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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_1PeptideAndProteinQuant.html">PeptideAndProteinQuant</a></li> </ul>
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<a href="#pub-types">Public Types</a> |
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<div class="title">PeptideAndProteinQuant Class Reference</div> </div>
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<p>Helper class for peptide and protein quantification based on feature data annotated with IDs.
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<a href="classOpenMS_1_1PeptideAndProteinQuant.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="PeptideAndProteinQuant_8h_source.html">OpenMS/ANALYSIS/QUANTITATION/PeptideAndProteinQuant.h</a>></code></p>
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<div class="dynheader">
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Inheritance diagram for PeptideAndProteinQuant:</div>
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<div class="dyncontent">
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<img src="classOpenMS_1_1PeptideAndProteinQuant.png" usemap="#PeptideAndProteinQuant_map" alt=""/>
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<map id="PeptideAndProteinQuant_map" name="PeptideAndProteinQuant_map">
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<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,151,24"/>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
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Classes</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html">PeptideData</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Quantitative and associated data for a peptide. <a href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html#details">More...</a><br/></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html">ProteinData</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Quantitative and associated data for a protein. <a href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html#details">More...</a><br/></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a></td></tr>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html" title="Statistics for processing summary. ">Statistics</a> for processing summary. <a href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html#details">More...</a><br/></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
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Public Types</h2></td></tr>
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<tr class="memitem:a5242f4ede25f6f7f0ec9f634244c78d6"><td class="memItemLeft" align="right" valign="top">typedef std::map< <a class="el" href="group__Concept.html#ga5162db95dc78bdf2e3a71d73bec703e9">UInt64</a>, <br class="typebreak"/>
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<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a></td></tr>
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<tr class="memdesc:a5242f4ede25f6f7f0ec9f634244c78d6"><td class="mdescLeft"> </td><td class="mdescRight">Mapping: sample ID -> abundance. <a href="#a5242f4ede25f6f7f0ec9f634244c78d6">More...</a><br/></td></tr>
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<tr class="separator:a5242f4ede25f6f7f0ec9f634244c78d6"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2750aa75b50972d89e20d01214ff1c01"><td class="memItemLeft" align="right" valign="top">typedef std::map< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a>, <br class="typebreak"/>
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<a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html">PeptideData</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a></td></tr>
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<tr class="memdesc:a2750aa75b50972d89e20d01214ff1c01"><td class="mdescLeft"> </td><td class="mdescRight">Mapping: peptide sequence (modified) -> peptide data. <a href="#a2750aa75b50972d89e20d01214ff1c01">More...</a><br/></td></tr>
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<tr class="separator:a2750aa75b50972d89e20d01214ff1c01"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a38f6c1fb46b4457f1fcde70b207f0cea"><td class="memItemLeft" align="right" valign="top">typedef std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <br class="typebreak"/>
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<a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html">ProteinData</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a></td></tr>
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<tr class="memdesc:a38f6c1fb46b4457f1fcde70b207f0cea"><td class="mdescLeft"> </td><td class="mdescRight">Mapping: protein accession -> protein data. <a href="#a38f6c1fb46b4457f1fcde70b207f0cea">More...</a><br/></td></tr>
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<tr class="separator:a38f6c1fb46b4457f1fcde70b207f0cea"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr class="memitem:af79b41ec5d82b1edafc0bef0366d386d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#af79b41ec5d82b1edafc0bef0366d386d">PeptideAndProteinQuant</a> ()</td></tr>
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<tr class="memdesc:af79b41ec5d82b1edafc0bef0366d386d"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#af79b41ec5d82b1edafc0bef0366d386d">More...</a><br/></td></tr>
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<tr class="separator:af79b41ec5d82b1edafc0bef0366d386d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:acc999d51d6f370ed969d0c89a65884b8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#acc999d51d6f370ed969d0c89a65884b8">~PeptideAndProteinQuant</a> ()</td></tr>
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<tr class="memdesc:acc999d51d6f370ed969d0c89a65884b8"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#acc999d51d6f370ed969d0c89a65884b8">More...</a><br/></td></tr>
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<tr class="separator:acc999d51d6f370ed969d0c89a65884b8"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a15012f9212859265c1d082c5f0fca7f0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a15012f9212859265c1d082c5f0fca7f0">quantifyPeptides</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &features)</td></tr>
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<tr class="memdesc:a15012f9212859265c1d082c5f0fca7f0"><td class="mdescLeft"> </td><td class="mdescRight">Compute peptide abundances from data in a feature map. <a href="#a15012f9212859265c1d082c5f0fca7f0">More...</a><br/></td></tr>
