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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_1ConsensusID.html">ConsensusID</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">ConsensusID Class Reference<div class="ingroups"><a class="el" href="group__Analysis__ID.html">Identification</a></div></div> </div>
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<div class="contents">
<p>Calculates a consensus ID from several ID runs.
<a href="classOpenMS_1_1ConsensusID.html#details">More...</a></p>
<p><code>#include <<a class="el" href="ConsensusID_8h_source.html">OpenMS/ANALYSIS/ID/ConsensusID.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for ConsensusID:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1ConsensusID.png" usemap="#ConsensusID_map" alt=""/>
<map id="ConsensusID_map" name="ConsensusID_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-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a2acada526be7b20cded75fbfa9145652"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a2acada526be7b20cded75fbfa9145652">ConsensusID</a> ()</td></tr>
<tr class="memdesc:a2acada526be7b20cded75fbfa9145652"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a2acada526be7b20cded75fbfa9145652">More...</a><br/></td></tr>
<tr class="separator:a2acada526be7b20cded75fbfa9145652"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b649f6bc70f3ef02d434996dd003e4a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a6b649f6bc70f3ef02d434996dd003e4a">apply</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:a6b649f6bc70f3ef02d434996dd003e4a"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the consensus ID for a set of <a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> instances of the same spectrum. <a href="#a6b649f6bc70f3ef02d434996dd003e4a">More...</a><br/></td></tr>
<tr class="separator:a6b649f6bc70f3ef02d434996dd003e4a"><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="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:ad81de9340a4eecf954b0b0ccbde00cae"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#ad81de9340a4eecf954b0b0ccbde00cae">ConsensusID</a> (const <a class="el" href="classOpenMS_1_1ConsensusID.html">ConsensusID</a> &)</td></tr>
<tr class="memdesc:ad81de9340a4eecf954b0b0ccbde00cae"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#ad81de9340a4eecf954b0b0ccbde00cae">More...</a><br/></td></tr>
<tr class="separator:ad81de9340a4eecf954b0b0ccbde00cae"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4cb9a059f4793e46d8c883e6177389e6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ConsensusID.html">ConsensusID</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a4cb9a059f4793e46d8c883e6177389e6">operator=</a> (const <a class="el" href="classOpenMS_1_1ConsensusID.html">ConsensusID</a> &)</td></tr>
<tr class="memdesc:a4cb9a059f4793e46d8c883e6177389e6"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#a4cb9a059f4793e46d8c883e6177389e6">More...</a><br/></td></tr>
<tr class="separator:a4cb9a059f4793e46d8c883e6177389e6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2ed2c84a38290b3b6409617a38cc2019"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a2ed2c84a38290b3b6409617a38cc2019">ranked_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:a2ed2c84a38290b3b6409617a38cc2019"><td class="mdescLeft"> </td><td class="mdescRight">Ranked algorithm. <a href="#a2ed2c84a38290b3b6409617a38cc2019">More...</a><br/></td></tr>
<tr class="separator:a2ed2c84a38290b3b6409617a38cc2019"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2bf744ef812266898863602b219b5565"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a2bf744ef812266898863602b219b5565">average_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:a2bf744ef812266898863602b219b5565"><td class="mdescLeft"> </td><td class="mdescRight">Average score algorithm. <a href="#a2bf744ef812266898863602b219b5565">More...</a><br/></td></tr>
<tr class="separator:a2bf744ef812266898863602b219b5565"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aac4b39d45a36f45b645f437a384cc9a3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#aac4b39d45a36f45b645f437a384cc9a3">PEPMatrix_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:aac4b39d45a36f45b645f437a384cc9a3"><td class="mdescLeft"> </td><td class="mdescRight">PEP and scoring matrix based algorithm. <a href="#aac4b39d45a36f45b645f437a384cc9a3">More...</a><br/></td></tr>
<tr class="separator:aac4b39d45a36f45b645f437a384cc9a3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8c51221e0ca66a208e5defb9a5e210e9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a8c51221e0ca66a208e5defb9a5e210e9">PEPIons_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:a8c51221e0ca66a208e5defb9a5e210e9"><td class="mdescLeft"> </td><td class="mdescRight">PEP and ion similarity based algorithm. <a href="#a8c51221e0ca66a208e5defb9a5e210e9">More...</a><br/></td></tr>
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<tr class="memitem:a6d67b03d590d4e41c0edbc7782090f06"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a6d67b03d590d4e41c0edbc7782090f06">Minimum_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:a6d67b03d590d4e41c0edbc7782090f06"><td class="mdescLeft"> </td><td class="mdescRight">use minimal PEP score <a href="#a6d67b03d590d4e41c0edbc7782090f06">More...</a><br/></td></tr>
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<tr class="memitem:a4648aae671dd1ed82f9bb41d7cf2350f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ConsensusID.html#a4648aae671dd1ed82f9bb41d7cf2350f">mapIdentifications_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &sorted_ids, const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids)</td></tr>
<tr class="memdesc:a4648aae671dd1ed82f9bb41d7cf2350f"><td class="mdescLeft"> </td><td class="mdescRight">Merge peptide hits from different engines. <a href="#a4648aae671dd1ed82f9bb41d7cf2350f">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></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:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
<tr class="separator:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </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>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
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<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<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>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Calculates a consensus ID from several ID runs. </p>
