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<a href="InternalCalibration_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> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <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> <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> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <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> <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> <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> <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> <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> <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> <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> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#ifndef OPENMS_FILTERING_CALIBRATION_INTERNALCALIBRATION_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FILTERING_CALIBRATION_INTERNALCALIBRATION_H</span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor"></span><span class="preprocessor">#include <<a class="code" href="FeatureMap_8h.html">OpenMS/KERNEL/FeatureMap.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="TransformationDescription_8h.html">OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="MzMLFile_8h.html">OpenMS/FORMAT/MzMLFile.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <<a class="code" href="TransformationXMLFile_8h.html">OpenMS/FORMAT/TransformationXMLFile.h</a>></span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <gsl/gsl_fit.h></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> {</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InternalCalibration.html"> 62</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1InternalCalibration.html">InternalCalibration</a> :</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a>,</div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  {</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="classOpenMS_1_1InternalCalibration.html">InternalCalibration</a>();</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InternalCalibration.html#ae8d33625af3ba7f0c0c231b94e89827d"> 71</a></span>  <a class="code" href="classOpenMS_1_1InternalCalibration.html#ae8d33625af3ba7f0c0c231b94e89827d">~InternalCalibration</a>(){}</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">void</span> calibrateMapSpectrumwise(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & exp, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & calibrated_exp, std::vector<DoubleReal> & ref_masses);</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">void</span> calibrateMapGlobally(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & exp, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & calibrated_exp, std::vector<DoubleReal> & ref_masses, <a class="code" href="classOpenMS_1_1String.html">String</a> trafo_file_name = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keywordtype">void</span> calibrateMapGlobally(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & exp, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & calibrated_exp, std::vector<PeptideIdentification> & ref_ids, <a class="code" href="classOpenMS_1_1String.html">String</a> trafo_file_name = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordtype">void</span> calibrateMapGlobally(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & feature_map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & calibrated_feature_map, <a class="code" href="classOpenMS_1_1String.html">String</a> trafo_file_name = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span> </div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordtype">void</span> calibrateMapGlobally(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & feature_map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & calibrated_feature_map, std::vector<PeptideIdentification> & ref_ids, <a class="code" href="classOpenMS_1_1String.html">String</a> trafo_file_name = <span class="stringliteral">""</span>);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordtype">void</span> calibrateMapList(std::vector<<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> > & exp_list, std::vector<<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> > & calibrated_exp_list, std::vector<DoubleReal> & ref_masses, std::vector<DoubleReal> & detected_background_masses);</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> </div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> </div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  <span class="keywordtype">void</span> makeLinearRegression_(std::vector<DoubleReal> & observed_masses, std::vector<DoubleReal> & theoretical_masses);</div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <span class="keywordtype">void</span> checkReferenceIds_(std::vector<PeptideIdentification> & pep_ids);</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> </div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordtype">void</span> checkReferenceIds_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & feature_map);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordtype">void</span> applyTransformation_(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & feature_map, <a class="code" href="classOpenMS_1_1FeatureMap.html">FeatureMap<></a> & calibrated_feature_map);</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a"> 161</a></span>  <a class="code" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> <a class="code" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a>;</div>
<div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  }; <span class="comment">// class InternalCalibration</span></div>
<div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div>
<div class="line"><a name="l00164"></a><span class="lineno"> 164</span> </div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c"> 166</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c">InternalCalibration::calibrateMapSpectrumwise</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & exp, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & calibrated_exp, std::vector<DoubleReal> & ref_masses)</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  {</div>
<div class="line"><a name="l00168"></a><span class="lineno"> 168</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="preprocessor"></span> std::cout.precision(writtenDigits<DoubleReal>());</div>
<div class="line"><a name="l00170"></a><span class="lineno"> 170</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00171"></a><span class="lineno"> 171</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  {</div>
