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<HTML>
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<TITLE>FeaFiModule< PeakType, FeatureType > Class Template 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_1FeaFiModule.html">FeaFiModule</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
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<div class="title">FeaFiModule< PeakType, FeatureType > Class Template Reference</div> </div>
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<div class="contents">
<p>Implements a module of the <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> algorithm.
<a href="classOpenMS_1_1FeaFiModule.html#details">More...</a></p>
<p><code>#include <<a class="el" href="FeaFiModule_8h_source.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeaFiModule.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for FeaFiModule< PeakType, FeatureType >:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1FeaFiModule.png" usemap="#FeaFiModule< PeakType, FeatureType >_map" alt=""/>
<map id="FeaFiModule< PeakType, FeatureType >_map" name="FeaFiModule< PeakType, FeatureType >_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="270,0,530,24"/>
<area href="classOpenMS_1_1ModelFitter.html" title="Tests a group of data points in an LC-MS map for goodness-of-fit with a 2D averagine model..." alt="ModelFitter< PeakType, FeatureType >" shape="rect" coords="0,112,260,136"/>
<area href="classOpenMS_1_1SimpleExtender.html" title="Simple feature extension algorithm. " alt="SimpleExtender< PeakType, FeatureType >" shape="rect" coords="270,112,530,136"/>
<area href="classOpenMS_1_1SimpleSeeder.html" title="Simple seeding class that uses the strongest peak as next seed. " alt="SimpleSeeder< PeakType, FeatureType >" shape="rect" coords="540,112,800,136"/>
</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 class="memitem:a21ea3968c35235b6b3cd78a2190280d9"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a></td></tr>
<tr class="memdesc:a21ea3968c35235b6b3cd78a2190280d9"><td class="mdescLeft"> </td><td class="mdescRight">Output feature map type. <a href="#a21ea3968c35235b6b3cd78a2190280d9">More...</a><br/></td></tr>
<tr class="separator:a21ea3968c35235b6b3cd78a2190280d9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adf6f376e844058d129ce8ba868276643"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643">MapType</a></td></tr>
<tr class="memdesc:adf6f376e844058d129ce8ba868276643"><td class="mdescLeft"> </td><td class="mdescRight">Input map type. <a href="#adf6f376e844058d129ce8ba868276643">More...</a><br/></td></tr>
<tr class="separator:adf6f376e844058d129ce8ba868276643"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae4e0f0c176662a323a6a64d29ff986dd"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html#a066042ae14211da37d4fa66d466bfa3e">MapType::SpectrumType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a></td></tr>
<tr class="memdesc:ae4e0f0c176662a323a6a64d29ff986dd"><td class="mdescLeft"> </td><td class="mdescRight">Input spectrum type. <a href="#ae4e0f0c176662a323a6a64d29ff986dd">More...</a><br/></td></tr>
<tr class="separator:ae4e0f0c176662a323a6a64d29ff986dd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a221361082f641c3fccc58e9bc66aeee1"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">PeakType::IntensityType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a></td></tr>
<tr class="memdesc:a221361082f641c3fccc58e9bc66aeee1"><td class="mdescLeft"> </td><td class="mdescRight">Input intensity type. <a href="#a221361082f641c3fccc58e9bc66aeee1">More...</a><br/></td></tr>
<tr class="separator:a221361082f641c3fccc58e9bc66aeee1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a181486a43da338e31f089df7661f50bb"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1Peak2D.html#a063d40a3528749f1a905ab04d76387e0">PeakType::CoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb">CoordinateType</a></td></tr>
<tr class="memdesc:a181486a43da338e31f089df7661f50bb"><td class="mdescLeft"> </td><td class="mdescRight">Input coordinate type. <a href="#a181486a43da338e31f089df7661f50bb">More...</a><br/></td></tr>
<tr class="separator:a181486a43da338e31f089df7661f50bb"><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:ad3fe3d27b98fcd12d996b358e30723fa"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa">FeaFiModule</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > *map, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > *features, <a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> *ff)</td></tr>
<tr class="memdesc:ad3fe3d27b98fcd12d996b358e30723fa"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#ad3fe3d27b98fcd12d996b358e30723fa">More...</a><br/></td></tr>
<tr class="separator:ad3fe3d27b98fcd12d996b358e30723fa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa14dc0b3522c854b9005fc9dd5c754d3"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#aa14dc0b3522c854b9005fc9dd5c754d3">~FeaFiModule</a> ()</td></tr>
