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<HTML>
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<TITLE>ItraqQuantifier Class Reference</TITLE>
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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a></li> </ul>
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<p>Does post-processing on raw iTRAQ channel quantitation.
<a href="classOpenMS_1_1ItraqQuantifier.html#details">More...</a></p>
<p><code>#include <<a class="el" href="ItraqQuantifier_8h_source.html">OpenMS/ANALYSIS/QUANTITATION/ItraqQuantifier.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for ItraqQuantifier:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1ItraqQuantifier.png" usemap="#ItraqQuantifier_map" alt=""/>
<map id="ItraqQuantifier_map" name="ItraqQuantifier_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"/>
<area href="classOpenMS_1_1ItraqConstants.html" title="Some constants used throughout iTRAQ classes. " alt="ItraqConstants" shape="rect" coords="143,0,276,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Statistics for quantitation performance and comparison of <a class="el" href="namespaceOpenMS_1_1NNLS.html">NNLS</a> vs. naive method (aka matrix inversion) <a href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a2db6873392e87c6d42bb6466354d05e4"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenMS_1_1ItraqConstants_1_1ChannelInfo.html">ItraqConstants::ChannelInfo</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a2db6873392e87c6d42bb6466354d05e4">ChannelInfo</a></td></tr>
<tr class="separator:a2db6873392e87c6d42bb6466354d05e4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a90c9c7b0430f6c9821987d342595f45b"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ItraqConstants::ChannelMapType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a90c9c7b0430f6c9821987d342595f45b">ChannelMapType</a></td></tr>
<tr class="separator:a90c9c7b0430f6c9821987d342595f45b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2977e178aa82b51a5d30ca756e503afd"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">ItraqConstants::IsotopeMatrices</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a2977e178aa82b51a5d30ca756e503afd">IsotopeMatrices</a></td></tr>
<tr class="separator:a2977e178aa82b51a5d30ca756e503afd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ItraqConstants"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ItraqConstants')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ItraqConstants.html">ItraqConstants</a></td></tr>
<tr class="memitem:a6d4d2da803a1940366d2d1c9df88a1da inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1da">ITRAQ_TYPES</a> { <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">FOURPLEX</a> = 0,
<a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">EIGHTPLEX</a>,
<a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daab2efab97bf0de95600be505f6f3f3e70">TMT_SIXPLEX</a>,
<a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa3fe6083b74a8c1bcd0a4731a10b452c0">SIZE_OF_ITRAQ_TYPES</a>
}</td></tr>
<tr class="separator:a6d4d2da803a1940366d2d1c9df88a1da inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0fd315ce2505dd774fe92abfcaa4786f inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="structOpenMS_1_1ItraqConstants_1_1ChannelInfo.html">ChannelInfo</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ChannelMapType</a></td></tr>
<tr class="memdesc:a0fd315ce2505dd774fe92abfcaa4786f inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">maps iTRAQ channel (e.g. 117) to more information <a href="#a0fd315ce2505dd774fe92abfcaa4786f">More...</a><br/></td></tr>
<tr class="separator:a0fd315ce2505dd774fe92abfcaa4786f inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aad56172226aab6ec420d03d72e692a17 inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">typedef std::vector< <a class="el" href="classOpenMS_1_1Matrix.html">Matrix</a><br class="typebreak"/>
< <a class="el" href="classdouble.html">double</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a></td></tr>
<tr class="memdesc:aad56172226aab6ec420d03d72e692a17 inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style <a href="#aad56172226aab6ec420d03d72e692a17">More...</a><br/></td></tr>