<div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  std::cout << <span class="stringliteral">"Input is empty."</span> << std::endl;</div>
<div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  }</div>
<div class="line"><a name="l00176"></a><span class="lineno"> 176</span> </div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">if</span> (exp[0].getType() != <a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>)</div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  {</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  std::cout << <span class="stringliteral">"Attention: this function is assuming peak data."</span> << std::endl;</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  }</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  calibrated_exp = exp;</div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_ref_peaks = ref_masses.size();</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordtype">bool</span> use_ppm = (<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">"mz_tolerance_unit"</span>) == <span class="stringliteral">"ppm"</span>) ? <span class="keyword">true</span> : <span class="keyword">false</span>;</div>
<div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz_tol = <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">"mz_tolerance"</span>);</div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"calibrate spectra"</span>);</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="comment">// for each spectrum</span></div>
<div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec = 0; spec < exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++spec)</div>
<div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  {</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="comment">// calibrate only MS1 spectra</span></div>
<div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordflow">if</span> (exp[spec].getMSLevel() != 1)</div>
<div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  {</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  }</div>
<div class="line"><a name="l00195"></a><span class="lineno"> 195</span> </div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  std::vector<DoubleReal> corr_masses, rel_errors, found_ref_masses;</div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  <a class="code" href="classunsigned_01int.html">UInt</a> corr_peaks = 0;</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak = 0; peak < exp[spec].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++peak)</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  {</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ref_peak = 0; ref_peak < num_ref_peaks; ++ref_peak)</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  {</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  <span class="keywordflow">if</span> (!use_ppm && fabs(exp[spec][peak].getMZ() - ref_masses[ref_peak]) < mz_tol)</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  {</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  found_ref_masses.push_back(ref_masses[ref_peak]);</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  corr_masses.push_back(exp[spec][peak].getMZ());</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  ++corr_peaks;</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  }</div>
<div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (use_ppm && fabs(exp[spec][peak].getMZ() - ref_masses[ref_peak]) / ref_masses[ref_peak] * 1e6 < mz_tol)</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  {</div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  found_ref_masses.push_back(ref_masses[ref_peak]);</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  corr_masses.push_back(exp[spec][peak].getMZ());</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  ++corr_peaks;</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  }</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  }</div>
<div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  }</div>
<div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordflow">if</span> (corr_peaks < 2)</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  {</div>
<div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  std::cout << <span class="stringliteral">"spec: "</span> << spec</div>
<div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  << <span class="stringliteral">" less than 2 reference masses were detected within a reasonable error range\n"</span>;</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  std::cout << <span class="stringliteral">"This spectrum cannot be calibrated!\n"</span>;</div>
<div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  }</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  <span class="comment">// determine rel error in ppm for the two reference masses</span></div>
<div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ref_peak = 0; ref_peak < found_ref_masses.size(); ++ref_peak)</div>
<div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  {</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  rel_errors.push_back((found_ref_masses[ref_peak] - corr_masses[ref_peak]) / corr_masses[ref_peak] * 1e6);</div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  }</div>
<div class="line"><a name="l00232"></a><span class="lineno"> 232</span> </div>
<div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <a class="code" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">makeLinearRegression_</a>(corr_masses, found_ref_masses);</div>
<div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div>
<div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="comment">// now calibrate the whole spectrum</span></div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> peak = 0; peak < calibrated_exp[spec].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++peak)</div>
<div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  {</div>
<div class="line"><a name="l00238"></a><span class="lineno"> 238</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span> <span class="preprocessor"></span> std::cout << calibrated_exp[spec][peak].getMZ() << <span class="stringliteral">"\t"</span>;</div>
<div class="line"><a name="l00240"></a><span class="lineno"> 240</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span> <span class="preprocessor"></span> <a class="code" href="classdouble.html">DoubleReal</a> mz = calibrated_exp[spec][peak].getMZ();</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  mz = <a class="code" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a>.<a class="code" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a>(mz);</div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  calibrated_exp[spec][peak].setMZ(mz);</div>
