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<a href="IDMapper_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Chris Bielow $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Marc Sturm, Hendrik Weisser $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_ANALYSIS_ID_IDMAPPER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_ANALYSIS_ID_IDMAPPER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="ConsensusMap_8h.html">OpenMS/KERNEL/ConsensusMap.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="LogStream_8h.html">OpenMS/CONCEPT/LogStream.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;algorithm&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;<span class="preprocessor">#include &lt;limits&gt;</span></div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;{</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html">   62</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1IDMapper.html">IDMapper</a> :</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;  {</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bba67a1f968d5f74b3bf8e123eea735db42">   66</a></span>&#160;    <span class="keyword">enum</span> <a class="code" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">Measure</a> {MEASURE_PPM = 0, MEASURE_DA};</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <a class="code" href="classOpenMS_1_1IDMapper.html">IDMapper</a>();</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <a class="code" href="classOpenMS_1_1IDMapper.html">IDMapper</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IDMapper.html">IDMapper</a> &amp; cp);</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <a class="code" href="classOpenMS_1_1IDMapper.html">IDMapper</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1IDMapper.html">IDMapper</a> &amp; rhs);</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> PeakType&gt;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#ad8c436deda857f332e4d843d002e0717">   90</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDMapper.html#ad8c436deda857f332e4d843d002e0717">annotate</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment&lt;PeakType&gt;</a> &amp; map, <span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; ids, <span class="keyword">const</span> std::vector&lt;ProteinIdentification&gt; &amp; protein_ids)</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;    {</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      checkHits_(ids);</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;      <span class="comment">//append protein identifications</span></div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;      map.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().insert(map.<a class="code" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().end(), protein_ids.begin(), protein_ids.end());</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      <span class="comment">//store mapping of scan RT to index</span></div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      std::multimap&lt;DoubleReal, Size&gt; experiment_precursors;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; map.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); i++)</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      {</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;        experiment_precursors.insert(std::make_pair(map[i].getRT(), i));</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      }</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;      <span class="comment">//store mapping of identification RT to index</span></div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;      std::multimap&lt;DoubleReal, Size&gt; identifications_precursors;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt; ids.size(); i++)</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;      {</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        identifications_precursors.insert(std::make_pair(ids[i].getMetaValue(<span class="stringliteral">&quot;RT&quot;</span>), i));</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      }</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;      <span class="comment">//calculate the actual mapping</span></div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;      std::multimap&lt;DoubleReal, Size&gt;::iterator experiment_iterator = experiment_precursors.begin();</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      std::multimap&lt;DoubleReal, Size&gt;::iterator identifications_iterator = identifications_precursors.begin();</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> matches(0);</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      <span class="keywordflow">while</span> (experiment_iterator != experiment_precursors.end() &amp;&amp; identifications_iterator != identifications_precursors.end())</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      {</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        <span class="keywordflow">while</span> (identifications_iterator != identifications_precursors.end())</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        {</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;          <span class="comment">// testing whether the retention times are within the precision threshold</span></div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;          <span class="keywordflow">if</span> (fabs(experiment_iterator-&gt;first - identifications_iterator-&gt;first) &lt; rt_tolerance_)</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;          {</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;            <span class="comment">// testing whether the m/z fits</span></div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;            <span class="keywordflow">if</span> (!map[experiment_iterator-&gt;second].getPrecursors().<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;            {</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;              <span class="keywordflow">if</span> (fabs((<a class="code" href="classdouble.html">DoubleReal</a>)(ids[identifications_iterator-&gt;second].getMetaValue(<span class="stringliteral">&quot;MZ&quot;</span>)) - map[experiment_iterator-&gt;second].getPrecursors()[0].getMZ()) &lt; mz_tolerance_)</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;              {</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;                <span class="keywordflow">if</span> (!