<tr class="separator:aad56172226aab6ec420d03d72e692a17 inherit pub_types_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:afd9955780214a974b6e81fc07dc20acb"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#afd9955780214a974b6e81fc07dc20acb">ItraqQuantifier</a> ()</td></tr>
<tr class="memdesc:afd9955780214a974b6e81fc07dc20acb"><td class="mdescLeft"> </td><td class="mdescRight">Constructor (assuming 4-plex experiment) <a href="#afd9955780214a974b6e81fc07dc20acb">More...</a><br/></td></tr>
<tr class="separator:afd9955780214a974b6e81fc07dc20acb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1c8dc4c9bdbd5ef1909b19c434bcb82b"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a1c8dc4c9bdbd5ef1909b19c434bcb82b">ItraqQuantifier</a> (<a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> itraq_type)</td></tr>
<tr class="memdesc:a1c8dc4c9bdbd5ef1909b19c434bcb82b"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with iTRAQ-type (either <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">ItraqConstants::FOURPLEX</a> or <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">ItraqConstants::EIGHTPLEX</a>) <a href="#a1c8dc4c9bdbd5ef1909b19c434bcb82b">More...</a><br/></td></tr>
<tr class="separator:a1c8dc4c9bdbd5ef1909b19c434bcb82b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7cb8ccdbd2178d5150f258fd7171860d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a7cb8ccdbd2178d5150f258fd7171860d">ItraqQuantifier</a> (<a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> itraq_type, const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:a7cb8ccdbd2178d5150f258fd7171860d"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with iTRAQ-type (either <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">ItraqConstants::FOURPLEX</a> or <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">ItraqConstants::EIGHTPLEX</a>) and <a class="el" href="classOpenMS_1_1Param.html" title="Management and storage of parameters / INI files. ">Param</a>. <a href="#a7cb8ccdbd2178d5150f258fd7171860d">More...</a><br/></td></tr>
<tr class="separator:a7cb8ccdbd2178d5150f258fd7171860d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae7e22bf384f6c39ed6efb537dab5d067"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#ae7e22bf384f6c39ed6efb537dab5d067">ItraqQuantifier</a> (const <a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> &cp)</td></tr>
<tr class="memdesc:ae7e22bf384f6c39ed6efb537dab5d067"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#ae7e22bf384f6c39ed6efb537dab5d067">More...</a><br/></td></tr>
<tr class="separator:ae7e22bf384f6c39ed6efb537dab5d067"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a578200a3e0c013ca5549d44045f795bc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a578200a3e0c013ca5549d44045f795bc">operator=</a> (const <a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> &rhs)</td></tr>
<tr class="memdesc:a578200a3e0c013ca5549d44045f795bc"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a578200a3e0c013ca5549d44045f795bc">More...</a><br/></td></tr>
<tr class="separator:a578200a3e0c013ca5549d44045f795bc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acdee771faf76f323d2d812ad19ce65f6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#acdee771faf76f323d2d812ad19ce65f6">run</a> (const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map_in, <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map_out)</td></tr>
<tr class="memdesc:acdee771faf76f323d2d812ad19ce65f6"><td class="mdescLeft"> </td><td class="mdescRight">using the raw iTRAQ intensities we apply isotope correction, normalization (using median) <a href="#acdee771faf76f323d2d812ad19ce65f6">More...</a><br/></td></tr>
<tr class="separator:acdee771faf76f323d2d812ad19ce65f6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a31fe1c7e0febd8b3de262dde54810cbb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a31fe1c7e0febd8b3de262dde54810cbb">getStats</a> () const </td></tr>
<tr class="separator:a31fe1c7e0febd8b3de262dde54810cbb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a592956c92badca126cec3abd62da8d67"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a592956c92badca126cec3abd62da8d67">setDefaultParams_</a> ()</td></tr>
<tr class="separator:a592956c92badca126cec3abd62da8d67"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a57fc3c4c5d65eeeaa91889c33aa44cdf"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a57fc3c4c5d65eeeaa91889c33aa44cdf">initIsotopeCorrections_</a> ()</td></tr>