<div class="line"><a name="l00244"></a><span class="lineno"> 244</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00245"></a><span class="lineno"> 245</span> <span class="preprocessor"></span> std::cout << calibrated_exp[spec][peak].getMZ() << std::endl;</div>
<div class="line"><a name="l00246"></a><span class="lineno"> 246</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00247"></a><span class="lineno"> 247</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  }</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(spec);</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  } <span class="comment">// for(Size spec=0;spec < exp.size(); ++spec)</span></div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  }</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span> </div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00255"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InternalCalibration.html#a2157a7fbbba00561b9bf8b26b469786d"> 255</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1InternalCalibration.html#ae16f418bb5c7ac54002dce6c81a59ca3">InternalCalibration::calibrateMapGlobally</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & exp,</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & calibrated_exp,</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  std::vector<PeptideIdentification> & ref_ids, <a class="code" href="classOpenMS_1_1String.html">String</a> trafo_file_name)</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  {</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordtype">bool</span> use_ppm = <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">"mz_tolerance_unit"</span>) == <span class="stringliteral">"ppm"</span> ? <span class="keyword">true</span> : <span class="keyword">false</span>;</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz_tolerance = <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">"mz_tolerance"</span>);</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keywordflow">if</span> (exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  {</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  std::cout << <span class="stringliteral">"Input is empty."</span> << std::endl;</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  }</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span> </div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordflow">if</span> (exp[0].getType() != <a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>)</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  {</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  std::cout << <span class="stringliteral">"Attention: this function is assuming peak data."</span> << std::endl;</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  }</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="comment">// check if the ids contain meta information about the peak positions</span></div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <a class="code" href="classOpenMS_1_1InternalCalibration.html#a103a7b7cbdc2702033468a091b4f6a26">checkReferenceIds_</a>(ref_ids);</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> </div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  std::vector<DoubleReal> theoretical_masses, observed_masses;</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p_id = 0; p_id < ref_ids.size(); ++p_id)</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  {</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p_h = 0; p_h < ref_ids[p_id].getHits().size(); ++p_h)</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  {</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge = ref_ids[p_id].getHits()[p_h].getCharge();</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <a class="code" href="classdouble.html">DoubleReal</a> theo_mass = ref_ids[p_id].getHits()[p_h].getSequence().getMonoWeight(<a class="code" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48a8b7c5cd8bd8eb51ee6d3fd0eac584679">Residue::Full</a>, charge) / (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)charge;</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="comment">// first find corresponding ms1-spectrum</span></div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">MSExperiment<InputPeakType>::ConstIterator</a> rt_iter = exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">RTBegin</a>(ref_ids[p_id].getMetaValue(<span class="stringliteral">"RT"</span>));</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keywordflow">while</span> (rt_iter != exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() && rt_iter->getMSLevel() != 1)</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  {</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  --rt_iter;</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  }</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="comment">// now find closest peak</span></div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">MSSpectrum<InputPeakType>::ConstIterator</a> mz_iter = rt_iter->MZBegin(ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>));</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="comment">//std::cout << mz_iter->getMZ() <<" "<<(DoubleReal)ref_ids[p_id].getMetaValue("MZ")<<"\t";</span></div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>) - mz_iter->getMZ();</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="comment">//std::cout << dist << "\t";</span></div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="keywordflow">if</span> ((mz_iter + 1) != rt_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>()</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  && fabs((mz_iter + 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) < fabs(dist)</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  && mz_iter != rt_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>()</div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  && fabs((mz_iter - 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) < fabs((mz_iter + 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>))) <span class="comment">// if mz_iter +1 has smaller dist than mz_iter and mz_iter-1</span></div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  {</div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="keywordflow">if</span> ((use_ppm &&</div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  fabs((mz_iter + 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) / (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>) * 1e06 < mz_tolerance) ||</div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  (!use_ppm && fabs((mz_iter + 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) < mz_tolerance))</div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  {</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="comment">//std::cout <<(mz_iter +1)->getMZ() - (DoubleReal)ref_ids[p_id].getMetaValue("MZ")<<"\t";</span></div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  observed_masses.push_back((mz_iter + 1)->getMZ());</div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  theoretical_masses.push_back(theo_mass);</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="comment">//std::cout << (mz_iter +1)->getMZ() << " ~ "<<theo_mass << " charge: "<<ref_ids[p_id].getHits()[p_h].getCharge()</span></div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="comment">//<< "\tplus 1"<< std::endl;</span></div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  }</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  }</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (mz_iter != rt_iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>()</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  && fabs((mz_iter - 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) < fabs(dist)) <span class="comment">// if mz_iter-1 has smaller dist than mz_iter</span></div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  {</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">if</span> ((use_ppm &&</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  fabs((mz_iter - 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) / (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>) * 1e06 < mz_tolerance) ||</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  (!use_ppm && fabs((mz_iter - 1)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) < mz_tolerance))</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  {</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="comment">//std::cout <<(mz_iter -1)->getMZ() - (DoubleReal)ref_ids[p_id].getMetaValue("MZ")<<"\t";</span></div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  observed_masses.push_back((mz_iter - 1)->getMZ());</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  theoretical_masses.push_back(theo_mass);</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="comment">//std::cout << (mz_iter -1)->getMZ() << " ~ "<<theo_mass << " charge: "<<ref_ids[p_id].getHits()[p_h].getCharge()</span></div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="comment">//<< "\tminus 1"<< std::endl;</span></div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  }</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  }</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  {</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">if</span> ((use_ppm &&</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  fabs((mz_iter)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) / (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>) * 1e06 < mz_tolerance) ||</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  (!use_ppm && fabs((mz_iter)->getMZ() - (<a class="code" href="classdouble.html">DoubleReal</a>)ref_ids[p_id].getMetaValue(<span class="stringliteral">"MZ"</span>)) < mz_tolerance))</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  {</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  observed_masses.push_back(mz_iter->getMZ());</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  theoretical_masses.push_back(theo_mass);</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span> <span class="comment">// std::cout <<"\t"<< mz_iter->getMZ() << " ~ "<<theo_mass<< " charge: "<<ref_ids[p_id].getHits()[p_h].getCharge()</span></div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span> <span class="comment">// << "\tat mz_iter"<< std::endl;</span></div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  }</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  }</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  }</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  }</div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span> </div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <a class="code" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">makeLinearRegression_</a>(observed_masses, theoretical_masses);</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keyword">static_cast<</span><a class="code" href="classOpenMS_1_1ExperimentalSettings.html">ExperimentalSettings</a> &<span class="keyword">></span>(calibrated_exp) = exp;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  calibrated_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">resize</a>(exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span> </div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="comment">// for each spectrum</span></div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec = 0; spec < exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++spec)</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  {</div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="comment">// calibrate only MS1 spectra</span></div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">if</span> (exp[spec].getMSLevel() != 1)</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  {</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  calibrated_exp[spec] = exp[spec];</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  }</div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="comment">// copy the spectrum meta data</span></div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  calibrated_exp[spec] = exp[spec];</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span> </div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> peak = 0; peak < exp[spec].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++peak)</div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  {</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> <span class="preprocessor"></span> std::cout << exp[spec][peak].getMZ() << <span class="stringliteral">"\t"</span>;</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> <span class="preprocessor"></span> <a class="code" href="classdouble.html">DoubleReal</a> mz = exp[spec][peak].getMZ();</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  mz = <a class="code" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a>.<a class="code" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a>(mz);</div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  calibrated_exp[spec][peak].setMZ(mz);</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span> <span class="preprocessor"></span> std::cout << calibrated_exp[spec][peak].getMZ() << std::endl;</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  }</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  } <span class="comment">// for(Size spec=0;spec < exp.size(); ++spec)</span></div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordflow">if</span> (trafo_file_name != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  {</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <a class="code" href="classOpenMS_1_1TransformationXMLFile.html">TransformationXMLFile</a>().<a class="code" href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">store</a>(trafo_file_name, <a class="code" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a>);</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  }</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  }</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span> </div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputPeakType></div>