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<tr class="separator:a15012f9212859265c1d082c5f0fca7f0"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:adb2cb00297803fb1d63ecbaf9f386e1d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#adb2cb00297803fb1d63ecbaf9f386e1d">quantifyPeptides</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus)</td></tr>
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<tr class="memdesc:adb2cb00297803fb1d63ecbaf9f386e1d"><td class="mdescLeft"> </td><td class="mdescRight">Compute peptide abundances from data in a consensus map. <a href="#adb2cb00297803fb1d63ecbaf9f386e1d">More...</a><br/></td></tr>
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<tr class="separator:adb2cb00297803fb1d63ecbaf9f386e1d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0f72e96b01ff3c6ad0d05335cfdcce97"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a0f72e96b01ff3c6ad0d05335cfdcce97">quantifyPeptides</a> (std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &proteins, std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &peptides)</td></tr>
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<tr class="memdesc:a0f72e96b01ff3c6ad0d05335cfdcce97"><td class="mdescLeft"> </td><td class="mdescRight">Compute peptide abundances from identification data (spectral counting) <a href="#a0f72e96b01ff3c6ad0d05335cfdcce97">More...</a><br/></td></tr>
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<tr class="separator:a0f72e96b01ff3c6ad0d05335cfdcce97"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:adc1ba5a6b19c8a97348525ce85ffb5f5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#adc1ba5a6b19c8a97348525ce85ffb5f5">quantifyProteins</a> (const <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> &proteins=<a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>())</td></tr>
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<tr class="memdesc:adc1ba5a6b19c8a97348525ce85ffb5f5"><td class="mdescLeft"> </td><td class="mdescRight">Compute protein abundances. <a href="#adc1ba5a6b19c8a97348525ce85ffb5f5">More...</a><br/></td></tr>
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<tr class="separator:adc1ba5a6b19c8a97348525ce85ffb5f5"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae1b1eb1f01c8cf0f6ef59c4b690eab2a"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#ae1b1eb1f01c8cf0f6ef59c4b690eab2a">getStatistics</a> ()</td></tr>
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<tr class="memdesc:ae1b1eb1f01c8cf0f6ef59c4b690eab2a"><td class="mdescLeft"> </td><td class="mdescRight">Get summary statistics. <a href="#ae1b1eb1f01c8cf0f6ef59c4b690eab2a">More...</a><br/></td></tr>
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<tr class="separator:ae1b1eb1f01c8cf0f6ef59c4b690eab2a"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9e3edddf9d6cfdf216143f3a61f1d166"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a9e3edddf9d6cfdf216143f3a61f1d166">getPeptideResults</a> ()</td></tr>
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<tr class="memdesc:a9e3edddf9d6cfdf216143f3a61f1d166"><td class="mdescLeft"> </td><td class="mdescRight">Get peptide abundance data. <a href="#a9e3edddf9d6cfdf216143f3a61f1d166">More...</a><br/></td></tr>
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<tr class="separator:a9e3edddf9d6cfdf216143f3a61f1d166"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3e55a01775fc867848b2ccc3fbf8ae3e"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a3e55a01775fc867848b2ccc3fbf8ae3e">getProteinResults</a> ()</td></tr>
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<tr class="memdesc:a3e55a01775fc867848b2ccc3fbf8ae3e"><td class="mdescLeft"> </td><td class="mdescRight">Get protein abundance data. <a href="#a3e55a01775fc867848b2ccc3fbf8ae3e">More...</a><br/></td></tr>
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<tr class="separator:a3e55a01775fc867848b2ccc3fbf8ae3e"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<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>
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<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
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Private Member Functions</h2></td></tr>
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<tr class="memitem:adf8ea35cdd453598839d1cb99ed0762c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#adf8ea35cdd453598839d1cb99ed0762c">getAnnotation_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &peptides)</td></tr>
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<tr class="memdesc:adf8ea35cdd453598839d1cb99ed0762c"><td class="mdescLeft"> </td><td class="mdescRight">Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications. <a href="#adf8ea35cdd453598839d1cb99ed0762c">More...</a><br/></td></tr>
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<tr class="separator:adf8ea35cdd453598839d1cb99ed0762c"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa9e62c706d726a6755bf27cd0723803f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#aa9e62c706d726a6755bf27cd0723803f">quantifyFeature_</a> (const <a class="el" href="classOpenMS_1_1FeatureHandle.html">FeatureHandle</a> &feature, const <a class="el" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> &hit)</td></tr>
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<tr class="memdesc:aa9e62c706d726a6755bf27cd0723803f"><td class="mdescLeft"> </td><td class="mdescRight">Gather quantitative information from a feature. <a href="#aa9e62c706d726a6755bf27cd0723803f">More...</a><br/></td></tr>
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<tr class="separator:aa9e62c706d726a6755bf27cd0723803f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3be41534a677c665572d841c7aa81a7f"><td class="memTemplParams" colspan="2">template<typename T > </td></tr>
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<tr class="memitem:a3be41534a677c665572d841c7aa81a7f"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a3be41534a677c665572d841c7aa81a7f">orderBest_</a> (const std::map< T, <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a> > abundances, std::vector< T > &result)</td></tr>
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<tr class="memdesc:a3be41534a677c665572d841c7aa81a7f"><td class="mdescLeft"> </td><td class="mdescRight">Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance. <a href="#a3be41534a677c665572d841c7aa81a7f">More...</a><br/></td></tr>
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<tr class="separator:a3be41534a677c665572d841c7aa81a7f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a6a664e360a175a716613a7c808aae3cd"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a6a664e360a175a716613a7c808aae3cd">quantifyPeptides_</a> ()</td></tr>
