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<HTML>
<HEAD>
<TITLE>MRMFeatureFinderScoring Class Reference</TITLE>
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<ul>
<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html">MRMFeatureFinderScoring</a></li> </ul>
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<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pri-methods">Private Member Functions</a> |
<a href="#pri-attribs">Private Attributes</a> |
<a href="classOpenMS_1_1MRMFeatureFinderScoring-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">MRMFeatureFinderScoring Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>The MRMFeatureFinder finds and scores peaks of transitions that coelute.
<a href="classOpenMS_1_1MRMFeatureFinderScoring.html#details">More...</a></p>
<p><code>#include <<a class="el" href="MRMFeatureFinderScoring_8h_source.html">OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for MRMFeatureFinderScoring:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1MRMFeatureFinderScoring.png" usemap="#MRMFeatureFinderScoring_map" alt=""/>
<map id="MRMFeatureFinderScoring_map" name="MRMFeatureFinderScoring_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,167,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="177,0,344,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader"></div></td></tr>
<tr class="memitem:a4910016b262f6723b82c4b1c4d6cdde7"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1ChromatogramPeak.html">ChromatogramPeak</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4910016b262f6723b82c4b1c4d6cdde7">RichPeakChromatogram</a></td></tr>
<tr class="memdesc:a4910016b262f6723b82c4b1c4d6cdde7"><td class="mdescLeft"> </td><td class="mdescRight">Type definitions. <a href="#a4910016b262f6723b82c4b1c4d6cdde7">More...</a><br/></td></tr>
<tr class="separator:a4910016b262f6723b82c4b1c4d6cdde7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8497becf96cdfaf51ba301262d81f126"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenSwath_1_1LightTransition.html">OpenSwath::LightTransition</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126">TransitionType</a></td></tr>
<tr class="separator:a8497becf96cdfaf51ba301262d81f126"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab93154c1962d6ccb0a7d8f548ea0a9da"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab93154c1962d6ccb0a7d8f548ea0a9da">TargetedExpType</a></td></tr>
<tr class="separator:ab93154c1962d6ccb0a7d8f548ea0a9da"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af71c1f3e928ced2c6264ed63155d8de0"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af71c1f3e928ced2c6264ed63155d8de0">PeptideType</a></td></tr>
<tr class="separator:af71c1f3e928ced2c6264ed63155d8de0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1e9fb94f05f21667db64366fe31b4357"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenSwath_1_1LightProtein.html">OpenSwath::LightProtein</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1e9fb94f05f21667db64366fe31b4357">ProteinType</a></td></tr>
<tr class="separator:a1e9fb94f05f21667db64366fe31b4357"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae3c1ad9ec2bbfe5e9e7bac70731091fb"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenSwath_1_1LightModification.html">OpenSwath::LightModification</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae3c1ad9ec2bbfe5e9e7bac70731091fb">ModificationType</a></td></tr>
<tr class="separator:ae3c1ad9ec2bbfe5e9e7bac70731091fb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0f6b08b724983b516b2529790b798a9f"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup</a><br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a>< <a class="el" href="classOpenMS_1_1ChromatogramPeak.html">ChromatogramPeak</a> ><br class="typebreak"/>
, <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126">TransitionType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f">MRMTransitionGroupType</a></td></tr>
<tr class="separator:a0f6b08b724983b516b2529790b798a9f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adc7399590e54bd7f438d16a0372803e7"><td class="memItemLeft" align="right" valign="top">typedef std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f">MRMTransitionGroupType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a></td></tr>
<tr class="separator:adc7399590e54bd7f438d16a0372803e7"><td class="memSeparator" colspan="2"> </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>
<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_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="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a524199abe99df52a9e136845038430dc"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a524199abe99df52a9e136845038430dc">MRMFeatureFinderScoring</a> ()</td></tr>
<tr class="memdesc:a524199abe99df52a9e136845038430dc"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a524199abe99df52a9e136845038430dc">More...</a><br/></td></tr>
<tr class="separator:a524199abe99df52a9e136845038430dc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abe114fcc3288c5769044a52effbd7e46"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#abe114fcc3288c5769044a52effbd7e46">~MRMFeatureFinderScoring</a> ()</td></tr>
