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<HTML>
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<TITLE>SimplePairFinder 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_1SimplePairFinder.html">SimplePairFinder</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-static-methods">Static Public Member Functions</a> |
<a href="#pro-methods">Protected Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> |
<a href="classOpenMS_1_1SimplePairFinder-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">SimplePairFinder Class Reference<div class="ingroups"><a class="el" href="group__FeatureGrouping.html">FeatureGrouping</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>This class implements a simple point pair finding algorithm.
<a href="classOpenMS_1_1SimplePairFinder.html#details">More...</a></p>
<p><code>#include <<a class="el" href="SimplePairFinder_8h_source.html">OpenMS/ANALYSIS/MAPMATCHING/SimplePairFinder.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for SimplePairFinder:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1SimplePairFinder.png" usemap="#SimplePairFinder_map" alt=""/>
<map id="SimplePairFinder_map" name="SimplePairFinder_map">
<area href="classOpenMS_1_1BaseGroupFinder.html" title="The base class of all element group finding algorithms. " alt="BaseGroupFinder" shape="rect" coords="71,56,204,80"/>
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,133,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="143,0,276,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:ad9a24952f8ba91d261de80ec8a07e3a2"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1BaseGroupFinder.html">BaseGroupFinder</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#ad9a24952f8ba91d261de80ec8a07e3a2">Base</a></td></tr>
<tr class="memdesc:ad9a24952f8ba91d261de80ec8a07e3a2"><td class="mdescLeft"> </td><td class="mdescRight">Base class. <a href="#ad9a24952f8ba91d261de80ec8a07e3a2">More...</a><br/></td></tr>
<tr class="separator:ad9a24952f8ba91d261de80ec8a07e3a2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a38be7c3c67e8913b3f816056cd99cc5b"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#a38be7c3c67e8913b3f816056cd99cc5b">SimplePairFinder</a> ()</td></tr>
<tr class="memdesc:a38be7c3c67e8913b3f816056cd99cc5b"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a38be7c3c67e8913b3f816056cd99cc5b">More...</a><br/></td></tr>
<tr class="separator:a38be7c3c67e8913b3f816056cd99cc5b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a06720fc0d99652e6a4875171c7f5f020"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#a06720fc0d99652e6a4875171c7f5f020">~SimplePairFinder</a> ()</td></tr>
<tr class="memdesc:a06720fc0d99652e6a4875171c7f5f020"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a06720fc0d99652e6a4875171c7f5f020">More...</a><br/></td></tr>
<tr class="separator:a06720fc0d99652e6a4875171c7f5f020"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afe5cf49fa30622901babefc6cd0cdc3c"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#afe5cf49fa30622901babefc6cd0cdc3c">run</a> (const std::vector< <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> > &input_maps, <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &result_map)</td></tr>
<tr class="memdesc:afe5cf49fa30622901babefc6cd0cdc3c"><td class="mdescLeft"> </td><td class="mdescRight">Run the algorithm. <a href="#afe5cf49fa30622901babefc6cd0cdc3c">More...</a><br/></td></tr>
<tr class="separator:afe5cf49fa30622901babefc6cd0cdc3c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1BaseGroupFinder"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1BaseGroupFinder')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1BaseGroupFinder.html">BaseGroupFinder</a></td></tr>
<tr class="memitem:a309c1c9b2533b83f8a0ca2a4714d754b inherit pub_methods_classOpenMS_1_1BaseGroupFinder"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BaseGroupFinder.html#a309c1c9b2533b83f8a0ca2a4714d754b">BaseGroupFinder</a> ()</td></tr>
<tr class="memdesc:a309c1c9b2533b83f8a0ca2a4714d754b inherit pub_methods_classOpenMS_1_1BaseGroupFinder"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a309c1c9b2533b83f8a0ca2a4714d754b">More...</a><br/></td></tr>
<tr class="separator:a309c1c9b2533b83f8a0ca2a4714d754b inherit pub_methods_classOpenMS_1_1BaseGroupFinder"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adefa09baf5e125a9b3f1c6a373f5f69a inherit pub_methods_classOpenMS_1_1BaseGroupFinder"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BaseGroupFinder.html#adefa09baf5e125a9b3f1c6a373f5f69a">~BaseGroupFinder</a> ()</td></tr>
<tr class="memdesc:adefa09baf5e125a9b3f1c6a373f5f69a inherit pub_methods_classOpenMS_1_1BaseGroupFinder"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#adefa09baf5e125a9b3f1c6a373f5f69a">More...</a><br/></td></tr>
<tr class="separator:adefa09baf5e125a9b3f1c6a373f5f69a inherit pub_methods_classOpenMS_1_1BaseGroupFinder"><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:aedd9bc32d9e13af233c2cbc3f06a0b68"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1BaseGroupFinder.html">BaseGroupFinder</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#aedd9bc32d9e13af233c2cbc3f06a0b68">create</a> ()</td></tr>
<tr class="memdesc:aedd9bc32d9e13af233c2cbc3f06a0b68"><td class="mdescLeft"> </td><td class="mdescRight">returns an instance of this class <a href="#aedd9bc32d9e13af233c2cbc3f06a0b68">More...</a><br/></td></tr>
<tr class="separator:aedd9bc32d9e13af233c2cbc3f06a0b68"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af73fd15708e50e77665070023a09cc87"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#af73fd15708e50e77665070023a09cc87">getProductName</a> ()</td></tr>
