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<a href="TransformationModel_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>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</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: $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: 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_MAPMATCHING_TRANSFORMATIONMODEL_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_TRANSFORMATIONMODEL_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="Param_8h.html">OpenMS/DATASTRUCTURES/Param.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_bspline.h&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;gsl/gsl_interp.h&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="l00052"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html">   52</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TransformationModel.html">TransformationModel</a></div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;  {</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#ac93bbaab8952124bfb6a32870b773ac1">   56</a></span>&#160;    <span class="keyword">typedef</span> std::pair&lt;DoubleReal, DoubleReal&gt; <a class="code" href="classOpenMS_1_1TransformationModel.html#ac93bbaab8952124bfb6a32870b773ac1">DataPoint</a>;</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">   58</a></span>&#160;    <span class="keyword">typedef</span> std::vector&lt;DataPoint&gt; <a class="code" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">DataPoints</a>;</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#a2b84910d6d7bd930ff4651f01616d95f">   61</a></span>&#160;    <a class="code" href="classOpenMS_1_1TransformationModel.html#a2b84910d6d7bd930ff4651f01616d95f">TransformationModel</a>() {}</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#a30dddf822bf60a5b250a5b3da95e2bd4">   64</a></span>&#160;    <a class="code" href="classOpenMS_1_1TransformationModel.html#a30dddf822bf60a5b250a5b3da95e2bd4">TransformationModel</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">TransformationModel::DataPoints</a> &amp;,</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;                        <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp;) :</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;      params_() {}</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"><a class="line" href="classOpenMS_1_1TransformationModel.html#a7f0376d313bdd03d5b99111f85a589bd">   69</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a7f0376d313bdd03d5b99111f85a589bd">~TransformationModel</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"><a class="line" href="classOpenMS_1_1TransformationModel.html#a1562399d507d343b4cb759a6e3d5470a">   72</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TransformationModel.html#a1562399d507d343b4cb759a6e3d5470a">evaluate</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> value)<span class="keyword"> const</span></div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;      <span class="keywordflow">return</span> value;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    }</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#a4d012735f1d877dc02a0041f459b7891">   78</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a4d012735f1d877dc02a0041f459b7891">getParameters</a>(<a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params)<span class="keyword"> const</span></div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;      params = params_;</div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    }</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#a39100a3d6235b7512df3d2731d016934">   84</a></span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a39100a3d6235b7512df3d2731d016934">getDefaultParameters</a>(<a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params)</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    {</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      params.<a class="code" href="classOpenMS_1_1Param.html#ac8bb3912a3ce86b15842e79d0b421204">clear</a>();</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    }</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModel.html#a20793411214daa54c7571bf9fccd5ccf">   91</a></span>&#160;    <a class="code" href="classOpenMS_1_1Param.html">Param</a> <a class="code" href="classOpenMS_1_1TransformationModel.html#a20793411214daa54c7571bf9fccd5ccf">params_</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;  };</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;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelLinear.html">  104</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TransformationModelLinear.html">TransformationModelLinear</a> :</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1TransformationModel.html">TransformationModel</a></div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;  {</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;    <a class="code" href="classOpenMS_1_1TransformationModelLinear.html">TransformationModelLinear</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">DataPoints</a> &amp; data, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params);</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    ~<a class="code" href="classOpenMS_1_1TransformationModelLinear.html">TransformationModelLinear</a>();</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> value) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    <span class="keyword">using</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a4d012735f1d877dc02a0041f459b7891">TransformationModel::getParameters</a>;</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;    <span class="keywordtype">void</span> getParameters(<a class="code" href="classdouble.html">DoubleReal</a> &amp; slope, <a class="code" href="classdouble.html">DoubleReal</a> &amp; intercept) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> getDefaultParameters(<a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params);</div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;    <span class="keywordtype">void</span> invert();</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelLinear.html#a7810770fb0835d5813492491bc0e5e87">  138</a></span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TransformationModelLinear.html#a7810770fb0835d5813492491bc0e5e87">slope_</a>, intercept_;</div>