<tr class="memdesc:abe114fcc3288c5769044a52effbd7e46"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#abe114fcc3288c5769044a52effbd7e46">More...</a><br/></td></tr>
<tr class="separator:abe114fcc3288c5769044a52effbd7e46"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af879ba2bc9bcc83bed021af39c24e9d6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af879ba2bc9bcc83bed021af39c24e9d6">pickExperiment</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a> > &chromatograms, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> > &output, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">TargetedExperiment</a> &transition_exp_, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a> > &swath_map)</td></tr>
<tr class="separator:af879ba2bc9bcc83bed021af39c24e9d6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a21e38df433d05118f343c33af60816e9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a21e38df433d05118f343c33af60816e9">pickExperiment</a> (<a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> input, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> > &output, <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> &transition_exp, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a> &transition_group_map)</td></tr>
<tr class="separator:a21e38df433d05118f343c33af60816e9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a193f9f32a57675b94563446bac729125"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a193f9f32a57675b94563446bac729125">mapExperimentToTransitionList</a> (<a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> input, <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> &transition_exp, <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a> &transition_group_map, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> trafo, <a class="el" href="classdouble.html">double</a> rt_extraction_window)</td></tr>
<tr class="separator:a193f9f32a57675b94563446bac729125"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9ac530b577855511cc32791aef8de7e4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9ac530b577855511cc32791aef8de7e4">setStrictFlag</a> (bool f)</td></tr>
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<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>
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</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:a1d7f11c2be93f8140f508487ba0ae718"><td class="memTemplParams" colspan="2">template<typename SpectrumT , typename TransitionT > </td></tr>
<tr class="memitem:a1d7f11c2be93f8140f508487ba0ae718"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1d7f11c2be93f8140f508487ba0ae718">scorePeakgroups_</a> (<a class="el" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup</a>< SpectrumT, TransitionT > &transition_group, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &trafo, <a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> > &output)</td></tr>
<tr class="memdesc:a1d7f11c2be93f8140f508487ba0ae718"><td class="mdescLeft"> </td><td class="mdescRight">Score all peak groups. <a href="#a1d7f11c2be93f8140f508487ba0ae718">More...</a><br/></td></tr>
<tr class="separator:a1d7f11c2be93f8140f508487ba0ae718"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a392c2beaccf8b9d8e6f5d3e766f1bc72"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a392c2beaccf8b9d8e6f5d3e766f1bc72">getAddedSpectra_</a> (<a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, <a class="el" href="classdouble.html">double</a> RT, int nr_spectra_to_add)</td></tr>
<tr class="memdesc:a392c2beaccf8b9d8e6f5d3e766f1bc72"><td class="mdescLeft"> </td><td class="mdescRight">Returns the addition of "nr_spectra_to_add" spectra around the given RT. <a href="#a392c2beaccf8b9d8e6f5d3e766f1bc72">More...</a><br/></td></tr>
<tr class="separator:a392c2beaccf8b9d8e6f5d3e766f1bc72"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7aa7123edb723725ec69f259c69d46d0"><td class="memTemplParams" colspan="2">template<typename SpectrumT , typename TransitionT > </td></tr>
<tr class="memitem:a7aa7123edb723725ec69f259c69d46d0"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7aa7123edb723725ec69f259c69d46d0">calculateSwathScores_</a> (<a class="el" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup</a>< SpectrumT, TransitionT > &transition_group, <a class="el" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> &mrmfeature_, <a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> swath_map, std::vector< <a class="el" href="classdouble.html">double</a> > &normalized_library_intensity, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html">OpenSwath_Scores</a> scores)</td></tr>
<tr class="separator:a7aa7123edb723725ec69f259c69d46d0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">Synchronize members with param class. <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:a22f959483c21d84714446ca1dda67305"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22f959483c21d84714446ca1dda67305">rt_extraction_window_</a></td></tr>
<tr class="separator:a22f959483c21d84714446ca1dda67305"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab5e0c18f8afa7476f40274195da56a95"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab5e0c18f8afa7476f40274195da56a95">quantification_cutoff_</a></td></tr>