<div class="line"><a name="l00375"></a><span class="lineno"><a class="line" href="classOpenMS_1_1InternalCalibration.html#ae16f418bb5c7ac54002dce6c81a59ca3"> 375</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1InternalCalibration.html#ae16f418bb5c7ac54002dce6c81a59ca3">InternalCalibration::calibrateMapGlobally</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & exp, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType></a> & calibrated_exp, std::vector<DoubleReal> & ref_masses, <a class="code" href="classOpenMS_1_1String.html">String</a> trafo_file_name)</div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  {</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  <span class="keywordflow">if</span> (exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  {</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  std::cout << <span class="stringliteral">"Input is empty."</span> << std::endl;</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  }</div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span> </div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">if</span> (exp[0].getType() != <a class="code" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>)</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  {</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  std::cout << <span class="stringliteral">"Attention: this function is assuming peak data."</span> << std::endl;</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  }</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span> </div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span> </div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_ref_peaks = ref_masses.size();</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="keywordtype">bool</span> use_ppm = (<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">"mz_tolerance_unit"</span>) == <span class="stringliteral">"ppm"</span>) ? <span class="keyword">true</span> : <span class="keyword">false</span>;</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz_tol = <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">"mz_tolerance"</span>);</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a>(0, exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(), <span class="stringliteral">"calibrate spectra"</span>);</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  std::vector<DoubleReal> corr_masses, rel_errors, found_ref_masses;</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <a class="code" href="classunsigned_01int.html">UInt</a> corr_peaks = 0;</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="comment">// for each spectrum</span></div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec = 0; spec < exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++spec)</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  {</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="comment">// calibrate only MS1 spectra</span></div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <span class="keywordflow">if</span> (exp[spec].getMSLevel() != 1)</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak = 0; peak < exp[spec].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++peak)</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  {</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ref_peak = 0; ref_peak < num_ref_peaks; ++ref_peak)</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  {</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="keywordflow">if</span> (!use_ppm && fabs(exp[spec][peak].getMZ() - ref_masses[ref_peak]) < mz_tol)</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  {</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  found_ref_masses.push_back(ref_masses[ref_peak]);</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  corr_masses.push_back(exp[spec][peak].getMZ());</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  ++corr_peaks;</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  }</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (use_ppm && fabs(exp[spec][peak].getMZ() - ref_masses[ref_peak]) / ref_masses[ref_peak] * 1e6 < mz_tol)</div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  {</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  found_ref_masses.push_back(ref_masses[ref_peak]);</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  corr_masses.push_back(exp[spec][peak].getMZ());</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  ++corr_peaks;</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  }</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  }</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  }</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  }</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordflow">if</span> (corr_peaks < 2)</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  {</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  std::cout << <span class="stringliteral">"Less than 2 reference masses were detected within a reasonable error range\n"</span>;</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  std::cout << <span class="stringliteral">"This spectrum cannot be calibrated!