<tr class="memdesc:af73fd15708e50e77665070023a09cc87"><td class="mdescLeft"> </td><td class="mdescRight">returns the name of this module <a href="#af73fd15708e50e77665070023a09cc87">More...</a><br/></td></tr>
<tr class="separator:af73fd15708e50e77665070023a09cc87"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_static_methods_classOpenMS_1_1BaseGroupFinder"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1BaseGroupFinder')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1BaseGroupFinder.html">BaseGroupFinder</a></td></tr>
<tr class="memitem:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1BaseGroupFinder"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BaseGroupFinder.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1BaseGroupFinder"><td class="mdescLeft"> </td><td class="mdescRight">Register all derived classes here. <a href="#a7899dbe105534dc1f81971dd71a26ff0">More...</a><br/></td></tr>
<tr class="separator:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1BaseGroupFinder"><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_1SimplePairFinder.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="memitem:a166830903bc21b91842891590ece7776"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#a166830903bc21b91842891590ece7776">similarity_</a> (<a class="el" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> const &left, <a class="el" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> const &right) const </td></tr>
<tr class="memdesc:a166830903bc21b91842891590ece7776"><td class="mdescLeft"> </td><td class="mdescRight">Compute the similarity for a pair of elements. <a href="#a166830903bc21b91842891590ece7776">More...</a><br/></td></tr>
<tr class="separator:a166830903bc21b91842891590ece7776"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1BaseGroupFinder"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1BaseGroupFinder')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1BaseGroupFinder.html">BaseGroupFinder</a></td></tr>
<tr class="memitem:ae6a31106f2c6fab5214e085fb5168903 inherit pro_methods_classOpenMS_1_1BaseGroupFinder"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1BaseGroupFinder.html#ae6a31106f2c6fab5214e085fb5168903">checkIds_</a> (const std::vector< <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> > &maps) const </td></tr>
<tr class="memdesc:ae6a31106f2c6fab5214e085fb5168903 inherit pro_methods_classOpenMS_1_1BaseGroupFinder"><td class="mdescLeft"> </td><td class="mdescRight">Checks if all file descriptions have disjoint map identifiers. <a href="#ae6a31106f2c6fab5214e085fb5168903">More...</a><br/></td></tr>
<tr class="separator:ae6a31106f2c6fab5214e085fb5168903 inherit pro_methods_classOpenMS_1_1BaseGroupFinder"><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:ad7021c206336463ef1afbfffce0214c9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#ad7021c206336463ef1afbfffce0214c9">diff_exponent_</a> [2]</td></tr>
<tr class="memdesc:ad7021c206336463ef1afbfffce0214c9"><td class="mdescLeft"> </td><td class="mdescRight">A parameter for <a class="el" href="classOpenMS_1_1SimplePairFinder.html#a166830903bc21b91842891590ece7776" title="Compute the similarity for a pair of elements. ">similarity_()</a>. <a href="#ad7021c206336463ef1afbfffce0214c9">More...</a><br/></td></tr>
<tr class="separator:ad7021c206336463ef1afbfffce0214c9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5e7d69f13cfc5c043544372b350ac59c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#a5e7d69f13cfc5c043544372b350ac59c">diff_intercept_</a> [2]</td></tr>
<tr class="memdesc:a5e7d69f13cfc5c043544372b350ac59c"><td class="mdescLeft"> </td><td class="mdescRight">A parameter for <a class="el" href="classOpenMS_1_1SimplePairFinder.html#a166830903bc21b91842891590ece7776" title="Compute the similarity for a pair of elements. ">similarity_()</a>. <a href="#a5e7d69f13cfc5c043544372b350ac59c">More...</a><br/></td></tr>
<tr class="separator:a5e7d69f13cfc5c043544372b350ac59c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a7afe0dfbb83327be42c67b1d1a2d43"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SimplePairFinder.html#a5a7afe0dfbb83327be42c67b1d1a2d43">pair_min_quality_</a></td></tr>
<tr class="memdesc:a5a7afe0dfbb83327be42c67b1d1a2d43"><td class="mdescLeft"> </td><td class="mdescRight">Minimal pair quality. <a href="#a5a7afe0dfbb83327be42c67b1d1a2d43">More...</a><br/></td></tr>
<tr class="separator:a5a7afe0dfbb83327be42c67b1d1a2d43"><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>
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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="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
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<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
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<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>This class implements a simple point pair finding algorithm. </p>
<p>It offers a method to find element pairs across two element maps.</p>
<p>The similarity value should express our confidence that one element might possibly be matched to the other. Larger quality values are better, the maximal similarity is one. Let <img class="formulaInl" alt="$\Delta_\textit{RT}$" src="form_9.png"/> and <img class="formulaInl" alt="$\Delta_\textit{MZ}$" src="form_10.png"/> be the absolute values of the RT and MZ differences in the data. Then the similarity value is </p>
<p class="formulaDsp">
<img class="formulaDsp" alt="\[ \frac{1}{ \big( 1 + \Delta_\textit{RT} \cdot \textit{diff\_intercept\_RT} \big)^\textit{diff\_exponent\_RT} \cdot \big( 1 + \Delta_\textit{MZ} \cdot \textit{diff\_intercept\_MZ} \big)^\textit{diff\_exponent\_MZ} } \]" src="form_11.png"/>
