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<a href="MRMFeatureAccessOpenMS_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>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</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>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
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<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Hannes Roest $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Hannes Roest $</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_OPENSWATH_DATAACCESS_MRMFEATUREACCESSOPENMS_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_OPENSWATH_DATAACCESS_MRMFEATUREACCESSOPENMS_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="ITransition_8h.html">OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ITransition.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;<a class="code" href="Feature_8h.html">OpenMS/KERNEL/Feature.h</a>&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MRMFeature_8h.html">OpenMS/KERNEL/MRMFeature.h</a>&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MRMTransitionGroup_8h.html">OpenMS/KERNEL/MRMTransitionGroup.h</a>&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="SignalToNoiseEstimatorMedian_8h.html">OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h</a>&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;<span class="preprocessor">#include &lt;boost/shared_ptr.hpp&gt;</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="comment">// These classes are minimal implementations of the interfaces defined in ITransition:</span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="comment">//  - IFeature</span></div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;<span class="comment">//  - IMRMFeature</span></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;<span class="comment">//  - ITransitionGroup</span></div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="comment">//  - ISignalToNoise</span></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;{</div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureOpenMS.html">   59</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1FeatureOpenMS.html">FeatureOpenMS</a> :</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenSwath_1_1IFeature.html">OpenSwath::IFeature</a></div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;  {</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;</div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">explicit</span> <a class="code" href="classOpenMS_1_1FeatureOpenMS.html">FeatureOpenMS</a>(<a class="code" href="classOpenMS_1_1Feature.html">Feature</a>&amp; feature);</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    ~<a class="code" href="classOpenMS_1_1FeatureOpenMS.html">FeatureOpenMS</a>();</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;    <span class="keywordtype">void</span> getRT(std::vector&lt;double&gt;&amp; rt);</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;    <span class="keywordtype">void</span> getIntensity(std::vector&lt;double&gt;&amp; intens);</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;    <span class="keywordtype">float</span> getIntensity();</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    <span class="keywordtype">double</span> getRT();</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;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="classOpenMS_1_1FeatureOpenMS.html#a939ce85624aad39ef8ee089c7cb7cf61">   77</a></span>&#160;    <a class="code" href="classOpenMS_1_1Feature.html">Feature</a>* <a class="code" href="classOpenMS_1_1FeatureOpenMS.html#a939ce85624aad39ef8ee089c7cb7cf61">feature_</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;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureOpenMS.html">   84</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html">MRMFeatureOpenMS</a> :</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenSwath_1_1IMRMFeature.html">OpenSwath::IMRMFeature</a></div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;  {</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;<span class="keyword">public</span>:</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">explicit</span> <a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html">MRMFeatureOpenMS</a>(<a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a>&amp; mrmfeature);</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;    ~<a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html">MRMFeatureOpenMS</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;    boost::shared_ptr&lt;OpenSwath::IFeature&gt; getFeature(std::string nativeID);</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    <span class="keywordtype">float</span> getIntensity();</div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <span class="keywordtype">double</span> getRT();</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureOpenMS.html#ac3101dd0466a177457529280bd151294">  100</a></span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a>&amp; <a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html#ac3101dd0466a177457529280bd151294">mrmfeature_</a>;</div>
<div class="line"><a name="l00101"></a><span class="lineno"><a class="line" href="classOpenMS_1_1MRMFeatureOpenMS.html#af8676c95915f43bd22c98ac117ea7730">  101</a></span>&#160;    std::map&lt;std::string, boost::shared_ptr&lt;FeatureOpenMS&gt; &gt; <a class="code" href="classOpenMS_1_1MRMFeatureOpenMS.html#af8676c95915f43bd22c98ac117ea7730">features_</a>;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;  };</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumT, <span class="keyword">typename</span> TransitionT&gt;</div>
