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<HTML>
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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_1IDMapper.html">IDMapper</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">IDMapper Class Reference</div> </div>
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<div class="contents">
<p>Annotates an <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> or <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> with peptide identifications.
<a href="classOpenMS_1_1IDMapper.html#details">More...</a></p>
<p><code>#include <<a class="el" href="IDMapper_8h_source.html">OpenMS/ANALYSIS/ID/IDMapper.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for IDMapper:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1IDMapper.png" usemap="#IDMapper_map" alt=""/>
<map id="IDMapper_map" name="IDMapper_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"/>
</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:afb571f7e4181db2c9a40dd64f8dce6bb"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">Measure</a> { <a class="el" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bba67a1f968d5f74b3bf8e123eea735db42">MEASURE_PPM</a> = 0,
<a class="el" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bba717bca94a64af975ef0f6f34ee5eb71b">MEASURE_DA</a>
}</td></tr>
<tr class="separator:afb571f7e4181db2c9a40dd64f8dce6bb"><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:aa249defd5397a4ca31ff6e919652c525"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#aa249defd5397a4ca31ff6e919652c525">IDMapper</a> ()</td></tr>
<tr class="memdesc:aa249defd5397a4ca31ff6e919652c525"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#aa249defd5397a4ca31ff6e919652c525">More...</a><br/></td></tr>
<tr class="separator:aa249defd5397a4ca31ff6e919652c525"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba5f61aa9535c14db4de3f0bc6c402c8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#aba5f61aa9535c14db4de3f0bc6c402c8">IDMapper</a> (const <a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a> &cp)</td></tr>
<tr class="memdesc:aba5f61aa9535c14db4de3f0bc6c402c8"><td class="mdescLeft"> </td><td class="mdescRight">Copy C'Tor. <a href="#aba5f61aa9535c14db4de3f0bc6c402c8">More...</a><br/></td></tr>
<tr class="separator:aba5f61aa9535c14db4de3f0bc6c402c8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a69e825f2611162c4a21980ca072aada5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a69e825f2611162c4a21980ca072aada5">operator=</a> (const <a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a> &rhs)</td></tr>
<tr class="memdesc:a69e825f2611162c4a21980ca072aada5"><td class="mdescLeft"> </td><td class="mdescRight">Assignment. <a href="#a69e825f2611162c4a21980ca072aada5">More...</a><br/></td></tr>
<tr class="separator:a69e825f2611162c4a21980ca072aada5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad8c436deda857f332e4d843d002e0717"><td class="memTemplParams" colspan="2">template<typename PeakType > </td></tr>
<tr class="memitem:ad8c436deda857f332e4d843d002e0717"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#ad8c436deda857f332e4d843d002e0717">annotate</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &map, const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids, const std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &protein_ids)</td></tr>
<tr class="memdesc:ad8c436deda857f332e4d843d002e0717"><td class="mdescLeft"> </td><td class="mdescRight">Mapping method for peak maps. <a href="#ad8c436deda857f332e4d843d002e0717">More...</a><br/></td></tr>
<tr class="separator:ad8c436deda857f332e4d843d002e0717"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8422c24016b4c5c9c358395cd307802d"><td class="memTemplParams" colspan="2">template<typename FeatureType > </td></tr>
<tr class="memitem:a8422c24016b4c5c9c358395cd307802d"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a8422c24016b4c5c9c358395cd307802d">annotate</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > &map, const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids, const std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false)</td></tr>
<tr class="memdesc:a8422c24016b4c5c9c358395cd307802d"><td class="mdescLeft"> </td><td class="mdescRight">Mapping method for feature maps. <a href="#a8422c24016b4c5c9c358395cd307802d">More...</a><br/></td></tr>
<tr class="separator:a8422c24016b4c5c9c358395cd307802d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac9d8f90a40a4e4ec544df79709a4ee51"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#ac9d8f90a40a4e4ec544df79709a4ee51">annotate</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &map, const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids, const std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &protein_ids, bool measure_from_subelements=false)</td></tr>
<tr class="memdesc:ac9d8f90a40a4e4ec544df79709a4ee51"><td class="mdescLeft"> </td><td class="mdescRight">Mapping method for consensus maps. <a href="#ac9d8f90a40a4e4ec544df79709a4ee51">More...</a><br/></td></tr>
<tr class="separator:ac9d8f90a40a4e4ec544df79709a4ee51"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-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_1IDMapper.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><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="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aca0a98d0a3600c175d4a0a36f14b1802"><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_1IDMapper.html#aca0a98d0a3600c175d4a0a36f14b1802">getAbsoluteMZTolerance_</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz) const </td></tr>
<tr class="separator:aca0a98d0a3600c175d4a0a36f14b1802"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8d416b4b6a5fa91fac9d4834ae02eb4a"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a8d416b4b6a5fa91fac9d4834ae02eb4a">isMatch_</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> rt_distance, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz_theoretical, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz_observed) const </td></tr>