<tr class="memdesc:a57fc3c4c5d65eeeaa91889c33aa44cdf"><td class="mdescLeft"> </td><td class="mdescRight">initialize <a href="#a57fc3c4c5d65eeeaa91889c33aa44cdf">More...</a><br/></td></tr>
<tr class="separator:a57fc3c4c5d65eeeaa91889c33aa44cdf"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acf4b9c1ca1c798bb0cddaa9f7c1ec13e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#acf4b9c1ca1c798bb0cddaa9f7c1ec13e">reconstructChannelInfo_</a> (const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map)</td></tr>
<tr class="separator:acf4b9c1ca1c798bb0cddaa9f7c1ec13e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a68aba708eecb5fc36a917a7452c1ea51"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a68aba708eecb5fc36a917a7452c1ea51">isIdentityCorrectionMatrix_</a> (const <a class="el" href="classOpenMS_1_1Matrix.html">Matrix</a>< <a class="el" href="classdouble.html">double</a> > &channel_frequency) const </td></tr>
<tr class="memdesc:a68aba708eecb5fc36a917a7452c1ea51"><td class="mdescLeft"> </td><td class="mdescRight">Check if the given channel_frequency matrix is an identity matrix. <a href="#a68aba708eecb5fc36a917a7452c1ea51">More...</a><br/></td></tr>
<tr class="separator:a68aba708eecb5fc36a917a7452c1ea51"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:ac0dd3c18dae25b85f52e27eae758046f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#ac0dd3c18dae25b85f52e27eae758046f">itraq_type_</a></td></tr>
<tr class="memdesc:ac0dd3c18dae25b85f52e27eae758046f"><td class="mdescLeft"> </td><td class="mdescRight">either <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">ItraqConstants::FOURPLEX</a> or <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">ItraqConstants::EIGHTPLEX</a> <a href="#ac0dd3c18dae25b85f52e27eae758046f">More...</a><br/></td></tr>
<tr class="separator:ac0dd3c18dae25b85f52e27eae758046f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a580627b7de9396a221f5156261902f88"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ChannelMapType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a580627b7de9396a221f5156261902f88">channel_map_</a></td></tr>
<tr class="separator:a580627b7de9396a221f5156261902f88"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a536e27ec83eafb6e43ed1e71ffdce2b5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a536e27ec83eafb6e43ed1e71ffdce2b5">isotope_corrections_</a></td></tr>
<tr class="memdesc:a536e27ec83eafb6e43ed1e71ffdce2b5"><td class="mdescLeft"> </td><td class="mdescRight">Matrices with isotope correction values (one for each plex-type) <a href="#a536e27ec83eafb6e43ed1e71ffdce2b5">More...</a><br/></td></tr>
<tr class="separator:a536e27ec83eafb6e43ed1e71ffdce2b5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aeab1440c4c51bf9ece15d6a94e4ddbdf"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html#aeab1440c4c51bf9ece15d6a94e4ddbdf">stats_</a></td></tr>
<tr class="memdesc:aeab1440c4c51bf9ece15d6a94e4ddbdf"><td class="mdescLeft"> </td><td class="mdescRight">stats for isotope correction <a href="#aeab1440c4c51bf9ece15d6a94e4ddbdf">More...</a><br/></td></tr>
<tr class="separator:aeab1440c4c51bf9ece15d6a94e4ddbdf"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_static_methods_classOpenMS_1_1ItraqConstants"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1ItraqConstants')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ItraqConstants.html">ItraqConstants</a></td></tr>
<tr class="memitem:acdc73dfefd9acbd2f6bc60315b34c192 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#acdc73dfefd9acbd2f6bc60315b34c192">getIsotopeMatrixAsStringList</a> (const int itraq_type, const <a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a> &isotope_corrections)</td></tr>
<tr class="memdesc:acdc73dfefd9acbd2f6bc60315b34c192 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">convert isotope correction matrix to stringlist <a href="#acdc73dfefd9acbd2f6bc60315b34c192">More...</a><br/></td></tr>
<tr class="separator:acdc73dfefd9acbd2f6bc60315b34c192 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a43810a076d4e9906bc4da9b316c04e48 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a43810a076d4e9906bc4da9b316c04e48">updateIsotopeMatrixFromStringList</a> (const int itraq_type, const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> &channels, <a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a> &isotope_corrections)</td></tr>
