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<HTML>
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<TITLE>FeatureDistance 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_1FeatureDistance.html">FeatureDistance</a></li> </ul>
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<a href="#nested-classes">Classes</a> |
<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pro-methods">Protected Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> |
<a href="classOpenMS_1_1FeatureDistance-members.html">List of all members</a> </div>
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<div class="title">FeatureDistance Class Reference<div class="ingroups"><a class="el" href="group__FeatureGrouping.html">FeatureGrouping</a></div></div> </div>
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<div class="contents">
<p>A functor class for the calculation of distances between features or consensus features.
<a href="classOpenMS_1_1FeatureDistance.html#details">More...</a></p>
<p><code>#include <<a class="el" href="FeatureDistance_8h_source.html">OpenMS/ANALYSIS/MAPMATCHING/FeatureDistance.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for FeatureDistance:</div>
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<img src="classOpenMS_1_1FeatureDistance.png" usemap="#FeatureDistance_map" alt=""/>
<map id="FeatureDistance_map" name="FeatureDistance_map">
<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"/>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Structure for storing distance parameters. <a href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html#details">More...</a><br/></td></tr>
<tr class="separator:"><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:a06315551e400d6d6b8bbbbf2c9090c7d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a06315551e400d6d6b8bbbbf2c9090c7d">FeatureDistance</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_intensity=1.0, bool force_constraints=false)</td></tr>
<tr class="memdesc:a06315551e400d6d6b8bbbbf2c9090c7d"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a06315551e400d6d6b8bbbbf2c9090c7d">More...</a><br/></td></tr>
<tr class="separator:a06315551e400d6d6b8bbbbf2c9090c7d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a720b5f6a3a1c9366578eb0acccad03ce"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a720b5f6a3a1c9366578eb0acccad03ce">~FeatureDistance</a> ()</td></tr>
<tr class="memdesc:a720b5f6a3a1c9366578eb0acccad03ce"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a720b5f6a3a1c9366578eb0acccad03ce">More...</a><br/></td></tr>
<tr class="separator:a720b5f6a3a1c9366578eb0acccad03ce"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a30635cd2165a8a08854f19031bbba4a0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a30635cd2165a8a08854f19031bbba4a0">operator=</a> (const <a class="el" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> &other)</td></tr>
<tr class="memdesc:a30635cd2165a8a08854f19031bbba4a0"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#a30635cd2165a8a08854f19031bbba4a0">More...</a><br/></td></tr>
<tr class="separator:a30635cd2165a8a08854f19031bbba4a0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a63d485487b6a06e482529a1c8aedc5b5"><td class="memItemLeft" align="right" valign="top">std::pair< bool, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a63d485487b6a06e482529a1c8aedc5b5">operator()</a> (const <a class="el" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> &left, const <a class="el" href="classOpenMS_1_1BaseFeature.html">BaseFeature</a> &right)</td></tr>
<tr class="memdesc:a63d485487b6a06e482529a1c8aedc5b5"><td class="mdescLeft"> </td><td class="mdescRight">Evaluation operator - checks constraints and computes the distance between two features. <a href="#a63d485487b6a06e482529a1c8aedc5b5">More...</a><br/></td></tr>
<tr class="separator:a63d485487b6a06e482529a1c8aedc5b5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-attribs"></a>
Static Public Attributes</h2></td></tr>
<tr class="memitem:ac2d2e8a0d437237b160e465808fdf20e"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a></td></tr>
<tr class="memdesc:ac2d2e8a0d437237b160e465808fdf20e"><td class="mdescLeft"> </td><td class="mdescRight">Value to return if max. difference is exceeded or if charge states don't match. <a href="#ac2d2e8a0d437237b160e465808fdf20e">More...</a><br/></td></tr>
<tr class="separator:ac2d2e8a0d437237b160e465808fdf20e"><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:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">Docu in base class. <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab7351868d7ff84a882b8c3cd14c6f601"><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_1FeatureDistance.html#ab7351868d7ff84a882b8c3cd14c6f601">distance_</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> diff, const <a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> &params) const </td></tr>
<tr class="memdesc:ab7351868d7ff84a882b8c3cd14c6f601"><td class="mdescLeft"> </td><td class="mdescRight">Computes a distance component given absolute difference and parameters. <a href="#ab7351868d7ff84a882b8c3cd14c6f601">More...</a><br/></td></tr>
<tr class="separator:ab7351868d7ff84a882b8c3cd14c6f601"><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:a3c454c044130ed7f7e5fe6c979d952af"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a3c454c044130ed7f7e5fe6c979d952af">params_rt_</a></td></tr>
<tr class="memdesc:a3c454c044130ed7f7e5fe6c979d952af"><td class="mdescLeft"> </td><td class="mdescRight">Storage of parameters for the individual distance components. <a href="#a3c454c044130ed7f7e5fe6c979d952af">More...</a><br/></td></tr>
