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<HTML>
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<TITLE>MapAlignmentAlgorithmPoseClustering Class Reference</TITLE>
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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pro-methods">Protected Member Functions</a> |
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<div class="title">MapAlignmentAlgorithmPoseClustering Class Reference<div class="ingroups"><a class="el" href="group__MapAlignment.html">MapAlignment</a></div></div> </div>
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<p>A map alignment algorithm based on pose clustering.
<a href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#details">More...</a></p>
<p><code>#include <<a class="el" href="MapAlignmentAlgorithmPoseClustering_8h_source.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering.h</a>></code></p>
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Inheritance diagram for MapAlignmentAlgorithmPoseClustering:</div>
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<div class="center">
<img src="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.png" usemap="#MapAlignmentAlgorithmPoseClustering_map" alt=""/>
<map id="MapAlignmentAlgorithmPoseClustering_map" name="MapAlignmentAlgorithmPoseClustering_map">
<area href="classOpenMS_1_1MapAlignmentAlgorithm.html" title="Base class for all map-alignment algorithms. " alt="MapAlignmentAlgorithm" shape="rect" coords="120,56,350,80"/>
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,230,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="240,0,470,24"/>
</map>
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<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:a53fe0bee083b9a6d33c5bc932dcc364b"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a53fe0bee083b9a6d33c5bc932dcc364b">MapAlignmentAlgorithmPoseClustering</a> ()</td></tr>
<tr class="memdesc:a53fe0bee083b9a6d33c5bc932dcc364b"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a53fe0bee083b9a6d33c5bc932dcc364b">More...</a><br/></td></tr>
<tr class="separator:a53fe0bee083b9a6d33c5bc932dcc364b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac01c739c961c93deb40ee0642dbe7a38"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#ac01c739c961c93deb40ee0642dbe7a38">~MapAlignmentAlgorithmPoseClustering</a> ()</td></tr>
<tr class="memdesc:ac01c739c961c93deb40ee0642dbe7a38"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#ac01c739c961c93deb40ee0642dbe7a38">More...</a><br/></td></tr>
<tr class="separator:ac01c739c961c93deb40ee0642dbe7a38"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8c5f81600ee8c144d0df1e00b21d0889"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a8c5f81600ee8c144d0df1e00b21d0889">align</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &map, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &trafo)</td></tr>
<tr class="separator:a8c5f81600ee8c144d0df1e00b21d0889"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a99f67b4668f938c5f121aa5422b5c870"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a99f67b4668f938c5f121aa5422b5c870">align</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> &map, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &trafo)</td></tr>
<tr class="separator:a99f67b4668f938c5f121aa5422b5c870"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9b631e34ccfb6e0dd940ce3403cb0880"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a9b631e34ccfb6e0dd940ce3403cb0880">align</a> (const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &map, <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> &trafo)</td></tr>
<tr class="separator:a9b631e34ccfb6e0dd940ce3403cb0880"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6110872a350e1ac11924dcc470cb6714"><td class="memTemplParams" colspan="2">template<typename MapType > </td></tr>
<tr class="memitem:a6110872a350e1ac11924dcc470cb6714"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a6110872a350e1ac11924dcc470cb6714">setReference</a> (const MapType &map)</td></tr>
<tr class="separator:a6110872a350e1ac11924dcc470cb6714"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1MapAlignmentAlgorithm')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td></tr>
<tr class="memitem:a2323adcbf2f7ef45c0a4c63f0001374a inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2323adcbf2f7ef45c0a4c63f0001374a">MapAlignmentAlgorithm</a> ()</td></tr>
<tr class="memdesc:a2323adcbf2f7ef45c0a4c63f0001374a inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a2323adcbf2f7ef45c0a4c63f0001374a">More...</a><br/></td></tr>
<tr class="separator:a2323adcbf2f7ef45c0a4c63f0001374a inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1423ba5efed91566183b0d264fe0c2fe inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a1423ba5efed91566183b0d264fe0c2fe">~MapAlignmentAlgorithm</a> ()</td></tr>
<tr class="memdesc:a1423ba5efed91566183b0d264fe0c2fe inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a1423ba5efed91566183b0d264fe0c2fe">More...</a><br/></td></tr>
<tr class="separator:a1423ba5efed91566183b0d264fe0c2fe inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2038727c06b2e23bf60e1d21d7179815 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2038727c06b2e23bf60e1d21d7179815">alignPeakMaps</a> (std::vector< <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a2038727c06b2e23bf60e1d21d7179815 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns peak maps. <a href="#a2038727c06b2e23bf60e1d21d7179815">More...</a><br/></td></tr>
<tr class="separator:a2038727c06b2e23bf60e1d21d7179815 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9e66a73174d03975d49a7e9b3f8854df inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a9e66a73174d03975d49a7e9b3f8854df">alignCompactFeatureMaps</a> (std::vector< std::vector< <a class="el" href="classOpenMS_1_1Peak2D.html">Peak2D</a> > > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a9e66a73174d03975d49a7e9b3f8854df inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns vectors of 2D peaks (memory efficient version of <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>) <a href="#a9e66a73174d03975d49a7e9b3f8854df">More...</a><br/></td></tr>
<tr class="separator:a9e66a73174d03975d49a7e9b3f8854df inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a32c9e0577b4455dbc2d3493079ef1c81 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a32c9e0577b4455dbc2d3493079ef1c81">alignFeatureMaps</a> (std::vector< <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a32c9e0577b4455dbc2d3493079ef1c81 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns feature maps. <a href="#a32c9e0577b4455dbc2d3493079ef1c81">More...</a><br/></td></tr>
<tr class="separator:a32c9e0577b4455dbc2d3493079ef1c81 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7385e8b646ae9d282c3c06abf1620083 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7385e8b646ae9d282c3c06abf1620083">alignConsensusMaps</a> (std::vector< <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a7385e8b646ae9d282c3c06abf1620083 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns consensus maps. <a href="#a7385e8b646ae9d282c3c06abf1620083">More...</a><br/></td></tr>