(ids[identifications_iterator-&gt;second].empty()))</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;                {</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;                  map[experiment_iterator-&gt;second].getPeptideIdentifications().push_back(ids[identifications_iterator-&gt;second]);</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;                  ++matches;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;                }</div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;              }</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;            }</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;          }</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;          ++identifications_iterator;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        }</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;        identifications_iterator = identifications_precursors.begin();</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;        ++experiment_iterator;</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;      }</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;      <span class="comment">// some statistics output</span></div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <a class="code" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a> &lt;&lt; <span class="stringliteral">&quot;Unassigned peptides: &quot;</span> &lt;&lt; ids.size() - matches &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span></div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;               &lt;&lt; <span class="stringliteral">&quot;Peptides assigned to a precursor: &quot;</span> &lt;&lt; matches &lt;&lt; std::endl;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;    }</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> FeatureType&gt;</div>
<div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#a8422c24016b4c5c9c358395cd307802d">  165</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1IDMapper.html#a8422c24016b4c5c9c358395cd307802d">annotate</a>(<a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap&lt;FeatureType&gt;</a> &amp; map, <span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; ids, <span class="keyword">const</span> std::vector&lt;ProteinIdentification&gt; &amp; protein_ids, <span class="keywordtype">bool</span> use_centroid_rt = <span class="keyword">false</span>, <span class="keywordtype">bool</span> use_centroid_mz = <span class="keyword">false</span>)</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;    {</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;      <span class="comment">// std::cout &lt;&lt; &quot;Starting annotation...&quot; &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;      checkHits_(ids);</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;      <span class="comment">// append protein identifications</span></div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      map.<a class="code" href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().insert(map.<a class="code" href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">getProteinIdentifications</a>().end(), protein_ids.begin(), protein_ids.end());</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;      <span class="comment">// check if all features have at least one convex hull</span></div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;      <span class="comment">// if not, use the centroid and the given tolerances</span></div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;      <span class="keywordflow">if</span> (!(use_centroid_rt &amp;&amp; use_centroid_mz))</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;      {</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;        <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1FeatureMap.html#ad436ba4f307bb17e3a999bf315125b33">FeatureMap&lt;FeatureType&gt;::Iterator</a> f_it = map.begin(); f_it != map.end(); ++f_it)</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;        {</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;          <span class="keywordflow">if</span> (f_it-&gt;getConvexHulls().empty())</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;          {</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;            use_centroid_rt = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;            use_centroid_mz = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;            <a class="code" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a> &lt;&lt; <span class="stringliteral">&quot;IDMapper warning: at least one feature has no convex hull - using centroid coordinates for matching&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;          }</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        }</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;      }</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;      <span class="keywordtype">bool</span> use_avg_mass = <span class="keyword">false</span>;           <span class="comment">// use avg. peptide masses for matching?</span></div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;      <span class="keywordflow">if</span> (use_centroid_mz &amp;&amp; (param_.getValue(<span class="stringliteral">&quot;mz_reference&quot;</span>) == <span class="stringliteral">&quot;peptide&quot;</span>))</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;      {</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;        <span class="comment">// if possible, check which m/z value is reported for features,</span></div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;        <span class="comment">// so the appropriate peptide mass can be used for matching</span></div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;        use_avg_mass = checkMassType_(map.