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<HTML>
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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1InternalCalibration.html">InternalCalibration</a></li> </ul>
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<div class="title">InternalCalibration Class Reference<div class="ingroups"><a class="el" href="group__SignalProcessing.html">SignalProcessing</a></div></div> </div>
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<p>A simple calibration method using linear interpolation of given reference masses.
<a href="classOpenMS_1_1InternalCalibration.html#details">More...</a></p>
<p><code>#include <<a class="el" href="InternalCalibration_8h_source.html">OpenMS/FILTERING/CALIBRATION/InternalCalibration.h</a>></code></p>
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Inheritance diagram for InternalCalibration:</div>
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<img src="classOpenMS_1_1InternalCalibration.png" usemap="#InternalCalibration_map" alt=""/>
<map id="InternalCalibration_map" name="InternalCalibration_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,133,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="143,0,276,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ab360aace93e2db7484fba988f30addca"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#ab360aace93e2db7484fba988f30addca">InternalCalibration</a> ()</td></tr>
<tr class="memdesc:ab360aace93e2db7484fba988f30addca"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#ab360aace93e2db7484fba988f30addca">More...</a><br/></td></tr>
<tr class="separator:ab360aace93e2db7484fba988f30addca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae8d33625af3ba7f0c0c231b94e89827d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#ae8d33625af3ba7f0c0c231b94e89827d">~InternalCalibration</a> ()</td></tr>
<tr class="memdesc:ae8d33625af3ba7f0c0c231b94e89827d"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#ae8d33625af3ba7f0c0c231b94e89827d">More...</a><br/></td></tr>
<tr class="separator:ae8d33625af3ba7f0c0c231b94e89827d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1651981607d6c86252b9ab64e5f7996c"><td class="memTemplParams" colspan="2">template<typename InputPeakType > </td></tr>
<tr class="memitem:a1651981607d6c86252b9ab64e5f7996c"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c">calibrateMapSpectrumwise</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > &exp, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > &calibrated_exp, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &ref_masses)</td></tr>
<tr class="memdesc:a1651981607d6c86252b9ab64e5f7996c"><td class="mdescLeft"> </td><td class="mdescRight">Calibrate a peak map using given reference masses with a separate calibration function for each spectrum. <a href="#a1651981607d6c86252b9ab64e5f7996c">More...</a><br/></td></tr>
<tr class="separator:a1651981607d6c86252b9ab64e5f7996c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae16f418bb5c7ac54002dce6c81a59ca3"><td class="memTemplParams" colspan="2">template<typename InputPeakType > </td></tr>
<tr class="memitem:ae16f418bb5c7ac54002dce6c81a59ca3"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#ae16f418bb5c7ac54002dce6c81a59ca3">calibrateMapGlobally</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > &exp, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > &calibrated_exp, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &ref_masses, <a class="el" href="classOpenMS_1_1String.html">String</a> trafo_file_name="")</td></tr>
<tr class="memdesc:ae16f418bb5c7ac54002dce6c81a59ca3"><td class="mdescLeft"> </td><td class="mdescRight">Calibrate a peak map using given reference masses with one calibration function for the whole map. <a href="#ae16f418bb5c7ac54002dce6c81a59ca3">More...</a><br/></td></tr>
<tr class="separator:ae16f418bb5c7ac54002dce6c81a59ca3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2157a7fbbba00561b9bf8b26b469786d"><td class="memTemplParams" colspan="2">template<typename InputPeakType > </td></tr>
<tr class="memitem:a2157a7fbbba00561b9bf8b26b469786d"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a2157a7fbbba00561b9bf8b26b469786d">calibrateMapGlobally</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > &exp, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > &calibrated_exp, std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ref_ids, <a class="el" href="classOpenMS_1_1String.html">String</a> trafo_file_name="")</td></tr>
<tr class="memdesc:a2157a7fbbba00561b9bf8b26b469786d"><td class="mdescLeft"> </td><td class="mdescRight">Calibrate a peak map using given reference ids with one calibration function for the whole map. <a href="#a2157a7fbbba00561b9bf8b26b469786d">More...</a><br/></td></tr>
<tr class="separator:a2157a7fbbba00561b9bf8b26b469786d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad8574a0bdbd6781d45cb93877732ce1b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#ad8574a0bdbd6781d45cb93877732ce1b">calibrateMapGlobally</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &feature_map, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &calibrated_feature_map, <a class="el" href="classOpenMS_1_1String.html">String</a> trafo_file_name="")</td></tr>
<tr class="memdesc:ad8574a0bdbd6781d45cb93877732ce1b"><td class="mdescLeft"> </td><td class="mdescRight">Calibrate an annotated feature map with one calibration function for the whole map. <a href="#ad8574a0bdbd6781d45cb93877732ce1b">More...</a><br/></td></tr>
<tr class="separator:ad8574a0bdbd6781d45cb93877732ce1b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a53035b66ce03545b53417e0f1fd684b7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a53035b66ce03545b53417e0f1fd684b7">calibrateMapGlobally</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &feature_map, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &calibrated_feature_map, std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ref_ids, <a class="el" href="classOpenMS_1_1String.html">String</a> trafo_file_name="")</td></tr>
<tr class="memdesc:a53035b66ce03545b53417e0f1fd684b7"><td class="mdescLeft"> </td><td class="mdescRight">Calibrate a feature map using given reference ids with one calibration function for the whole map. <a href="#a53035b66ce03545b53417e0f1fd684b7">More...</a><br/></td></tr>