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<tr class="memdesc:a6a664e360a175a716613a7c808aae3cd"><td class="mdescLeft"> </td><td class="mdescRight">Compute overall peptide abundances. <a href="#a6a664e360a175a716613a7c808aae3cd">More...</a><br/></td></tr>
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<tr class="separator:a6a664e360a175a716613a7c808aae3cd"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad0a33eaa5e799cbc4188fd5298871ed6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#ad0a33eaa5e799cbc4188fd5298871ed6">normalizePeptides_</a> ()</td></tr>
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<tr class="memdesc:ad0a33eaa5e799cbc4188fd5298871ed6"><td class="mdescLeft"> </td><td class="mdescRight">Normalize peptide abundances across samples by (multiplicative) scaling to equal medians. <a href="#ad0a33eaa5e799cbc4188fd5298871ed6">More...</a><br/></td></tr>
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<tr class="separator:ad0a33eaa5e799cbc4188fd5298871ed6"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ad516940e16385964f87ae4223d098912"><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_1PeptideAndProteinQuant.html#ad516940e16385964f87ae4223d098912">getAccession_</a> (const std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > &pep_accessions, std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > &accession_to_leader)</td></tr>
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<tr class="memdesc:ad516940e16385964f87ae4223d098912"><td class="mdescLeft"> </td><td class="mdescRight">Get the "canonical" protein accession from the list of protein accessions of a peptide. <a href="#ad516940e16385964f87ae4223d098912">More...</a><br/></td></tr>
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<tr class="separator:ad516940e16385964f87ae4223d098912"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2fca327094707629d72e9f9a56016267"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2fca327094707629d72e9f9a56016267">countPeptides_</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &peptides)</td></tr>
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<tr class="memdesc:a2fca327094707629d72e9f9a56016267"><td class="mdescLeft"> </td><td class="mdescRight">Count the number of identifications (best hits only) of each peptide sequence. <a href="#a2fca327094707629d72e9f9a56016267">More...</a><br/></td></tr>
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<tr class="separator:a2fca327094707629d72e9f9a56016267"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
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<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">Clear all data when parameters are set. <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
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<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
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Private Attributes</h2></td></tr>
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<tr class="memitem:adf2156f63e081adc052ffa6fbfe14fb4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#adf2156f63e081adc052ffa6fbfe14fb4">stats_</a></td></tr>
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<tr class="memdesc:adf2156f63e081adc052ffa6fbfe14fb4"><td class="mdescLeft"> </td><td class="mdescRight">Processing statistics for output in the end. <a href="#adf2156f63e081adc052ffa6fbfe14fb4">More...</a><br/></td></tr>
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<tr class="separator:adf2156f63e081adc052ffa6fbfe14fb4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a9c294e9f368e113196bb5306dd4ba1f6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a9c294e9f368e113196bb5306dd4ba1f6">pep_quant_</a></td></tr>
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<tr class="memdesc:a9c294e9f368e113196bb5306dd4ba1f6"><td class="mdescLeft"> </td><td class="mdescRight">Peptide quantification data. <a href="#a9c294e9f368e113196bb5306dd4ba1f6">More...</a><br/></td></tr>
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<tr class="separator:a9c294e9f368e113196bb5306dd4ba1f6"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af075fa02d32cdcabfb6de54142f9d3ca"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#af075fa02d32cdcabfb6de54142f9d3ca">prot_quant_</a></td></tr>
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<tr class="memdesc:af075fa02d32cdcabfb6de54142f9d3ca"><td class="mdescLeft"> </td><td class="mdescRight">Protein quantification data. <a href="#af075fa02d32cdcabfb6de54142f9d3ca">More...</a><br/></td></tr>
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<tr class="separator:af075fa02d32cdcabfb6de54142f9d3ca"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
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Additional Inherited Members</h2></td></tr>
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<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>
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<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>
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<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>
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<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
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<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>
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<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>
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<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<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="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </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>
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<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
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<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
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<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
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<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>
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<div class="textblock"><p>Helper class for peptide and protein quantification based on feature data annotated with IDs. </p>
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<p>This class is used by <a class="el" href="TOPP_ProteinQuantifier.html">ProteinQuantifier</a>. See there for further documentation.</p>
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<B>Parameters of this class are:</B><BR><BR>