\n"</span>;</div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  }</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span> </div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  <span class="comment">// calculate the (linear) calibration function</span></div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  <a class="code" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">makeLinearRegression_</a>(corr_masses, found_ref_masses);</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keyword">static_cast<</span><a class="code" href="classOpenMS_1_1ExperimentalSettings.html">ExperimentalSettings</a> &<span class="keyword">></span>(calibrated_exp) = exp;</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  calibrated_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">resize</a>(exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>());</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> </div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="comment">// apply the calibration function to each peak</span></div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spec = 0; spec < exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++spec)</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  {</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  <span class="comment">// calibrate only MS1 spectra</span></div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  <span class="keywordflow">if</span> (exp[spec].getMSLevel() != 1)</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  {</div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  calibrated_exp[spec] = exp[spec];</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  }</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span> </div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="comment">// copy the spectrum data</span></div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  calibrated_exp[spec] = exp[spec];</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span> </div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> peak = 0; peak < exp[spec].<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++peak)</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  {</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span> <span class="preprocessor"></span> std::cout << exp[spec][peak].getMZ() << <span class="stringliteral">"\t"</span>;</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span> <span class="preprocessor"></span> <a class="code" href="classdouble.html">DoubleReal</a> mz = exp[spec][peak].getMZ();</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  mz = <a class="code" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a>.<a class="code" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">apply</a>(mz);</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  calibrated_exp[spec][peak].setMZ(mz);</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span> </div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span> <span class="preprocessor">#ifdef DEBUG_CALIBRATION</span></div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span> <span class="preprocessor"></span> std::cout << calibrated_exp[spec][peak].getMZ() << std::endl;</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  }</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a>(spec);</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  } <span class="comment">// for(Size spec=0;spec < exp.size(); ++spec)</span></div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <a class="code" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a>();</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">if</span> (trafo_file_name != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  {</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <a class="code" href="classOpenMS_1_1TransformationXMLFile.html">TransformationXMLFile</a>().<a class="code" href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">store</a>(trafo_file_name, <a class="code" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a>);</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  }</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  }</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> </div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span> <span class="preprocessor">#endif // OPENMS_FILTERING_CALIBRATION_INTERNALCALIBRATION_H</span></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1InternalCalibration_html_ae16f418bb5c7ac54002dce6c81a59ca3"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html#ae16f418bb5c7ac54002dce6c81a59ca3">OpenMS::InternalCalibration::calibrateMapGlobally</a></div><div class="ttdeci">void calibrateMapGlobally(const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< DoubleReal > &ref_masses, String trafo_file_name="")</div><div class="ttdoc">Calibrate a peak map using given reference masses with one calibration function for the whole map...</div><div class="ttdef"><b>Definition:</b> InternalCalibration.h:375</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">OpenMS::SpectrumSettings::PEAKS</a></div><div class="ttdoc">Peak data (also called centroided data or stick data) </div><div class="ttdef"><b>Definition:</b> SpectrumSettings.h:74</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_1FeatureMap_html"><div class="ttname"><a href="classOpenMS_1_1FeatureMap.html">OpenMS::FeatureMap<></a></div></div>
<div class="ttc" id="classOpenMS_1_1InternalCalibration_html_a28e0d24d3052fd9cf4c732ca85b2f3b9"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">OpenMS::InternalCalibration::makeLinearRegression_</a></div><div class="ttdeci">void makeLinearRegression_(std::vector< DoubleReal > &observed_masses, std::vector< DoubleReal > &theoretical_masses)</div><div class="ttdoc">the actual calibration function </div></div>
<div class="ttc" id="classOpenMS_1_1InternalCalibration_html"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html">OpenMS::InternalCalibration</a></div><div class="ttdoc">A simple calibration method using linear interpolation of given reference masses. ...</div><div class="ttdef"><b>Definition:</b> InternalCalibration.h:62</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a4895afe86c2aa0747ae0411c58c82114"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a4895afe86c2aa0747ae0411c58c82114">OpenMS::MSSpectrum::ConstIterator</a></div><div class="ttdeci">ContainerType::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:125</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a2387033802383edbdc95f9bbb12a707e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">OpenMS::MSExperiment::begin</a></div><div class="ttdeci">Iterator begin()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:147</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac2bc824d6ff2633ec34793c9e918d479"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">OpenMS::MSExperiment::resize</a></div><div class="ttdeci">void resize(Size s)</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:122</div></div>