<tr class="separator:a7385e8b646ae9d282c3c06abf1620083 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4f223602464cbafef563871036b5dfc1 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a4f223602464cbafef563871036b5dfc1">alignPeptideIdentifications</a> (std::vector< std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a4f223602464cbafef563871036b5dfc1 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns peptide identifications. <a href="#a4f223602464cbafef563871036b5dfc1">More...</a><br/></td></tr>
<tr class="separator:a4f223602464cbafef563871036b5dfc1 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aef01d65c73bbdd9f550309195007622b inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#aef01d65c73bbdd9f550309195007622b">setReference</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> reference_index=0, const <a class="el" href="classOpenMS_1_1String.html">String</a> &reference_file="")</td></tr>
<tr class="memdesc:aef01d65c73bbdd9f550309195007622b inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Defines a reference for the alignment. <a href="#aef01d65c73bbdd9f550309195007622b">More...</a><br/></td></tr>
<tr class="separator:aef01d65c73bbdd9f550309195007622b inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE! <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of progress log being used. <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the progress display. <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the current progress. <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Ends the progress display. <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:a9584ec9238430832ac2c381039513247"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a9584ec9238430832ac2c381039513247">create</a> ()</td></tr>
<tr class="memdesc:a9584ec9238430832ac2c381039513247"><td class="mdescLeft"> </td><td class="mdescRight">Creates a new instance of this class (for <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) <a href="#a9584ec9238430832ac2c381039513247">More...</a><br/></td></tr>
<tr class="separator:a9584ec9238430832ac2c381039513247"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8d4600093afb26cff7d7db82a1837e9f"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a8d4600093afb26cff7d7db82a1837e9f">getProductName</a> ()</td></tr>
<tr class="memdesc:a8d4600093afb26cff7d7db82a1837e9f"><td class="mdescLeft"> </td><td class="mdescRight">Returns the product name (for the <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) <a href="#a8d4600093afb26cff7d7db82a1837e9f">More...</a><br/></td></tr>
<tr class="separator:a8d4600093afb26cff7d7db82a1837e9f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td></tr>
<tr class="memitem:acc270843ebe2525547c6ac01bf341234 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &model_type, const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &params, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &trafos)</td></tr>
<tr class="memdesc:acc270843ebe2525547c6ac01bf341234 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Fits a model with given parameters to the transformations. <a href="#acc270843ebe2525547c6ac01bf341234">More...</a><br/></td></tr>
<tr class="separator:acc270843ebe2525547c6ac01bf341234 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Register all derived classes in this method. <a href="#a7899dbe105534dc1f81971dd71a26ff0">More...</a><br/></td></tr>
<tr class="separator:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a776f7572fc4f466e9527ca233471920d"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
<tr class="memdesc:a776f7572fc4f466e9527ca233471920d"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
<tr class="separator:a776f7572fc4f466e9527ca233471920d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a58e8fabd0acee7c3d34db7c304db762e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PoseClusteringAffineSuperimposer.html">PoseClusteringAffineSuperimposer</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a58e8fabd0acee7c3d34db7c304db762e">superimposer_</a></td></tr>
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<tr class="memitem:afa65b41aa65348bd4396b9bef84e7ac7"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StablePairFinder.html">StablePairFinder</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#afa65b41aa65348bd4396b9bef84e7ac7">pairfinder_</a></td></tr>
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<tr class="memitem:a0a180d56906b4980aa2719fc500cd2de"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a0a180d56906b4980aa2719fc500cd2de">reference_</a></td></tr>
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<tr class="memitem:a04e32c6e5d826c09e14323f0226f69b8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#a04e32c6e5d826c09e14323f0226f69b8">max_num_peaks_considered_</a></td></tr>
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<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>
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<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>
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<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>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<tr class="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>
<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
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<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
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<tr class="memitem:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td></tr>
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<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
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<tr class="memitem:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StopWatch.html">StopWatch</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a6d9750520313ea7f843d7a49cb2e9e5f">stop_watch_</a></td></tr>
<tr class="separator:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">time_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:af1497f3100deeebaa43b434c3c59597d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#af1497f3100deeebaa43b434c3c59597d">MapAlignmentAlgorithmPoseClustering</a> (const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> &)</td></tr>
<tr class="memdesc:af1497f3100deeebaa43b434c3c59597d"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor intentionally not implemented -> private. <a href="#af1497f3100deeebaa43b434c3c59597d">More...</a><br/></td></tr>
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<tr class="memitem:afc9953f4d61eafd60dfd077a2fbdc529"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html#afc9953f4d61eafd60dfd077a2fbdc529">operator=</a> (const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> &)</td></tr>
<tr class="memdesc:afc9953f4d61eafd60dfd077a2fbdc529"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator intentionally not implemented -> private. <a href="#afc9953f4d61eafd60dfd077a2fbdc529">More...</a><br/></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
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<tr class="inherit_header pro_static_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