<a class="code" href="classOpenMS_1_1FeatureMap.html#ae131ea2ec923582f86aa9805e72241ad">getDataProcessing</a>());</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;      }</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;      <span class="comment">// calculate feature bounding boxes only once:</span></div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;      std::vector&lt;DBoundingBox&lt;2&gt; &gt; boxes;</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> min_rt = std::numeric_limits&lt;DoubleReal&gt;::max(),</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;                 max_rt = -std::numeric_limits&lt;DoubleReal&gt;::max();</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;      <span class="comment">// std::cout &lt;&lt; &quot;Precomputing bounding boxes...&quot; &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;      boxes.reserve(map.size());</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1FeatureMap.html#ad436ba4f307bb17e3a999bf315125b33">FeatureMap&lt;FeatureType&gt;::Iterator</a> f_it = map.begin();</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;           f_it != map.end(); ++f_it)</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;      {</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;        <a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> box;</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;        <span class="keywordflow">if</span> (!(use_centroid_rt &amp;&amp; use_centroid_mz))</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;        {</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;          box = f_it-&gt;getConvexHull().getBoundingBox();</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;        }</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;        <span class="keywordflow">if</span> (use_centroid_rt)</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;        {</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;          box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a9f4dd5aa564dcc541a0d5a271e22e6a0">setMinX</a>(f_it-&gt;getRT());</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;          box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#adcf69cae2f91d868b8defd2b12aad4ed">setMaxX</a>(f_it-&gt;getRT());</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;        }</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;        <span class="keywordflow">if</span> (use_centroid_mz)</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;        {</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;          box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a3faa28974e310e9743446f1c184496a6">setMinY</a>(f_it-&gt;getMZ());</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;          box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a71b4e57973d9ad60975b774f4eeaef06">setMaxY</a>(f_it-&gt;getMZ());</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        }</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;        increaseBoundingBox_(box);</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;        boxes.push_back(box);</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;        min_rt = std::min(min_rt, box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>().getX());</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;        max_rt = std::max(max_rt, box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>().getX());</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;      }</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;      <span class="comment">// hash bounding boxes of features by RT:</span></div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;      <span class="comment">// RT range is partitioned into slices (bins) of 1 second; every feature</span></div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;      <span class="comment">// that overlaps a certain slice is hashed into the corresponding bin</span></div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;      std::vector&lt;std::vector&lt;SignedSize&gt; &gt; hash_table;</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;      <span class="comment">// make sure the RT hash table has indices &gt;= 0 and doesn&#39;t waste space</span></div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;      <span class="comment">// in the beginning:</span></div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;      <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> offset(0);</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;      <span class="keywordflow">if</span> (map.size() &gt; 0)</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;      {</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;        <span class="comment">// std::cout &lt;&lt; &quot;Setting up hash table...&quot; &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;        offset = <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>(floor(min_rt));</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;        <span class="comment">// this only works if features were found</span></div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;        hash_table.resize(<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>(floor(max_rt)) - offset + 1);</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = 0; index &lt; boxes.size(); ++index)</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;        {</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;          <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> &amp; box = boxes[index];</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;          <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> i = <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>(floor(box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">minPosition</a>().getX()));</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;               i &lt;= <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>(floor(box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">maxPosition</a>().getX())); ++i)</div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;          {</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;            hash_table[i - offset].push_back(index);</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;          }</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;        }</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;      }</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;      <span class="keywordflow">else</span></div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;      {</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;        <a class="code" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a> &lt;&lt; <span class="stringliteral">&quot;IDMapper received an empty FeatureMap! All peptides are mapped as &#39;unassigned&#39;!