<tr class="separator:a3c454c044130ed7f7e5fe6c979d952af"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9948c1e2a2d6bd3dd35744cc96ad255b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a9948c1e2a2d6bd3dd35744cc96ad255b">params_mz_</a></td></tr>
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<tr class="memitem:a8f146b0e2104c805a7a8ebf75e9def04"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a8f146b0e2104c805a7a8ebf75e9def04">params_intensity_</a></td></tr>
<tr class="separator:a8f146b0e2104c805a7a8ebf75e9def04"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a42bbf59694a9e5f5057c7229c3e5bc5e"><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_1FeatureDistance.html#a42bbf59694a9e5f5057c7229c3e5bc5e">total_weight_reciprocal_</a></td></tr>
<tr class="memdesc:a42bbf59694a9e5f5057c7229c3e5bc5e"><td class="mdescLeft"> </td><td class="mdescRight">Reciprocal value of the total weight in the distance function. <a href="#a42bbf59694a9e5f5057c7229c3e5bc5e">More...</a><br/></td></tr>
<tr class="separator:a42bbf59694a9e5f5057c7229c3e5bc5e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a247d330613019e713377dbdf503f78b7"><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_1FeatureDistance.html#a247d330613019e713377dbdf503f78b7">max_intensity_</a></td></tr>
<tr class="memdesc:a247d330613019e713377dbdf503f78b7"><td class="mdescLeft"> </td><td class="mdescRight">Maximum intensity of features (for normalization) <a href="#a247d330613019e713377dbdf503f78b7">More...</a><br/></td></tr>
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<tr class="memitem:ad08b3e80b01e59cb4986dba46f212234"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#ad08b3e80b01e59cb4986dba46f212234">ignore_charge_</a></td></tr>
<tr class="memdesc:ad08b3e80b01e59cb4986dba46f212234"><td class="mdescLeft"> </td><td class="mdescRight">Compute a distance even if charge states don't match? <a href="#ad08b3e80b01e59cb4986dba46f212234">More...</a><br/></td></tr>
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<tr class="memitem:a744a160e6b8a32a60e7ea7ed535421aa"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureDistance.html#a744a160e6b8a32a60e7ea7ed535421aa">force_constraints_</a></td></tr>
<tr class="memdesc:a744a160e6b8a32a60e7ea7ed535421aa"><td class="mdescLeft"> </td><td class="mdescRight">Always return <a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a> if "max. difference" constraints are not met? <a href="#a744a160e6b8a32a60e7ea7ed535421aa">More...</a><br/></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>
<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>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A functor class for the calculation of distances between features or consensus features. </p>
<p>It implements a customizable distance function of the following form:</p>
<p class="formulaDsp">
<img class="formulaDsp" alt="\[ w_{RT} \cdot \left( \frac{\left| RT_1 - RT_2 \right|}{\Delta RT_{max}} \right)^{p_{RT}} + w_{MZ} \cdot \left( \frac{\left| MZ_1 - MZ_2 \right|}{\Delta MZ_{max}} \right)^{p_{MZ}} + w_{int} \cdot \left( \frac{\left| int_1 - int_2 \right|}{int_{max}} \right)^{p_{int}} \]" src="form_0.png"/>
</p>
<p>This function returns a normalized distance between zero and one (unless constraints are violated, see below).</p>
<p><img class="formulaInl" alt="$ RT_i $" src="form_1.png"/>, <img class="formulaInl" alt="$ MZ_i $" src="form_2.png"/>, and <img class="formulaInl" alt="$ int_i $" src="form_3.png"/> are the RT, m/z, and intensity values of the respective feature.</p>
<p><img class="formulaInl" alt="$ {\Delta RT_{max}} $" src="form_4.png"/> and <img class="formulaInl" alt="$ {\Delta MZ_{max}} $" src="form_5.png"/> are the maximum allowed differences in RT and m/z, respectively. They are specified by the parameters <code>distance_RT:max_difference</code> and <code>distance_MZ:max_difference</code>, and are used for normalization. If an absolute difference exceeds the specified maximum, the behavior depends on the value used for <code>check_constraints</code> in the constructor: If "false", the distance will be computed normally, but may become greater than 1; if "true", the fixed value <a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a> is returned.</p>
<p><img class="formulaInl" alt="$ int_{max} $" src="form_6.png"/> is the maximum intensity that can occur for features compared by this distance function. It is not a parameter specified by the user, but depends on the data at hand and is thus set in the constructor (via parameter <code>max_intensity</code>).</p>
<p><img class="formulaInl" alt="$ w_X $" src="form_7.png"/> is the weight of distance component X, specified by the parameter <code>distance_X:weight</code>. The weights can be used to increase or decrease the contribution of RT, m/z, or intensity in the distance function. (Note that the default weight for the intensity component is zero, i.e. intensity is not considered by default.)</p>
<p><img class="formulaInl" alt="$ p_X $" src="form_8.png"/> is the exponent for distance component X, specified by the parameter <code>distance_X:exponent</code>. Normalized differences are taken to this power. This makes it possible to compare values using linear, quadratic, etc. distance.</p>
<p>By default, two features are only compared if they have the same charge state (or charge state 0 for "undefined") - otherwise, <a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a> is returned. This behavior can be changed by the <code>ignore_charge</code> parameter.</p>