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<p>Choosing diff_exponent: This parameter controls the growth rate of the penalty for differences. It is for example possible to search for pairs using the absolute distance in RT (which should not be very susceptible to outliers) and the squared distance in MZ (where small difference occur frequently, but large differences indicate a mismatch).</p>
<p>Choosing diff_intercept: Since we are taking the reciprocal value ("1/..."), we include an offset to avoid division by zero in case <img class="formulaInl" alt="$\Delta=0$" src="form_12.png"/>. To set this parameter, ask yourself: How much worse is a difference of 1 compared to no difference?</p>
<p>The following image illustrates the influence of these parameters: </p>
<div class="image">
<img src="SimplePairFinder.png" alt="SimplePairFinder.png"/>
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Influence of the parameters intercept and exponent</div></div>
<B>Parameters of this class are:</B><BR><BR>
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<td style="vertical-align:top"><i>similarity:pair_min_quality</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.01</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Minimum required pair quality.</td>
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<td style="vertical-align:top"><i>similarity:diff_intercept:RT</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">This parameter controls the asymptotic decay rate for large differences (for more details see the similarity measurement).</td>
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<td style="vertical-align:top"><i>similarity:diff_intercept:MZ</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">This parameter controls the asymptotic decay rate for large differences (for more details see the similarity measurement).</td>
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<td style="vertical-align:top"><i>similarity:diff_exponent:RT</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">This parameter is important for small differences (for more details see the similarity measurement).</td>
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<td style="vertical-align:top"><i>similarity:diff_exponent:MZ</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">This parameter is important for small differences (for more details see the similarity measurement).</td>
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<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.
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</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1BaseGroupFinder.html">BaseGroupFinder</a> <a class="el" href="classOpenMS_1_1SimplePairFinder.html#ad9a24952f8ba91d261de80ec8a07e3a2">Base</a></td>
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<p>Base class. </p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<p>Constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1SimplePairFinder.html">SimplePairFinder</a> </td>
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<p>Destructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<p>returns an instance of this class </p>
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<p>returns the name of this module </p>
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<td class="memname">virtual void run </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> > & </td>
<td class="paramname"><em>input_maps</em>, </td>
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<p>Run the algorithm. </p>
<dl class="section note"><dt>Note</dt><dd>Exactly two <em>input</em> maps must be provided. </dd>
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All two <em>input</em> maps must be provided.</dd></dl>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1IllegalArgument.html" title="A method or algorithm argument contains illegal values. ">Exception::IllegalArgument</a></td><td>is thrown if the input data is not valid. </td></tr>
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<p>Implements <a class="el" href="classOpenMS_1_1BaseGroupFinder.html#ac755b617b353190b1af9291688c49b5b">BaseGroupFinder</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> similarity_ </td>
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<p>Compute the similarity for a pair of elements. </p>
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<td class="memname">virtual void updateMembers_ </td>
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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#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> diff_exponent_[2]</td>
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<p>A parameter for <a class="el" href="classOpenMS_1_1SimplePairFinder.html#a166830903bc21b91842891590ece7776" title="Compute the similarity for a pair of elements. ">similarity_()</a>. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> diff_intercept_[2]</td>
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<p>A parameter for <a class="el" href="classOpenMS_1_1SimplePairFinder.html#a166830903bc21b91842891590ece7776" title="Compute the similarity for a pair of elements. ">similarity_()</a>. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> pair_min_quality_</td>
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<p>Minimal pair quality. </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 11:19:26 using doxygen 1.8.5</font></TD>
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