&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;      }</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;      <span class="comment">// for statistics:</span></div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> matches_none = 0, matches_single = 0, matches_multi = 0;</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;      <span class="comment">// std::cout &lt;&lt; &quot;Finding matches...&quot; &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;      <span class="comment">// iterate over peptide IDs:</span></div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;      <span class="keywordflow">for</span> (std::vector&lt;PeptideIdentification&gt;::const_iterator id_it =</div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;             ids.begin(); id_it != ids.end(); ++id_it)</div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;      {</div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;        <span class="comment">// std::cout &lt;&lt; &quot;Peptide ID: &quot; &lt;&lt; id_it - ids.begin() &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;        <span class="keywordflow">if</span> (id_it-&gt;getHits().empty()) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;        <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> mz_values;</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;        <a class="code" href="classdouble.html">DoubleReal</a> rt_value;</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;        <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> charges;</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;        getIDDetails_(*id_it, rt_value, mz_values, charges, use_avg_mass);</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;        <span class="keywordflow">if</span> ((rt_value &lt; min_rt) || (rt_value &gt; max_rt))             <span class="comment">// RT out of bounds</span></div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;        {</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;          map.<a class="code" href="classOpenMS_1_1FeatureMap.html#a001ea2eb2a9c05266a69f50594f25604">getUnassignedPeptideIdentifications</a>().push_back(*id_it);</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;          ++matches_none;</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;          <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;        }</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;        <span class="comment">// iterate over candidate features:</span></div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = <a class="code" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>(floor(rt_value)) - offset;</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> matching_features = 0;</div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;        <span class="keywordflow">for</span> (std::vector&lt;SignedSize&gt;::iterator hash_it =</div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;               hash_table[index].begin(); hash_it != hash_table[index].end();</div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;             ++hash_it)</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;        {</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;          <a class="code" href="classOpenMS_1_1Feature.html">Feature</a> &amp; feat = map[*hash_it];</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;          <span class="comment">// need to check the charge state?</span></div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;          <span class="keywordtype">bool</span> check_charge = !ignore_charge_;</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;          <span class="keywordflow">if</span> (check_charge &amp;&amp; (mz_values.size() == 1))               <span class="comment">// check now</span></div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;          {</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;            <span class="keywordflow">if</span> (!charges.<a class="code" href="classOpenMS_1_1IntList.html#ac2d1b0c3af7939b2b7d5e74607166d9c">contains</a>(feat.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>())) <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;            check_charge = <span class="keyword">false</span>;                 <span class="comment">// don&#39;t need to check later</span></div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;          }</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;          <span class="comment">// iterate over m/z values (only one if &quot;mz_ref.&quot; is &quot;precursor&quot;):</span></div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;          <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> index = 0;</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;          <span class="keywordflow">for</span> (DoubleList::iterator mz_it = mz_values.begin();</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;               mz_it != mz_values.end(); ++mz_it, ++index)</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;          {</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;            <span class="keywordflow">if</span> (check_charge &amp;&amp; (charges[index] != feat.<a class="code" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">getCharge</a>()))</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;            {</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;              <span class="keywordflow">continue</span>;                   <span class="comment">// charge states need to match</span></div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;            }</div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;            <a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;2&gt;</a> id_pos(rt_value, *mz_it);</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;            <span class="keywordflow">if</span> (boxes[*hash_it].encloses(id_pos))                 <span class="comment">// potential match</span></div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;            {</div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;              <span class="keywordflow">if</span> (use_centroid_mz)</div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;              {</div>
