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<a href="BaseModel_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>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">//  * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</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="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<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: Clemens Groepl $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: $</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_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_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_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_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="DPeak_8h.html">OpenMS/KERNEL/DPeak.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="keyword">namespace </span>OpenMS</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;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;  <span class="keyword">template</span> &lt;UInt D&gt;</div>
<div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html">   51</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1BaseModel.html">BaseModel</a> :</div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</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;</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div>
<div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#acbd54f28a23dc263a3c81b7c45a3e1e1">   57</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1BaseModel.html#acbd54f28a23dc263a3c81b7c45a3e1e1">IntensityType</a>;</div>
<div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a063d40a3528749f1a905ab04d76387e0">   58</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1BaseModel.html#a063d40a3528749f1a905ab04d76387e0">CoordinateType</a>;</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a49ac71825a631fc5537551e33ad4b72c">   59</a></span>&#160;    <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1DPosition.html">DPosition&lt;D&gt;</a> <a class="code" href="classOpenMS_1_1BaseModel.html#a49ac71825a631fc5537551e33ad4b72c">PositionType</a>;</div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a19e7594d894168936a9d0b0a11c4f2c3">   60</a></span>&#160;    <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1DPeak.html">DPeak&lt;D&gt;::Type</a> <a class="code" href="classOpenMS_1_1BaseModel.html#a19e7594d894168936a9d0b0a11c4f2c3">PeakType</a>;</div>
<div class="line"><a name="l00061"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a8846ea396fc3690dc69387998cf7cb85">   61</a></span>&#160;    <span class="keyword">typedef</span> std::vector&lt;PeakType&gt; <a class="code" href="classOpenMS_1_1BaseModel.html#a8846ea396fc3690dc69387998cf7cb85">SamplesType</a>;</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a4022784bf4c4e048bc478d31db45e833">   65</a></span>&#160;    <a class="code" href="classOpenMS_1_1BaseModel.html#a4022784bf4c4e048bc478d31db45e833">BaseModel</a>() :</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(<span class="stringliteral">&quot;BaseModel&quot;</span>)</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    {</div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;cutoff&quot;</span>, 0.0, <span class="stringliteral">&quot;Low intensity cutoff of the model.  Peaks below this intensity are not considered part of the model.&quot;</span>);</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    }</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_1BaseModel.html#a1b7eded8c20032546668ffe7b0ac67f6">   72</a></span>&#160;    <a class="code" href="classOpenMS_1_1BaseModel.html#a1b7eded8c20032546668ffe7b0ac67f6">BaseModel</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseModel.html">BaseModel</a> &amp; source) :</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>(source),</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;      <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a>(source.<a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a>)</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="l00077"></a><span class="lineno">   77</span>&#160;</div>
<div class="line"><a name="l00079"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a8a30701c8fabac6b006ed2f77ffad5e7">   79</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a8a30701c8fabac6b006ed2f77ffad5e7">~BaseModel</a>()</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    {</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_1BaseModel.html#aa77887521d929a9565d179067f19b4ef">   84</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1BaseModel.html">BaseModel</a> &amp; <a class="code" href="classOpenMS_1_1BaseModel.html#aa77887521d929a9565d179067f19b4ef">operator=</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseModel.html">BaseModel</a> &amp; source)</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;      <span class="keywordflow">if</span> (&amp;source == <span class="keyword">this</span>) <span class="keywordflow">return</span> *<span class="keyword">this</span>;</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;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">DefaultParamHandler::operator=</a>(source);</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a> = source.