<div class="line"><a name="l00140"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelLinear.html#aa5d41f3562d8f5dfc128c7fe47202275">  140</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TransformationModelLinear.html#aa5d41f3562d8f5dfc128c7fe47202275">data_given_</a>;</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelLinear.html#ab4bda0318b186ad5113740ee5102ddb6">  142</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TransformationModelLinear.html#ab4bda0318b186ad5113740ee5102ddb6">symmetric_</a>;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;  };</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="l00155"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelInterpolated.html">  155</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html">TransformationModelInterpolated</a> :</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1TransformationModel.html">TransformationModel</a></div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;  {</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;    <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html">TransformationModelInterpolated</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">DataPoints</a> &amp; data,</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;                                    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params);</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;    ~<a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html">TransformationModelInterpolated</a>();</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> value) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> getDefaultParameters(<a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params);</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelInterpolated.html#a5dcd911499a1cc60f5c0edaebf489469">  178</a></span>&#160;    std::vector&lt;double&gt; x_, <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html#a5dcd911499a1cc60f5c0edaebf489469">y_</a>;</div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelInterpolated.html#a5f31775800bbb46b35b5791def1f3acc">  180</a></span>&#160;    <span class="keywordtype">size_t</span> <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html#a5f31775800bbb46b35b5791def1f3acc">size_</a>;</div>
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelInterpolated.html#a413a5250121cb0862f2b50c631638b53">  182</a></span>&#160;    gsl_interp_accel * <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html#a413a5250121cb0862f2b50c631638b53">acc_</a>;</div>
<div class="line"><a name="l00184"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelInterpolated.html#a5d4133d03390cdba412a59cf73989bf8">  184</a></span>&#160;    gsl_interp * <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html#a5d4133d03390cdba412a59cf73989bf8">interp_</a>;</div>
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelInterpolated.html#a90c614c6e2883eb7d55c547d655d2a59">  186</a></span>&#160;    <a class="code" href="classOpenMS_1_1TransformationModelLinear.html">TransformationModelLinear</a> * <a class="code" href="classOpenMS_1_1TransformationModelInterpolated.html#a90c614c6e2883eb7d55c547d655d2a59">lm_</a>;</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;</div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html">  199</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html">TransformationModelBSpline</a> :</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1TransformationModel.html">TransformationModel</a></div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;  {</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;    <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html">TransformationModelBSpline</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">DataPoints</a> &amp; data, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params);</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;    ~<a class="code" href="classOpenMS_1_1TransformationModelBSpline.html">TransformationModelBSpline</a>();</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;    <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">evaluate</a>(<span class="keyword">const</span> <a class="code" href="classdouble.html">DoubleReal</a> value) <span class="keyword">const</span>;</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> getDefaultParameters(<a class="code" href="classOpenMS_1_1Param.html">Param</a> &amp; params);</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;    <span class="keywordtype">void</span> getQuantiles_(<span class="keyword">const</span> gsl_vector * x, <span class="keyword">const</span> std::vector&lt;double&gt; &amp;</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;                       quantiles, gsl_vector * results);</div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;    <span class="keywordtype">void</span> computeFit_();</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;    <span class="keywordtype">void</span> computeLinear_(<span class="keyword">const</span> <span class="keywordtype">double</span> pos, <span class="keywordtype">double</span> &amp; slope, <span class="keywordtype">double</span> &amp; offset,</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;                        <span class="keywordtype">double</span> &amp; sd_err);</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;</div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#af7c121b6b5a496337911ff3b050020e4">  238</a></span>&#160;    gsl_vector * x_, * <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#af7c121b6b5a496337911ff3b050020e4">y_</a>, * w_, * bsplines_, * coeffs_;</div>
<div class="line"><a name="l00240"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#a6cb8e740b31a1022e10832841e82775c">  240</a></span>&#160;    gsl_matrix * <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#a6cb8e740b31a1022e10832841e82775c">cov_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#a5f3eb60791ca332b2e7fd2770bb0152b">  242</a></span>&#160;    gsl_bspline_workspace * <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#a5f3eb60791ca332b2e7fd2770bb0152b">workspace_</a>;</div>