<div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;                <span class="comment">// only one m/z value to check, which was alredy incorporated</span></div>
<div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;                <span class="comment">// into the overall bounding box -&gt; success!</span></div>
<div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;                feat.<a class="code" href="classOpenMS_1_1BaseFeature.html#a9f20adb44d57c28c422619779488de17">getPeptideIdentifications</a>().push_back(*id_it);</div>
<div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;                ++matching_features;</div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;                <span class="keywordflow">break</span>;                     <span class="comment">// &quot;mz_it&quot; loop</span></div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;              }</div>
<div class="line"><a name="l00319"></a><span class="lineno">  319</span>&#160;              <span class="comment">// else: check all the mass traces</span></div>
<div class="line"><a name="l00320"></a><span class="lineno">  320</span>&#160;              <span class="keywordtype">bool</span> found_match = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00321"></a><span class="lineno">  321</span>&#160;              <span class="keywordflow">for</span> (std::vector&lt;ConvexHull2D&gt;::iterator ch_it =</div>
<div class="line"><a name="l00322"></a><span class="lineno">  322</span>&#160;                     feat.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().begin(); ch_it !=</div>
<div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;                   feat.<a class="code" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">getConvexHulls</a>().end(); ++ch_it)</div>
<div class="line"><a name="l00324"></a><span class="lineno">  324</span>&#160;              {</div>
<div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;                <a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> box = ch_it-&gt;getBoundingBox();</div>
<div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;                <span class="keywordflow">if</span> (use_centroid_rt)</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;                {</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;                  box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a9f4dd5aa564dcc541a0d5a271e22e6a0">setMinX</a>(feat.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>());</div>
<div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;                  box.<a class="code" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#adcf69cae2f91d868b8defd2b12aad4ed">setMaxX</a>(feat.<a class="code" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">getRT</a>());</div>
<div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;                }</div>
<div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;                increaseBoundingBox_(box);</div>
<div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;                <span class="keywordflow">if</span> (box.<a class="code" href="classOpenMS_1_1DBoundingBox.html#ac55b302033b5b9d7c78a223db8cfaffb">encloses</a>(id_pos))                     <span class="comment">// success!</span></div>
<div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;                {</div>
<div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;                  feat.<a class="code" href="classOpenMS_1_1BaseFeature.html#a9f20adb44d57c28c422619779488de17">getPeptideIdentifications</a>().push_back(*id_it);</div>
<div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;                  ++matching_features;</div>
<div class="line"><a name="l00336"></a><span class="lineno">  336</span>&#160;                  found_match = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00337"></a><span class="lineno">  337</span>&#160;                  <span class="keywordflow">break</span>;                       <span class="comment">// &quot;ch_it&quot; loop</span></div>
<div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;                }</div>
<div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;              }</div>
<div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;              <span class="keywordflow">if</span> (found_match) <span class="keywordflow">break</span>;                   <span class="comment">// &quot;mz_it&quot; loop</span></div>
<div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;            }</div>
<div class="line"><a name="l00342"></a><span class="lineno">  342</span>&#160;          }</div>
<div class="line"><a name="l00343"></a><span class="lineno">  343</span>&#160;        }</div>
<div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;        <span class="keywordflow">if</span> (matching_features == 0)</div>
<div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;        {</div>
<div class="line"><a name="l00346"></a><span class="lineno">  346</span>&#160;          map.<a class="code" href="classOpenMS_1_1FeatureMap.html#a001ea2eb2a9c05266a69f50594f25604">getUnassignedPeptideIdentifications</a>().push_back(*id_it);</div>
<div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;          ++matches_none;</div>
<div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;        }</div>
<div class="line"><a name="l00349"></a><span class="lineno">  349</span>&#160;        <span class="keywordflow">else</span> <span class="keywordflow">if</span> (matching_features == 1) ++matches_single;</div>
