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<a href="ChromatogramTools_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>
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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: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Andreas Bertsch $</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_KERNEL_CHROMATOGRAMTOOLS_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_KERNEL_CHROMATOGRAMTOOLS_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="Map_8h.html">OpenMS/DATASTRUCTURES/Map.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="Types_8h.html">OpenMS/CONCEPT/Types.h</a>&gt;</span></div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="MSChromatogram_8h.html">OpenMS/KERNEL/MSChromatogram.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="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.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="RangeUtils_8h.html">OpenMS/KERNEL/RangeUtils.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="LogStream_8h.html">OpenMS/CONCEPT/LogStream.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="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;{</div>
<div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramTools.html">   55</a></span>&#160;  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a></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">   57</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    <a class="code" href="classOpenMS_1_1ChromatogramTools.html#a41bd54ebbe20b4f33112d5a1e979a870">ChromatogramTools</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_1ChromatogramTools.html#afda6458ea9e5f8f923907a7afe8c9e63">   65</a></span>&#160;    <a class="code" href="classOpenMS_1_1ChromatogramTools.html#afda6458ea9e5f8f923907a7afe8c9e63">ChromatogramTools</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ChromatogramTools.html">ChromatogramTools</a> &amp; <span class="comment">/*rhs*/</span>)</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    {}</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_1ChromatogramTools.html#adc92fcb859234049c3cebcd178b41ff0">   69</a></span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1ChromatogramTools.html#adc92fcb859234049c3cebcd178b41ff0">~ChromatogramTools</a>()</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;    {}</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;</div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> ExperimentType&gt;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">   86</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">convertChromatogramsToSpectra</a>(ExperimentType &amp; exp)</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;      <span class="keywordflow">for</span> (std::vector&lt;<a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram&lt;&gt;</a> &gt;::const_iterator it = exp.getChromatograms().begin(); it != exp.getChromatograms().end(); ++it)</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      {</div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        <span class="comment">// for each peak add a new spectrum</span></div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;        <span class="keywordflow">for</span> (<span class="keyword">typename</span> ExperimentType::ChromatogramType::const_iterator pit = it-&gt;begin(); pit != it-&gt;end(); ++pit)</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;          <span class="keyword">typename</span> ExperimentType::SpectrumType spec;</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="comment">// add precursor and product peaks to spectrum settings</span></div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;          spec.getPrecursors().push_back(it-&gt;getPrecursor());</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;          spec.getProducts().push_back(it-&gt;getProduct());</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;          spec.setRT(pit-&gt;getRT());</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;          spec.setMSLevel(2);</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;          spec.setInstrumentSettings(it-&gt;getInstrumentSettings());</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;          spec.setAcquisitionInfo(it-&gt;getAcquisitionInfo());</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;          spec.setSourceFile(it-&gt;getSourceFile());</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;          <span class="comment">// TODO implement others</span></div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;          <span class="keywordflow">if</span> (it-&gt;getChromatogramType() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</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;            spec.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>);</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;          }</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;          <span class="keywordflow">if</span> (it-&gt;getChromatogramType() == <a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa">ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM</a>)</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;          {</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;            spec.getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>);</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;          }</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;          <span class="comment">// new spec contains one peak, with product m/z and intensity</span></div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;          <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">ExperimentType::PeakType</a> peak;</div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;          peak.<a class="code" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">setMZ</a>(it-&gt;getMZ());</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;          peak.setIntensity(pit-&gt;getIntensity());</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;          spec.push_back(peak);</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;          exp.addSpectrum(spec);</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">  123</span>&#160;      exp.setChromatograms(std::vector&lt;<a class="code" href="classOpenMS_1_1MSChromatogram.html">MSChromatogram&lt;&gt;</a> &gt;());</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;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> ExperimentType&gt;</div>