<tr class="memdesc:a43810a076d4e9906bc4da9b316c04e48 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">convert strings to isotope correction matrix rows <a href="#a43810a076d4e9906bc4da9b316c04e48">More...</a><br/></td></tr>
<tr class="separator:a43810a076d4e9906bc4da9b316c04e48 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5d051e73fafba18f1b313041d8534e32 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a5d051e73fafba18f1b313041d8534e32">initChannelMap</a> (const int itraq_type, <a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ChannelMapType</a> &map)</td></tr>
<tr class="memdesc:a5d051e73fafba18f1b313041d8534e32 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">information about an iTRAQ channel <a href="#a5d051e73fafba18f1b313041d8534e32">More...</a><br/></td></tr>
<tr class="separator:a5d051e73fafba18f1b313041d8534e32 inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae287c6892c0ff0bdfa292cbf7e7a4cdf inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#ae287c6892c0ff0bdfa292cbf7e7a4cdf">updateChannelMap</a> (const <a class="el" href="classOpenMS_1_1StringList.html">StringList</a> &active_channels, <a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ChannelMapType</a> &map)</td></tr>
<tr class="memdesc:ae287c6892c0ff0bdfa292cbf7e7a4cdf inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">activate & annotate channels <a href="#ae287c6892c0ff0bdfa292cbf7e7a4cdf">More...</a><br/></td></tr>
<tr class="separator:ae287c6892c0ff0bdfa292cbf7e7a4cdf inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0d893f462f971cf06a513ac1d4a3d12a inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1Matrix.html">Matrix</a>< <a class="el" href="classdouble.html">double</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a0d893f462f971cf06a513ac1d4a3d12a">translateIsotopeMatrix</a> (const int &itraq_type, const <a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a> &isotope_corrections)</td></tr>
<tr class="memdesc:a0d893f462f971cf06a513ac1d4a3d12a inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">translate isotope correction matrix in -2,-1,+1,+2 form into 114,115,116,117 format <a href="#a0d893f462f971cf06a513ac1d4a3d12a">More...</a><br/></td></tr>
<tr class="separator:a0d893f462f971cf06a513ac1d4a3d12a inherit pub_static_methods_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_static_attribs_classOpenMS_1_1ItraqConstants"><td colspan="2" onclick="javascript:toggleInherit('pub_static_attribs_classOpenMS_1_1ItraqConstants')"><img src="closed.png" alt="-"/> Static Public Attributes inherited from <a class="el" href="classOpenMS_1_1ItraqConstants.html">ItraqConstants</a></td></tr>
<tr class="memitem:a8d48199718eb5ba0d5c270eecd423f6d inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a8d48199718eb5ba0d5c270eecd423f6d">CHANNEL_COUNT</a> []</td></tr>
<tr class="separator:a8d48199718eb5ba0d5c270eecd423f6d inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad271dd9921791a8c6c9448ed1657e646 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#ad271dd9921791a8c6c9448ed1657e646">CHANNELS_FOURPLEX</a> [4][1]</td></tr>
<tr class="memdesc:ad271dd9921791a8c6c9448ed1657e646 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">channel names for 4plex( 114, 115, 116, 117) <a href="#ad271dd9921791a8c6c9448ed1657e646">More...</a><br/></td></tr>
<tr class="separator:ad271dd9921791a8c6c9448ed1657e646 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adac316ab7529e6004c173ba1248a1fe5 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#adac316ab7529e6004c173ba1248a1fe5">CHANNELS_EIGHTPLEX</a> [8][1]</td></tr>
<tr class="memdesc:adac316ab7529e6004c173ba1248a1fe5 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">channel names for 8plex( 113, 114, 115, 116, 117, 118, 119, 121) <a href="#adac316ab7529e6004c173ba1248a1fe5">More...</a><br/></td></tr>
<tr class="separator:adac316ab7529e6004c173ba1248a1fe5 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2c78d3b888d30c21fbe5ce7614749fe7 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a2c78d3b888d30c21fbe5ce7614749fe7">CHANNELS_TMT_SIXPLEX</a> [6][1]</td></tr>
<tr class="memdesc:a2c78d3b888d30c21fbe5ce7614749fe7 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">channel names for 6plex TMT with CID fragmentation( 126, 127, 128, 129, 130, 131) <a href="#a2c78d3b888d30c21fbe5ce7614749fe7">More...</a><br/></td></tr>