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</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A map alignment algorithm based on pose clustering. </p>
<p>Pose clustering analyzes pair distances to find the most probable transformation of retention times. The algorithm choses the x most intensity peaks/features per map. This is modeled via the parameter 'max_num_peaks_considered', which in turn influences the runtime and stability of the results. Bigger values prolong computation, smaller values might lead to no or unstable trafos. Set to -1 to use all features (might take very long for large maps).</p>
<p>For further details see: <br/>
Eva Lange et.al <br/>
A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data <br/>
ISMB/ECCB 2007</p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><b>max_num_peaks_considered</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1000</td>
<td style="vertical-align:top">min: -1</td><td style="vertical-align:top">The maximal number of peaks/features to be considered per map. To use all, set to '-1'.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>superimposer:mz_pair_max_distance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>superimposer:rt_pair_distance_fraction</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). </td>
</tr>
<tr>
<td style="vertical-align:top"><b>superimposer:num_used_points</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2000</td>
<td style="vertical-align:top">min: -1</td><td style="vertical-align:top">Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>superimposer:scaling_bucket_size</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.005</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>superimposer:shift_bucket_size</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>superimposer:max_shift</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1000</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Maximal shift which is considered during histogramming. This applies for both directions.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>superimposer:max_scaling</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>superimposer:dump_buckets</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>superimposer:dump_pairs</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top"></td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>pairfinder:second_nearest_gap</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>pairfinder:use_identifications</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).</td>
</tr>
<tr>
<td style="vertical-align:top"><b>pairfinder:ignore_charge</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Compare features normally even if their charge states are different</td>
</tr>
<tr>
<td style="vertical-align:top"><b>pairfinder:<span title="Distance component based on RT differences">distance_RT</span>:max_difference</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Maximum allowed difference in RT in seconds</td>
</tr>
<tr>
<td style="vertical-align:top"><i>pairfinder:<span title="Distance component based on RT differences">distance_RT</span>:exponent</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)</td>
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<td style="vertical-align:top"><i>pairfinder:<span title="Distance component based on RT differences">distance_RT</span>:weight</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">RT distances are weighted by this factor</td>
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<td style="vertical-align:top"><b>pairfinder:<span title="Distance component based on m/z differences">distance_MZ</span>:max_difference</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.3</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Maximum allowed difference in m/z (unit defined by 'unit')</td>
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<td style="vertical-align:top"><b>pairfinder:<span title="Distance component based on m/z differences">distance_MZ</span>:unit</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">Da</td>
<td style="vertical-align:top">Da, ppm</td><td style="vertical-align:top">Unit of the 'max_difference' parameter</td>
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<td style="vertical-align:top"><i>pairfinder:<span title="Distance component based on m/z differences">distance_MZ</span>:exponent</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)</td>
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<td style="vertical-align:top"><i>pairfinder:<span title="Distance component based on m/z differences">distance_MZ</span>:weight</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">m/z distances are weighted by this factor</td>
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<td style="vertical-align:top"><i>pairfinder:<span title="Distance component based on differences in relative intensity">distance_intensity</span>:exponent</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)</td>
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<td style="vertical-align:top"><i>pairfinder:<span title="Distance component based on differences in relative intensity">distance_intensity</span>:weight</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Distances based on relative intensity are weighted by this factor</td>
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<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> </td>
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<p>Default constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> </td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a> & </td>
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<p>Copy constructor intentionally not implemented -> private. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void align </td>
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<p>Creates a new instance of this class (for <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) </p>
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<p>Returns the product name (for the <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">MapAlignmentAlgorithmPoseClustering</a>& operator= </td>
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<p>Assignment operator intentionally not implemented -> private. </p>
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<td class="memname">void setReference </td>
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<p>References <a class="el" href="classOpenMS_1_1ConsensusMap.html#addd3e7ab2d02c8ff9377da76cf2fcaff">ConsensusMap::convert()</a>.</p>
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<p>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. </p>
<p>Also call it at the end of the derived classes' copy constructor and assignment operator.</p>
<p>The default implementation is empty. </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"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> max_num_peaks_considered_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> reference_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1PoseClusteringAffineSuperimposer.html">PoseClusteringAffineSuperimposer</a> superimposer_</td>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5</font></TD>
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