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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_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">SvmTheoreticalSpectrumGeneratorTrainer Class Reference<div class="ingroups"><a class="el" href="group__Chemistry.html">Chemistry</a></div></div> </div>
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<p>Train SVM models that are used by <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html" title="Simulates ms2 spectra with support vector machines. ">SvmTheoreticalSpectrumGenerator</a>.
<a href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#details">More...</a></p>
<p><code>#include <<a class="el" href="SvmTheoreticalSpectrumGeneratorTrainer_8h_source.html">OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGeneratorTrainer.h</a>></code></p>
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Inheritance diagram for SvmTheoreticalSpectrumGeneratorTrainer:</div>
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<img src="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.png" usemap="#SvmTheoreticalSpectrumGeneratorTrainer_map" alt=""/>
<map id="SvmTheoreticalSpectrumGeneratorTrainer_map" name="SvmTheoreticalSpectrumGeneratorTrainer_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,250,24"/>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a1a2e1388e76267ed2975f1b1fab63dbc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a1a2e1388e76267ed2975f1b1fab63dbc">operator=</a> (const <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> &tsg)</td></tr>
<tr class="memdesc:a1a2e1388e76267ed2975f1b1fab63dbc"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#a1a2e1388e76267ed2975f1b1fab63dbc">More...</a><br/></td></tr>
<tr class="separator:a1a2e1388e76267ed2975f1b1fab63dbc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8358d338088e35cc6554d3bca81d3ffa"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a8358d338088e35cc6554d3bca81d3ffa">trainModel</a> (const <a class="el" href="group__Kernel.html#gac459ab9d68b68f31561c7763c7da61ef">PeakMap</a> &spectra, const std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > &annotations, <a class="el" href="classOpenMS_1_1String.html">String</a> filename, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> precursor_charge)</td></tr>
<tr class="memdesc:a8358d338088e35cc6554d3bca81d3ffa"><td class="mdescLeft"> </td><td class="mdescRight">trains an SVM for each ion_type and stores them in files <filename>_residue_loss_charge.svm <a href="#a8358d338088e35cc6554d3bca81d3ffa">More...</a><br/></td></tr>
<tr class="separator:a8358d338088e35cc6554d3bca81d3ffa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acfb5bd3e29e2e5599b24699cd6a45e78"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#acfb5bd3e29e2e5599b24699cd6a45e78">normalizeIntensity</a> (<a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &S) const </td></tr>
<tr class="memdesc:acfb5bd3e29e2e5599b24699cd6a45e78"><td class="mdescLeft"> </td><td class="mdescRight">Normalizes the intensity of the peaks in the input data. <a href="#acfb5bd3e29e2e5599b24699cd6a45e78">More...</a><br/></td></tr>
<tr class="separator:acfb5bd3e29e2e5599b24699cd6a45e78"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors and Destructors</div></td></tr>
<tr class="memitem:a0897faeb79cec6bf33a3f4293f8fb1ff"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a0897faeb79cec6bf33a3f4293f8fb1ff">SvmTheoreticalSpectrumGeneratorTrainer</a> ()</td></tr>
<tr class="memdesc:a0897faeb79cec6bf33a3f4293f8fb1ff"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a0897faeb79cec6bf33a3f4293f8fb1ff">More...</a><br/></td></tr>
<tr class="separator:a0897faeb79cec6bf33a3f4293f8fb1ff"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a49bc5bfcae67bec7302b21b2d961bfbe"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a49bc5bfcae67bec7302b21b2d961bfbe">SvmTheoreticalSpectrumGeneratorTrainer</a> (const <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> &source)</td></tr>
<tr class="memdesc:a49bc5bfcae67bec7302b21b2d961bfbe"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a49bc5bfcae67bec7302b21b2d961bfbe">More...</a><br/></td></tr>
<tr class="separator:a49bc5bfcae67bec7302b21b2d961bfbe"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a86aaff1c12c22a751882bca11b97fb14"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a86aaff1c12c22a751882bca11b97fb14">~SvmTheoreticalSpectrumGeneratorTrainer</a> ()</td></tr>
<tr class="memdesc:a86aaff1c12c22a751882bca11b97fb14"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a86aaff1c12c22a751882bca11b97fb14">More...</a><br/></td></tr>
<tr class="separator:a86aaff1c12c22a751882bca11b97fb14"><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:ab57a4cf426cb7d62cf37cba617c0abc3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#ab57a4cf426cb7d62cf37cba617c0abc3">writeTrainingFile_</a> (std::vector< <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a0e03c0c3820c2614965d5e8c0032909d">DescriptorSet</a> > &training_input, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &training_output, <a class="el" href="classOpenMS_1_1String.html">String</a> filename)</td></tr>
<tr class="memdesc:ab57a4cf426cb7d62cf37cba617c0abc3"><td class="mdescLeft"> </td><td class="mdescRight">Write a training file that can be passed to libsvm command line tools. <a href="#ab57a4cf426cb7d62cf37cba617c0abc3">More...</a><br/></td></tr>
<tr class="separator:ab57a4cf426cb7d62cf37cba617c0abc3"><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:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
<tr class="separator:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-types"></a>
Private Types</h2></td></tr>
<tr class="memitem:aa0fba1591fc5bc36390fe46a58c5e043"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">SvmTheoreticalSpectrumGenerator::IonType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a></td></tr>
<tr class="separator:aa0fba1591fc5bc36390fe46a58c5e043"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0e03c0c3820c2614965d5e8c0032909d"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">SvmTheoreticalSpectrumGenerator::DescriptorSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a0e03c0c3820c2614965d5e8c0032909d">DescriptorSet</a></td></tr>
<tr class="separator:a0e03c0c3820c2614965d5e8c0032909d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7d4b9e812b80dbcfc155f259e3b29438"><td class="memItemLeft" align="right" valign="top">typedef std::map< std::pair<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> >, std::vector<br class="typebreak"/>
< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a7d4b9e812b80dbcfc155f259e3b29438">ObservedIntensMap</a></td></tr>
<tr class="separator:a7d4b9e812b80dbcfc155f259e3b29438"><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:ae04a1b0f94c76c06ccdd617bd9b57d5a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#ae04a1b0f94c76c06ccdd617bd9b57d5a">countIntensities_</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spectrum, const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &annotation, <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a> type, std::map< std::pair< <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> >, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > &observed_intensities, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> tolerance, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_regions)</td></tr>
<tr class="memdesc:ae04a1b0f94c76c06ccdd617bd9b57d5a"><td class="mdescLeft"> </td><td class="mdescRight">stores the observed intensities for each sector-type combination in a vector <a href="#ae04a1b0f94c76c06ccdd617bd9b57d5a">More...</a><br/></td></tr>