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<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
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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>top</b></td>
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<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
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<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)</td>
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<td style="vertical-align:top"><b>average</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">median</td>
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<td style="vertical-align:top">median, mean, sum</td><td style="vertical-align:top">Averaging method used to compute protein abundances from peptide abundances</td>
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<td style="vertical-align:top"><b>include_all</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)</td>
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<td style="vertical-align:top"><b>filter_charge</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;<BR>for proteins, abundances will be computed based only on the most prevalent charge of each peptide.<BR>By default, abundances are summed over all charge states.</td>
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<td style="vertical-align:top"><b><span title="Additional options for consensus maps (and identification results comprising multiple runs)">consensus</span>:normalize</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Scale peptide abundances so that medians of all samples are equal</td>
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<td style="vertical-align:top"><b><span title="Additional options for consensus maps (and identification results comprising multiple runs)">consensus</span>:fix_peptides</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Use the same peptides for protein quantification across all samples.<BR>With 'top 0', all peptides that occur in every sample are considered.<BR>Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,<BR>breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!).</td>
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<UL style="margin-top:0px;">
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<LI> If a section name is documented, the documentation is displayed as tooltip.
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<LI> Advanced parameter names are italic.
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</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef std::map<<a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a>, <a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1PeptideData.html">PeptideData</a>> <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a></td>
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<p>Mapping: peptide sequence (modified) -> peptide data. </p>
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<td class="memname">typedef std::map<<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1ProteinData.html">ProteinData</a>> <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a></td>
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<p>Mapping: protein accession -> protein data. </p>
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<td class="memname">typedef std::map<<a class="el" href="group__Concept.html#ga5162db95dc78bdf2e3a71d73bec703e9">UInt64</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a></td>
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<p>Mapping: sample ID -> abundance. </p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html">PeptideAndProteinQuant</a> </td>
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<td class="paramname"></td><td>)</td>
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<td class="memname">~<a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html">PeptideAndProteinQuant</a> </td>
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<td class="paramname"></td><td>)</td>
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<span class="mlabels"><span class="mlabel">inline</span></span> </td>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void countPeptides_ </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<td class="paramname"><em>peptides</em></td><td>)</td>
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<p>Count the number of identifications (best hits only) of each peptide sequence. </p>
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<p>The peptide hits in <code>peptides</code> are sorted by score in the process. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> getAccession_ </td>
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<td class="paramtype">const std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td>
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<td class="paramname"><em>pep_accessions</em>, </td>
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<td class="paramtype">std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td>
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<td class="paramname"><em>accession_to_leader</em> </td>
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<p>Get the "canonical" protein accession from the list of protein accessions of a peptide. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">pep_accessions</td><td>Protein accessions of a peptide </td></tr>
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<tr><td class="paramname">accession_to_leader</td><td>Captures information about indistinguishable proteins (maps accession to accession of group leader)</td></tr>
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<p>If there is no information about indistinguishable proteins (from protXML) available, a canonical accession exists only for proteotypic peptides - it's the single accession for the respective peptide.</p>
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<p>Otherwise, a peptide has a canonical accession if it maps only to proteins of one indistinguishable group. In this case, the canonical accession is that of the group leader.</p>
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<p>If there is no canonical accession, the empty string is returned. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeptideHit.html">PeptideHit</a> getAnnotation_ </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<td class="paramname"><em>peptides</em></td><td>)</td>
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<p>Get the "canonical" annotation (a single peptide hit) of a feature/consensus feature from the associated list of peptide identifications. </p>
