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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_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">MapAlignmentEvaluationAlgorithm Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span></div> </div>
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<p>Base class for all Caap evaluation algorithms.
<a href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#details">More...</a></p>
<p><code>#include <<a class="el" href="MapAlignmentEvaluationAlgorithm_8h_source.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentEvaluationAlgorithm.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for MapAlignmentEvaluationAlgorithm:</div>
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<img src="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.png" usemap="#MapAlignmentEvaluationAlgorithm_map" alt=""/>
<map id="MapAlignmentEvaluationAlgorithm_map" name="MapAlignmentEvaluationAlgorithm_map">
<area href="classOpenMS_1_1MapAlignmentEvaluationAlgorithmPrecision.html" title="Caap evaluation algorithm to obtain a precision value. " alt="MapAlignmentEvaluationAlgorithmPrecision" shape="rect" coords="0,56,257,80"/>
<area href="classOpenMS_1_1MapAlignmentEvaluationAlgorithmRecall.html" title="Caap evaluation algorithm to obtain a recall value. " alt="MapAlignmentEvaluationAlgorithmRecall" shape="rect" coords="267,56,524,80"/>
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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:a3ff45d7c5953b4f1950d17639e9534ab"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#a3ff45d7c5953b4f1950d17639e9534ab">MapAlignmentEvaluationAlgorithm</a> ()</td></tr>
<tr class="memdesc:a3ff45d7c5953b4f1950d17639e9534ab"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a3ff45d7c5953b4f1950d17639e9534ab">More...</a><br/></td></tr>
<tr class="separator:a3ff45d7c5953b4f1950d17639e9534ab"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac5c6c9fde1ece5542135447846268c90"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#ac5c6c9fde1ece5542135447846268c90">~MapAlignmentEvaluationAlgorithm</a> ()</td></tr>
<tr class="memdesc:ac5c6c9fde1ece5542135447846268c90"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#ac5c6c9fde1ece5542135447846268c90">More...</a><br/></td></tr>
<tr class="separator:ac5c6c9fde1ece5542135447846268c90"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a242e005f981c9992d9d8852cf7b7f09f"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#a242e005f981c9992d9d8852cf7b7f09f">evaluate</a> (const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &conensus_map_in, const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map_gt, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &rt_dev, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &mz_dev, const <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> &int_dev, const bool use_charge, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &out)=0</td></tr>
<tr class="memdesc:a242e005f981c9992d9d8852cf7b7f09f"><td class="mdescLeft"> </td><td class="mdescRight">Applies the algorithm. The input consensus map is compared to the ground truth. <a href="#a242e005f981c9992d9d8852cf7b7f09f">More...</a><br/></td></tr>
<tr class="separator:a242e005f981c9992d9d8852cf7b7f09f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6e8c3ab60723fffb3f65998d0c14a44"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#ae6e8c3ab60723fffb3f65998d0c14a44">isSameHandle</a> (const <a class="el" href="classOpenMS_1_1FeatureHandle.html">FeatureHandle</a> &lhs, const <a class="el" href="classOpenMS_1_1FeatureHandle.html">FeatureHandle</a> &rhs, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &rt_dev, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &mz_dev, const <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> &int_dev, const bool use_charge)</td></tr>
<tr class="memdesc:ae6e8c3ab60723fffb3f65998d0c14a44"><td class="mdescLeft"> </td><td class="mdescRight">Decides if two features are the same, based on maximum allowed deviations for retention time, m/z and intensity. <a href="#ae6e8c3ab60723fffb3f65998d0c14a44">More...</a><br/></td></tr>
<tr class="separator:ae6e8c3ab60723fffb3f65998d0c14a44"><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:a7899dbe105534dc1f81971dd71a26ff0"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0"><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"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-types"></a>
Protected Types</h2></td></tr>
<tr class="memitem:a2c233ffe5523da73c521648a3b57d0e4"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
ConsensusFeature::HandleSetType::const_iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#a2c233ffe5523da73c521648a3b57d0e4">HandleIterator</a></td></tr>
<tr class="separator:a2c233ffe5523da73c521648a3b57d0e4"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a2db5a06cbcbd76bdb98e60d24012cbb9"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#a2db5a06cbcbd76bdb98e60d24012cbb9">MapAlignmentEvaluationAlgorithm</a> (const <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> &)</td></tr>
<tr class="memdesc:a2db5a06cbcbd76bdb98e60d24012cbb9"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor is not implemented -> private. <a href="#a2db5a06cbcbd76bdb98e60d24012cbb9">More...</a><br/></td></tr>
<tr class="separator:a2db5a06cbcbd76bdb98e60d24012cbb9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac2d26e1911341a6d63dfa00b0204242a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#ac2d26e1911341a6d63dfa00b0204242a">operator=</a> (const <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> &)</td></tr>
<tr class="memdesc:ac2d26e1911341a6d63dfa00b0204242a"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator is not implemented -> private. <a href="#ac2d26e1911341a6d63dfa00b0204242a">More...</a><br/></td></tr>
<tr class="separator:ac2d26e1911341a6d63dfa00b0204242a"><td class="memSeparator" colspan="2"> </td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Base class for all Caap evaluation algorithms. </p>
<p>These algorithms evaluates alignment results against a ground truth. </p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef ConsensusFeature::HandleSetType::const_iterator <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html#a2c233ffe5523da73c521648a3b57d0e4">HandleIterator</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
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<p>Default constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> & </td>
<td class="paramname"></td><td>)</td>
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<p>Copy constructor is not implemented -> private. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">virtual void evaluate </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td>
<td class="paramname"><em>conensus_map_in</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td>
<td class="paramname"><em>consensus_map_gt</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
<td class="paramname"><em>rt_dev</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
<td class="paramname"><em>mz_dev</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> & </td>
<td class="paramname"><em>int_dev</em>, </td>
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<td class="paramtype">const bool </td>
<td class="paramname"><em>use_charge</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
<td class="paramname"><em>out</em> </td>
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<td>)</td>
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<p>Applies the algorithm. The input consensus map is compared to the ground truth. </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithmPrecision.html#a04f0dd3d4175f3f37413fddefa3315f1">MapAlignmentEvaluationAlgorithmPrecision</a>, and <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithmRecall.html#a04f0dd3d4175f3f37413fddefa3315f1">MapAlignmentEvaluationAlgorithmRecall</a>.</p>
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<td class="memname">bool isSameHandle </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureHandle.html">FeatureHandle</a> & </td>
<td class="paramname"><em>lhs</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureHandle.html">FeatureHandle</a> & </td>
<td class="paramname"><em>rhs</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
<td class="paramname"><em>rt_dev</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
<td class="paramname"><em>mz_dev</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> & </td>
<td class="paramname"><em>int_dev</em>, </td>
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<td class="paramtype">const bool </td>
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<p>Decides if two features are the same, based on maximum allowed deviations for retention time, m/z and intensity. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MapAlignmentEvaluationAlgorithm.html">MapAlignmentEvaluationAlgorithm</a> & </td>
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<p>Assignment operator is not implemented -> private. </p>
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<td class="memname">static void registerChildren </td>
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<p>Register all derived classes in this method. </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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