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<HTML>
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<TITLE>ChromatogramExtractor Class Reference</TITLE>
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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_1ChromatogramExtractor.html">ChromatogramExtractor</a></li>  </ul>
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<div class="header">
  <div class="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pri-methods">Private Member Functions</a> &#124;
<a href="#pri-attribs">Private Attributes</a> &#124;
<a href="classOpenMS_1_1ChromatogramExtractor-members.html">List of all members</a>  </div>
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<div class="title">ChromatogramExtractor Class Reference</div>  </div>
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<p>The <a class="el" href="classOpenMS_1_1ChromatogramExtractor.html" title="The ChromatogramExtractor extracts chromatograms from a mzML file. ">ChromatogramExtractor</a> extracts chromatograms from a mzML file.  
 <a href="classOpenMS_1_1ChromatogramExtractor.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="ChromatogramExtractor_8h_source.html">OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for ChromatogramExtractor:</div>
<div class="dyncontent">
 <div class="center">
  <img src="classOpenMS_1_1ChromatogramExtractor.png" usemap="#ChromatogramExtractor_map" alt=""/>
  <map id="ChromatogramExtractor_map" name="ChromatogramExtractor_map">
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="0,0,145,24"/>
</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:aebc0d6b93b7fbc4d7a7b1230d55489a0"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#aebc0d6b93b7fbc4d7a7b1230d55489a0">ChromatogramExtractor</a> ()</td></tr>
<tr class="memdesc:aebc0d6b93b7fbc4d7a7b1230d55489a0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Constructor.  <a href="#aebc0d6b93b7fbc4d7a7b1230d55489a0">More...</a><br/></td></tr>
<tr class="separator:aebc0d6b93b7fbc4d7a7b1230d55489a0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1409f6f0d2531350d7b9e7b0dd4601fc"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#a1409f6f0d2531350d7b9e7b0dd4601fc">~ChromatogramExtractor</a> ()</td></tr>
<tr class="memdesc:a1409f6f0d2531350d7b9e7b0dd4601fc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Destructor.  <a href="#a1409f6f0d2531350d7b9e7b0dd4601fc">More...</a><br/></td></tr>
<tr class="separator:a1409f6f0d2531350d7b9e7b0dd4601fc"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab8e5068d0d5799146b80ea6282ff0a6c"><td class="memTemplParams" colspan="2">template&lt;typename ExperimentT &gt; </td></tr>
<tr class="memitem:ab8e5068d0d5799146b80ea6282ff0a6c"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#ab8e5068d0d5799146b80ea6282ff0a6c">extractChromatograms</a> (const ExperimentT &amp;input, ExperimentT &amp;output, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &amp;transition_exp, <a class="el" href="classdouble.html">double</a> extract_window, bool ppm, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <a class="el" href="classdouble.html">double</a> rt_extraction_window, <a class="el" href="classOpenMS_1_1String.html">String</a> filter)</td></tr>
<tr class="memdesc:ab8e5068d0d5799146b80ea6282ff0a6c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Extract chromatograms defined by the <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> from the input map and write them to the output map.  <a href="#ab8e5068d0d5799146b80ea6282ff0a6c">More...</a><br/></td></tr>
<tr class="separator:ab8e5068d0d5799146b80ea6282ff0a6c"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a476e590e0e0491b81412da274dd84eb8"><td class="memTemplParams" colspan="2">template&lt;typename SpectrumT &gt; </td></tr>
<tr class="memitem:a476e590e0e0491b81412da274dd84eb8"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#a476e590e0e0491b81412da274dd84eb8">extract_value_tophat</a> (const SpectrumT &amp;input, const <a class="el" href="classdouble.html">double</a> &amp;mz, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp;peak_idx, <a class="el" href="classdouble.html">double</a> &amp;integrated_intensity, const <a class="el" href="classdouble.html">double</a> &amp;extract_window, const bool ppm)</td></tr>
<tr class="separator:a476e590e0e0491b81412da274dd84eb8"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8ae1f016ab62bf4c23427e15495e0784"><td class="memTemplParams" colspan="2">template&lt;typename SpectrumT &gt; </td></tr>
<tr class="memitem:a8ae1f016ab62bf4c23427e15495e0784"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#a8ae1f016ab62bf4c23427e15495e0784">extract_value_bartlett</a> (const SpectrumT &amp;input, const <a class="el" href="classdouble.html">double</a> &amp;mz, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp;peak_idx, <a class="el" href="classdouble.html">double</a> &amp;integrated_intensity, const <a class="el" href="classdouble.html">double</a> &amp;extract_window, const bool ppm)</td></tr>
