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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_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a></li> </ul>
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<div class="title">SvmTheoreticalSpectrumGenerator Class Reference<div class="ingroups"><a class="el" href="group__Chemistry.html">Chemistry</a></div></div> </div>
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<p>Simulates ms2 spectra with support vector machines.
<a href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#details">More...</a></p>
<p><code>#include <<a class="el" href="SvmTheoreticalSpectrumGenerator_8h_source.html">OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h</a>></code></p>
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Inheritance diagram for SvmTheoreticalSpectrumGenerator:</div>
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<img src="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.png" usemap="#SvmTheoreticalSpectrumGenerator_map" alt=""/>
<map id="SvmTheoreticalSpectrumGenerator_map" name="SvmTheoreticalSpectrumGenerator_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,209,24"/>
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<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_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">DescriptorSet</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">A set of descriptors for a single training row. <a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </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_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">nested class <a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </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_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">SvmModelParameterSet</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Simple container storing the model parameters required for simulation. <a href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.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-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a5c8a302c628f40855e96653849c430e7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a5c8a302c628f40855e96653849c430e7">simulate</a> (<a class="el" href="group__Kernel.html#gae09df17325d781f23b1486a2db006e0d">RichPeakSpectrum</a> &spectrum, const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &peptide, const gsl_rng *rng, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_charge)</td></tr>
<tr class="memdesc:a5c8a302c628f40855e96653849c430e7"><td class="mdescLeft"> </td><td class="mdescRight">Generate the MS/MS according to the given probabilistic model. <a href="#a5c8a302c628f40855e96653849c430e7">More...</a><br/></td></tr>
<tr class="separator:a5c8a302c628f40855e96653849c430e7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a78f61ac2dd03bcba8e09ca20cd7d68e3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a78f61ac2dd03bcba8e09ca20cd7d68e3">load</a> ()</td></tr>
<tr class="memdesc:a78f61ac2dd03bcba8e09ca20cd7d68e3"><td class="mdescLeft"> </td><td class="mdescRight">Load a trained Svm and Prob. models. <a href="#a78f61ac2dd03bcba8e09ca20cd7d68e3">More...</a><br/></td></tr>
<tr class="separator:a78f61ac2dd03bcba8e09ca20cd7d68e3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7fd878e35881deccde0faca564b096fe"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a7fd878e35881deccde0faca564b096fe">getIonTypes</a> ()</td></tr>
<tr class="memdesc:a7fd878e35881deccde0faca564b096fe"><td class="mdescLeft"> </td><td class="mdescRight">return the set of ion types that are modeled by the loaded SVMs <a href="#a7fd878e35881deccde0faca564b096fe">More...</a><br/></td></tr>
<tr class="separator:a7fd878e35881deccde0faca564b096fe"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors and Destructors</div></td></tr>
<tr class="memitem:ae92979470fc04a8a12b4355af95fdf35"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ae92979470fc04a8a12b4355af95fdf35">SvmTheoreticalSpectrumGenerator</a> ()</td></tr>
<tr class="memdesc:ae92979470fc04a8a12b4355af95fdf35"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#ae92979470fc04a8a12b4355af95fdf35">More...</a><br/></td></tr>
<tr class="separator:ae92979470fc04a8a12b4355af95fdf35"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9edd4dc9e81412353100b1868cfa3977"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a9edd4dc9e81412353100b1868cfa3977">SvmTheoreticalSpectrumGenerator</a> (const <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> &source)</td></tr>
<tr class="memdesc:a9edd4dc9e81412353100b1868cfa3977"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a9edd4dc9e81412353100b1868cfa3977">More...</a><br/></td></tr>
<tr class="separator:a9edd4dc9e81412353100b1868cfa3977"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abe42c0ace1d34032d5ffadafd1a1f7e6"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#abe42c0ace1d34032d5ffadafd1a1f7e6">operator=</a> (const <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> &tsg)</td></tr>
<tr class="memdesc:abe42c0ace1d34032d5ffadafd1a1f7e6"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#abe42c0ace1d34032d5ffadafd1a1f7e6">More...</a><br/></td></tr>
<tr class="separator:abe42c0ace1d34032d5ffadafd1a1f7e6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a97041cb50650200be0742292b5680d22"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a97041cb50650200be0742292b5680d22">~SvmTheoreticalSpectrumGenerator</a> ()</td></tr>
<tr class="memdesc:a97041cb50650200be0742292b5680d22"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a97041cb50650200be0742292b5680d22">More...</a><br/></td></tr>
<tr class="separator:a97041cb50650200be0742292b5680d22"><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-types"></a>
Protected Types</h2></td></tr>
<tr class="memitem:ad0f94e7ae2de2380f906f0e3110d58cc"><td class="memItemLeft" align="right" valign="top">typedef std::map< <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a>, <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_1SvmTheoreticalSpectrumGenerator.html#ad0f94e7ae2de2380f906f0e3110d58cc">IntensityMap</a></td></tr>