<tr class="memdesc:aa14dc0b3522c854b9005fc9dd5c754d3"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#aa14dc0b3522c854b9005fc9dd5c754d3">More...</a><br/></td></tr>
<tr class="separator:aa14dc0b3522c854b9005fc9dd5c754d3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4698fa90bfbdd5729e0e25c62345ff0d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">getPeakIntensity</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index) const </td></tr>
<tr class="memdesc:a4698fa90bfbdd5729e0e25c62345ff0d"><td class="mdescLeft"> </td><td class="mdescRight">Returns the intensity of a peak. <a href="#a4698fa90bfbdd5729e0e25c62345ff0d">More...</a><br/></td></tr>
<tr class="separator:a4698fa90bfbdd5729e0e25c62345ff0d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a606049d47faacd506705556d333849a2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb">CoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">getPeakMz</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index) const </td></tr>
<tr class="memdesc:a606049d47faacd506705556d333849a2"><td class="mdescLeft"> </td><td class="mdescRight">Returns the m/z of a peak. <a href="#a606049d47faacd506705556d333849a2">More...</a><br/></td></tr>
<tr class="separator:a606049d47faacd506705556d333849a2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8e5564d7b686645a7d7d6f5aed8cd494"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb">CoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">getPeakRt</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index) const </td></tr>
<tr class="memdesc:a8e5564d7b686645a7d7d6f5aed8cd494"><td class="mdescLeft"> </td><td class="mdescRight">Returns the retention time of a peak. <a href="#a8e5564d7b686645a7d7d6f5aed8cd494">More...</a><br/></td></tr>
<tr class="separator:a8e5564d7b686645a7d7d6f5aed8cd494"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9f755c03fd9b7a485fec02224cc858d7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a9f755c03fd9b7a485fec02224cc858d7">getNextMz</a> (<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index) const </td></tr>
<tr class="memdesc:a9f755c03fd9b7a485fec02224cc858d7"><td class="mdescLeft"> </td><td class="mdescRight">fills <code>index</code> with the index of next peak in m/z dimension <a href="#a9f755c03fd9b7a485fec02224cc858d7">More...</a><br/></td></tr>
<tr class="separator:a9f755c03fd9b7a485fec02224cc858d7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a62c6d0208b4fc2bc51e55eea8ea1ce9d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a62c6d0208b4fc2bc51e55eea8ea1ce9d">getPrevMz</a> (<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index) const </td></tr>
<tr class="memdesc:a62c6d0208b4fc2bc51e55eea8ea1ce9d"><td class="mdescLeft"> </td><td class="mdescRight">fills <code>index</code> with the index of previous peak in m/z dimension <a href="#a62c6d0208b4fc2bc51e55eea8ea1ce9d">More...</a><br/></td></tr>
<tr class="separator:a62c6d0208b4fc2bc51e55eea8ea1ce9d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adf52c00b457571ad74d59a5d6fd12d1a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#adf52c00b457571ad74d59a5d6fd12d1a">getNextRt</a> (<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index)</td></tr>
<tr class="memdesc:adf52c00b457571ad74d59a5d6fd12d1a"><td class="mdescLeft"> </td><td class="mdescRight">fills <code>index</code> with the index of the nearest peak in the next scan <a href="#adf52c00b457571ad74d59a5d6fd12d1a">More...</a><br/></td></tr>
<tr class="separator:adf52c00b457571ad74d59a5d6fd12d1a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad4efb644d8a117edfaf7f0f5a9b34e0a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#ad4efb644d8a117edfaf7f0f5a9b34e0a">getPrevRt</a> (<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">FeatureFinderDefs::IndexPair</a> &index)</td></tr>
<tr class="memdesc:ad4efb644d8a117edfaf7f0f5a9b34e0a"><td class="mdescLeft"> </td><td class="mdescRight">fills <code>index</code> with the index of the nearest peak in the previous scan <a href="#ad4efb644d8a117edfaf7f0f5a9b34e0a">More...</a><br/></td></tr>
<tr class="separator:ad4efb644d8a117edfaf7f0f5a9b34e0a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac641d17ba54cde66c331d17bdee355e8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#ac641d17ba54cde66c331d17bdee355e8">addConvexHull</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">FeatureFinderDefs::IndexSet</a> &set, <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &feature) const </td></tr>
<tr class="memdesc:ac641d17ba54cde66c331d17bdee355e8"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the convex hull of a index <code>set</code> and adds it to the <code>feature</code>. <a href="#ac641d17ba54cde66c331d17bdee355e8">More...</a><br/></td></tr>