<tr class="separator:a53035b66ce03545b53417e0f1fd684b7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a34c53fde5084c75359a06d124b2ff4e6"><td class="memTemplParams" colspan="2">template<typename InputPeakType > </td></tr>
<tr class="memitem:a34c53fde5084c75359a06d124b2ff4e6"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a34c53fde5084c75359a06d124b2ff4e6">calibrateMapList</a> (std::vector< <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > > &exp_list, std::vector< <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > > &calibrated_exp_list, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &ref_masses, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &detected_background_masses)</td></tr>
<tr class="separator:a34c53fde5084c75359a06d124b2ff4e6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE! <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of progress log being used. <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the progress display. <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the current progress. <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Ends the progress display. <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a28e0d24d3052fd9cf4c732ca85b2f3b9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">makeLinearRegression_</a> (std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &observed_masses, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &theoretical_masses)</td></tr>
<tr class="memdesc:a28e0d24d3052fd9cf4c732ca85b2f3b9"><td class="mdescLeft"> </td><td class="mdescRight">the actual calibration function <a href="#a28e0d24d3052fd9cf4c732ca85b2f3b9">More...</a><br/></td></tr>
<tr class="separator:a28e0d24d3052fd9cf4c732ca85b2f3b9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a103a7b7cbdc2702033468a091b4f6a26"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a103a7b7cbdc2702033468a091b4f6a26">checkReferenceIds_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &pep_ids)</td></tr>
<tr class="memdesc:a103a7b7cbdc2702033468a091b4f6a26"><td class="mdescLeft"> </td><td class="mdescRight">check if reference ids contain RT and MZ information as meta values <a href="#a103a7b7cbdc2702033468a091b4f6a26">More...</a><br/></td></tr>
<tr class="separator:a103a7b7cbdc2702033468a091b4f6a26"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a07623ac12844eccc462ed506a97209bd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a07623ac12844eccc462ed506a97209bd">checkReferenceIds_</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &feature_map)</td></tr>
<tr class="memdesc:a07623ac12844eccc462ed506a97209bd"><td class="mdescLeft"> </td><td class="mdescRight">check if reference ids contain RT and MZ information as meta values <a href="#a07623ac12844eccc462ed506a97209bd">More...</a><br/></td></tr>
<tr class="separator:a07623ac12844eccc462ed506a97209bd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a143d5d335c0bd74c729fd0a3742c5577"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a143d5d335c0bd74c729fd0a3742c5577">applyTransformation_</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &feature_map, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &calibrated_feature_map)</td></tr>
<tr class="memdesc:a143d5d335c0bd74c729fd0a3742c5577"><td class="mdescLeft"> </td><td class="mdescRight">apply transformation to all features (including subordinates and convex hulls) <a href="#a143d5d335c0bd74c729fd0a3742c5577">More...</a><br/></td></tr>
<tr class="separator:a143d5d335c0bd74c729fd0a3742c5577"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
<tr class="separator:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a0846853a0279b29f089c7c8d19e0ad4a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">trafo_</a></td></tr>
<tr class="memdesc:a0846853a0279b29f089c7c8d19e0ad4a"><td class="mdescLeft"> </td><td class="mdescRight">here the transformation is stored <a href="#a0846853a0279b29f089c7c8d19e0ad4a">More...</a><br/></td></tr>
<tr class="separator:a0846853a0279b29f089c7c8d19e0ad4a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
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<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
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<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
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<tr class="memitem:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">time_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
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<tr class="inherit_header pro_static_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A simple calibration method using linear interpolation of given reference masses. </p>
<p>This class implements a simle calibration method: given a list of reference masses, the relative errors of the peaks in the data are approximated by linear interpolation and subtracted from the data.</p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><b>mz_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Allowed tolerance between peak and reference m/z.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>mz_tolerance_unit</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">Da</td>
<td style="vertical-align:top">Da, ppm</td><td style="vertical-align:top">Unit for mz_tolerance.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>rt_tolerance</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Allowed tolerance between peak and reference rt.</td>
</tr>
</table>
<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1InternalCalibration.html">InternalCalibration</a> </td>
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<p>Default constructor. </p>
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<td class="memname">~<a class="el" href="classOpenMS_1_1InternalCalibration.html">InternalCalibration</a> </td>
<td>(</td>
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<p>Destructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void applyTransformation_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>feature_map</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>calibrated_feature_map</em> </td>