<tr class="separator:a8ae1f016ab62bf4c23427e15495e0784"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a6935de84f69c85bfdf90e5119f705c07"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#a6935de84f69c85bfdf90e5119f705c07">extract_value_tophat</a> (const std::vector&lt; <a class="el" href="classdouble.html">double</a> &gt;::const_iterator &amp;mz_start, std::vector&lt; <a class="el" href="classdouble.html">double</a> &gt;::const_iterator &amp;mz_it, const std::vector&lt; <a class="el" href="classdouble.html">double</a> &gt;::const_iterator &amp;mz_end, std::vector&lt; <a class="el" href="classdouble.html">double</a> &gt;::const_iterator &amp;int_it, const <a class="el" href="classdouble.html">double</a> &amp;mz, <a class="el" href="classdouble.html">double</a> &amp;integrated_intensity, <a class="el" href="classdouble.html">double</a> &amp;extract_window, bool ppm)</td></tr>
<tr class="separator:a6935de84f69c85bfdf90e5119f705c07"><td class="memSeparator" colspan="2">&#160;</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="-"/>&#160;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">&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</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>&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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> &amp;label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</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">&#160;</td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:acc6dd6bb5820778b452b8adf9334421e"><td class="memTemplParams" colspan="2">template&lt;class SpectrumSettingsT , class ChromatogramT &gt; </td></tr>
<tr class="memitem:acc6dd6bb5820778b452b8adf9334421e"><td class="memTemplItemLeft" align="right" valign="top">void&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#acc6dd6bb5820778b452b8adf9334421e">prepareSpectra_</a> (SpectrumSettingsT &amp;settings, std::vector&lt; ChromatogramT &gt; &amp;chromatograms, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &amp;transition_exp)</td></tr>
<tr class="memdesc:acc6dd6bb5820778b452b8adf9334421e"><td class="mdescLeft">&#160;</td><td class="mdescRight">This populates the chromatograms vector with empty chromatograms (but sets their meta-information)  <a href="#acc6dd6bb5820778b452b8adf9334421e">More...</a><br/></td></tr>
<tr class="separator:acc6dd6bb5820778b452b8adf9334421e"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:acee142f4f394a06534b33c828b42f7ec"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#acee142f4f394a06534b33c828b42f7ec">outsideExtractionWindow_</a> (const <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html">ReactionMonitoringTransition</a> &amp;transition, <a class="el" href="classdouble.html">double</a> current_rt, const <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &amp;trafo, <a class="el" href="classdouble.html">double</a> rt_extraction_window)</td></tr>
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Private Attributes</h2></td></tr>
<tr class="memitem:ae505eef01d0c7c8b342bac83fcd81f23"><td class="memItemLeft" align="right" valign="top">std::map&lt; <a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a>, <a class="el" href="classdouble.html">double</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html#ae505eef01d0c7c8b342bac83fcd81f23">PeptideRTMap_</a></td></tr>
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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="-"/>&#160;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 &#160;</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>, 
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<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft">&#160;</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="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>&#160;</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>&#160;</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:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</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 *&#160;</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&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
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<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int&#160;</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>The <a class="el" href="classOpenMS_1_1ChromatogramExtractor.html" title="The ChromatogramExtractor extracts chromatograms from a mzML file. ">ChromatogramExtractor</a> extracts chromatograms from a mzML file. </p>
<p>It will take as input a set of (TraML) transitions and will extract the signal of the provided map at the product ion m/z values specified by the transitions. The map is thus assumed to be an MS2 map from a SWATH / DIA experiment. </p>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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          <td class="memname"><a class="el" href="classOpenMS_1_1ChromatogramExtractor.html">ChromatogramExtractor</a> </td>
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<p>Constructor. </p>