<tr class="separator:ac641d17ba54cde66c331d17bdee355e8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a365c5cf67d48519199fe00cb5688d628"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643">MapType</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">map_</a></td></tr>
<tr class="memdesc:a365c5cf67d48519199fe00cb5688d628"><td class="mdescLeft"> </td><td class="mdescRight">Input data pointer. <a href="#a365c5cf67d48519199fe00cb5688d628">More...</a><br/></td></tr>
<tr class="separator:a365c5cf67d48519199fe00cb5688d628"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5f09052343ef99616ad653897841ce3e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e">features_</a></td></tr>
<tr class="memdesc:a5f09052343ef99616ad653897841ce3e"><td class="mdescLeft"> </td><td class="mdescRight">Output data pointer. <a href="#a5f09052343ef99616ad653897841ce3e">More...</a><br/></td></tr>
<tr class="separator:a5f09052343ef99616ad653897841ce3e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adf68cb378c76b322b2cc4dbb2c145a3e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a></td></tr>
<tr class="memdesc:adf68cb378c76b322b2cc4dbb2c145a3e"><td class="mdescLeft"> </td><td class="mdescRight">Pointer to the calling <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> that is used to access the feature flags and report progress. <a href="#adf68cb378c76b322b2cc4dbb2c145a3e">More...</a><br/></td></tr>
<tr class="separator:adf68cb378c76b322b2cc4dbb2c145a3e"><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>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:aa769c6ab217b68ae46061d722ff7f5d1"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#aa769c6ab217b68ae46061d722ff7f5d1">FeaFiModule</a> ()</td></tr>
<tr class="memdesc:aa769c6ab217b68ae46061d722ff7f5d1"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#aa769c6ab217b68ae46061d722ff7f5d1">More...</a><br/></td></tr>
<tr class="separator:aa769c6ab217b68ae46061d722ff7f5d1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a58dbffc498123ad5d8d371843a9e6d5b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a58dbffc498123ad5d8d371843a9e6d5b">operator=</a> (const <a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> &)</td></tr>
<tr class="memdesc:a58dbffc498123ad5d8d371843a9e6d5b"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#a58dbffc498123ad5d8d371843a9e6d5b">More...</a><br/></td></tr>
<tr class="separator:a58dbffc498123ad5d8d371843a9e6d5b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a239ff63fbbaceeffe49a9143c6b20dfe"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a239ff63fbbaceeffe49a9143c6b20dfe">FeaFiModule</a> (const <a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> &)</td></tr>
<tr class="memdesc:a239ff63fbbaceeffe49a9143c6b20dfe"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#a239ff63fbbaceeffe49a9143c6b20dfe">More...</a><br/></td></tr>
<tr class="separator:a239ff63fbbaceeffe49a9143c6b20dfe"><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:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
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<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>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><h3>template<class PeakType, class FeatureType><br/>
class OpenMS::FeaFiModule< PeakType, FeatureType ></h3>
<p>Implements a module of the <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> algorithm. </p>
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<p>Input coordinate type. </p>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><FeatureType> <a class="el" href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a></td>
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<p>Output feature map type. </p>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">PeakType::IntensityType</a> <a class="el" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a></td>
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<p>Input intensity type. </p>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>> <a class="el" href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643">MapType</a></td>
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<p>Input map type. </p>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html#a066042ae14211da37d4fa66d466bfa3e">MapType::SpectrumType</a> <a class="el" href="classOpenMS_1_1FeaFiModule.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a></td>
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<p>Input spectrum type. </p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td>(</td>
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<td class="paramname"><em>map</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > * </td>
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<p>Constructor. </p>
<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a5f09052343ef99616ad653897841ce3e">FeaFiModule< PeakType, FeatureType >::features_</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#adf68cb378c76b322b2cc4dbb2c145a3e">FeaFiModule< PeakType, FeatureType >::ff_</a>, and <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>.</p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> </td>