<tr class="separator:ab5e0c18f8afa7476f40274195da56a95"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a1ef597bca1204743aea62db7e5854c"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4a1ef597bca1204743aea62db7e5854c">use_coelution_score_</a></td></tr>
<tr class="separator:a4a1ef597bca1204743aea62db7e5854c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae129fad3b127a2c3b2e326957d8790f6"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae129fad3b127a2c3b2e326957d8790f6">use_shape_score_</a></td></tr>
<tr class="separator:ae129fad3b127a2c3b2e326957d8790f6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02cbed9db0f88714f00b408ce1b2cd89"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a02cbed9db0f88714f00b408ce1b2cd89">use_rt_score_</a></td></tr>
<tr class="separator:a02cbed9db0f88714f00b408ce1b2cd89"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9f60459941531734092771fbffbbff74"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a9f60459941531734092771fbffbbff74">use_library_score_</a></td></tr>
<tr class="separator:a9f60459941531734092771fbffbbff74"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac8d7f0bcfd4cb2e7d52cab65e7df6158"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac8d7f0bcfd4cb2e7d52cab65e7df6158">use_elution_model_score_</a></td></tr>
<tr class="separator:ac8d7f0bcfd4cb2e7d52cab65e7df6158"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a576420b6d768fd10d4346e472d5fd2aa"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a576420b6d768fd10d4346e472d5fd2aa">use_intensity_score_</a></td></tr>
<tr class="separator:a576420b6d768fd10d4346e472d5fd2aa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a75a21d4281da11d37c8da3535d1d84b6"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a75a21d4281da11d37c8da3535d1d84b6">use_total_xic_score_</a></td></tr>
<tr class="separator:a75a21d4281da11d37c8da3535d1d84b6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac64852f39c2bec2f316e47ae6dec9252"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac64852f39c2bec2f316e47ae6dec9252">use_nr_peaks_score_</a></td></tr>
<tr class="separator:ac64852f39c2bec2f316e47ae6dec9252"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aea920562de500ac98b46bbb0e89ccdfc"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#aea920562de500ac98b46bbb0e89ccdfc">use_sn_score_</a></td></tr>
<tr class="separator:aea920562de500ac98b46bbb0e89ccdfc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5014ed66263ea3caf2b85109c996ebb4"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a5014ed66263ea3caf2b85109c996ebb4">stop_report_after_feature_</a></td></tr>
<tr class="separator:a5014ed66263ea3caf2b85109c996ebb4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2b03153c17ac2f3ace8b5d471a98dd53"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a2b03153c17ac2f3ace8b5d471a98dd53">add_up_spectra_</a></td></tr>
<tr class="separator:a2b03153c17ac2f3ace8b5d471a98dd53"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a22727bee734eaaa5b46b0c81d64de04f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a22727bee734eaaa5b46b0c81d64de04f">spacing_for_spectra_resampling_</a></td></tr>
<tr class="separator:a22727bee734eaaa5b46b0c81d64de04f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67ca9455fcfa3f2bf40502a88ea0b776"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a67ca9455fcfa3f2bf40502a88ea0b776">write_convex_hull_</a></td></tr>
<tr class="separator:a67ca9455fcfa3f2bf40502a88ea0b776"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0ae9ca9c54d967fe064dd3b5939dabd2"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0ae9ca9c54d967fe064dd3b5939dabd2">strict_</a></td></tr>
<tr class="separator:a0ae9ca9c54d967fe064dd3b5939dabd2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a18149f9f24aaea0ec584e290620fbd20"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a18149f9f24aaea0ec584e290620fbd20">rt_normalization_factor_</a></td></tr>
<tr class="separator:a18149f9f24aaea0ec584e290620fbd20"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae505eef01d0c7c8b342bac83fcd81f23"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a>, <a class="el" href="classdouble.html">double</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae505eef01d0c7c8b342bac83fcd81f23">PeptideRTMap_</a></td></tr>
<tr class="separator:ae505eef01d0c7c8b342bac83fcd81f23"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f80a0cb2acd6063fc093e3d79aa04b0"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a>, <br class="typebreak"/>
const <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af71c1f3e928ced2c6264ed63155d8de0">PeptideType</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a7f80a0cb2acd6063fc093e3d79aa04b0">PeptideRefMap_</a></td></tr>
<tr class="separator:a7f80a0cb2acd6063fc093e3d79aa04b0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abfbb890cd21227a2434d240018c1e7a8"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a>, <br class="typebreak"/>