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<p>apply transformation to all features (including subordinates and convex hulls) </p>
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<td class="memname">void calibrateMapGlobally </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > & </td>
<td class="paramname"><em>exp</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > & </td>
<td class="paramname"><em>calibrated_exp</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>ref_masses</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> </td>
<td class="paramname"><em>trafo_file_name</em> = <code>""</code> </td>
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<p>Calibrate a peak map using given reference masses with one calibration function for the whole map. </p>
<p>The calibration function is calculated for the whole map. For the matching of the reference masses and the peaks the parameter mz_tolerance is used to calculate a window around the reference masses. If more than one peak is found within this window the closest peak is taken. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">exp</td><td>the uncalibrated peak map </td></tr>
<tr><td class="paramname">calibrated_exp</td><td>the calibrated peak map </td></tr>
<tr><td class="paramname">ref_masses</td><td>the reference m/z values </td></tr>
<tr><td class="paramname">trafo_file_name</td><td>file where the transformation function of the calibration is stored </td></tr>
</table>
</dd>
</dl>
<p>References <a class="el" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">TransformationDescription::apply()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">ProgressLogger::endProgress()</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">InternalCalibration::makeLinearRegression_()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">MSExperiment< PeakT, ChromatogramPeakT >::resize()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">ProgressLogger::setProgress()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">ProgressLogger::startProgress()</a>, <a class="el" href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">TransformationXMLFile::store()</a>, and <a class="el" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">InternalCalibration::trafo_</a>.</p>
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<td class="memname">void calibrateMapGlobally </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > & </td>
<td class="paramname"><em>exp</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > & </td>
<td class="paramname"><em>calibrated_exp</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
<td class="paramname"><em>ref_ids</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> </td>
<td class="paramname"><em>trafo_file_name</em> = <code>""</code> </td>
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<p>Calibrate a peak map using given reference ids with one calibration function for the whole map. </p>
<p>Calibrate a map using given peptide identifications. The calibration function is calculated for the whole map. The m/z-values of the reference identifications are calculated through the given sequence and charge of the peptide. For the matching of the reference masses and the peaks the parameter mz_tolerance is used to calculate a window around the reference masses. If more than one peak is found within this window the closest peak is taken. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">exp</td><td>the uncalibrated peak map </td></tr>
<tr><td class="paramname">calibrated_exp</td><td>the calibrated peak map </td></tr>
<tr><td class="paramname">ref_ids</td><td>the reference peptide identifications </td></tr>
<tr><td class="paramname">trafo_file_name</td><td>file where the transformation function of the calibration is stored </td></tr>
</table>
</dd>
</dl>
<p>References <a class="el" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">TransformationDescription::apply()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">MSExperiment< PeakT, ChromatogramPeakT >::begin()</a>, <a class="el" href="classOpenMS_1_1InternalCalibration.html#a103a7b7cbdc2702033468a091b4f6a26">InternalCalibration::checkReferenceIds_()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">MSExperiment< PeakT, ChromatogramPeakT >::end()</a>, <a class="el" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48a8b7c5cd8bd8eb51ee6d3fd0eac584679">Residue::Full</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">InternalCalibration::makeLinearRegression_()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">MSExperiment< PeakT, ChromatogramPeakT >::resize()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">MSExperiment< PeakT, ChromatogramPeakT >::RTBegin()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="classOpenMS_1_1TransformationXMLFile.html#abdddea80e737ce717013609e58e755f0">TransformationXMLFile::store()</a>, and <a class="el" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">InternalCalibration::trafo_</a>.</p>
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<td class="memname">void calibrateMapGlobally </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>feature_map</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>calibrated_feature_map</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> </td>
<td class="paramname"><em>trafo_file_name</em> = <code>""</code> </td>
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<p>Calibrate an annotated feature map with one calibration function for the whole map. </p>
<p>Calibrate an annotated (!) feature map using the features' identifications. The calibration function is calculated for the whole map. The m/z-values of the reference identifications are calculated through the given sequence and charge of the peptide. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">feature_map</td><td>the uncalibrated feature map (annotated with peptide ids) </td></tr>
<tr><td class="paramname">calibrated_feature_map</td><td>the calibrated feature map </td></tr>
<tr><td class="paramname">trafo_file_name</td><td>file where the transformation function of the calibration is stored </td></tr>