<div class="line"><a name="l00138"></a><span class="lineno"><a class="line" href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">  138</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">convertSpectraToChromatograms</a>(ExperimentType &amp; exp, <span class="keywordtype">bool</span> remove_spectra = <span class="keyword">false</span>)</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;      <span class="keyword">typedef</span> <span class="keyword">typename</span> ExperimentType::SpectrumType SpectrumType;</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;      <a class="code" href="classOpenMS_1_1Map.html">Map&lt;DoubleReal, Map&lt;DoubleReal, std::vector&lt;SpectrumType&gt;</a> &gt; &gt; chroms;</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;      <span class="keywordflow">for</span> (<span class="keyword">typename</span> ExperimentType::ConstIterator it = exp.begin(); it != exp.end(); ++it)</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;        <span class="comment">// TODO other types</span></div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        <span class="keywordflow">if</span> (it-&gt;getInstrumentSettings().getScanMode() == <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>)</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;          <span class="comment">// exactly one precursor and one product ion</span></div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;          <span class="keywordflow">if</span> (it-&gt;getPrecursors().size() == 1 &amp;&amp; it-&gt;size() == 1)</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;          {</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;            chroms[it-&gt;getPrecursors().begin()-&gt;getMZ()][it-&gt;begin()-&gt;getMZ()].push_back(*it);</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;          }</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;          <span class="comment">// Exactly one precursor and more than one product ion.</span></div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;          <span class="comment">// This is how some converters (e.g. ReAdW 4.0.2) store SRM data,</span></div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;          <span class="comment">// collecting all information from one precursor in a single</span></div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;          <span class="comment">// pseudo-spectrum</span></div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;          <span class="keywordflow">else</span> <span class="keywordflow">if</span> (it-&gt;getPrecursors().size() == 1 &amp;&amp; it-&gt;size() &gt; 0)</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="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak_idx = 0; peak_idx &lt; it-&gt;size(); peak_idx++)</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;              <span class="comment">// copy spectrum and delete all data, but keep metadata, then add single peak</span></div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;              SpectrumType dummy = *it;</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;              dummy.clear(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;              dummy.push_back((*it)[peak_idx]);</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;              chroms[it-&gt;getPrecursors().begin()-&gt;getMZ()][(*it)[peak_idx].getMZ()].push_back(dummy);</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;          }</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;          {</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;            <a class="code" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a> &lt;&lt; <span class="stringliteral">&quot;ChromatogramTools: need exactly one precursor (given &quot;</span> &lt;&lt; it-&gt;getPrecursors().size() &lt;&lt;</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;            <span class="stringliteral">&quot;) and one or more product ions (&quot;</span> &lt;&lt; it-&gt;size() &lt;&lt; <span class="stringliteral">&quot;), skipping conversion of this spectrum to chromatogram.&quot;</span> &lt;&lt; std::endl;</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;          }</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;        }</div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;        {</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;          <span class="comment">// This does not makes sense to warn here, because it would also warn on simple mass spectra...</span></div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;          <span class="comment">// TODO think what to to here</span></div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;          <span class="comment">//LOG_WARN &lt;&lt; &quot;ChromatogramTools: cannot convert other chromatrogram spectra types than &#39;Selected Reaction Monitoring&#39;, skipping conversion.