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<a href="FeatureDistance_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>
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<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hendrik Weisser $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Clemens Groepl, Hendrik Weisser, Chris Bielow $</span></div>
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<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_MAPMATCHING_FEATUREDISTANCE_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_MAPMATCHING_FEATUREDISTANCE_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="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.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="BaseFeature_8h.html">OpenMS/KERNEL/BaseFeature.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;limits&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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;{</div>
<div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html">   76</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> :</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;  {</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">   81</a></span>&#160;    <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a>(<a class="code" href="classdouble.html">DoubleReal</a> max_intensity = 1.0,</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;                    <span class="keywordtype">bool</span> force_constraints = <span class="keyword">false</span>);</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a>();</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    <a class="code" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> &amp; other);</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;    std::pair&lt;bool, DoubleReal&gt; operator()(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> &amp; left,</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;                                           <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> &amp; right);</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00108"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">  108</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a></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"><a class="line" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a96ddc0648f545442920fe809a32748cb">  110</a></span>&#160;      <a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a96ddc0648f545442920fe809a32748cb">DistanceParams_</a>() {}</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;</div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#aa5ed70e5ae48b3fe67720bc2faa5db44">  112</a></span>&#160;      <a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#aa5ed70e5ae48b3fe67720bc2faa5db44">DistanceParams_</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a> &amp; what, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; global)</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      {</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;        <a class="code" href="classOpenMS_1_1Param.html">Param</a> param = global.<a class="code" href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">copy</a>(<span class="stringliteral">&quot;distance_&quot;</span> + what + <span class="stringliteral">&quot;:&quot;</span>, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;        <span class="keywordflow">if</span> (what == <span class="stringliteral">&quot;MZ&quot;</span>) max_diff_ppm = param.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;unit&quot;</span>) == <span class="stringliteral">&quot;ppm&quot;</span>;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        <span class="keywordflow">else</span> max_diff_ppm = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        max_difference = param.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;max_difference&quot;</span>);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        exponent = param.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;exponent&quot;</span>);</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;        weight = param.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;weight&quot;</span>);</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        norm_factor = 1 / max_difference;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        relevant = (weight != 0.0) &amp;&amp; (exponent != 0.0);</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        <span class="keywordflow">if</span> (!relevant) weight = 0.0;</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;      }</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"><a class="line" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a912b8ba7b2a6ccc272b1423bcb9d769b">  125</a></span>&#160;      <a class="code" href="classdouble.html">DoubleReal</a> max_difference, exponent, <a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a912b8ba7b2a6ccc272b1423bcb9d769b">weight</a>, norm_factor;</div>
<div class="line"><a name="l00126"></a><span class="lineno"><a class="line" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a398fb09ef444497b2e3506b5b229b187">  126</a></span>&#160;      <span class="keywordtype">bool</span> max_diff_ppm, <a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a398fb09ef444497b2e3506b5b229b187">relevant</a>;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    };</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;    <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> distance_(<a class="code" href="classdouble.html">DoubleReal</a> diff, <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> &amp; params) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;</div>
<div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html#a3c454c044130ed7f7e5fe6c979d952af">  136</a></span>&#160;    <a class="code" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> <a class="code" href="classOpenMS_1_1FeatureDistance.html#a3c454c044130ed7f7e5fe6c979d952af">params_rt_</a>, params_mz_, params_intensity_;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;</div>
<div class="line"><a name="l00139"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html#a42bbf59694a9e5f5057c7229c3e5bc5e">  139</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureDistance.html#a42bbf59694a9e5f5057c7229c3e5bc5e">total_weight_reciprocal_</a>;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html#a247d330613019e713377dbdf503f78b7">  142</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1FeatureDistance.html#a247d330613019e713377dbdf503f78b7">max_intensity_</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;</div>