<div class="line"><a name="l00109"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html">  109</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html">TransitionGroupOpenMS</a> :</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    <span class="keyword">public</span> <a class="code" href="structOpenSwath_1_1ITransitionGroup.html">OpenSwath::ITransitionGroup</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">  112</span>&#160;<span class="keyword">public</span>:</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"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html#abaa13e20104269f5f8809f567a69bf6a">  114</a></span>&#160;    <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html#abaa13e20104269f5f8809f567a69bf6a">TransitionGroupOpenMS</a>(<a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup&lt;SpectrumT, TransitionT&gt;</a>&amp; trgroup) :</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      trgroup_(trgroup)</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;    {</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    }</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html#a4294b6e408a1778efecb341f7388641f">  119</a></span>&#160;    <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html#a4294b6e408a1778efecb341f7388641f">~TransitionGroupOpenMS</a>()</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;    }</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;</div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html#aee37e9309344d91a82e996b2e7fb905e">  123</a></span>&#160;    std::size_t <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html#aee37e9309344d91a82e996b2e7fb905e">size</a>()</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;    {</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;      <span class="keywordflow">return</span> trgroup_.size();</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="l00128"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html#a4ea1bbd785ddf4b059305b1a083fc757">  128</a></span>&#160;    std::vector&lt;std::string&gt; <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html#a4ea1bbd785ddf4b059305b1a083fc757">getNativeIDs</a>()</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    {</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;      std::vector&lt;std::string&gt; result;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;      <span class="keywordflow">for</span> (std::size_t i = 0; i &lt; this-&gt;size(); i++)</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;        result.push_back(trgroup_.getChromatograms()[i].getNativeID());</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;      }</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;      <span class="keywordflow">return</span> result;</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;</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html#a52528ca964940be1aa820fbd58f423c5">  138</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html#a52528ca964940be1aa820fbd58f423c5">getLibraryIntensities</a>(std::vector&lt;double&gt;&amp; intensities)</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;      trgroup_.getLibraryIntensity(intensities);</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    }</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TransitionGroupOpenMS.html#a853b6412a4f65c2c9f4781da007d6cfe">  144</a></span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup&lt;SpectrumT, TransitionT&gt;</a>&amp; <a class="code" href="classOpenMS_1_1TransitionGroupOpenMS.html#a853b6412a4f65c2c9f4781da007d6cfe">trgroup_</a>;</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;  };</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;  <span class="keyword">template</span> &lt;<span class="keyword">typename</span> PeakT&gt;</div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SignalToNoiseOpenMS.html">  152</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SignalToNoiseOpenMS.html">SignalToNoiseOpenMS</a> :</div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;    <span class="keyword">public</span> <a class="code" href="structOpenSwath_1_1ISignalToNoise.html">OpenSwath::ISignalToNoise</a></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">public</span>:</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SignalToNoiseOpenMS.html#a61e58ed574e6196deffeaf53220a0816">  157</a></span>&#160;    <a class="code" href="classOpenMS_1_1SignalToNoiseOpenMS.html#a61e58ed574e6196deffeaf53220a0816">SignalToNoiseOpenMS</a>(<a class="code" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt;PeakT&gt;</a>&amp; chromat,</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;                        <span class="keywordtype">double</span> sn_win_len_, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> sn_bin_count_) :</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;      chromatogram_(chromat), sn_()</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;    {</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;      <a class="code" href="classOpenMS_1_1Param.html">OpenMS::Param</a> snt_parameters = sn_.getParameters();</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;      snt_parameters.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;win_len&quot;</span>, sn_win_len_);</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;      snt_parameters.