<a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <span class="keywordflow">return</span> *<span class="keyword">this</span>;</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="l00095"></a><span class="lineno">   95</span>&#160;    <span class="keyword">static</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a>();</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1BaseModel.html#acbd54f28a23dc263a3c81b7c45a3e1e1">IntensityType</a> <a class="code" href="classOpenMS_1_1BaseModel.html#a0a066871875d83652f697288d3cffb54">getIntensity</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a49ac71825a631fc5537551e33ad4b72c">PositionType</a> &amp; pos) <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">  101</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">isContained</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DPosition.html">PositionType</a> &amp; pos)<span class="keyword"> const</span></div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;      <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a0a066871875d83652f697288d3cffb54">getIntensity</a>(pos) &gt;= <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a>;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    }</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> PeakType&gt;</div>
<div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a3f199844dfcde21b2620c13e2faf97cc">  111</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a3f199844dfcde21b2620c13e2faf97cc">fillIntensity</a>(<a class="code" href="classOpenMS_1_1BaseModel.html#a19e7594d894168936a9d0b0a11c4f2c3">PeakType</a> &amp; peak)<span class="keyword"> const</span></div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      peak.setIntensity(<a class="code" href="classOpenMS_1_1BaseModel.html#a0a066871875d83652f697288d3cffb54">getIntensity</a>(peak.getPosition()));</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;    }</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> PeakIterator&gt;</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a31ea86f73d57cb3640eba84bcb4b1952">  120</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a31ea86f73d57cb3640eba84bcb4b1952">fillIntensities</a>(<a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a> begin, <a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a> end)<span class="keyword"> const</span></div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a> it = begin; it != end; ++it)</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;        <a class="code" href="classOpenMS_1_1BaseModel.html#a3f199844dfcde21b2620c13e2faf97cc">fillIntensity</a>(*it);</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      }</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;</div>
<div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#ae9f0af9f4fda60ae3a46a0f16a4833e7">  129</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classdouble.html">IntensityType</a> <a class="code" href="classOpenMS_1_1BaseModel.html#ae9f0af9f4fda60ae3a46a0f16a4833e7">getCutOff</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;      <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a>;</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="l00135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#a464bd13b1e846ea0bc7bb0632f8e7256">  135</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a464bd13b1e846ea0bc7bb0632f8e7256">setCutOff</a>(<a class="code" href="classdouble.html">IntensityType</a> cut_off)</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;      <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a> = cut_off;</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;      <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;cutoff&quot;</span>, <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a>);</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="l00142"></a><span class="lineno">  142</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#aa991d84566612935e53c0d6c0019de11">getSamples</a>(<a class="code" href="classOpenMS_1_1BaseModel.html#a8846ea396fc3690dc69387998cf7cb85">SamplesType</a> &amp; cont) <span class="keyword">const</span> = 0;</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_1BaseModel.html#ade88650afe70db899c99697e03958cc5">  145</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#ade88650afe70db899c99697e03958cc5">getSamples</a>(std::ostream &amp; os)</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    {</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;      <a class="code" href="classOpenMS_1_1BaseModel.html#a8846ea396fc3690dc69387998cf7cb85">SamplesType</a> samples;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;      <a class="code" href="classOpenMS_1_1BaseModel.html#aa991d84566612935e53c0d6c0019de11">getSamples</a>(samples);</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> SamplesType::const_iterator it = samples.begin(); it != samples.end(); ++it)</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;        os &lt;&lt; *it &lt;&lt; std::endl;</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;    }</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;<span class="keyword">protected</span>:</div>