<div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;        <span class="keywordflow">else</span> ++matches_multi;</div>
<div class="line"><a name="l00351"></a><span class="lineno">  351</span>&#160;      }</div>
<div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;</div>
<div class="line"><a name="l00353"></a><span class="lineno">  353</span>&#160;      <span class="comment">// some statistics output</span></div>
<div class="line"><a name="l00354"></a><span class="lineno">  354</span>&#160;      <a class="code" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a> &lt;&lt; <span class="stringliteral">&quot;Unassigned peptides: &quot;</span> &lt;&lt; matches_none &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span></div>
<div class="line"><a name="l00355"></a><span class="lineno">  355</span>&#160;               &lt;&lt; <span class="stringliteral">&quot;Peptides assigned to exactly one feature: &quot;</span> &lt;&lt; matches_single &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span></div>
<div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;               &lt;&lt; <span class="stringliteral">&quot;Peptides assigned to multiple features: &quot;</span> &lt;&lt; matches_multi &lt;&lt; <span class="stringliteral">&quot;\n&quot;</span></div>
<div class="line"><a name="l00357"></a><span class="lineno">  357</span>&#160;               &lt;&lt; map.<a class="code" href="classOpenMS_1_1FeatureMap.html#a4f40a3d8606e7855a7b3c12620bf9f58">getAnnotationStatistics</a>()</div>
<div class="line"><a name="l00358"></a><span class="lineno">  358</span>&#160;               &lt;&lt; std::endl;</div>
<div class="line"><a name="l00359"></a><span class="lineno">  359</span>&#160;</div>
<div class="line"><a name="l00360"></a><span class="lineno">  360</span>&#160;    }</div>
<div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;</div>
<div class="line"><a name="l00375"></a><span class="lineno">  375</span>&#160;    <span class="keywordtype">void</span> annotate(<a class="code" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp; map, <span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; ids, <span class="keyword">const</span> std::vector&lt;ProteinIdentification&gt; &amp; protein_ids, <span class="keywordtype">bool</span> measure_from_subelements = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;</div>
<div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;    <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;</div>
<div class="line"><a name="l00381"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#a73f60e6ff36e6b7fd8f631003521843c">  381</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1IDMapper.html#a73f60e6ff36e6b7fd8f631003521843c">rt_tolerance_</a>;</div>
<div class="line"><a name="l00383"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#aa0d44a6be23374eb5d1f099ef8b4ca82">  383</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1IDMapper.html#aa0d44a6be23374eb5d1f099ef8b4ca82">mz_tolerance_</a>;</div>
<div class="line"><a name="l00385"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#a1324e22761bf35562937e88a4a58d8b5">  385</a></span>&#160;    <a class="code" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">Measure</a> <a class="code" href="classOpenMS_1_1IDMapper.html#a1324e22761bf35562937e88a4a58d8b5">measure_</a>;</div>
<div class="line"><a name="l00387"></a><span class="lineno"><a class="line" href="classOpenMS_1_1IDMapper.html#ad08b3e80b01e59cb4986dba46f212234">  387</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1IDMapper.html#ad08b3e80b01e59cb4986dba46f212234">ignore_charge_</a>;</div>
<div class="line"><a name="l00388"></a><span class="lineno">  388</span>&#160;</div>
<div class="line"><a name="l00392"></a><span class="lineno">  392</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> getAbsoluteMZTolerance_(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> mz) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00393"></a><span class="lineno">  393</span>&#160;</div>
<div class="line"><a name="l00395"></a><span class="lineno">  395</span>&#160;    <span class="keywordtype">bool</span> isMatch_(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> rt_distance, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> mz_theoretical, <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> mz_observed) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00396"></a><span class="lineno">  396</span>&#160;</div>
<div class="line"><a name="l00398"></a><span class="lineno">  398</span>&#160;    <span class="keywordtype">void</span> checkHits_(<span class="keyword">const</span> std::vector&lt;PeptideIdentification&gt; &amp; ids) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00399"></a><span class="lineno">  399</span>&#160;</div>
<div class="line"><a name="l00403"></a><span class="lineno">  403</span>&#160;    <span class="keywordtype">void</span> getIDDetails_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &amp; <span class="keywordtype">id</span>, <a class="code" href="classdouble.html">DoubleReal</a> &amp; rt_pep, <a class="code" href="classOpenMS_1_1DoubleList.html">DoubleList</a> &amp; mz_values, <a class="code" href="classOpenMS_1_1IntList.html">IntList</a> &amp; charges, <span class="keywordtype">bool</span> use_avg_mass = <span class="keyword">false</span>) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00404"></a><span class="lineno">  404</span>&#160;</div>
<div class="line"><a name="l00406"></a><span class="lineno">  406</span>&#160;    <span class="keywordtype">void</span> increaseBoundingBox_(<a class="code" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox&lt;2&gt;</a> &amp; box);</div>
<div class="line"><a name="l00407"></a><span class="lineno">  407</span>&#160;</div>
<div class="line"><a name="l00410"></a><span class="lineno">  410</span>&#160;    <span class="keywordtype">bool</span> checkMassType_(<span class="keyword">const</span> std::vector&lt;DataProcessing&gt; &amp; processing) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00411"></a><span class="lineno">  411</span>&#160;</div>
<div class="line"><a name="l00412"></a><span class="lineno">  412</span>&#160;  };</div>