&quot; &lt;&lt; std::endl;</span></div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;          <span class="comment">//</span></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;</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;      <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1Map.html">Map&lt;DoubleReal, Map&lt;DoubleReal, std::vector&lt;SpectrumType&gt;</a> &gt; &gt;::const_iterator it1 = chroms.begin();</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;      <span class="keywordflow">for</span> (; it1 != chroms.end(); ++it1)</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;      {</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;        <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1Map.html">Map&lt;DoubleReal, std::vector&lt;SpectrumType&gt;</a> &gt;::const_iterator it2 = it1-&gt;second.begin();</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        <span class="keywordflow">for</span> (; it2 != it1-&gt;second.end(); ++it2)</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;          <span class="keyword">typename</span> ExperimentType::ChromatogramType chrom;</div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;          chrom.setPrecursor(*it2-&gt;second.begin()-&gt;getPrecursors().begin());</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;          <a class="code" href="classOpenMS_1_1Product.html">Product</a> prod;</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;          prod.<a class="code" href="classOpenMS_1_1Product.html#a94893c6a36a1281bfd8ff45c0199bd35">setMZ</a>(it2-&gt;first);</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;          chrom.setProduct(prod);</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;          chrom.setInstrumentSettings(it2-&gt;second.begin()-&gt;getInstrumentSettings());</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;          chrom.setAcquisitionInfo(it2-&gt;second.begin()-&gt;getAcquisitionInfo());</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;          chrom.setSourceFile(it2-&gt;second.begin()-&gt;getSourceFile());</div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;          <span class="keyword">typename</span> std::vector&lt;SpectrumType&gt;::const_iterator it3 = it2-&gt;second.begin();</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;          <span class="keywordflow">for</span> (; it3 != it2-&gt;second.end(); ++it3)</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;          {</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;            <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">ExperimentType::ChromatogramType::PeakType</a> p;</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;            p.<a class="code" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">setRT</a>(it3-&gt;getRT());</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;            p.setIntensity(it3-&gt;begin()-&gt;getIntensity());</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;            chrom.push_back(p);</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;          }</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;          chrom.setNativeID(<span class="stringliteral">&quot;chromatogram=&quot;</span> + it2-&gt;second.begin()-&gt;getNativeID());               <span class="comment">// TODO native id?</span></div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;          chrom.setChromatogramType(<a class="code" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>);</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;          exp.addChromatogram(chrom);</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;        }</div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;      }</div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;      <span class="keywordflow">if</span> (remove_spectra)</div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;      {</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;        exp.getSpectra().erase(remove_if(exp.begin(), exp.end(), <a class="code" href="classOpenMS_1_1HasScanMode.html">HasScanMode&lt;SpectrumType&gt;</a>(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>)), exp.end());</div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;      }</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;    }</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;  };</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;} <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;<span class="preprocessor">#endif // OPENMS_KERNEL_CHROMATOGRAMTOOLS_H</span></div>
<div class="ttc" id="Types_8h_html"><div class="ttname"><a href="Types_8h.html">Types.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_adc92fcb859234049c3cebcd178b41ff0"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#adc92fcb859234049c3cebcd178b41ff0">OpenMS::ChromatogramTools::~ChromatogramTools</a></div><div class="ttdeci">virtual ~ChromatogramTools()</div><div class="ttdoc">destructor </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:69</div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a2694f0775c46d9076355cb85d9815425"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">OpenMS::Peak2D::setMZ</a></div><div class="ttdeci">void setMZ(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the m/z coordinate (index 1) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:197</div></div>