<div class="line"><a name="l00156"></a><span class="lineno"><a class="line" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">  156</a></span>&#160;    <a class="code" href="classdouble.html">IntensityType</a> <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</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"><a class="line" href="classOpenMS_1_1BaseModel.html#a776f7572fc4f466e9527ca233471920d">  158</a></span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1BaseModel.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a>()</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;    {</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;      <a class="code" href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">cut_off_</a> = (<a class="code" href="classdouble.html">double</a>)<a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">&quot;cutoff&quot;</span>);</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    }</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;  };</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;}</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;<span class="preprocessor">#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_BASEMODEL_H</span></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a761b1937850c141d0c6fff0e4d633a04"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">OpenMS::DefaultParamHandler::defaults_</a></div><div class="ttdeci">Param defaults_</div><div class="ttdoc">Container for default parameters. This member should be filled in the constructor of derived classes!...</div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:155</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_a432099944e11263aa20aaf8ea1389790"><div class="ttname"><a href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">OpenMS::Param::setValue</a></div><div class="ttdeci">void setValue(const String &amp;key, const DataValue &amp;value, const String &amp;description=&quot;&quot;, const StringList &amp;tags=StringList())</div><div class="ttdoc">Sets a value. </div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_acbd54f28a23dc263a3c81b7c45a3e1e1"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#acbd54f28a23dc263a3c81b7c45a3e1e1">OpenMS::BaseModel::IntensityType</a></div><div class="ttdeci">DoubleReal IntensityType</div><div class="ttdef"><b>Definition:</b> BaseModel.h:57</div></div>
<div class="ttc" id="DPeak_8h_html"><div class="ttname"><a href="DPeak_8h.html">DPeak.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::DefaultParamHandler::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">Container for current parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a3f199844dfcde21b2620c13e2faf97cc"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a3f199844dfcde21b2620c13e2faf97cc">OpenMS::BaseModel::fillIntensity</a></div><div class="ttdeci">void fillIntensity(PeakType &amp;peak) const </div><div class="ttdoc">Convenience function to set the intensity of a peak to the predicted intensity at its current positio...</div><div class="ttdef"><b>Definition:</b> BaseModel.h:111</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="namespaceOpenMS_1_1OptimizationFunctions_html_a335cff277df421bfa0ce8d2412f02134"><div class="ttname"><a href="namespaceOpenMS_1_1OptimizationFunctions.html#a335cff277df421bfa0ce8d2412f02134">OpenMS::OptimizationFunctions::PeakIterator</a></div><div class="ttdeci">RawDataVector::iterator PeakIterator</div><div class="ttdoc">Raw data iterator type. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a31ea86f73d57cb3640eba84bcb4b1952"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a31ea86f73d57cb3640eba84bcb4b1952">OpenMS::BaseModel::fillIntensities</a></div><div class="ttdeci">void fillIntensities(PeakIterator begin, PeakIterator end) const </div><div class="ttdoc">Convenience function that applies fillIntensity() to an iterator range. </div><div class="ttdef"><b>Definition:</b> BaseModel.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_ae9f0af9f4fda60ae3a46a0f16a4833e7"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#ae9f0af9f4fda60ae3a46a0f16a4833e7">OpenMS::BaseModel::getCutOff</a></div><div class="ttdeci">virtual IntensityType getCutOff() const </div><div class="ttdoc">get cutoff value </div><div class="ttdef"><b>Definition:</b> BaseModel.h:129</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="classOpenMS_1_1BaseModel_html_a776f7572fc4f466e9527ca233471920d"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a776f7572fc4f466e9527ca233471920d">OpenMS::BaseModel::updateMembers_</a></div><div class="ttdeci">virtual void updateMembers_()</div><div class="ttdoc">This method is used to update extra member variables at the end of the setParameters() method...</div><div class="ttdef"><b>Definition:</b> BaseModel.h:158</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_ade88650afe70db899c99697e03958cc5"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#ade88650afe70db899c99697e03958cc5">OpenMS::BaseModel::getSamples</a></div><div class="ttdeci">virtual void getSamples(std::ostream &amp;os)</div><div class="ttdoc">fill stream with reasonable set of samples from the model (i.e. for printing) </div><div class="ttdef"><b>Definition:</b> BaseModel.h:145</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_aa991d84566612935e53c0d6c0019de11"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#aa991d84566612935e53c0d6c0019de11">OpenMS::BaseModel::getSamples</a></div><div class="ttdeci">virtual void getSamples(SamplesType &amp;cont) const =0</div><div class="ttdoc">get reasonable set of samples from the model (i.e. for printing) </div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition&lt; D &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a49ac71825a631fc5537551e33ad4b72c"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a49ac71825a631fc5537551e33ad4b72c">OpenMS::BaseModel::PositionType</a></div><div class="ttdeci">DPosition&lt; D &gt; PositionType</div><div class="ttdef"><b>Definition:</b> BaseModel.