<tr class="separator:a2c78d3b888d30c21fbe5ce7614749fe7 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9f42f5978c59c080821c1a2ba802470b inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classdouble.html">double</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a9f42f5978c59c080821c1a2ba802470b">ISOTOPECORRECTIONS_FOURPLEX</a> [4][4]</td></tr>
<tr class="memdesc:a9f42f5978c59c080821c1a2ba802470b inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">default isotope correction matrix (4 plex) <a href="#a9f42f5978c59c080821c1a2ba802470b">More...</a><br/></td></tr>
<tr class="separator:a9f42f5978c59c080821c1a2ba802470b inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a54b5a4e63da8563b898389c9ba7871c3 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classdouble.html">double</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a54b5a4e63da8563b898389c9ba7871c3">ISOTOPECORRECTIONS_EIGHTPLEX</a> [8][4]</td></tr>
<tr class="memdesc:a54b5a4e63da8563b898389c9ba7871c3 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">default isotope correction matrix (8 plex) <a href="#a54b5a4e63da8563b898389c9ba7871c3">More...</a><br/></td></tr>
<tr class="separator:a54b5a4e63da8563b898389c9ba7871c3 inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa54aeea3eb3dfa93820330748e655abf inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classdouble.html">double</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ItraqConstants.html#aa54aeea3eb3dfa93820330748e655abf">ISOTOPECORRECTIONS_TMT_SIXPLEX</a> [6][4]</td></tr>
<tr class="memdesc:aa54aeea3eb3dfa93820330748e655abf inherit pub_static_attribs_classOpenMS_1_1ItraqConstants"><td class="mdescLeft"> </td><td class="mdescRight">default isotope correction matrix (6 plex TMT) <a href="#aa54aeea3eb3dfa93820330748e655abf">More...</a><br/></td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<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>Does post-processing on raw iTRAQ channel quantitation. </p>
<p>Using the raw consensus map from <a class="el" href="classOpenMS_1_1ItraqChannelExtractor.html" title="[experimental class] extracts the iTRAQ channels from tandem MS data and stores intensity values in a...">ItraqChannelExtractor</a>, a non-negative isotope correction, normalization (using median) and [optionally] protein inference is computed.</p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
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<td style="vertical-align:top"><i>isotope_correction</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Enable isotope correction (highly recommended).</td>
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<td style="vertical-align:top"><i>do_normalization</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Normalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!</td>
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<td style="vertical-align:top"><b>channel_reference</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">114</td>
<td style="vertical-align:top">min: 114 max: 117</td><td style="vertical-align:top">Number of the reference channel (114-117 for 4plex).</td>
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<td style="vertical-align:top"><i><span title="Isotope correction matrices for 4plex and 8plex. Only one of them will be used (depending on iTRAQ mode).">isotope_correction</span>:4plex</i></td>
<td style="vertical-align:top">string list</td><td style="vertical-align:top">[114:0/1/5.9/0.2, 115:0/2/5.6/0.1, 116:0/3/4.5/0.1, 117:0.1/4/3.5/0.1]</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'.</td>
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<td style="vertical-align:top"><i><span title="Isotope correction matrices for 4plex and 8plex. Only one of them will be used (depending on iTRAQ mode).">isotope_correction</span>:8plex</i></td>
<td style="vertical-align:top">string list</td><td style="vertical-align:top">[113:0/0/6.89/0.22, 114:0/0.94/5.9/0.16, 115:0/1.88/4.9/0.1, 116:0/2.82/3.9/0.07, 117:0.06/3.77/2.99/0, 118:0.09/4.71/1.88/0, 119:0.14/5.66/0.87/0, 121:0.27/7.44/0.18/0]</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'.</td>
</tr>
</table>
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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.