<tr class="separator:ad0f94e7ae2de2380f906f0e3110d58cc"><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:a01b2ecfa118e5ad632ece3b09987856c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a01b2ecfa118e5ad632ece3b09987856c">scaleSingleFeature_</a> (<a class="el" href="classdouble.html">double</a> &value, <a class="el" href="classdouble.html">double</a> feature_min, <a class="el" href="classdouble.html">double</a> feature_max, <a class="el" href="classdouble.html">double</a> lower=-1.0, <a class="el" href="classdouble.html">double</a> upper=1.0)</td></tr>
<tr class="memdesc:a01b2ecfa118e5ad632ece3b09987856c"><td class="mdescLeft"> </td><td class="mdescRight">scale value to the intervall [lower,max] given the maximal and minimal entries for a feature <a href="#a01b2ecfa118e5ad632ece3b09987856c">More...</a><br/></td></tr>
<tr class="separator:a01b2ecfa118e5ad632ece3b09987856c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a86741b436e08eeda23dade3f17cda970"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a86741b436e08eeda23dade3f17cda970">scaleDescriptorSet_</a> (<a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">DescriptorSet</a> &desc, <a class="el" href="classdouble.html">double</a> lower, <a class="el" href="classdouble.html">double</a> upper)</td></tr>
<tr class="memdesc:a86741b436e08eeda23dade3f17cda970"><td class="mdescLeft"> </td><td class="mdescRight">scale value to the intervall [lower,max] given the maximal and minimal entries for a feature <a href="#a86741b436e08eeda23dade3f17cda970">More...</a><br/></td></tr>
<tr class="separator:a86741b436e08eeda23dade3f17cda970"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6acbe0fad4e8185aafb37154bb1027d3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a6acbe0fad4e8185aafb37154bb1027d3">generateDescriptorSet_</a> (<a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> peptide, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> position, <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a> type, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_charge, <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1DescriptorSet.html">DescriptorSet</a> &desc_set)</td></tr>
<tr class="memdesc:a6acbe0fad4e8185aafb37154bb1027d3"><td class="mdescLeft"> </td><td class="mdescRight">generate the desciptors for an input peptide and a given fragmentation position <a href="#a6acbe0fad4e8185aafb37154bb1027d3">More...</a><br/></td></tr>
<tr class="separator:a6acbe0fad4e8185aafb37154bb1027d3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a16bbdf903607a343a04bfc5cb306b4c9"><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_1SvmTheoreticalSpectrumGenerator.html#a16bbdf903607a343a04bfc5cb306b4c9">ResidueTypeToString_</a> (<a class="el" href="classOpenMS_1_1Residue.html#a7651af21f9cf8ed6445415903fc6cb48">Residue::ResidueType</a> type)</td></tr>
<tr class="memdesc:a16bbdf903607a343a04bfc5cb306b4c9"><td class="mdescLeft"> </td><td class="mdescRight">Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation. <a href="#a16bbdf903607a343a04bfc5cb306b4c9">More...</a><br/></td></tr>
<tr class="separator:a16bbdf903607a343a04bfc5cb306b4c9"><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_1SvmTheoreticalSpectrumGenerator.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="pro-static-methods"></a>
Static Protected Member Functions</h2></td></tr>
<tr class="memitem:ab408467129a1ccf78eedf1fec417e122"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab408467129a1ccf78eedf1fec417e122">initializeMaps_</a> ()</td></tr>
<tr class="memdesc:ab408467129a1ccf78eedf1fec417e122"><td class="mdescLeft"> </td><td class="mdescRight">initialized the maps <a href="#ab408467129a1ccf78eedf1fec417e122">More...</a><br/></td></tr>
<tr class="separator:ab408467129a1ccf78eedf1fec417e122"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:ab4f4b9381d8d1c6ede3ef66028cd6b42"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab4f4b9381d8d1c6ede3ef66028cd6b42">precursor_charge_</a></td></tr>
<tr class="memdesc:ab4f4b9381d8d1c6ede3ef66028cd6b42"><td class="mdescLeft"> </td><td class="mdescRight">charge of the precursors used for training <a href="#ab4f4b9381d8d1c6ede3ef66028cd6b42">More...</a><br/></td></tr>
<tr class="separator:ab4f4b9381d8d1c6ede3ef66028cd6b42"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a442a4d1a69906395b7ac683b15344229"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">SvmModelParameterSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a442a4d1a69906395b7ac683b15344229">mp_</a></td></tr>
<tr class="memdesc:a442a4d1a69906395b7ac683b15344229"><td class="mdescLeft"> </td><td class="mdescRight">set of model parameters read from model file <a href="#a442a4d1a69906395b7ac683b15344229">More...</a><br/></td></tr>
<tr class="separator:a442a4d1a69906395b7ac683b15344229"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6c6c1213fef424b3e47b9f16e0afed1"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a>, bool > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ae6c6c1213fef424b3e47b9f16e0afed1">hide_type_</a></td></tr>
<tr class="memdesc:ae6c6c1213fef424b3e47b9f16e0afed1"><td class="mdescLeft"> </td><td class="mdescRight">whether ion types are hidden or not <a href="#ae6c6c1213fef424b3e47b9f16e0afed1">More...</a><br/></td></tr>
<tr class="separator:ae6c6c1213fef424b3e47b9f16e0afed1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-static-attribs"></a>
Static Protected Attributes</h2></td></tr>
<tr class="memitem:a6488f3ef2246dcc142791a66eab4bf7a"><td class="memItemLeft" align="right" valign="top">static std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a6488f3ef2246dcc142791a66eab4bf7a">aa_to_index_</a></td></tr>
<tr class="memdesc:a6488f3ef2246dcc142791a66eab4bf7a"><td class="mdescLeft"> </td><td class="mdescRight">map AA to integers <a href="#a6488f3ef2246dcc142791a66eab4bf7a">More...</a><br/></td></tr>