<div class="ttc" id="classOpenMS_1_1TransformationXMLFile_html_abdddea80e737ce717013609e58e755f0"><div class="ttname"><a href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">OpenMS::TransformationXMLFile::store</a></div><div class="ttdeci">void store(String filename, const TransformationDescription &transformation)</div><div class="ttdoc">Stores the data in an TransformationXML file. </div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ab45dae688fc5d8983727abffa4389003"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">OpenMS::MSExperiment::end</a></div><div class="ttdeci">Iterator end()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_adb2f0f3e10754ca4dc7be677f15689a3"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">OpenMS::MSExperiment::RTBegin</a></div><div class="ttdeci">ConstIterator RTBegin(CoordinateType rt) const </div><div class="ttdoc">Fast search for spectrum range begin. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:349</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_1TransformationXMLFile_html"><div class="ttname"><a href="classOpenMS_1_1TransformationXMLFile.html">OpenMS::TransformationXMLFile</a></div><div class="ttdoc">Used to load and store TransformationXML files. </div><div class="ttdef"><b>Definition:</b> TransformationXMLFile.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a1cc1012b0cdaea97f58d571af1ff45de"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">OpenMS::ProgressLogger::endProgress</a></div><div class="ttdeci">void endProgress() const </div><div class="ttdoc">Ends the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1InternalCalibration_html_ae8d33625af3ba7f0c0c231b94e89827d"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html#ae8d33625af3ba7f0c0c231b94e89827d">OpenMS::InternalCalibration::~InternalCalibration</a></div><div class="ttdeci">~InternalCalibration()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> InternalCalibration.h:71</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 & getValue(const String &key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html_aa280f8d4730c216c58a3edd091b99767"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">OpenMS::TransformationDescription::apply</a></div><div class="ttdeci">DoubleReal apply(DoubleReal value) const </div><div class="ttdoc">Applies the transformation to value. </div></div>
<div class="ttc" id="classOpenMS_1_1Residue_html_a7651af21f9cf8ed6445415903fc6cb48a8b7c5cd8bd8eb51ee6d3fd0eac584679"><div class="ttname"><a href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48a8b7c5cd8bd8eb51ee6d3fd0eac584679">OpenMS::Residue::Full</a></div><div class="ttdef"><b>Definition:</b> Residue.h:363</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1InternalCalibration_html_a1651981607d6c86252b9ab64e5f7996c"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c">OpenMS::InternalCalibration::calibrateMapSpectrumwise</a></div><div class="ttdeci">void calibrateMapSpectrumwise(const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< DoubleReal > &ref_masses)</div><div class="ttdoc">Calibrate a peak map using given reference masses with a separate calibration function for each spect...</div><div class="ttdef"><b>Definition:</b> InternalCalibration.h:166</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_aee0a1a68d0fab63eefa6e14010b4a7f0"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#aee0a1a68d0fab63eefa6e14010b4a7f0">OpenMS::MSExperiment::ConstIterator</a></div><div class="ttdeci">std::vector< SpectrumType >::const_iterator ConstIterator</div><div class="ttdoc">Non-mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:103</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="classOpenMS_1_1InternalCalibration_html_a103a7b7cbdc2702033468a091b4f6a26"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html#a103a7b7cbdc2702033468a091b4f6a26">OpenMS::InternalCalibration::checkReferenceIds_</a></div><div class="ttdeci">void checkReferenceIds_(std::vector< PeptideIdentification > &pep_ids)</div><div class="ttdoc">check if reference ids contain RT and MZ information as meta values </div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_af1c45ecd71b5041b70319249e8e73591"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">OpenMS::ProgressLogger::startProgress</a></div><div class="ttdeci">void startProgress(SignedSize begin, SignedSize end, const String &label) const </div><div class="ttdoc">Initializes the progress display. </div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ac6e61de369e994009e36f344f99c15ad"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">OpenMS::MSExperiment::empty</a></div><div class="ttdeci">bool empty() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:127</div></div>
<div class="ttc" id="TransformationDescription_8h_html"><div class="ttname"><a href="TransformationDescription_8h.html">TransformationDescription.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html_a8852277abd03220cc7b80d6c1bed6fed"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">OpenMS::ProgressLogger::setProgress</a></div><div class="ttdeci">void setProgress(SignedSize value) const </div><div class="ttdoc">Sets the current progress. </div></div>
<div class="ttc" id="classOpenMS_1_1TransformationDescription_html"><div class="ttname"><a href="classOpenMS_1_1TransformationDescription.html">OpenMS::TransformationDescription</a></div><div class="ttdoc">Generic description of a coordinate transformation. </div><div class="ttdef"><b>Definition:</b> TransformationDescription.h:59</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="TransformationXMLFile_8h_html"><div class="ttname"><a href="TransformationXMLFile_8h.html">TransformationXMLFile.h</a></div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1ExperimentalSettings_html"><div class="ttname"><a href="classOpenMS_1_1ExperimentalSettings.html">OpenMS::ExperimentalSettings</a></div><div class="ttdoc">Description of the experimental settings. </div><div class="ttdef"><b>Definition:</b> ExperimentalSettings.h:59</div></div>
<div class="ttc" id="MzMLFile_8h_html"><div class="ttname"><a href="MzMLFile_8h.html">MzMLFile.h</a></div></div>
<div class="ttc" id="FeatureMap_8h_html"><div class="ttname"><a href="FeatureMap_8h.html">FeatureMap.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1InternalCalibration_html_a0846853a0279b29f089c7c8d19e0ad4a"><div class="ttname"><a href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">OpenMS::InternalCalibration::trafo_</a></div><div class="ttdeci">TransformationDescription trafo_</div><div class="ttdoc">here the transformation is stored </div><div class="ttdef"><b>Definition:</b> InternalCalibration.h:161</div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
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