<div class="ttc" id="classOpenMS_1_1Product_html"><div class="ttname"><a href="classOpenMS_1_1Product.html">OpenMS::Product</a></div><div class="ttdoc">Product meta information. </div><div class="ttdef"><b>Definition:</b> Product.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_a180cb4974eaf3d4dea0de5326b132951"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#a180cb4974eaf3d4dea0de5326b132951">OpenMS::ChromatogramTools::convertChromatogramsToSpectra</a></div><div class="ttdeci">void convertChromatogramsToSpectra(ExperimentType &amp;exp)</div><div class="ttdoc">converts the chromatogram to a list of spectra with instrument settings SRM </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1MSChromatogram_html"><div class="ttname"><a href="classOpenMS_1_1MSChromatogram.html">OpenMS::MSChromatogram</a></div><div class="ttdoc">The representation of a chromatogram. </div><div class="ttdef"><b>Definition:</b> MSChromatogram.h:53</div></div>
<div class="ttc" id="RangeUtils_8h_html"><div class="ttname"><a href="RangeUtils_8h.html">RangeUtils.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1HasScanMode_html"><div class="ttname"><a href="classOpenMS_1_1HasScanMode.html">OpenMS::HasScanMode</a></div><div class="ttdoc">Predicate that determines if a spectrum has a certain scan mode. </div><div class="ttdef"><b>Definition:</b> RangeUtils.h:215</div></div>
<div class="ttc" id="namespaceOpenMS_html_a013338b7bdbb5c3b4c78666656070e23"><div class="ttname"><a href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">OpenMS::PeakType</a></div><div class="ttdeci">Peak2D PeakType</div><div class="ttdef"><b>Definition:</b> MassTrace.h:49</div></div>
<div class="ttc" id="Map_8h_html"><div class="ttname"><a href="Map_8h.html">Map.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Product_html_a94893c6a36a1281bfd8ff45c0199bd35"><div class="ttname"><a href="classOpenMS_1_1Product.html#a94893c6a36a1281bfd8ff45c0199bd35">OpenMS::Product::setMZ</a></div><div class="ttdeci">void setMZ(DoubleReal mz)</div><div class="ttdoc">sets the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">OpenMS::InstrumentSettings::SRM</a></div><div class="ttdoc">Selected reaction monitoring scan   Synonyms: &amp;#39;Multiple reaction monitoring scan&amp;#39;, &amp;#39;SRM scan&amp;#39;, &amp;#39;MRM scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:60</div></div>
<div class="ttc" id="LogStream_8h_html_aea3f57d6dcc5b4ac957e2679e87dde27"><div class="ttname"><a href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a></div><div class="ttdeci">#define LOG_WARN</div><div class="ttdoc">Macro if a warning, a piece of information which should be read by the user, should be logged...</div><div class="ttdef"><b>Definition:</b> LogStream.h:451</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Peak2D_html_a396c5ebcac2e70f9b9a478bb2456985b"><div class="ttname"><a href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">OpenMS::Peak2D::setRT</a></div><div class="ttdeci">void setRT(CoordinateType coordinate)</div><div class="ttdoc">Mutable access to the RT coordinate (index 0) </div><div class="ttdef"><b>Definition:</b> Peak2D.h:209</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_af3ff28dcfb8f80c33a57605672ebb0b1"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#af3ff28dcfb8f80c33a57605672ebb0b1">OpenMS::ChromatogramTools::convertSpectraToChromatograms</a></div><div class="ttdeci">void convertSpectraToChromatograms(ExperimentType &amp;exp, bool remove_spectra=false)</div><div class="ttdoc">converts e.g. SRM spectra to chromatograms </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:138</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">OpenMS::InstrumentSettings::SIM</a></div><div class="ttdoc">Selected ion monitoring scan   Synonyms: &amp;#39;Multiple ion monitoring scan&amp;#39;, &amp;#39;SIM scan&amp;#39;, &amp;#39;MIM scan&amp;#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_afda6458ea9e5f8f923907a7afe8c9e63"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#afda6458ea9e5f8f923907a7afe8c9e63">OpenMS::ChromatogramTools::ChromatogramTools</a></div><div class="ttdeci">ChromatogramTools(const ChromatogramTools &amp;)</div><div class="ttdoc">copy constructor </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:65</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html_a41bd54ebbe20b4f33112d5a1e979a870"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html#a41bd54ebbe20b4f33112d5a1e979a870">OpenMS::ChromatogramTools::ChromatogramTools</a></div><div class="ttdeci">ChromatogramTools()</div><div class="ttdoc">default constructor </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">OpenMS::ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:74</div></div>
<div class="ttc" id="LogStream_8h_html"><div class="ttname"><a href="LogStream_8h.html">LogStream.h</a></div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="MSChromatogram_8h_html"><div class="ttname"><a href="MSChromatogram_8h.html">MSChromatogram.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramSettings_html_a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa"><div class="ttname"><a href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bdace5f1115eae62ba8c2527d50f67548aa">OpenMS::ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM</a></div><div class="ttdef"><b>Definition:</b> ChromatogramSettings.h:73</div></div>
<div class="ttc" id="classOpenMS_1_1ChromatogramTools_html"><div class="ttname"><a href="classOpenMS_1_1ChromatogramTools.html">OpenMS::ChromatogramTools</a></div><div class="ttdoc">Conversion class to interconvert chromatograms. </div><div class="ttdef"><b>Definition:</b> ChromatogramTools.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1Map_html"><div class="ttname"><a href="classOpenMS_1_1Map.html">OpenMS::Map</a></div><div class="ttdoc">Map class based on the STL map (containing serveral convenience functions) </div><div class="ttdef"><b>Definition:</b> Map.h:50</div></div>
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<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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