<tr class="separator:ae04a1b0f94c76c06ccdd617bd9b57d5a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a967de7dce1f37e5c4370b3cb17b1ed"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a4a967de7dce1f37e5c4370b3cb17b1ed">trainSecondaryTypes_</a> (<a class="el" href="classOpenMS_1_1TextFile.html">TextFile</a> &info_outfile, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_regions, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> number_of_intensity_levels, <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a7d4b9e812b80dbcfc155f259e3b29438">ObservedIntensMap</a> &observed_intensities, const std::vector< <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a> > &ion_types, const std::vector< bool > &is_primary)</td></tr>
<tr class="memdesc:a4a967de7dce1f37e5c4370b3cb17b1ed"><td class="mdescLeft"> </td><td class="mdescRight">trains the Bayesian secondary peak types models <a href="#a4a967de7dce1f37e5c4370b3cb17b1ed">More...</a><br/></td></tr>
<tr class="separator:a4a967de7dce1f37e5c4370b3cb17b1ed"><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 pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Train SVM models that are used by <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html" title="Simulates ms2 spectra with support vector machines. ">SvmTheoreticalSpectrumGenerator</a>. </p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><b>write_training_files</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to true no models are trained but files (<Filename>_<ion_type>_training.dat) are produced for the selected primary ion types. They can be used as input for LibSVM command line tools</td>
</tr>
<tr>
<td style="vertical-align:top"><b>number_intensity_levels</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">7</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">The number of intensity bins (for secondary type models)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>number_regions</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">The number of regions each spectrum is split to (for secondary type models)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>parent_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2.5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">The maximum difference between theoretical and experimental parent mass to accept training spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>peak_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">The maximum mass error for a peak to the expected mass of some ion type</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_b_ions</b></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">Train simulator for b-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_y_ions</b></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">Train simulator for y-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_a_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for a-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_c_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for c-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_x_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for x-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_z_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for z-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_losses</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_b2_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for doubly charged b-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>add_y2_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Train simulator for double charged y-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:svc_type</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Type of the SVC: 0=C_SVC 1=NU_SVC</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:svr_type</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Type of the SVR: 0=EPSILON_SVR 1=NU_SVR</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:scaling</b></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">Apply scaling of feature values</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:scaling_lower</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Lower bound for scaling</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:scaling_upper</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Upper bound for scaling</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:n_fold</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">n_fold cross validation is performed</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:grid</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Perform grid search</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:additive_cv</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Additive step size (if false multiplicative)</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:kernel_type</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0 max: 3</td><td style="vertical-align:top">Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:degree</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">For POLY</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:gamma</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">For POLY/RBF/SIGMOID</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:C</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Cost of constraint violation</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:nu</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">For NU_SVC, ONE_CLASS and NU_SVR</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:balancing</b></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">Use class balanced SVC training</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:degree_start</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">starting point of degree</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:degree_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size point of degree</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:degree_stop</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">4</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of degree</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:gamma_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1e-05</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">starting point of gamma</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:gamma_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size point of gamma</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:gamma_stop</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of gamma</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:c_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">starting point of c</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:c_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size of c</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:c_stop</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1000</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of c</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:nu_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.3</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">starting point of nu</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:nu_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size of nu</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - classification