const <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1e9fb94f05f21667db64366fe31b4357">ProteinType</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#abfbb890cd21227a2434d240018c1e7a8">ProteinRefMap_</a></td></tr>
<tr class="separator:abfbb890cd21227a2434d240018c1e7a8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac63df47f07bf98212d84b4edb37d1a86"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenSwath_1_1MRMScoring.html">OpenSwath::MRMScoring</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ac63df47f07bf98212d84b4edb37d1a86">mrmscore_</a></td></tr>
<tr class="separator:ac63df47f07bf98212d84b4edb37d1a86"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a608c6b3c9c5f225e40f35260f1f6cc9e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1DIAScoring.html">OpenMS::DIAScoring</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a608c6b3c9c5f225e40f35260f1f6cc9e">diascoring_</a></td></tr>
<tr class="separator:a608c6b3c9c5f225e40f35260f1f6cc9e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a40b8bcf6f0f15147e7e6e88a46e1e35f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1EmgScoring.html">OpenMS::EmgScoring</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a40b8bcf6f0f15147e7e6e88a46e1e35f">emgscoring_</a></td></tr>
<tr class="separator:a40b8bcf6f0f15147e7e6e88a46e1e35f"><td class="memSeparator" colspan="2"> </td></tr>
</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 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: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>
<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>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<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="inherit_header pro_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>The MRMFeatureFinder finds and scores peaks of transitions that coelute. </p>
<p>It does so using an internal peakpicker for each chromatogram and then creating consensus / meta-peaks (MRMFeatures) that contain the information of all corresponding chromatograms at the peak-position. It then goes on to score those MRMFeatures using different criteria described in the MRMScoring class.</p>
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<td class="memname">typedef <a class="el" href="structOpenSwath_1_1LightModification.html">OpenSwath::LightModification</a> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ae3c1ad9ec2bbfe5e9e7bac70731091fb">ModificationType</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup</a><<a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a> <<a class="el" href="classOpenMS_1_1ChromatogramPeak.html">ChromatogramPeak</a>>, <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126">TransitionType</a>> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f">MRMTransitionGroupType</a></td>
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<td class="memname">typedef <a class="el" href="structOpenSwath_1_1LightPeptide.html">OpenSwath::LightPeptide</a> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#af71c1f3e928ced2c6264ed63155d8de0">PeptideType</a></td>
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<td class="memname">typedef <a class="el" href="structOpenSwath_1_1LightProtein.html">OpenSwath::LightProtein</a> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a1e9fb94f05f21667db64366fe31b4357">ProteinType</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><<a class="el" href="classOpenMS_1_1ChromatogramPeak.html">ChromatogramPeak</a>> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a4910016b262f6723b82c4b1c4d6cdde7">RichPeakChromatogram</a></td>
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<p>Type definitions. </p>
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<td class="memname">typedef <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#ab93154c1962d6ccb0a7d8f548ea0a9da">TargetedExpType</a></td>
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<td class="memname">typedef std::map<<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a0f6b08b724983b516b2529790b798a9f">MRMTransitionGroupType</a>> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a></td>
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<td class="memname">typedef <a class="el" href="structOpenSwath_1_1LightTransition.html">OpenSwath::LightTransition</a> <a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#a8497becf96cdfaf51ba301262d81f126">TransitionType</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html">MRMFeatureFinderScoring</a> </td>
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<p>Constructor. </p>
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<td class="memname">~<a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html">MRMFeatureFinderScoring</a> </td>
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<p>Destructor. </p>
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<td class="memname">void calculateSwathScores_ </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup</a>< SpectrumT, TransitionT > & </td>
<td class="paramname"><em>transition_group</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MRMFeature.html">MRMFeature</a> & </td>
<td class="paramname"><em>mrmfeature_</em>, </td>