<tr class="memdesc:a8d416b4b6a5fa91fac9d4834ae02eb4a"><td class="mdescLeft"> </td><td class="mdescRight">check if distance constraint is fulfilled (using <code>rt_tolerance_</code>, <code>mz_tolerance_</code> and <code>measure_</code>) <a href="#a8d416b4b6a5fa91fac9d4834ae02eb4a">More...</a><br/></td></tr>
<tr class="separator:a8d416b4b6a5fa91fac9d4834ae02eb4a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8295835c054b639df085f1eac7dcae26"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a8295835c054b639df085f1eac7dcae26">checkHits_</a> (const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids) const </td></tr>
<tr class="memdesc:a8295835c054b639df085f1eac7dcae26"><td class="mdescLeft"> </td><td class="mdescRight">helper function that checks if all peptide hits are annotated with RT and MZ meta values <a href="#a8295835c054b639df085f1eac7dcae26">More...</a><br/></td></tr>
<tr class="separator:a8295835c054b639df085f1eac7dcae26"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae03e7ce5f8e570c74af27cdfbe88d63d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#ae03e7ce5f8e570c74af27cdfbe88d63d">getIDDetails_</a> (const <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &id, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &rt_pep, <a class="el" href="classOpenMS_1_1DoubleList.html">DoubleList</a> &mz_values, <a class="el" href="classOpenMS_1_1IntList.html">IntList</a> &charges, bool use_avg_mass=false) const </td></tr>
<tr class="separator:ae03e7ce5f8e570c74af27cdfbe88d63d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2402977138ef4c565818163516b4bfe2"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a2402977138ef4c565818163516b4bfe2">increaseBoundingBox_</a> (<a class="el" href="classOpenMS_1_1DBoundingBox.html">DBoundingBox</a>< 2 > &box)</td></tr>
<tr class="memdesc:a2402977138ef4c565818163516b4bfe2"><td class="mdescLeft"> </td><td class="mdescRight">increase a bounding box by the given RT and m/z tolerances <a href="#a2402977138ef4c565818163516b4bfe2">More...</a><br/></td></tr>
<tr class="separator:a2402977138ef4c565818163516b4bfe2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a601aa4a522119339bb02264698bd589e"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a601aa4a522119339bb02264698bd589e">checkMassType_</a> (const std::vector< <a class="el" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a> > &processing) const </td></tr>
<tr class="separator:a601aa4a522119339bb02264698bd589e"><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:a73f60e6ff36e6b7fd8f631003521843c"><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_1IDMapper.html#a73f60e6ff36e6b7fd8f631003521843c">rt_tolerance_</a></td></tr>
<tr class="memdesc:a73f60e6ff36e6b7fd8f631003521843c"><td class="mdescLeft"> </td><td class="mdescRight">Allowed RT deviation. <a href="#a73f60e6ff36e6b7fd8f631003521843c">More...</a><br/></td></tr>
<tr class="separator:a73f60e6ff36e6b7fd8f631003521843c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa0d44a6be23374eb5d1f099ef8b4ca82"><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_1IDMapper.html#aa0d44a6be23374eb5d1f099ef8b4ca82">mz_tolerance_</a></td></tr>
<tr class="memdesc:aa0d44a6be23374eb5d1f099ef8b4ca82"><td class="mdescLeft"> </td><td class="mdescRight">Allowed m/z deviation. <a href="#aa0d44a6be23374eb5d1f099ef8b4ca82">More...</a><br/></td></tr>
<tr class="separator:aa0d44a6be23374eb5d1f099ef8b4ca82"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1324e22761bf35562937e88a4a58d8b5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">Measure</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#a1324e22761bf35562937e88a4a58d8b5">measure_</a></td></tr>
<tr class="memdesc:a1324e22761bf35562937e88a4a58d8b5"><td class="mdescLeft"> </td><td class="mdescRight">Measure used for m/z. <a href="#a1324e22761bf35562937e88a4a58d8b5">More...</a><br/></td></tr>
<tr class="separator:a1324e22761bf35562937e88a4a58d8b5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad08b3e80b01e59cb4986dba46f212234"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IDMapper.html#ad08b3e80b01e59cb4986dba46f212234">ignore_charge_</a></td></tr>
<tr class="memdesc:ad08b3e80b01e59cb4986dba46f212234"><td class="mdescLeft"> </td><td class="mdescRight">Ignore charge states during matching? <a href="#ad08b3e80b01e59cb4986dba46f212234">More...</a><br/></td></tr>
<tr class="separator:ad08b3e80b01e59cb4986dba46f212234"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Annotates an <a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> or <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> with peptide identifications. </p>
<p>ProteinIdentifications are assigned to the whole map.</p>
<p>The retention time and mass-to-charge ratio of the <a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> have to be given in the <a class="el" href="classOpenMS_1_1MetaInfoInterface.html" title="Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). ">MetaInfoInterface</a> as the values "MZ" and "RT".</p>
<p>m/z-matching on peptide side can be done either with the precursor m/z value of the peptide identification or with the theoretical masses of the peptide hits (see "mz_reference" parameter).</p>
<p>See the documentation of the individual <code>annotate</code> methods for more in-depth information.</p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><b>rt_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">RT tolerance (in seconds) for the matching</td>
</tr>
<tr>
<td style="vertical-align:top"><b>mz_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">20</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">m/z tolerance (in ppm or Da) for the matching</td>
</tr>
<tr>
<td style="vertical-align:top"><b>mz_measure</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">ppm</td>