<tr class="separator:a6488f3ef2246dcc142791a66eab4bf7a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaf924b0e5c8dd84daeb1705aaf1d01bc"><td class="memItemLeft" align="right" valign="top">static std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <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_1SvmTheoreticalSpectrumGenerator.html#aaf924b0e5c8dd84daeb1705aaf1d01bc">hydrophobicity_</a></td></tr>
<tr class="memdesc:aaf924b0e5c8dd84daeb1705aaf1d01bc"><td class="mdescLeft"> </td><td class="mdescRight">hydrophobicity values for each AA <a href="#aaf924b0e5c8dd84daeb1705aaf1d01bc">More...</a><br/></td></tr>
<tr class="separator:aaf924b0e5c8dd84daeb1705aaf1d01bc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a08803b692e19f653b8c0a1a62fcda611"><td class="memItemLeft" align="right" valign="top">static std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <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_1SvmTheoreticalSpectrumGenerator.html#a08803b692e19f653b8c0a1a62fcda611">helicity_</a></td></tr>
<tr class="memdesc:a08803b692e19f653b8c0a1a62fcda611"><td class="mdescLeft"> </td><td class="mdescRight">helicity values for each AA <a href="#a08803b692e19f653b8c0a1a62fcda611">More...</a><br/></td></tr>
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<tr class="memitem:a3af386eefaea14316abc3da0c3a6bbee"><td class="memItemLeft" align="right" valign="top">static std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <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_1SvmTheoreticalSpectrumGenerator.html#a3af386eefaea14316abc3da0c3a6bbee">basicity_</a></td></tr>
<tr class="memdesc:a3af386eefaea14316abc3da0c3a6bbee"><td class="mdescLeft"> </td><td class="mdescRight">basicity values for each AA <a href="#a3af386eefaea14316abc3da0c3a6bbee">More...</a><br/></td></tr>
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<tr class="memitem:ab1cb112813b80accd3a3adf8aac0f8c8"><td class="memItemLeft" align="right" valign="top">static bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ab1cb112813b80accd3a3adf8aac0f8c8">initializedMaps_</a></td></tr>
<tr class="memdesc:ab1cb112813b80accd3a3adf8aac0f8c8"><td class="mdescLeft"> </td><td class="mdescRight">flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized <a href="#ab1cb112813b80accd3a3adf8aac0f8c8">More...</a><br/></td></tr>
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Friends</h2></td></tr>
<tr class="memitem:a44946b9432a4504dfeb43f7ac732d018"><td class="memItemLeft" align="right" valign="top">class </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#a44946b9432a4504dfeb43f7ac732d018">SvmTheoreticalSpectrumGeneratorTrainer</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Simulates ms2 spectra with support vector machines. </p>
<p>The models are generated with the <a class="el" href="UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a>. <br/>
Two modes are supported:<br/>
</p>
<ul>
<li>Only a prediction of abundant/missing is performed and for abundant peaks are generated with user defined intensity. <br/>
</li>
<li>The intensity is predicted using SVM-regression (only for the primary ion types b and y). For the secondary types a Bayesian model is used.</li>
</ul>
<p>Currently, only a test model is shipped with <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a>.<br/>
Please find trained models at: <a href="http://sourceforge.net/projects/open-ms/files/Supplementary/Simulation/">http://sourceforge.net/projects/open-ms/files/Supplementary/Simulation/</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>svm_mode</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">whether to predict abundant/missing using SVC (0) or predict intensities using SVR (1)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>model_file_name</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">examples/simulation/SvmMSim.model</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Name of the probabilistic Model file</td>
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<tr>
<td style="vertical-align:top"><b>add_isotopes</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 1 isotope peaks of the product ion peaks are added</td>
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<tr>
<td style="vertical-align:top"><b>max_isotope</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">Defines the maximal isotopic peak which is added, add_isotopes must be set to 1</td>
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<tr>
<td style="vertical-align:top"><b>add_metainfo</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">Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++</td>
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<tr>
<td style="vertical-align:top"><b>add_first_prefix_ion</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 e.g. b1 ions are added</td>
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<tr>
<td style="vertical-align:top"><b>hide_y_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">Add peaks of y-ions to the spectrum</td>
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<tr>
<td style="vertical-align:top"><b>hide_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">Add peaks of y-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_b_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">Add peaks of b-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_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">Add peaks of b-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_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">Add peaks of a-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_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">Add peaks of c-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_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">Add peaks of x-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_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">Add peaks of z-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>hide_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">Adds common losses to those ion expect to have them, only water and ammonia loss is considered</td>