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<p>destructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> </td>
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<p>Not implemented. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType > & </td>
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<p>Not implemented. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void addConvexHull </td>
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<p>Calculates the convex hull of a index <code>set</code> and adds it to the <code>feature</code>. </p>
<p>References <a class="el" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">Feature::getConvexHulls()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018a35008b046ec2687e53152082281d0867">Peak2D::MZ</a>, and <a class="el" href="classOpenMS_1_1Peak2D.html#ac2d92631c8f762c7e9afe43f11e1f018af388fcb6d444ef59841ef549ca6ee0da">Peak2D::RT</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">ModelFitter< PeakType, FeatureType >::fit()</a>.</p>
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<td class="memname">void getNextMz </td>
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<p>fills <code>index</code> with the index of next peak in m/z dimension </p>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1Precondition.html" title="Precondition failed exception. ">Exception::Precondition</a></td><td>is thrown if an invalid index is given </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#a36b5d54b1a3a55b7cf46576fd849c299">SimpleExtender< PeakType, FeatureType >::moveMzUp_()</a>.</p>
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<td class="memname">void getNextRt </td>
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<p>fills <code>index</code> with the index of the nearest peak in the next scan </p>
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<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#af79f8c231da6a9d674c28941d313d315">SimpleExtender< PeakType, FeatureType >::moveRtUp_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a221361082f641c3fccc58e9bc66aeee1">IntensityType</a> getPeakIntensity </td>
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<p>Returns the intensity of a peak. </p>
<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#a8597c0a5982f48f9a8387e286b0251b0">SimpleExtender< PeakType, FeatureType >::checkNeighbour_()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">ModelFitter< PeakType, FeatureType >::doProjectionDim_()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a520ad36c37273100004a5dca3c2a6c24">ModelFitter< PeakType, FeatureType >::evaluate_()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">SimpleExtender< PeakType, FeatureType >::extend()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">ModelFitter< PeakType, FeatureType >::fit()</a>, and <a class="el" href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">SimpleSeeder< PeakType, FeatureType >::initialize_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a181486a43da338e31f089df7661f50bb">CoordinateType</a> getPeakMz </td>
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<p>Returns the m/z of a peak. </p>
<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">ModelFitter< PeakType, FeatureType >::doProjectionDim_()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a520ad36c37273100004a5dca3c2a6c24">ModelFitter< PeakType, FeatureType >::evaluate_()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">SimpleExtender< PeakType, FeatureType >::extend()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">ModelFitter< PeakType, FeatureType >::fit()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#af560e97f4f00d467116a5791bcdf7ca5">SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_()</a>, and <a class="el" href="classOpenMS_1_1SimpleExtender.html#a0d642765897747c34debb18095cde304">SimpleExtender< PeakType, FeatureType >::writeDebugFile_()</a>.</p>
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<p>Returns the retention time of a peak. </p>
<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1ModelFitter.html#a9e49d9564896fee1216a006f907d139d">ModelFitter< PeakType, FeatureType >::doProjectionDim_()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">SimpleExtender< PeakType, FeatureType >::extend()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">ModelFitter< PeakType, FeatureType >::fit()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#af560e97f4f00d467116a5791bcdf7ca5">SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_()</a>, and <a class="el" href="classOpenMS_1_1SimpleExtender.html#a0d642765897747c34debb18095cde304">SimpleExtender< PeakType, FeatureType >::writeDebugFile_()</a>.</p>
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<td class="memname">void getPrevMz </td>