<div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#a5f31775800bbb46b35b5791def1f3acc">  244</a></span>&#160;    <span class="keywordtype">size_t</span> <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#a5f31775800bbb46b35b5791def1f3acc">size_</a>, ncoeffs_;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;    <span class="comment">// First/last breakpoint</span></div>
<div class="line"><a name="l00246"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#a81e624028b355f1db94e8b8ef1d69090">  246</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#a81e624028b355f1db94e8b8ef1d69090">xmin_</a>, xmax_;</div>
<div class="line"><a name="l00248"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#ae535452dee4f82226a418315a190aae3">  248</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#ae535452dee4f82226a418315a190aae3">slope_min_</a>, slope_max_, offset_min_, offset_max_;</div>
<div class="line"><a name="l00250"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransformationModelBSpline.html#ab393e3c6aa6eceec678d048c0604a82d">  250</a></span>&#160;    <span class="keywordtype">double</span> sd_err_left_, <a class="code" href="classOpenMS_1_1TransformationModelBSpline.html#ab393e3c6aa6eceec678d048c0604a82d">sd_err_right_</a>;</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;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;} <span class="comment">// end of namespace OpenMS</span></div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;<span class="preprocessor">#endif // OPENMS_ANALYSIS_MAPMATCHING_TRANSFORMATIONMODEL_H</span></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a20793411214daa54c7571bf9fccd5ccf"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a20793411214daa54c7571bf9fccd5ccf">OpenMS::TransformationModel::params_</a></div><div class="ttdeci">Param params_</div><div class="ttdoc">Parameters. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a2b84910d6d7bd930ff4651f01616d95f"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a2b84910d6d7bd930ff4651f01616d95f">OpenMS::TransformationModel::TransformationModel</a></div><div class="ttdeci">TransformationModel()</div><div class="ttdoc">Constructor. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html_a5f31775800bbb46b35b5791def1f3acc"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html#a5f31775800bbb46b35b5791def1f3acc">OpenMS::TransformationModelInterpolated::size_</a></div><div class="ttdeci">size_t size_</div><div class="ttdoc">Number of data points. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:180</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_a6cb8e740b31a1022e10832841e82775c"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#a6cb8e740b31a1022e10832841e82775c">OpenMS::TransformationModelBSpline::cov_</a></div><div class="ttdeci">gsl_matrix * cov_</div><div class="ttdoc">Covariance matrix. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:240</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a30dddf822bf60a5b250a5b3da95e2bd4"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a30dddf822bf60a5b250a5b3da95e2bd4">OpenMS::TransformationModel::TransformationModel</a></div><div class="ttdeci">TransformationModel(const TransformationModel::DataPoints &amp;, const Param &amp;)</div><div class="ttdoc">Alternative constructor (derived classes should implement this one!) </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:64</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html">OpenMS::TransformationModelBSpline</a></div><div class="ttdoc">B-spline model for transformations. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:199</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_ae535452dee4f82226a418315a190aae3"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#ae535452dee4f82226a418315a190aae3">OpenMS::TransformationModelBSpline::slope_min_</a></div><div class="ttdeci">double slope_min_</div><div class="ttdoc">Parameters for linear extrapolation. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:248</div></div>
<div class="ttc" id="Param_8h_html"><div class="ttname"><a href="Param_8h.html">Param.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html_a5d4133d03390cdba412a59cf73989bf8"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html#a5d4133d03390cdba412a59cf73989bf8">OpenMS::TransformationModelInterpolated::interp_</a></div><div class="ttdeci">gsl_interp * interp_</div><div class="ttdoc">Interpolation function. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:184</div></div>
<div class="ttc" id="namespaceOpenMS_1_1OptimizationFunctions_html_aacf12ce6c8657d87174c792d19c318bf"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">OpenMS::OptimizationFunctions::evaluate</a></div><div class="ttdeci">int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)</div><div class="ttdoc">Driver function for the evaluation of function and jacobian. </div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_ac8bb3912a3ce86b15842e79d0b421204"><div class="ttname"><a href="classOpenMS_1_1Param.html#ac8bb3912a3ce86b15842e79d0b421204">OpenMS::Param::clear</a></div><div class="ttdeci">void clear()</div><div class="ttdoc">Deletes all entries. </div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelLinear_html"><div class="ttname"><a href="classOpenMS_1_1TransformationModelLinear.html">OpenMS::TransformationModelLinear</a></div><div class="ttdoc">Linear model for transformations. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:104</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_a5f31775800bbb46b35b5791def1f3acc"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#a5f31775800bbb46b35b5791def1f3acc">OpenMS::TransformationModelBSpline::size_</a></div><div class="ttdeci">size_t size_</div><div class="ttdoc">Number of data points and coefficients. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:244</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html_a413a5250121cb0862f2b50c631638b53"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html#a413a5250121cb0862f2b50c631638b53">OpenMS::TransformationModelInterpolated::acc_</a></div><div class="ttdeci">gsl_interp_accel * acc_</div><div class="ttdoc">Look-up accelerator. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_a5f3eb60791ca332b2e7fd2770bb0152b"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#a5f3eb60791ca332b2e7fd2770bb0152b">OpenMS::TransformationModelBSpline::workspace_</a></div><div class="ttdeci">gsl_bspline_workspace * workspace_</div><div class="ttdoc">B-spline workspace. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:242</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a4d012735f1d877dc02a0041f459b7891"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a4d012735f1d877dc02a0041f459b7891">OpenMS::TransformationModel::getParameters</a></div><div class="ttdeci">void getParameters(Param &amp;params) const </div><div class="ttdoc">Gets the (actual) parameters. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_af7c121b6b5a496337911ff3b050020e4"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#af7c121b6b5a496337911ff3b050020e4">OpenMS::TransformationModelBSpline::y_</a></div><div class="ttdeci">gsl_vector * y_</div><div class="ttdef"><b>Definition:</b> TransformationModel.h:238</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_a81e624028b355f1db94e8b8ef1d69090"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#a81e624028b355f1db94e8b8ef1d69090">OpenMS::TransformationModelBSpline::xmin_</a></div><div class="ttdeci">double xmin_</div><div class="ttdef"><b>Definition:</b> TransformationModel.h:246</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelBSpline_html_ab393e3c6aa6eceec678d048c0604a82d"><div class="ttname"><a href="classOpenMS_1_1TransformationModelBSpline.html#ab393e3c6aa6eceec678d048c0604a82d">OpenMS::TransformationModelBSpline::sd_err_right_</a></div><div class="ttdeci">double sd_err_right_</div><div class="ttdef"><b>Definition:</b> TransformationModel.h:250</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_1TransformationModel_html_ac93bbaab8952124bfb6a32870b773ac1"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#ac93bbaab8952124bfb6a32870b773ac1">OpenMS::TransformationModel::DataPoint</a></div><div class="ttdeci">std::pair&lt; DoubleReal, DoubleReal &gt; DataPoint</div><div class="ttdoc">Coordinate pair. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelLinear_html_ab4bda0318b186ad5113740ee5102ddb6"><div class="ttname"><a href="classOpenMS_1_1TransformationModelLinear.html#ab4bda0318b186ad5113740ee5102ddb6">OpenMS::TransformationModelLinear::symmetric_</a></div><div class="ttdeci">bool symmetric_</div><div class="ttdoc">Use symmetric regression? </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:142</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelLinear_html_a7810770fb0835d5813492491bc0e5e87"><div class="ttname"><a href="classOpenMS_1_1TransformationModelLinear.html#a7810770fb0835d5813492491bc0e5e87">OpenMS::TransformationModelLinear::slope_</a></div><div class="ttdeci">DoubleReal slope_</div><div class="ttdoc">Parameters of the linear model. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a4067970d097e9b2f62de2058276b0c24"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a4067970d097e9b2f62de2058276b0c24">OpenMS::TransformationModel::DataPoints</a></div><div class="ttdeci">std::vector&lt; DataPoint &gt; DataPoints</div><div class="ttdoc">Vector of coordinate pairs. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html_a90c614c6e2883eb7d55c547d655d2a59"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html#a90c614c6e2883eb7d55c547d655d2a59">OpenMS::TransformationModelInterpolated::lm_</a></div><div class="ttdeci">TransformationModelLinear * lm_</div><div class="ttdoc">Linear model for extrapolation. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:186</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html">OpenMS::TransformationModel</a></div><div class="ttdoc">Base class for transformation models. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a1562399d507d343b4cb759a6e3d5470a"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a1562399d507d343b4cb759a6e3d5470a">OpenMS::TransformationModel::evaluate</a></div><div class="ttdeci">virtual DoubleReal evaluate(const DoubleReal value) const </div><div class="ttdoc">Evaluates the model at the given value. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a7f0376d313bdd03d5b99111f85a589bd"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a7f0376d313bdd03d5b99111f85a589bd">OpenMS::TransformationModel::~TransformationModel</a></div><div class="ttdeci">virtual ~TransformationModel()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModel_html_a39100a3d6235b7512df3d2731d016934"><div class="ttname"><a href="classOpenMS_1_1TransformationModel.html#a39100a3d6235b7512df3d2731d016934">OpenMS::TransformationModel::getDefaultParameters</a></div><div class="ttdeci">static void getDefaultParameters(Param &amp;params)</div><div class="ttdoc">Gets the default parameters. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:84</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html">OpenMS::TransformationModelInterpolated</a></div><div class="ttdoc">Interpolation model for transformations. </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelLinear_html_aa5d41f3562d8f5dfc128c7fe47202275"><div class="ttname"><a href="classOpenMS_1_1TransformationModelLinear.html#aa5d41f3562d8f5dfc128c7fe47202275">OpenMS::TransformationModelLinear::data_given_</a></div><div class="ttdeci">bool data_given_</div><div class="ttdoc">Was the model estimated from data? </div><div class="ttdef"><b>Definition:</b> TransformationModel.h:140</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationModelInterpolated_html_a5dcd911499a1cc60f5c0edaebf489469"><div class="ttname"><a href="classOpenMS_1_1TransformationModelInterpolated.html#a5dcd911499a1cc60f5c0edaebf489469">OpenMS::TransformationModelInterpolated::y_</a></div><div class="ttdeci">std::vector&lt; double &gt; y_</div><div class="ttdef"><b>Definition:</b> TransformationModel.h:178</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:22 using doxygen 1.8.5</font></TD>
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