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</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1ItraqConstants_1_1ChannelInfo.html">ItraqConstants::ChannelInfo</a> <a class="el" href="classOpenMS_1_1ItraqQuantifier.html#a2db6873392e87c6d42bb6466354d05e4">ChannelInfo</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ItraqConstants::ChannelMapType</a> <a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ChannelMapType</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">ItraqConstants::IsotopeMatrices</a> <a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> </td>
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<p>Constructor (assuming 4-plex experiment) </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td>
<td class="paramname"><em>itraq_type</em></td><td>)</td>
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<p>Constructor with iTRAQ-type (either <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">ItraqConstants::FOURPLEX</a> or <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">ItraqConstants::EIGHTPLEX</a>) </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> </td>
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<td class="paramname"><em>itraq_type</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td>
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<p>Constructor with iTRAQ-type (either <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">ItraqConstants::FOURPLEX</a> or <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">ItraqConstants::EIGHTPLEX</a>) and <a class="el" href="classOpenMS_1_1Param.html" title="Management and storage of parameters / INI files. ">Param</a>. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a> </td>
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<td class="paramname"><em>cp</em></td><td>)</td>
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<p>copy constructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a> getStats </td>
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<td class="memname">void initIsotopeCorrections_ </td>
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<p>initialize </p>
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<td class="memname">bool isIdentityCorrectionMatrix_ </td>
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<p>Check if the given channel_frequency matrix is an identity matrix. </p>
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<tr><td class="paramname">The</td><td>matrix to check. </td></tr>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqQuantifier.html">ItraqQuantifier</a>& operator= </td>
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<td class="paramname"><em>rhs</em></td><td>)</td>
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<p>assignment operator </p>
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<td class="memname">void reconstructChannelInfo_ </td>
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<td class="memname">void run </td>
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<p>using the raw iTRAQ intensities we apply isotope correction, normalization (using median) </p>
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<tr><td class="paramname">consensus_map_in</td><td>Raw iTRAQ intensities from previous step </td></tr>
<tr><td class="paramname">consensus_map_out</td><td>Post-processed iTRAQ ratios for peptides</td></tr>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1FailedAPICall.html" title="A call to an external library (other than OpenMS) went wrong. ">Exception::FailedAPICall</a></td><td>is least-squares fit fails </td></tr>
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1InvalidParameter.html" title="Exception indicating that an invalid parameter was handed over to an algorithm. ">Exception::InvalidParameter</a></td><td>if parameter is invalid (e.g. reference_channel) </td></tr>
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<p>This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. </p>
<p>Also call it at the end of the derived classes' copy constructor and assignment operator.</p>
<p>The default implementation is empty. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqConstants.html#a0fd315ce2505dd774fe92abfcaa4786f">ChannelMapType</a> channel_map_</td>
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<p>map the channel-name (e.g., 114) onto its channel_info the channel-description is also the id-string in the mapList section of the <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ItraqConstants.html#aad56172226aab6ec420d03d72e692a17">IsotopeMatrices</a> isotope_corrections_</td>
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<p>Matrices with isotope correction values (one for each plex-type) </p>
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<td class="memname"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> itraq_type_</td>
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<p>either <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daa4b799820f50b498cee50217a0a93760f">ItraqConstants::FOURPLEX</a> or <a class="el" href="classOpenMS_1_1ItraqConstants.html#a6d4d2da803a1940366d2d1c9df88a1daac6909f119e72c78fdaf35e5cb7db4d45">ItraqConstants::EIGHTPLEX</a> </p>
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<td class="memname"><a class="el" href="structOpenMS_1_1ItraqQuantifier_1_1ItraqQuantifierStats.html">ItraqQuantifierStats</a> stats_</td>
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<p>stats for isotope correction </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 11:19:27 using doxygen 1.8.5</font></TD>
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