<div class="line"><a name="l00413"></a><span class="lineno">  413</span>&#160;</div>
<div class="line"><a name="l00414"></a><span class="lineno">  414</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00415"></a><span class="lineno">  415</span>&#160;</div>
<div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_ID_IDMAPPER_H</span></div>
<div class="ttc" id="classOpenMS_1_1DBoundingBox_html_ac55b302033b5b9d7c78a223db8cfaffb"><div class="ttname"><a href="classOpenMS_1_1DBoundingBox.html#ac55b302033b5b9d7c78a223db8cfaffb">OpenMS::DBoundingBox::encloses</a></div><div class="ttdeci">bool encloses(const PositionType &amp;position) const </div><div class="ttdoc">Checks whether this range contains a certain point. </div><div class="ttdef"><b>Definition:</b> DBoundingBox.h:159</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_ac80a487ac41c375532f8bff16871ae15"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">OpenMS::BaseFeature::getCharge</a></div><div class="ttdeci">const ChargeType &amp; getCharge() const </div><div class="ttdoc">Non-mutable access to charge state. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_adcf69cae2f91d868b8defd2b12aad4ed"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#adcf69cae2f91d868b8defd2b12aad4ed">OpenMS::Internal::DIntervalBase::setMaxX</a></div><div class="ttdeci">void setMaxX(CoordinateType const c)</div><div class="ttdoc">Mutator for min_ coordinate of the larger point. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:278</div></div>
<div class="ttc" id="classOpenMS_1_1BaseFeature_html_a9f20adb44d57c28c422619779488de17"><div class="ttname"><a href="classOpenMS_1_1BaseFeature.html#a9f20adb44d57c28c422619779488de17">OpenMS::BaseFeature::getPeptideIdentifications</a></div><div class="ttdeci">const std::vector&lt; PeptideIdentification &gt; &amp; getPeptideIdentifications() const </div><div class="ttdoc">returns a const reference to the PeptideIdentification vector </div></div>
<div class="ttc" id="classOpenMS_1_1IntList_html_ac2d1b0c3af7939b2b7d5e74607166d9c"><div class="ttname"><a href="classOpenMS_1_1IntList.html#ac2d1b0c3af7939b2b7d5e74607166d9c">OpenMS::IntList::contains</a></div><div class="ttdeci">bool contains(Int s) const </div><div class="ttdoc">Returns if a string is contains in the list. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a3faa28974e310e9743446f1c184496a6"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a3faa28974e310e9743446f1c184496a6">OpenMS::Internal::DIntervalBase::setMinY</a></div><div class="ttdeci">void setMinY(CoordinateType const c)</div><div class="ttdoc">Mutator for max_ coordinate of the smaller point. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:271</div></div>
<div class="ttc" id="ConsensusMap_8h_html"><div class="ttname"><a href="ConsensusMap_8h.html">ConsensusMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_acef58bf2531b77d0191c4780739281c6"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">OpenMS::FeatureMap::getProteinIdentifications</a></div><div class="ttdeci">const std::vector&lt; ProteinIdentification &gt; &amp; getProteinIdentifications() const </div><div class="ttdoc">non-mutable access to the protein identifications </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:410</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_1ExperimentalSettings_html_acef58bf2531b77d0191c4780739281c6"><div class="ttname"><a href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">OpenMS::ExperimentalSettings::getProteinIdentifications</a></div><div class="ttdeci">const std::vector&lt; ProteinIdentification &gt; &amp; getProteinIdentifications() const </div><div class="ttdoc">returns a const reference to the protein ProteinIdentification vector </div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a4f40a3d8606e7855a7b3c12620bf9f58"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a4f40a3d8606e7855a7b3c12620bf9f58">OpenMS::FeatureMap::getAnnotationStatistics</a></div><div class="ttdeci">AnnotationStatistics getAnnotationStatistics() const </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:520</div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_a8422c24016b4c5c9c358395cd307802d"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#a8422c24016b4c5c9c358395cd307802d">OpenMS::IDMapper::annotate</a></div><div class="ttdeci">void annotate(FeatureMap&lt; FeatureType &gt; &amp;map, const std::vector&lt; PeptideIdentification &gt; &amp;ids, const std::vector&lt; ProteinIdentification &gt; &amp;protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false)</div><div class="ttdoc">Mapping method for feature maps. </div><div class="ttdef"><b>Definition:</b> IDMapper.h:165</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap</a></div><div class="ttdoc">A container for features. </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:111</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a71b4e57973d9ad60975b774f4eeaef06"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a71b4e57973d9ad60975b774f4eeaef06">OpenMS::Internal::DIntervalBase::setMaxY</a></div><div class="ttdeci">void setMaxY(CoordinateType const c)</div><div class="ttdoc">Mutator for max_ coordinate of the larger point. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:285</div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html">OpenMS::IDMapper</a></div><div class="ttdoc">Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. </div><div class="ttdef"><b>Definition:</b> IDMapper.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_a001ea2eb2a9c05266a69f50594f25604"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#a001ea2eb2a9c05266a69f50594f25604">OpenMS::FeatureMap::getUnassignedPeptideIdentifications</a></div><div class="ttdeci">const std::vector&lt; PeptideIdentification &gt; &amp; getUnassignedPeptideIdentifications() const </div><div class="ttdoc">non-mutable access to the unassigned peptide identifications </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:428</div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_afb571f7e4181db2c9a40dd64f8dce6bb"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">OpenMS::IDMapper::Measure</a></div><div class="ttdeci">Measure</div><div class="ttdef"><b>Definition:</b> IDMapper.h:66</div></div>