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<td class="paramtype"><a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> </td>
<td class="paramname"><em>swath_map</em>, </td>
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<p>References <a class="el" href="classOpenMS_1_1MRMFeature.html#a8d4bb3e3b2f22cdaa1855d09f5d98a41">MRMFeature::addScore()</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#a6509c5d12cc9ba3417f9d46314345bc9">OpenSwath_Scores::calculate_swath_lda_prescore()</a>, <a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a8ae154a5964d69f913d864b169b7310e">OpenSwathDataAccessHelper::convertPeptideToAASequence()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">Peak2D::getRT()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions()</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#a78dbcf0489fbf0d53d650d37c74ee164">OpenSwath_Scores::isotope_correlation</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#a3f0b0d733e7992afe009dd65591e0a2e">OpenSwath_Scores::isotope_overlap</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#ad86382490f14d6cc1b62611513b5e27f">OpenSwath_Scores::massdev_score</a>, <a class="el" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">Feature::setOverallQuality()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">MRMTransitionGroup< SpectrumType, TransitionType >::size()</a>, <a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a>, and <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#ad17f08a1a1d14810389bf7f585e95e8b">OpenSwath_Scores::yseries_score</a>.</p>
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<td class="memname"><a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a> getAddedSpectra_ </td>
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<p>Returns the addition of "nr_spectra_to_add" spectra around the given RT. </p>
<p>References <a class="el" href="classOpenMS_1_1SpectrumAddition.html#a66af26742cdb048bacaed720d147f7fb">SpectrumAddition::addUpSpectra()</a>, and <a class="el" href="namespaceOpenSwath.html#a93e7d6a13eb66ccae0357dbae6f33523">OpenSwath::SpectrumPtr</a>.</p>
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<td class="memname">void mapExperimentToTransitionList </td>
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<p>References <a class="el" href="classOpenMS_1_1OpenSwathDataAccessHelper.html#a0476f3ea925f584d9064efee48c7db6a">OpenSwathDataAccessHelper::convertTargetedExp()</a>, <a class="el" href="classOpenMS_1_1SimpleOpenMSSpectraFactory.html#a645eefe3725b60ffcf44f9ae01f0c19d">SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr()</a>, and <a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a>.</p>
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<td class="paramtype"><a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html">OpenSwath::LightTargetedExperiment</a> & </td>
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<td class="paramname"><em>trafo</em>, </td>
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<td class="paramtype"><a class="el" href="namespaceOpenSwath.html#a63af68177a01f914ee1944977ba796ee">OpenSwath::SpectrumAccessPtr</a> </td>
<td class="paramname"><em>swath_map</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MRMFeatureFinderScoring.html#adc7399590e54bd7f438d16a0372803e7">TransitionGroupMapType</a> & </td>
<td class="paramname"><em>transition_group_map</em> </td>
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<p>References <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms()</a>, <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html#a75e5e77ae24708d28d8f3df92fcb84de">LightTargetedExperiment::getPeptides()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">FeatureMap< FeatureT >::getProteinIdentifications()</a>, <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html#a6d58ec7403247e88dbee94e859389c19">LightTargetedExperiment::getProteins()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions()</a>, <a class="el" href="structOpenSwath_1_1LightTargetedExperiment.html#a23a85c8da00a9f39f0c9ce6e15bc5a32">LightTargetedExperiment::getTransitions()</a>, <a class="el" href="structOpenSwath_1_1LightPeptide.html#afd0d68c6d31ff249f3ae8662162663c3">LightPeptide::id</a>, <a class="el" href="structOpenSwath_1_1LightProtein.html#afd0d68c6d31ff249f3ae8662162663c3">LightProtein::id</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroupPicker.html#acce2a9f0fe8d27893f6a027a4598e8ba">MRMTransitionGroupPicker::pickTransitionGroup()</a>, <a class="el" href="structOpenSwath_1_1LightPeptide.html#ae5ee906bf451a6150d80754f4068dc58">LightPeptide::rt</a>, <a class="el" href="MRMFeatureFinderScoring_8h.html#a1f18f099a1e85e5ad0256530ab97cd3a">run_identifier</a>, <a class="el" href="structOpenSwath_1_1LightProtein.html#a9a2b94a2b0e3195ef7ea3a13187c17b9">LightProtein::sequence</a>, <a class="el" href="classOpenMS_1_1ProteinHit.html#aba1fff7a176ff80d53f932769e606980">ProteinHit::setAccession()</a>, <a class="el" href="classOpenMS_1_1ProteinIdentification.html#a86f5c6d7c17c3aa94ec734e2a4fb50fa">ProteinIdentification::setHits()</a>, <a class="el" href="classOpenMS_1_1ProteinIdentification.html#a00f1456779f764c2738c35be2c04f6e8">ProteinIdentification::setIdentifier()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">DefaultParamHandler::setParameters()</a>, and <a class="el" href="classOpenMS_1_1ProteinHit.html#a2b8bf5f3febdb76461bdea9ff39d6b6d">ProteinHit::setSequence()</a>.</p>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MRMTransitionGroup.html">MRMTransitionGroup</a>< SpectrumT, TransitionT > & </td>