</tr>
<tr>
<td style="vertical-align:top"><b>y_intensity</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">Intensity of the y-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>b_intensity</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">Intensity of the b-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>a_intensity</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">Intensity of the a-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>c_intensity</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">Intensity of the c-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>x_intensity</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">Intensity of the x-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>z_intensity</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">Intensity of the z-ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>relative_loss_intensity</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">Intensity of loss ions, in relation to the intact ion intensity</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>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef std::map<<a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html#ad0f94e7ae2de2380f906f0e3110d58cc">IntensityMap</a></td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </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_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> </td>
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<p>Default constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</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_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a> </td>
<td>(</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"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> generateDescriptorSet_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> </td>
<td class="paramname"><em>peptide</em>, </td>
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<td class="paramname"><em>position</em>, </td>
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<td class="paramname"><em>type</em>, </td>
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<td class="paramname"><em>precursor_charge</em>, </td>
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<td class="paramname"><em>desc_set</em> </td>
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<p>generate the desciptors for an input peptide and a given fragmentation position </p>
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<td class="memname">const std::vector<<a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1IonType.html">IonType</a>>& getIonTypes </td>
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<p>return the set of ion types that are modeled by the loaded SVMs </p>
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<td class="memname">static void initializeMaps_ </td>
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<p>initialized the maps </p>
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<td class="memname">void load </td>
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<p>Load a trained Svm and Prob. models. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGenerator.html">SvmTheoreticalSpectrumGenerator</a>& operator= </td>
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<p>Assignment operator. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> ResidueTypeToString_ </td>
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<p>Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation. </p>
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<td class="memname">void scaleDescriptorSet_ </td>
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<p>scale value to the intervall [lower,max] given the maximal and minimal entries for a feature </p>
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<p>scale value to the intervall [lower,max] given the maximal and minimal entries for a feature </p>
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<td class="memname">void simulate </td>
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<p>Generate the MS/MS according to the given probabilistic model. </p>
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<p>This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. </p>
<p>Also call it at the end of the derived classes' copy constructor and assignment operator.</p>
<p>The default implementation is empty. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Friends And Related Function Documentation</h2>
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<td class="memname">friend class <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">SvmTheoreticalSpectrumGeneratorTrainer</a></td>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname">std::map<<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>> aa_to_index_</td>
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<p>map AA to integers </p>
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<p>basicity values for each AA </p>
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<p>helicity values for each AA </p>
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<p>whether ion types are hidden or not </p>
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<p>hydrophobicity values for each AA </p>
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<p>flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized </p>
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<td class="memname"><a class="el" href="structOpenMS_1_1SvmTheoreticalSpectrumGenerator_1_1SvmModelParameterSet.html">SvmModelParameterSet</a> mp_</td>
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<p>set of model parameters read from model file </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> precursor_charge_</td>
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<p>charge of the precursors used for training </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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