<td style="vertical-align:top">ppm, Da</td><td style="vertical-align:top">unit of 'mz_tolerance' (ppm or Da)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>mz_reference</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">precursor</td>
<td style="vertical-align:top">precursor, peptide</td><td style="vertical-align:top">source of m/z values for peptide identifications</td>
</tr>
<tr>
<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">For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.</td>
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<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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<td class="memname">enum <a class="el" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">Measure</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="afb571f7e4181db2c9a40dd64f8dce6bba67a1f968d5f74b3bf8e123eea735db42"></a>MEASURE_PPM</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="afb571f7e4181db2c9a40dd64f8dce6bba717bca94a64af975ef0f6f34ee5eb71b"></a>MEASURE_DA</em> </td><td class="fielddoc">
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a> </td>
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<p>Default constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a> & </td>
<td class="paramname"><em>cp</em></td><td>)</td>
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<p>Copy C'Tor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void annotate </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
<td class="paramname"><em>map</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
<td class="paramname"><em>ids</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > & </td>
<td class="paramname"><em>protein_ids</em> </td>
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<p>Mapping method for peak maps. </p>
<p>The identifications stored in a <a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> instance can be added to the corresponding spectrum.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">map</td><td><a class="el" href="classOpenMS_1_1MSExperiment.html" title="Representation of a mass spectrometry experiment. ">MSExperiment</a> to receive the identifications </td></tr>
<tr><td class="paramname">ids</td><td><a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> for the ConsensusFeatures </td></tr>
<tr><td class="paramname">protein_ids</td><td><a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> for the <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a></td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1MissingInformation.html" title="Not all required information provided. ">Exception::MissingInformation</a></td><td>is thrown if the <a class="el" href="classOpenMS_1_1MetaInfoInterface.html" title="Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). ">MetaInfoInterface</a> of <code>ids</code> does not contain 'MZ' and 'RT'. </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1ExperimentalSettings.html#acef58bf2531b77d0191c4780739281c6">ExperimentalSettings::getProteinIdentifications()</a>, <a class="el" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TOPPViewBase.html#a998e79e7149ca4ef1ca8fa1625ffa250">TOPPViewBase::annotateWithID()</a>.</p>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
<td class="paramname"><em>ids</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > & </td>
<td class="paramname"><em>protein_ids</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>use_centroid_rt</em> = <code>false</code>, </td>
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<td class="paramname"><em>use_centroid_mz</em> = <code>false</code> </td>
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<p>Mapping method for feature maps. </p>
<p>If <em>all</em> features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if <code>use_centroid_rt</code> or <code>use_centroid_mz</code> are true.</p>
<p>In any case, tolerance in RT and m/z dimension is applied according to the global parameters <code>rt_tolerance</code> and <code>mz_tolerance</code>. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value.</p>
<p>If several features (incl. tolerance) overlap the position of a peptide identification, the identification is annotated to all of them.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">map</td><td><a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> to receive the identifications </td></tr>
<tr><td class="paramname">ids</td><td><a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> for the ConsensusFeatures </td></tr>
<tr><td class="paramname">protein_ids</td><td><a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> for the <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> </td></tr>
<tr><td class="paramname">use_centroid_rt</td><td>Whether to use the RT value of feature centroids even if convex hulls are present </td></tr>
<tr><td class="paramname">use_centroid_mz</td><td>Whether to use the m/z value of feature centroids even if convex hulls are present</td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1MissingInformation.html" title="Not all required information provided. ">Exception::MissingInformation</a></td><td>is thrown if the <a class="el" href="classOpenMS_1_1MetaInfoInterface.html" title="Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). ">MetaInfoInterface</a> of <code>ids</code> does not contain "MZ" and "RT" </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1IntList.html#ac2d1b0c3af7939b2b7d5e74607166d9c">IntList::contains()</a>, <a class="el" href="classOpenMS_1_1DBoundingBox.html#ac55b302033b5b9d7c78a223db8cfaffb">DBoundingBox< D >::encloses()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a4f40a3d8606e7855a7b3c12620bf9f58">FeatureMap< FeatureT >::getAnnotationStatistics()</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">BaseFeature::getCharge()</a>, <a class="el" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">Feature::getConvexHulls()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#ae131ea2ec923582f86aa9805e72241ad">FeatureMap< FeatureT >::getDataProcessing()</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#a9f20adb44d57c28c422619779488de17">BaseFeature::getPeptideIdentifications()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#acef58bf2531b77d0191c4780739281c6">FeatureMap< FeatureT >::getProteinIdentifications()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#ab4e0f356f837ce58e57695da114adce3">Peak2D::getRT()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a001ea2eb2a9c05266a69f50594f25604">FeatureMap< FeatureT >::getUnassignedPeptideIdentifications()</a>, <a class="el" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a>, <a class="el" href="LogStream_8h.html#aea3f57d6dcc5b4ac957e2679e87dde27">LOG_WARN</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">DIntervalBase< D >::maxPosition()</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">DIntervalBase< D >::minPosition()</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#adcf69cae2f91d868b8defd2b12aad4ed">DIntervalBase< D >::setMaxX()</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a71b4e57973d9ad60975b774f4eeaef06">DIntervalBase< D >::setMaxY()</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a9f4dd5aa564dcc541a0d5a271e22e6a0">DIntervalBase< D >::setMinX()</a>, and <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a3faa28974e310e9743446f1c184496a6">DIntervalBase< D >::setMinY()</a>.</p>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td>
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<p>Mapping method for consensus maps. </p>
<p>If several consensus features lie inside the allowed deviation, the peptide identifications are mapped to all the consensus features.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">map</td><td><a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> to receive the identifications </td></tr>
<tr><td class="paramname">ids</td><td><a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> for the ConsensusFeatures </td></tr>
<tr><td class="paramname">protein_ids</td><td><a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> for the <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> </td></tr>
<tr><td class="paramname">measure_from_subelements</td><td>Do distance estimate from FeatureHandles instead of Centroid</td></tr>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1MissingInformation.html" title="Not all required information provided. ">Exception::MissingInformation</a></td><td>is thrown if the <a class="el" href="classOpenMS_1_1MetaInfoInterface.html" title="Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). ">MetaInfoInterface</a> of <code>ids</code> does not contain 'MZ' and 'RT' </td></tr>
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<td class="memname">void checkHits_ </td>
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<p>helper function that checks if all peptide hits are annotated with RT and MZ meta values </p>
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<td class="paramname"><em>processing</em></td><td>)</td>
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<p>try to determine the type of m/z value reported for features, return whether average peptide masses should be used for matching </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getAbsoluteMZTolerance_ </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<p>compute absolute Da tolerance, for a given m/z, when <code>measure</code> is MEASURE_DA, the value is unchanged, for MEASURE_PPM it is computed according to currently allowed ppm tolerance </p>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> & </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1DoubleList.html">DoubleList</a> & </td>
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<p>get RT, m/z and charge value(s) of a <a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a></p>
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<li>multiple m/z values are returned if "mz_reference" is set to "peptide" (one for each <a class="el" href="classOpenMS_1_1PeptideHit.html" title="Representation of a peptide hit. ">PeptideHit</a>)</li>
<li>one m/z value is returned if "mz_reference" is set to "precursor" </li>
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<td class="memname">void increaseBoundingBox_ </td>
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<p>increase a bounding box by the given RT and m/z tolerances </p>
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<td class="paramname"><em>rt_distance</em>, </td>
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<td class="paramname"><em>mz_theoretical</em>, </td>
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<td class="paramname"><em>mz_observed</em> </td>
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<p>check if distance constraint is fulfilled (using <code>rt_tolerance_</code>, <code>mz_tolerance_</code> and <code>measure_</code>) </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1IDMapper.html">IDMapper</a>& operator= </td>
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<p>Assignment. </p>
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<p>This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. </p>
<p>Also call it at the end of the derived classes' copy constructor and assignment operator.</p>
<p>The default implementation is empty. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<p>Ignore charge states during matching? </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1IDMapper.html#afb571f7e4181db2c9a40dd64f8dce6bb">Measure</a> measure_</td>
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<p>Measure used for m/z. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz_tolerance_</td>
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<p>Allowed m/z deviation. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> rt_tolerance_</td>
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<p>Allowed RT deviation. </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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