<a class="code" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">setValue</a>(<span class="stringliteral">&quot;bin_count&quot;</span>, sn_bin_count_);</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;      sn_.setParameters(snt_parameters);</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;      sn_.init(chromatogram_);</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;    }</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;</div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SignalToNoiseOpenMS.html#aa8258c9d408eb3cae327b829e11da99f">  168</a></span>&#160;    <span class="keywordtype">double</span> <a class="code" href="classOpenMS_1_1SignalToNoiseOpenMS.html#aa8258c9d408eb3cae327b829e11da99f">getValueAtRT</a>(<span class="keywordtype">double</span> RT)</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;    {</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;      <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt;PeakT&gt;::const_iterator</a> it = chromatogram_.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a808327302a2ba3fb630ea132d32db942">MZBegin</a>(RT);</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;      <span class="keywordflow">return</span> sn_.getSignalToNoise(*it);</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;    }</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;<span class="keyword">private</span>:</div>
<div class="line"><a name="l00175"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SignalToNoiseOpenMS.html#aa19d795e2d1ba7c351821264f53b97cd">  175</a></span>&#160;    <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum&lt;PeakT&gt;</a>&amp; <a class="code" href="classOpenMS_1_1SignalToNoiseOpenMS.html#aa19d795e2d1ba7c351821264f53b97cd">chromatogram_</a>;</div>
<div class="line"><a name="l00176"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SignalToNoiseOpenMS.html#ad266ac449c82a55c7dcacff54455bb6c">  176</a></span>&#160;    <a class="code" href="classOpenMS_1_1SignalToNoiseEstimatorMedian.html">OpenMS::SignalToNoiseEstimatorMedian&lt;OpenMS::MSSpectrum&lt;PeakT&gt;</a> &gt; <a class="code" href="classOpenMS_1_1SignalToNoiseOpenMS.html#ad266ac449c82a55c7dcacff54455bb6c">sn_</a>;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;  };</div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;}</div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html_abaa13e20104269f5f8809f567a69bf6a"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html#abaa13e20104269f5f8809f567a69bf6a">OpenMS::TransitionGroupOpenMS::TransitionGroupOpenMS</a></div><div class="ttdeci">TransitionGroupOpenMS(MRMTransitionGroup&lt; SpectrumT, TransitionT &gt; &amp;trgroup)</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1FeatureOpenMS.html">OpenMS::FeatureOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH Feature Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:59</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="MRMFeature_8h_html"><div class="ttname"><a href="MRMFeature_8h.html">MRMFeature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseOpenMS_html_ad266ac449c82a55c7dcacff54455bb6c"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseOpenMS.html#ad266ac449c82a55c7dcacff54455bb6c">OpenMS::SignalToNoiseOpenMS::sn_</a></div><div class="ttdeci">OpenMS::SignalToNoiseEstimatorMedian&lt; OpenMS::MSSpectrum&lt; PeakT &gt; &gt; sn_</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:176</div></div>
<div class="ttc" id="ITransition_8h_html"><div class="ttname"><a href="ITransition_8h.html">ITransition.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseOpenMS_html_aa19d795e2d1ba7c351821264f53b97cd"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseOpenMS.html#aa19d795e2d1ba7c351821264f53b97cd">OpenMS::SignalToNoiseOpenMS::chromatogram_</a></div><div class="ttdeci">const OpenMS::MSSpectrum&lt; PeakT &gt; &amp; chromatogram_</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:175</div></div>
<div class="ttc" id="classOpenMS_1_1FeatureOpenMS_html_a939ce85624aad39ef8ee089c7cb7cf61"><div class="ttname"><a href="classOpenMS_1_1FeatureOpenMS.html#a939ce85624aad39ef8ee089c7cb7cf61">OpenMS::FeatureOpenMS::feature_</a></div><div class="ttdeci">Feature * feature_</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:77</div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html_a4ea1bbd785ddf4b059305b1a083fc757"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html#a4ea1bbd785ddf4b059305b1a083fc757">OpenMS::TransitionGroupOpenMS::getNativeIDs</a></div><div class="ttdeci">std::vector&lt; std::string &gt; getNativeIDs()</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:128</div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html_a853b6412a4f65c2c9f4781da007d6cfe"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html#a853b6412a4f65c2c9f4781da007d6cfe">OpenMS::TransitionGroupOpenMS::trgroup_</a></div><div class="ttdeci">const MRMTransitionGroup&lt; SpectrumT, TransitionT &gt; &amp; trgroup_</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html">OpenMS::TransitionGroupOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH Transition Group Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:109</div></div>
<div class="ttc" id="Feature_8h_html"><div class="ttname"><a href="Feature_8h.html">Feature.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a808327302a2ba3fb630ea132d32db942"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a808327302a2ba3fb630ea132d32db942">OpenMS::MSSpectrum::MZBegin</a></div><div class="ttdeci">Iterator MZBegin(CoordinateType mz)</div><div class="ttdoc">Binary search for peak range begin. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:506</div></div>