<p>This class combines several ID runs using one of several, available algorithms.</p>
<B>Parameters of this class are:</B><BR><BR>
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<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>algorithm</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">PEPMatrix</td>
<td style="vertical-align:top">ranked, average, PEPMatrix, PEPIons, Minimum</td><td style="vertical-align:top">Algorithm used for the consensus scoring.<BR>ranked -- reorders the hits according to a consensus score computed from the ranks in the input runs. The score is normalized to the interval (0,100). The PeptideIdentifications do not need to have the same score type.<BR>average -- reorders the hits according to the average score of the input runs. Make sure to use PeptideIdentifications with the same score type only!<BR>PEPMatrix -- calculates a consensus score based on posterior error probabilities and scoring matrices for siimilarity. This algorithm uses the PAM30MS matrix to score sequences not listed by all engines. Make sure to use PeptideIdentifications with score types converted to PEPs only!<BR>PEPIons -- calculates a consensus score based on posterior error probabilities and fragment ion siimilarity. Make sure to use PeptideIdentifications with score types converted to PEPs only!<BR>Minimum -- calculates a consensus score based on the minimal score. Make sure to use PeptideIdentifications with score types converted to PEPs only!<BR></td>
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<td style="vertical-align:top"><b>considered_hits</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">The number of top hits that are used for the consensus scoring.</td>
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<td style="vertical-align:top"><b>number_of_runs</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The number of runs used as input. This information is used in 'Ranked' and 'Average' to compute the new scores. If not given, the number of input identifications is taken.</td>
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<td style="vertical-align:top"><b>PEPIons:MinNumberOfFragments</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The minimal number of similar (between two suggested sequences) fragment ion masses that is necessary to evaluate the shared peak count similarity (SPC).</td>
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<td style="vertical-align:top"><b>PEPIons:common</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1.1</td>
<td style="vertical-align:top">min: 0 max: 1.1</td><td style="vertical-align:top">Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -> pep 1 with score x1 and engine2 -> pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 >= common, Note that 0 <= degree of similarity <= 1. Values > 1 will disable this option.</td>
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<td style="vertical-align:top"><b>PEPMatrix:common</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1.1</td>
<td style="vertical-align:top">min: 0 max: 1.1</td><td style="vertical-align:top">Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -> pep 1 with score x1 and engine2 -> pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 >= common, Note that 0 <= degree of similarity <= 1. Values > 1 will disable this option.</td>
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<td style="vertical-align:top"><b>PEPMatrix:penalty</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Give the gap penalty (the same penalty will be used for opening and extension) as a positive integer</td>
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<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ConsensusID.html">ConsensusID</a> </td>
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<p>Default constructor. </p>
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<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusID.html">ConsensusID</a> & </td>
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<p>Not implemented. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void apply </td>
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<td class="paramname"><em>ids</em></td><td>)</td>
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<p>Calculates the consensus ID for a set of <a class="el" href="classOpenMS_1_1PeptideIdentification.html" title="Represents the peptide hits for a spectrum. ">PeptideIdentification</a> instances of the same spectrum. </p>
<dl class="section note"><dt>Note</dt><dd>Make sure that the score orientation (<a class="el" href="classOpenMS_1_1PeptideIdentification.html#a7ae34a5d293424fbf091a3fa7218ccfb" title="returns the peptide score orientation ">PeptideIdentification::isHigherScoreBetter()</a>)is set properly! </dd></dl>
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<td class="memname">void average_ </td>
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<td class="paramname"><em>ids</em></td><td>)</td>
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<p>Average score algorithm. </p>
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<td class="paramname"><em>sorted_ids</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<p>Merge peptide hits from different engines. </p>
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<td class="memname">void Minimum_ </td>
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<td class="paramname"><em>ids</em></td><td>)</td>
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<p>use minimal PEP score </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ConsensusID.html">ConsensusID</a>& operator= </td>
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<p>Not implemented. </p>
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<td class="paramname"><em>ids</em></td><td>)</td>
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<p>PEP and ion similarity based algorithm. </p>
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<p>PEP and scoring matrix based algorithm. </p>
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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<p>Ranked algorithm. </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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