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<td class="memname">void calibrateMapGlobally </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>feature_map</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>calibrated_feature_map</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
<td class="paramname"><em>ref_ids</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> </td>
<td class="paramname"><em>trafo_file_name</em> = <code>""</code> </td>
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<p>Calibrate a feature map using given reference ids with one calibration function for the whole map. </p>
<p>Calibrate a feature map using given peptide identifications. The calibration function is calculated for the whole map. Even if the features are already annotated with peptide ids these annotations are ignored for the calibration, only the reference ids are used. The m/z-values of the reference identifications are calculated through the given sequence and charge of the peptide. The reference ids are mapped onto the <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> using <a class="el" href="classOpenMS_1_1IDMapper.html" title="Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. ">IDMapper</a> with the mz_tolerance and rt_tolerance parameters. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">feature_map</td><td>the uncalibrated feature map </td></tr>
<tr><td class="paramname">calibrated_feature_map</td><td>the calibrated feature map </td></tr>
<tr><td class="paramname">ref_ids</td><td>the reference peptide identifications </td></tr>
<tr><td class="paramname">trafo_file_name</td><td>file where the transformation function of the calibration is stored </td></tr>
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<td class="memname">void calibrateMapList </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > > & </td>
<td class="paramname"><em>exp_list</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > > & </td>
<td class="paramname"><em>calibrated_exp_list</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>ref_masses</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>detected_background_masses</em> </td>
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<td class="memname">void calibrateMapSpectrumwise </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > & </td>
<td class="paramname"><em>exp</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< InputPeakType > & </td>
<td class="paramname"><em>calibrated_exp</em>, </td>
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<td class="paramname"><em>ref_masses</em> </td>
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<p>Calibrate a peak map using given reference masses with a separate calibration function for each spectrum. </p>
<p>The calibration function is calculated for each spectrum separately. If not enough reference masses are found for a spectrum it is left uncalibrated. For the matching of the reference masses and the peaks, the parameter mz_tolerance is used to calculate a window around the reference masses. If more than one peak is found within this window the closest peak is taken. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">exp</td><td>the uncalibrated peak map </td></tr>
<tr><td class="paramname">calibrated_exp</td><td>the calibrated peak map </td></tr>
<tr><td class="paramname">ref_masses</td><td>the reference m/z values </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">TransformationDescription::apply()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">ProgressLogger::endProgress()</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="classOpenMS_1_1InternalCalibration.html#a28e0d24d3052fd9cf4c732ca85b2f3b9">InternalCalibration::makeLinearRegression_()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="classOpenMS_1_1SpectrumSettings.html#ab7b974cef152e339967fce62f49de0d9a07c53159ed2cb4665a4f16711140f4b5">SpectrumSettings::PEAKS</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">ProgressLogger::setProgress()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">ProgressLogger::startProgress()</a>, and <a class="el" href="classOpenMS_1_1InternalCalibration.html#a0846853a0279b29f089c7c8d19e0ad4a">InternalCalibration::trafo_</a>.</p>
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<td class="memname">void checkReferenceIds_ </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
<td class="paramname"><em>pep_ids</em></td><td>)</td>
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<p>check if reference ids contain RT and MZ information as meta values </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1InternalCalibration.html#a2157a7fbbba00561b9bf8b26b469786d">InternalCalibration::calibrateMapGlobally()</a>.</p>
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<td class="memname">void checkReferenceIds_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
<td class="paramname"><em>feature_map</em></td><td>)</td>
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<p>check if reference ids contain RT and MZ information as meta values </p>
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<td class="memname">void makeLinearRegression_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>observed_masses</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>theoretical_masses</em> </td>
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<p>the actual calibration function </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1InternalCalibration.html#a2157a7fbbba00561b9bf8b26b469786d">InternalCalibration::calibrateMapGlobally()</a>, and <a class="el" href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c">InternalCalibration::calibrateMapSpectrumwise()</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo_</td>
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<p>here the transformation is stored </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1InternalCalibration.html#a2157a7fbbba00561b9bf8b26b469786d">InternalCalibration::calibrateMapGlobally()</a>, and <a class="el" href="classOpenMS_1_1InternalCalibration.html#a1651981607d6c86252b9ab64e5f7996c">InternalCalibration::calibrateMapSpectrumwise()</a>.</p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5</font></TD>
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