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a4022784bf4c4e048bc478d31db45e833"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a4022784bf4c4e048bc478d31db45e833">OpenMS::BaseModel::BaseModel</a></div><div class="ttdeci">BaseModel()</div><div class="ttdoc">Default constructor. </div><div class="ttdef"><b>Definition:</b> BaseModel.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a063d40a3528749f1a905ab04d76387e0"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a063d40a3528749f1a905ab04d76387e0">OpenMS::BaseModel::CoordinateType</a></div><div class="ttdeci">DoubleReal CoordinateType</div><div class="ttdef"><b>Definition:</b> BaseModel.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_aca183c4ace75384f91bc04579eada9bc"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#aca183c4ace75384f91bc04579eada9bc">OpenMS::BaseModel::isContained</a></div><div class="ttdeci">virtual bool isContained(const PositionType &amp;pos) const </div><div class="ttdoc">check if position pos is part of the model regarding the models cut-off. </div><div class="ttdef"><b>Definition:</b> BaseModel.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a8a30701c8fabac6b006ed2f77ffad5e7"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a8a30701c8fabac6b006ed2f77ffad5e7">OpenMS::BaseModel::~BaseModel</a></div><div class="ttdeci">virtual ~BaseModel()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> BaseModel.h:79</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_ae6b6d68036a573a44f6609460ba2dfb6"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">OpenMS::DefaultParamHandler::operator=</a></div><div class="ttdeci">virtual DefaultParamHandler &amp; operator=(const DefaultParamHandler &amp;rhs)</div><div class="ttdoc">Assignment operator. </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_1BaseModel_html"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html">OpenMS::BaseModel</a></div><div class="ttdoc">Abstract base class for all D-dimensional models. </div><div class="ttdef"><b>Definition:</b> BaseModel.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a7899dbe105534dc1f81971dd71a26ff0"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a7899dbe105534dc1f81971dd71a26ff0">OpenMS::BaseModel::registerChildren</a></div><div class="ttdeci">static void registerChildren()</div><div class="ttdoc">register all derived classes here (implemented in file BaseModel_impl.h) </div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_ad6d5d8772d106965522adadadea1b6e9"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#ad6d5d8772d106965522adadadea1b6e9">OpenMS::BaseModel::cut_off_</a></div><div class="ttdeci">IntensityType cut_off_</div><div class="ttdef"><b>Definition:</b> BaseModel.h:156</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a0a066871875d83652f697288d3cffb54"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a0a066871875d83652f697288d3cffb54">OpenMS::BaseModel::getIntensity</a></div><div class="ttdeci">virtual IntensityType getIntensity(const PositionType &amp;pos) const =0</div><div class="ttdoc">access model predicted intensity at position pos </div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a8846ea396fc3690dc69387998cf7cb85"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a8846ea396fc3690dc69387998cf7cb85">OpenMS::BaseModel::SamplesType</a></div><div class="ttdeci">std::vector&lt; PeakType &gt; SamplesType</div><div class="ttdef"><b>Definition:</b> BaseModel.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_aa77887521d929a9565d179067f19b4ef"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#aa77887521d929a9565d179067f19b4ef">OpenMS::BaseModel::operator=</a></div><div class="ttdeci">virtual BaseModel &amp; operator=(const BaseModel &amp;source)</div><div class="ttdoc">assignment operator </div><div class="ttdef"><b>Definition:</b> BaseModel.h:84</div></div>
<div class="ttc" id="structOpenMS_1_1DPeak_html"><div class="ttname"><a href="structOpenMS_1_1DPeak.html">OpenMS::DPeak</a></div><div class="ttdoc">Metafunction to choose among Peak1D respectively Peak2D through a template argument. </div><div class="ttdef"><b>Definition:</b> DPeak.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a19e7594d894168936a9d0b0a11c4f2c3"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a19e7594d894168936a9d0b0a11c4f2c3">OpenMS::BaseModel::PeakType</a></div><div class="ttdeci">DPeak&lt; D &gt;::Type PeakType</div><div class="ttdef"><b>Definition:</b> BaseModel.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a464bd13b1e846ea0bc7bb0632f8e7256"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a464bd13b1e846ea0bc7bb0632f8e7256">OpenMS::BaseModel::setCutOff</a></div><div class="ttdeci">virtual void setCutOff(IntensityType cut_off)</div><div class="ttdoc">set cutoff value </div><div class="ttdef"><b>Definition:</b> BaseModel.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1BaseModel_html_a1b7eded8c20032546668ffe7b0ac67f6"><div class="ttname"><a href="classOpenMS_1_1BaseModel.html#a1b7eded8c20032546668ffe7b0ac67f6">OpenMS::BaseModel::BaseModel</a></div><div class="ttdeci">BaseModel(const BaseModel &amp;source)</div><div class="ttdoc">copy constructor </div><div class="ttdef"><b>Definition:</b> BaseModel.h:72</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 11:19:11 using doxygen 1.8.5</font></TD>
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