_</div><div class="ttdef"><b>Definition:</b> SpectraMerger.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1ClusterHierarchical_html"><div class="ttname"><a href="classOpenMS_1_1ClusterHierarchical.html">OpenMS::ClusterHierarchical</a></div><div class="ttdoc">Hierarchical clustering with generic clustering functions. </div><div class="ttdef"><b>Definition:</b> ClusterHierarchical.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumAlignment_html_a1e695a5349c395939217edc717effe84"><div class="ttname"><a href="classOpenMS_1_1SpectrumAlignment.html#a1e695a5349c395939217edc717effe84">OpenMS::SpectrumAlignment::getSpectrumAlignment</a></div><div class="ttdeci">void getSpectrumAlignment(std::vector< std::pair< Size, Size > > &alignment, const SpectrumType &s1, const SpectrumType &s2) const </div><div class="ttdef"><b>Definition:</b> SpectrumAlignment.h:83</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_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1SpectraMerger_1_1SpectraDistance___html_aaf258e1a9846d9b238ee4b3005ad3ee9"><div class="ttname"><a href="classOpenMS_1_1SpectraMerger_1_1SpectraDistance__.html#aaf258e1a9846d9b238ee4b3005ad3ee9">OpenMS::SpectraMerger::SpectraDistance_::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> SpectraMerger.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1MissingInformation_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1MissingInformation.html">OpenMS::Exception::MissingInformation</a></div><div class="ttdoc">Not all required information provided. </div><div class="ttdef"><b>Definition:</b> Exception.h:196</div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html"><div class="ttname"><a href="classOpenMS_1_1IntList.html">OpenMS::IntList</a></div><div class="ttdoc">Int list. </div><div class="ttdef"><b>Definition:</b> IntList.h:56</div></div>
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