<div class="line"><a name="l00145"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html#ad08b3e80b01e59cb4986dba46f212234">  145</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureDistance.html#ad08b3e80b01e59cb4986dba46f212234">ignore_charge_</a>;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00148"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureDistance.html#a744a160e6b8a32a60e7ea7ed535421aa">  148</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1FeatureDistance.html#a744a160e6b8a32a60e7ea7ed535421aa">force_constraints_</a>;</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;  };</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;<span class="preprocessor">#endif  // OPENMS_ANALYSIS_MAPMATCHING_FEATUREDISTANCE_H</span></div>
<div class="ttc" id="classOpenMS_1_1FeatureDistance_html"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html">OpenMS::FeatureDistance</a></div><div class="ttdoc">A functor class for the calculation of distances between features or consensus features. </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:76</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureDistance_1_1DistanceParams___html"><div class="ttname"><a href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">OpenMS::FeatureDistance::DistanceParams_</a></div><div class="ttdoc">Structure for storing distance parameters. </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureDistance_html_ac2d2e8a0d437237b160e465808fdf20e"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">OpenMS::FeatureDistance::infinity</a></div><div class="ttdeci">static const DoubleReal infinity</div><div class="ttdoc">Value to return if max. difference is exceeded or if charge states don&amp;#39;t match. </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:81</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureDistance_1_1DistanceParams___html_a96ddc0648f545442920fe809a32748cb"><div class="ttname"><a href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a96ddc0648f545442920fe809a32748cb">OpenMS::FeatureDistance::DistanceParams_::DistanceParams_</a></div><div class="ttdeci">DistanceParams_()</div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:110</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></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_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="classOpenMS_1_1Param_html_a25319a96118d2373efc5af9c8679b98b"><div class="ttname"><a href="classOpenMS_1_1Param.html#a25319a96118d2373efc5af9c8679b98b">OpenMS::Param::copy</a></div><div class="ttdeci">Param copy(const String &amp;prefix, bool remove_prefix=false) const </div><div class="ttdoc">Returns a new Param object containing all entries that start with prefix. </div></div>
<div class="ttc" id="structOpenMS_1_1FeatureDistance_1_1DistanceParams___html_aa5ed70e5ae48b3fe67720bc2faa5db44"><div class="ttname"><a href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#aa5ed70e5ae48b3fe67720bc2faa5db44">OpenMS::FeatureDistance::DistanceParams_::DistanceParams_</a></div><div class="ttdeci">DistanceParams_(const String &amp;what, const Param &amp;global)</div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:112</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue &amp; getValue(const String &amp;key) const </div><div class="ttdoc">Returns a value of a parameter. </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_1FeatureDistance_html_a3c454c044130ed7f7e5fe6c979d952af"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html#a3c454c044130ed7f7e5fe6c979d952af">OpenMS::FeatureDistance::params_rt_</a></div><div class="ttdeci">DistanceParams_ params_rt_</div><div class="ttdoc">Storage of parameters for the individual distance components. </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:136</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureDistance_html_a42bbf59694a9e5f5057c7229c3e5bc5e"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html#a42bbf59694a9e5f5057c7229c3e5bc5e">OpenMS::FeatureDistance::total_weight_reciprocal_</a></div><div class="ttdeci">DoubleReal total_weight_reciprocal_</div><div class="ttdoc">Reciprocal value of the total weight in the distance function. </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:139</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_1FeatureDistance_html_a744a160e6b8a32a60e7ea7ed535421aa"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html#a744a160e6b8a32a60e7ea7ed535421aa">OpenMS::FeatureDistance::force_constraints_</a></div><div class="ttdeci">bool force_constraints_</div><div class="ttdoc">Always return infinity if &amp;quot;max. difference&amp;quot; constraints are not met? </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureDistance_html_ad08b3e80b01e59cb4986dba46f212234"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html#ad08b3e80b01e59cb4986dba46f212234">OpenMS::FeatureDistance::ignore_charge_</a></div><div class="ttdeci">bool ignore_charge_</div><div class="ttdoc">Compute a distance even if charge states don&amp;#39;t match? </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:145</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_1FeatureDistance_html_a247d330613019e713377dbdf503f78b7"><div class="ttname"><a href="classOpenMS_1_1FeatureDistance.html#a247d330613019e713377dbdf503f78b7">OpenMS::FeatureDistance::max_intensity_</a></div><div class="ttdeci">DoubleReal max_intensity_</div><div class="ttdoc">Maximum intensity of features (for normalization) </div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:142</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureDistance_1_1DistanceParams___html_a912b8ba7b2a6ccc272b1423bcb9d769b"><div class="ttname"><a href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a912b8ba7b2a6ccc272b1423bcb9d769b">OpenMS::FeatureDistance::DistanceParams_::weight</a></div><div class="ttdeci">DoubleReal weight</div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:125</div></div>
<div class="ttc" id="structOpenMS_1_1FeatureDistance_1_1DistanceParams___html_a398fb09ef444497b2e3506b5b229b187"><div class="ttname"><a href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#a398fb09ef444497b2e3506b5b229b187">OpenMS::FeatureDistance::DistanceParams_::relevant</a></div><div class="ttdeci">bool relevant</div><div class="ttdef"><b>Definition:</b> FeatureDistance.h:126</div></div>
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