<dl class="section note"><dt>Note</dt><dd>Peptide identifications annotated to features are not taken into account here, because they are stored in a format that is not suitable for rapid comparison.</dd></dl>
<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>
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<td style="vertical-align:top"><b>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>
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<td style="vertical-align:top"><b><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><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>
</tr>
<tr>
<td style="vertical-align:top"><i><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><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>
</tr>
<tr>
<td style="vertical-align:top"><b><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>
</tr>
<tr>
<td style="vertical-align:top"><i><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>
</tr>
<tr>
<td style="vertical-align:top"><i><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>
</tr>
<tr>
<td style="vertical-align:top"><i><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>
</tr>
<tr>
<td style="vertical-align:top"><i><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>
</tr>
</table>
<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_1FeatureDistance.html">FeatureDistance</a> </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>max_intensity</em> = <code>1.0</code>, </td>
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<td class="paramname"><em>force_constraints</em> = <code>false</code> </td>
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<p>Constructor. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">max_intensity</td><td>Maximum intensity of features (for normalization) </td></tr>
<tr><td class="paramname">force_constraints</td><td>Check "max. difference" constraints given in the parameters and return <a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a> if violated? </td></tr>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>Destructor. </p>
</div>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> distance_ </td>
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<td class="paramname"><em>diff</em>, </td>
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<td class="paramtype">const <a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> & </td>
<td class="paramname"><em>params</em> </td>
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<p>Computes a distance component given absolute difference and parameters. </p>
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<td class="memname">std::pair<bool, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> operator() </td>
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<p>Evaluation operator - checks constraints and computes the distance between two features. </p>
<dl class="section return"><dt>Returns</dt><dd>In the first element, whether constraints were satisfied; in the second element, the distance (<a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a> if constraints were violated and <a class="el" href="classOpenMS_1_1FeatureDistance.html#a744a160e6b8a32a60e7ea7ed535421aa">force_constraints_</a> is true). </dd></dl>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureDistance.html">FeatureDistance</a> & </td>
<td class="paramname"><em>other</em></td><td>)</td>
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<p>Assignment operator. </p>
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<td class="memname">void updateMembers_ </td>
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<p>Docu in base class. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname">bool force_constraints_</td>
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<p>Always return <a class="el" href="classOpenMS_1_1FeatureDistance.html#ac2d2e8a0d437237b160e465808fdf20e">infinity</a> if "max. difference" constraints are not met? </p>
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<td class="memname">bool ignore_charge_</td>
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<p>Compute a distance even if charge states don't match? </p>
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<td class="memname">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> infinity</td>
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<p>Value to return if max. difference is exceeded or if charge states don't match. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_intensity_</td>
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<p>Maximum intensity of features (for normalization) </p>
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<td class="memname"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> params_intensity_</td>
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<td class="memname"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> params_mz_</td>
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<td class="memname"><a class="el" href="structOpenMS_1_1FeatureDistance_1_1DistanceParams__.html">DistanceParams_</a> params_rt_</td>
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<p>Storage of parameters for the individual distance components. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> total_weight_reciprocal_</td>
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<p>Reciprocal value of the total weight in the distance function. </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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