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          <td class="memname">~<a class="el" href="classOpenMS_1_1ChromatogramExtractor.html">ChromatogramExtractor</a> </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="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &amp;&#160;</td>
          <td class="paramname"><em>peak_idx</em>, </td>
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          <td class="paramtype"><a class="el" href="classdouble.html">double</a> &amp;&#160;</td>
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          <td class="memname">void extract_value_tophat </td>
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          <td class="memname">void extractChromatograms </td>
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          <td class="paramtype"><a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a>&#160;</td>
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<p>Extract chromatograms defined by the <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> from the input map and write them to the output map. </p>

<p>References <a class="el" href="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">TargetedExperiment::getPeptides()</a>, <a class="el" href="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">TargetedExperiment::getTransitions()</a>, <a class="el" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a76010eef1edc0406cc2375c25d2a433d">Peptide::id</a>, <a class="el" href="classOpenMS_1_1TransformationDescription.html#a7fa1616cc61c19a5efcc863c950f7f30">TransformationDescription::invert()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a04646756cfb9003cfa0fdbe7bafef165">Peptide::rts</a>, and <a class="el" href="classOpenMS_1_1TargetedExperiment.html#abc7d814820a48da344e780a775dfc5ac">TargetedExperiment::sortTransitionsByProductMZ()</a>.</p>

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<p>References <a class="el" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">TransformationDescription::apply()</a>, and <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html#a8d50acc4d8e15a1bb76c3d321679f300">ReactionMonitoringTransition::getPeptideRef()</a>.</p>

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          <td class="memname">void prepareSpectra_ </td>
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          <td class="paramtype">SpectrumSettingsT &amp;&#160;</td>
          <td class="paramname"><em>settings</em>, </td>
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          <td class="paramtype">std::vector&lt; ChromatogramT &gt; &amp;&#160;</td>
          <td class="paramname"><em>chromatograms</em>, </td>
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          <td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &amp;&#160;</td>
          <td class="paramname"><em>transition_exp</em>&#160;</td>
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          <td>)</td>
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<p>This populates the chromatograms vector with empty chromatograms (but sets their meta-information) </p>

<p>References <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html#ad368341c22d3447e324134c47adff081">ReactionMonitoringTransition::getNativeID()</a>, <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html#a8d50acc4d8e15a1bb76c3d321679f300">ReactionMonitoringTransition::getPeptideRef()</a>, <a class="el" href="classOpenMS_1_1TargetedExperiment.html#a81362aa067155119d3122af3555227f9">TargetedExperiment::getPeptides()</a>, <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html#aeaba1d2d17aad5f9a659c1b66ac77989">ReactionMonitoringTransition::getPrecursorMZ()</a>, <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html#ac6730e2e483fad81620fb1adfde156e8">ReactionMonitoringTransition::getProductMZ()</a>, <a class="el" href="classOpenMS_1_1TargetedExperiment.html#af3100e829c8edc47e845f2c73c0de0c2">TargetedExperiment::getTransitions()</a>, <a class="el" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a76010eef1edc0406cc2375c25d2a433d">Peptide::id</a>, <a class="el" href="classOpenMS_1_1ChromatogramSettings.html#a68c34f5f5adf5049a53084716add11bda812e4fa5ee617ea84709d7350aaad07c">ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM</a>, <a class="el" href="classOpenMS_1_1TargetedExperimentHelper_1_1Peptide.html#a3d81a52752fe56b49914dbe273521b5d">Peptide::sequence</a>, <a class="el" href="classOpenMS_1_1Precursor.html#a046066b9d4e7b06a0ce6b883346689f6">Precursor::setIsolationWindowLowerOffset()</a>, <a class="el" href="classOpenMS_1_1Precursor.html#a3c61b885b58c7b8ed6c09913229342d3">Precursor::setIsolationWindowUpperOffset()</a>, <a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">MetaInfoInterface::setMetaValue()</a>, <a class="el" href="classOpenMS_1_1Product.html#a94893c6a36a1281bfd8ff45c0199bd35">Product::setMZ()</a>, and <a class="el" href="classOpenMS_1_1Peak1D.html#ab9c4ce5d172a75d6de2c6f5f1847c9ab">Peak1D::setMZ()</a>.</p>

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<h2 class="groupheader">Member Data Documentation</h2>
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          <td class="memname">std::map&lt;<a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a>, <a class="el" href="classdouble.html">double</a>&gt; PeptideRTMap_</td>
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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 11:19:26 using doxygen 1.8.5</font></TD>
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