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<p>fills <code>index</code> with the index of previous peak in m/z dimension </p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1FeatureFinderDefs_1_1NoSuccessor.html" title="Exception that is thrown if a method an invalid IndexPair is given. ">FeatureFinderDefs::NoSuccessor</a></td><td>is thrown if there is no previous peak </td></tr>
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1Precondition.html" title="Precondition failed exception. ">Exception::Precondition</a></td><td>is thrown if an invalid index is given </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#a9c6a1a832b915ac89376cec9dbf009b7">SimpleExtender< PeakType, FeatureType >::moveMzDown_()</a>.</p>
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<td class="memname">void getPrevRt </td>
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<p>fills <code>index</code> with the index of the nearest peak in the previous scan </p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1Precondition.html" title="Precondition failed exception. ">Exception::Precondition</a></td><td>is thrown if an invalid index is given </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1FeaFiModule.html#a365c5cf67d48519199fe00cb5688d628">FeaFiModule< PeakType, FeatureType >::map_</a>, <a class="el" href="group__Conditions.html#ga45a74ea28109e7e1ed992fbd2ee97778">OPENMS_PRECONDITION</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#a7f4bbff96a2ea0e3d46711022de26b29">SimpleExtender< PeakType, FeatureType >::moveRtDown_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeaFiModule.html">FeaFiModule</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType > & </td>
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<p>Not implemented. </p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeaFiModule.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a>* features_</td>
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<p>Output data pointer. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa">FeaFiModule< PeakType, FeatureType >::FeaFiModule()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a>* ff_</td>
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<p>Pointer to the calling <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> that is used to access the feature flags and report progress. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#a8597c0a5982f48f9a8387e286b0251b0">SimpleExtender< PeakType, FeatureType >::checkNeighbour_()</a>, <a class="el" href="classOpenMS_1_1SimpleExtender.html#a1139a06b7cf1886d1977e5afcfddfea6">SimpleExtender< PeakType, FeatureType >::extend()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa">FeaFiModule< PeakType, FeatureType >::FeaFiModule()</a>, <a class="el" href="classOpenMS_1_1ModelFitter.html#a9a599157dfa0c832cf50f5596342c73e">ModelFitter< PeakType, FeatureType >::fit()</a>, <a class="el" href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">SimpleSeeder< PeakType, FeatureType >::initialize_()</a>, and <a class="el" href="classOpenMS_1_1SimpleSeeder.html#a9101eb2633f34b26a1436b3d8e1e7522">SimpleSeeder< PeakType, FeatureType >::nextSeed()</a>.</p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1FeaFiModule.html#adf6f376e844058d129ce8ba868276643">MapType</a>* map_</td>
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<p>Input data pointer. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SimpleExtender.html#af7842efcd3ecab40cf021f5cae359dbe">SimpleExtender< PeakType, FeatureType >::computePeakPriority_()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#ad3fe3d27b98fcd12d996b358e30723fa">FeaFiModule< PeakType, FeatureType >::FeaFiModule()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#a9f755c03fd9b7a485fec02224cc858d7">FeaFiModule< PeakType, FeatureType >::getNextMz()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#adf52c00b457571ad74d59a5d6fd12d1a">FeaFiModule< PeakType, FeatureType >::getNextRt()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#a4698fa90bfbdd5729e0e25c62345ff0d">FeaFiModule< PeakType, FeatureType >::getPeakIntensity()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#a606049d47faacd506705556d333849a2">FeaFiModule< PeakType, FeatureType >::getPeakMz()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#a8e5564d7b686645a7d7d6f5aed8cd494">FeaFiModule< PeakType, FeatureType >::getPeakRt()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#a62c6d0208b4fc2bc51e55eea8ea1ce9d">FeaFiModule< PeakType, FeatureType >::getPrevMz()</a>, <a class="el" href="classOpenMS_1_1FeaFiModule.html#ad4efb644d8a117edfaf7f0f5a9b34e0a">FeaFiModule< PeakType, FeatureType >::getPrevRt()</a>, and <a class="el" href="classOpenMS_1_1SimpleSeeder.html#a6aca068dd3cf1a6c7e78091c9bdae961">SimpleSeeder< PeakType, FeatureType >::initialize_()</a>.</p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5</font></TD>
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