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<p>Only the best-scoring peptide hit of each ID in <code>peptides</code> is taken into account. The hits of each ID must already be sorted! If there's more than one ID and the best hits are not identical by sequence, or if there's no peptide ID, an empty peptide hit (for "ambiguous/no annotation") is returned. Protein accessions from identical peptide hits are accumulated. </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a>& getPeptideResults </td>
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<td class="paramname"></td><td>)</td>
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<p>Get peptide abundance data. </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a>& getProteinResults </td>
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<td class="paramname"></td><td>)</td>
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<p>Get protein abundance data. </p>
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<td class="memname">const <a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a>& getStatistics </td>
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<p>Get summary statistics. </p>
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<td class="memname">void normalizePeptides_ </td>
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<p>Normalize peptide abundances across samples by (multiplicative) scaling to equal medians. </p>
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<td class="memname">void orderBest_ </td>
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<td class="paramtype">const std::map< T, <a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a5242f4ede25f6f7f0ec9f634244c78d6">SampleAbundances</a> > </td>
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<td class="paramname"><em>abundances</em>, </td>
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<td class="paramtype">std::vector< T > & </td>
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<td class="paramname"><em>result</em> </td>
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<p>Order keys (charges/peptides for peptide/protein quantification) according to how many samples they allow to quantify, breaking ties by total abundance. </p>
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<p>The keys of <code>abundances</code> are stored ordered in <code>result</code>, best first. </p>
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<td class="memname">void quantifyFeature_ </td>
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<td class="paramname"><em>feature</em>, </td>
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<p>Gather quantitative information from a feature. </p>
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<p>Store quantitative information from <code>feature</code> in member <code>pep_quant_</code>, based on the peptide annotation in <code>hit</code>. If <code>hit</code> is empty ("ambiguous/no annotation"), nothing is stored. </p>
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<td class="memname">void quantifyPeptides </td>
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<td class="paramname"><em>features</em></td><td>)</td>
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<p>Compute peptide abundances from data in a feature map. </p>
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<p>Parameters should be set before using this method, as setting parameters will clear all results. </p>
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<td class="memname">void quantifyPeptides </td>
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<td class="paramname"><em>consensus</em></td><td>)</td>
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<p>Compute peptide abundances from data in a consensus map. </p>
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<p>Parameters should be set before using this method, as setting parameters will clear all results. </p>
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<td class="memname">void quantifyPeptides </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > & </td>
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<td class="paramname"><em>proteins</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<p>Compute peptide abundances from identification data (spectral counting) </p>
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<p>Parameters should be set before using this method, as setting parameters will clear all results. </p>
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<p>Compute overall peptide abundances. </p>
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<p>Based on quantitative data for individual charge states (derived from annotated features) in member <code>pep_quant_</code>, compute overall abundances for all peptides and store them also in <code>pep_quant_</code>. </p>
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<td class="memname">void quantifyProteins </td>
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<td class="paramname"><em>proteins</em> = <code><a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a>()</code></td><td>)</td>
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<p>Compute protein abundances. </p>
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<p>Peptide abundances must be computed first with <code>quantifyPeptides</code>. Optional information about groups of indistinguishable proteins (from ProteinProphet) can be supplied via <code>proteins</code>. </p>
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<td class="memname">void updateMembers_ </td>
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<p>Clear all data when parameters are set. </p>
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<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a2750aa75b50972d89e20d01214ff1c01">PeptideQuant</a> pep_quant_</td>
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<p>Peptide quantification data. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeptideAndProteinQuant.html#a38f6c1fb46b4457f1fcde70b207f0cea">ProteinQuant</a> prot_quant_</td>
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<p>Protein quantification data. </p>
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<td class="memname"><a class="el" href="structOpenMS_1_1PeptideAndProteinQuant_1_1Statistics.html">Statistics</a> stats_</td>
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<p>Processing statistics for output in the end. </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
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