<div class="ttc" id="classOpenMS_1_1ConsensusMap_html"><div class="ttname"><a href="classOpenMS_1_1ConsensusMap.html">OpenMS::ConsensusMap</a></div><div class="ttdoc">A container for consensus elements. </div><div class="ttdef"><b>Definition:</b> ConsensusMap.h:60</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="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="classOpenMS_1_1FeatureMap_html_ae131ea2ec923582f86aa9805e72241ad"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#ae131ea2ec923582f86aa9805e72241ad">OpenMS::FeatureMap::getDataProcessing</a></div><div class="ttdeci">const std::vector&lt; DataProcessing &gt; &amp; getDataProcessing() const </div><div class="ttdoc">returns a const reference to the description of the applied data processing </div><div class="ttdef"><b>Definition:</b> FeatureMap.h:446</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_aa0d44a6be23374eb5d1f099ef8b4ca82"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#aa0d44a6be23374eb5d1f099ef8b4ca82">OpenMS::IDMapper::mz_tolerance_</a></div><div class="ttdeci">DoubleReal mz_tolerance_</div><div class="ttdoc">Allowed m/z deviation. </div><div class="ttdef"><b>Definition:</b> IDMapper.h:383</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition&lt; 2 &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html_ad99bb8ba2103d6c52ee10ae6369b46e7"><div class="ttname"><a href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">OpenMS::Feature::getConvexHulls</a></div><div class="ttdeci">const std::vector&lt; ConvexHull2D &gt; &amp; getConvexHulls() const </div><div class="ttdoc">Non-mutable access to the convex hulls. </div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_ad08b3e80b01e59cb4986dba46f212234"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#ad08b3e80b01e59cb4986dba46f212234">OpenMS::IDMapper::ignore_charge_</a></div><div class="ttdeci">bool ignore_charge_</div><div class="ttdoc">Ignore charge states during matching? </div><div class="ttdef"><b>Definition:</b> IDMapper.h:387</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureMap_html_ad436ba4f307bb17e3a999bf315125b33"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html#ad436ba4f307bb17e3a999bf315125b33">OpenMS::FeatureMap::Iterator</a></div><div class="ttdeci">Base::iterator Iterator</div><div class="ttdef"><b>Definition:</b> FeatureMap.h:154</div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</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_1Internal_1_1DIntervalBase_html_a84873a73e9e222a574dccff3bc2d860e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">OpenMS::Internal::DIntervalBase::minPosition</a></div><div class="ttdeci">PositionType const &amp; minPosition() const </div><div class="ttdoc">Accessor to minimum position. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:121</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="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_1MSExperiment_html_ac6e61de369e994009e36f344f99c15ad"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">OpenMS::MSExperiment::empty</a></div><div class="ttdeci">bool empty() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_a9f4dd5aa564dcc541a0d5a271e22e6a0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a9f4dd5aa564dcc541a0d5a271e22e6a0">OpenMS::Internal::DIntervalBase::setMinX</a></div><div class="ttdeci">void setMinX(CoordinateType const c)</div><div class="ttdoc">Mutator for min_ coordinate of the smaller point. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:264</div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_a1324e22761bf35562937e88a4a58d8b5"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#a1324e22761bf35562937e88a4a58d8b5">OpenMS::IDMapper::measure_</a></div><div class="ttdeci">Measure measure_</div><div class="ttdoc">Measure used for m/z. </div><div class="ttdef"><b>Definition:</b> IDMapper.h:385</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1DIntervalBase_html_ac093fc547d9a49aef9950f6cd92b5588"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">OpenMS::Internal::DIntervalBase::maxPosition</a></div><div class="ttdeci">PositionType const &amp; maxPosition() const </div><div class="ttdoc">Accessor to maximum position. </div><div class="ttdef"><b>Definition:</b> DIntervalBase.h:127</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_1DBoundingBox_html"><div class="ttname"><a href="classOpenMS_1_1DBoundingBox.html">OpenMS::DBoundingBox</a></div><div class="ttdoc">A D-dimensional bounding box. </div><div class="ttdef"><b>Definition:</b> DBoundingBox.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_a73f60e6ff36e6b7fd8f631003521843c"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#a73f60e6ff36e6b7fd8f631003521843c">OpenMS::IDMapper::rt_tolerance_</a></div><div class="ttdeci">DoubleReal rt_tolerance_</div><div class="ttdoc">Allowed RT deviation. </div><div class="ttdef"><b>Definition:</b> IDMapper.h:381</div></div>
<div class="ttc" id="classOpenMS_1_1IDMapper_html_ad8c436deda857f332e4d843d002e0717"><div class="ttname"><a href="classOpenMS_1_1IDMapper.html#ad8c436deda857f332e4d843d002e0717">OpenMS::IDMapper::annotate</a></div><div class="ttdeci">void annotate(MSExperiment&lt; PeakType &gt; &amp;map, const std::vector&lt; PeptideIdentification &gt; &amp;ids, const std::vector&lt; ProteinIdentification &gt; &amp;protein_ids)</div><div class="ttdoc">Mapping method for peak maps. </div><div class="ttdef"><b>Definition:</b> IDMapper.h:90</div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DoubleList_html"><div class="ttname"><a href="classOpenMS_1_1DoubleList.html">OpenMS::DoubleList</a></div><div class="ttdoc">DoubleReal list. </div><div class="ttdef"><b>Definition:</b> DoubleList.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1PeptideIdentification_html"><div class="ttname"><a href="classOpenMS_1_1PeptideIdentification.html">OpenMS::PeptideIdentification</a></div><div class="ttdoc">Represents the peptide hits for a spectrum. </div><div class="ttdef"><b>Definition:</b> PeptideIdentification.h:63</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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