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<p>Score all peak groups. </p>
<p>References <a class="el" href="classOpenMS_1_1PeptideHit.html#a49d90d2fa65c45386e5725386d7741fe">PeptideHit::addProteinAccession()</a>, <a class="el" href="classOpenMS_1_1TransformationDescription.html#aa280f8d4730c216c58a3edd091b99767">TransformationDescription::apply()</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#aca437d1a16d43a1e055a4fc295a2aa1e">OpenSwath_Scores::calculate_lda_prescore()</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#ac7a01742e0b867bc9ab9d91829d0d890">OpenSwath_Scores::elution_model_fit_score</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#aeb40871b8728dab160318bc38fc23e3a">OpenSwath_Scores::get_quick_lda_score()</a>, <a class="el" href="structOpenSwath_1_1LightPeptide.html#a49ce0caa2ae22c1439eaf0fd861bf37f">LightPeptide::getChargeState()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a84fbe2b625d0885f5e93397ed2122202">MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a5c92d3ef5e22a80e2188a8fd81af3e5a">MRMTransitionGroup< SpectrumType, TransitionType >::getFeaturesMuteable()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#aff73c863c0c2c6ff6173deac72567709">MRMTransitionGroup< SpectrumType, TransitionType >::getLibraryIntensity()</a>, <a class="el" href="structOpenSwath_1_1LightTransition.html#a4c4914efae99b51076cec9814268707c">LightTransition::getPeptideRef()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a72f3eb6e4f2beacf59fb94d10fffd9ba">MRMTransitionGroup< SpectrumType, TransitionType >::getTransition()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#aedcd02941cf31e259bb9394850653bbc">MRMTransitionGroup< SpectrumType, TransitionType >::getTransitionGroupID()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a3599bdfacba1b03fa680b7e183dc80ce">MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions()</a>, <a class="el" href="structOpenSwath_1_1LightProtein.html#afd0d68c6d31ff249f3ae8662162663c3">LightProtein::id</a>, <a class="el" href="classOpenMS_1_1PeptideIdentification.html#ae558057222f754e972e0257de2fe3c2d">PeptideIdentification::insertHit()</a>, <a class="el" href="classOpenMS_1_1TransformationDescription.html#a7fa1616cc61c19a5efcc863c950f7f30">TransformationDescription::invert()</a>, <a class="el" href="namespaceOpenSwath.html#a657df1b62b2200d972968d1151992d7f">OpenSwath::ISignalToNoisePtr</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#a4d7c492ccfc19c4162d9616011a060da">OpenSwath_Scores::library_corr</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#aba3edbdb6d99fdd71b262d1e938b4e89">OpenSwath_Scores::library_rmsd</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#a3626f9b563a3d7134f3849e62579c03b">OpenSwath_Scores::log_sn_score</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#a2d04130c2720f68f9dd1b541b0e5eaba">OpenSwath_Scores::norm_rt_score</a>, <a class="el" href="namespaceOpenSwath.html#a546b9a9117f4207e3cfc9ef2ea4aad3d">OpenSwath::normalize()</a>, <a class="el" href="namespaceOpenSwath_1_1Scoring.html#afa39e794c622d1fdfc2d702517fffc80">OpenSwath::Scoring::normalize_sum()</a>, <a class="el" href="structOpenSwath_1_1LightPeptide.html#a85ef381b973761bfb8afbe31ba8c010f">LightPeptide::protein_ref</a>, <a class="el" href="MRMFeatureFinderScoring_8h.html#a1f18f099a1e85e5ad0256530ab97cd3a">run_identifier</a>, <a class="el" href="structOpenSwath_1_1LightPeptide.html#a9a2b94a2b0e3195ef7ea3a13187c17b9">LightPeptide::sequence</a>, <a class="el" href="classOpenMS_1_1PeptideHit.html#aca40a4630f5f8a0568899b74a62dcd4b">PeptideHit::setCharge()</a>, <a class="el" href="classOpenMS_1_1PeptideIdentification.html#a00f1456779f764c2738c35be2c04f6e8">PeptideIdentification::setIdentifier()</a>, <a class="el" href="classOpenMS_1_1PeptideHit.html#a2e9b7c12f6d8fa7415aa0aca69208f42">PeptideHit::setScore()</a>, <a class="el" href="classOpenMS_1_1PeptideHit.html#a209d1e10f38a766c3f73c9666e89e14d">PeptideHit::setSequence()</a>, <a class="el" href="classOpenMS_1_1MRMTransitionGroup.html#a9d78a687cf2a391198bb3cbc08bc06cb">MRMTransitionGroup< SpectrumType, TransitionType >::size()</a>, <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#ab8dfbfc3eaa57313e0e5481894017995">OpenSwath_Scores::xcorr_coelution_score</a>, and <a class="el" href="structOpenMS_1_1OpenSwath__Scores.html#aa050ad09c86fd7f50842c59d49e6fea7">OpenSwath_Scores::xcorr_shape_score</a>.</p>
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<td class="memname">void setStrictFlag </td>
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<p>Synchronize members with param class. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname">int add_up_spectra_</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 11:19:27 using doxygen 1.8.5</font></TD>
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