<div class="ttc" id="structOpenSwath_1_1ITransitionGroup_html"><div class="ttname"><a href="structOpenSwath_1_1ITransitionGroup.html">OpenSwath::ITransitionGroup</a></div><div class="ttdef"><b>Definition:</b> ITransition.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureOpenMS_html_af8676c95915f43bd22c98ac117ea7730"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureOpenMS.html#af8676c95915f43bd22c98ac117ea7730">OpenMS::MRMFeatureOpenMS::features_</a></div><div class="ttdeci">std::map&lt; std::string, boost::shared_ptr&lt; FeatureOpenMS &gt; &gt; features_</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1MRMTransitionGroup_html"><div class="ttname"><a href="classOpenMS_1_1MRMTransitionGroup.html">OpenMS::MRMTransitionGroup&lt; SpectrumT, TransitionT &gt;</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html_aee37e9309344d91a82e996b2e7fb905e"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html#aee37e9309344d91a82e996b2e7fb905e">OpenMS::TransitionGroupOpenMS::size</a></div><div class="ttdeci">std::size_t size()</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:123</div></div>
<div class="ttc" id="classOpenSwath_1_1IFeature_html"><div class="ttname"><a href="classOpenSwath_1_1IFeature.html">OpenSwath::IFeature</a></div><div class="ttdef"><b>Definition:</b> ITransition.h:46</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum</a></div><div class="ttdoc">The representation of a 1D spectrum. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseOpenMS.html">OpenMS::SignalToNoiseOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH SignalToNoise Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:152</div></div>
<div class="ttc" id="MRMTransitionGroup_8h_html"><div class="ttname"><a href="MRMTransitionGroup_8h.html">MRMTransitionGroup.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html_a52528ca964940be1aa820fbd58f423c5"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html#a52528ca964940be1aa820fbd58f423c5">OpenMS::TransitionGroupOpenMS::getLibraryIntensities</a></div><div class="ttdeci">void getLibraryIntensities(std::vector&lt; double &gt; &amp;intensities)</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseOpenMS_html_a61e58ed574e6196deffeaf53220a0816"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseOpenMS.html#a61e58ed574e6196deffeaf53220a0816">OpenMS::SignalToNoiseOpenMS::SignalToNoiseOpenMS</a></div><div class="ttdeci">SignalToNoiseOpenMS(OpenMS::MSSpectrum&lt; PeakT &gt; &amp;chromat, double sn_win_len_, unsigned int sn_bin_count_)</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:157</div></div>
<div class="ttc" id="SignalToNoiseEstimatorMedian_8h_html"><div class="ttname"><a href="SignalToNoiseEstimatorMedian_8h.html">SignalToNoiseEstimatorMedian.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Feature_html"><div class="ttname"><a href="classOpenMS_1_1Feature.html">OpenMS::Feature</a></div><div class="ttdoc">An LC-MS feature. </div><div class="ttdef"><b>Definition:</b> Feature.h:66</div></div>
<div class="ttc" id="classOpenMS_1_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_1SignalToNoiseEstimatorMedian_html"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseEstimatorMedian.html">OpenMS::SignalToNoiseEstimatorMedian</a></div><div class="ttdoc">Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram ba...</div><div class="ttdef"><b>Definition:</b> SignalToNoiseEstimatorMedian.h:71</div></div>
<div class="ttc" id="classOpenSwath_1_1IMRMFeature_html"><div class="ttname"><a href="classOpenSwath_1_1IMRMFeature.html">OpenSwath::IMRMFeature</a></div><div class="ttdef"><b>Definition:</b> ITransition.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureOpenMS_html_ac3101dd0466a177457529280bd151294"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureOpenMS.html#ac3101dd0466a177457529280bd151294">OpenMS::MRMFeatureOpenMS::mrmfeature_</a></div><div class="ttdeci">const MRMFeature &amp; mrmfeature_</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1TransitionGroupOpenMS_html_a4294b6e408a1778efecb341f7388641f"><div class="ttname"><a href="classOpenMS_1_1TransitionGroupOpenMS.html#a4294b6e408a1778efecb341f7388641f">OpenMS::TransitionGroupOpenMS::~TransitionGroupOpenMS</a></div><div class="ttdeci">~TransitionGroupOpenMS()</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:119</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeature_html"><div class="ttname"><a href="classOpenMS_1_1MRMFeature.html">OpenMS::MRMFeature</a></div><div class="ttdoc">A multi-chromatogram MRM feature. </div><div class="ttdef"><b>Definition:</b> MRMFeature.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1SignalToNoiseOpenMS_html_aa8258c9d408eb3cae327b829e11da99f"><div class="ttname"><a href="classOpenMS_1_1SignalToNoiseOpenMS.html#aa8258c9d408eb3cae327b829e11da99f">OpenMS::SignalToNoiseOpenMS::getValueAtRT</a></div><div class="ttdeci">double getValueAtRT(double RT)</div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:168</div></div>
<div class="ttc" id="structOpenSwath_1_1ISignalToNoise_html"><div class="ttname"><a href="structOpenSwath_1_1ISignalToNoise.html">OpenSwath::ISignalToNoise</a></div><div class="ttdef"><b>Definition:</b> ITransition.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1MRMFeatureOpenMS_html"><div class="ttname"><a href="classOpenMS_1_1MRMFeatureOpenMS.html">OpenMS::MRMFeatureOpenMS</a></div><div class="ttdoc">An implementation of the OpenSWATH MRM Feature Access interface using OpenMS. </div><div class="ttdef"><b>Definition:</b> MRMFeatureAccessOpenMS.h:84</div></div>
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