of missing/abundant">svc</span>:nu_stop</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.6</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">stopping point of nu</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:kernel_type</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0 max: 3</td><td style="vertical-align:top">Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:degree</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">For POLY</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:gamma</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">For POLY/RBF/SIGMOID</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:C</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Cost of constraint violation</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:p</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">The epsilon for the loss function in epsilon-SVR</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:nu</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">For NU_SVC, ONE_CLASS and NU_SVR</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:degree_start</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">starting point of degree</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:degree_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size point of degree</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:degree_stop</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">4</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of degree</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:gamma_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1e-05</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">starting point of gamma</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:gamma_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size point of gamma</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:gamma_stop</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of gamma</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:p_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1e-05</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">starting point of p</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:p_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size point of p</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:p_stop</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of p</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:c_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">starting point of c</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:c_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size of c</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:c_stop</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1000</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">stopping point of c</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:nu_start</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.3</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">starting point of nu</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:nu_step_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">step size of nu</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation">svm</span>:<span title="Parameters for svm - regression of peak intensities">svr</span>:nu_stop</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.6</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">stopping point of nu</td>
</tr>
</table>
<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
<p>This class implements the algorithm used by the homonymous tool which can be used to train models for MS/MS spectrum simulation.<br/>
For the primary ion types (y, b) a SVM is trained using the libSVM library.<br/>
All important libSVM parameters are accessible as parameters.<br/>
Please refer to the libSVM manuals for detailed description of the parameters. Default values are choses as in the svm-training tool delivered with libSVM.<br/>
For the secondary types (a, c, x, z, losses, b2, y2) a simple Bayesian model is used. </p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">SvmTheoreticalSpectrumGenerator::DescriptorSet</a> <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a0e03c0c3820c2614965d5e8c0032909d">DescriptorSet</a></td>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">SvmTheoreticalSpectrumGenerator::IonType</a> <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a></td>
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<td class="memname">typedef std::map<std::pair<<a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>>, std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> > <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#a7d4b9e812b80dbcfc155f259e3b29438">ObservedIntensMap</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_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> </td>
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<p>Default constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<p>Copy constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a> </td>
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<p>Destructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void countIntensities_ </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
<td class="paramname"><em>spectrum</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a> </td>
<td class="paramname"><em>type</em>, </td>
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<td class="paramtype">std::map< std::pair< <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> >, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > & </td>
<td class="paramname"><em>observed_intensities</em>, </td>
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<td class="paramname"><em>number_of_regions</em> </td>
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<p>stores the observed intensities for each sector-type combination in a vector </p>
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<td class="memname">void normalizeIntensity </td>
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<p>Normalizes the intensity of the peaks in the input data. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a>& operator= </td>
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<p>Assignment operator. </p>
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<td class="memname">void trainModel </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#gac459ab9d68b68f31561c7763c7da61ef">PeakMap</a> & </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> </td>
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<p>trains an SVM for each ion_type and stores them in files <filename>_residue_loss_charge.svm </p>
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<td class="memname">void trainSecondaryTypes_ </td>
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<td class="paramname"><em>number_of_intensity_levels</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html#aa0fba1591fc5bc36390fe46a58c5e043">IonType</a> > & </td>
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<p>trains the Bayesian secondary peak types models </p>
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<td class="memname">void writeTrainingFile_ </td>
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<p>Write a training file that can be passed to libsvm command line tools. </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 11:19:28 using doxygen 1.8.5</font></TD>
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