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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_1RTSimulation.html">RTSimulation</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">RTSimulation Class Reference<div class="ingroups"><a class="el" href="group__Simulation.html">Simulation</a></div></div> </div>
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<p>Simulates/Predicts retention times for peptides or peptide separation.
<a href="classOpenMS_1_1RTSimulation.html#details">More...</a></p>
<p><code>#include <<a class="el" href="RTSimulation_8h_source.html">OpenMS/SIMULATION/RTSimulation.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for RTSimulation:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1RTSimulation.png" usemap="#RTSimulation_map" alt=""/>
<map id="RTSimulation_map" name="RTSimulation_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,133,24"/>
</map>
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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:abcc157a2a6906a52dd4ac330174f93f5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#abcc157a2a6906a52dd4ac330174f93f5">operator=</a> (const <a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a> &source)</td></tr>
<tr class="memdesc:abcc157a2a6906a52dd4ac330174f93f5"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#abcc157a2a6906a52dd4ac330174f93f5">More...</a><br/></td></tr>
<tr class="separator:abcc157a2a6906a52dd4ac330174f93f5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a127b17b4ac01a548052f7c1fac05f11b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a127b17b4ac01a548052f7c1fac05f11b">predictRT</a> (<a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &features)</td></tr>
<tr class="memdesc:a127b17b4ac01a548052f7c1fac05f11b"><td class="mdescLeft"> </td><td class="mdescRight">Predict retention times for given peptide features based for <a class="el" href="classOpenMS_1_1HPLC.html" title="Representation of a HPLC experiment. ">HPLC</a> or CE. <a href="#a127b17b4ac01a548052f7c1fac05f11b">More...</a><br/></td></tr>
<tr class="separator:a127b17b4ac01a548052f7c1fac05f11b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0f66312fff6e3881b6384ed786cfffce"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a0f66312fff6e3881b6384ed786cfffce">predictContaminantsRT</a> (<a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &)</td></tr>
<tr class="memdesc:a0f66312fff6e3881b6384ed786cfffce"><td class="mdescLeft"> </td><td class="mdescRight">Set retention times randomly for given contaminants. <a href="#a0f66312fff6e3881b6384ed786cfffce">More...</a><br/></td></tr>
<tr class="separator:a0f66312fff6e3881b6384ed786cfffce"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afffd136fa6fd02f50c50c461e660b8f6"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#afffd136fa6fd02f50c50c461e660b8f6">isRTColumnOn</a> () const </td></tr>
<tr class="memdesc:afffd136fa6fd02f50c50c461e660b8f6"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if a RT column was simulated. <a href="#afffd136fa6fd02f50c50c461e660b8f6">More...</a><br/></td></tr>
<tr class="separator:afffd136fa6fd02f50c50c461e660b8f6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a826df0019cfb51d6cd7435448f3efff1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a826df0019cfb51d6cd7435448f3efff1">wrapSVM</a> (std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > &peptide_sequences, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &predicted_retention_times)</td></tr>
<tr class="memdesc:a826df0019cfb51d6cd7435448f3efff1"><td class="mdescLeft"> </td><td class="mdescRight">Wrapper for the SVM RT Prediction (<a class="el" href="classOpenMS_1_1HPLC.html" title="Representation of a HPLC experiment. ">HPLC</a>) using AASequences. <a href="#a826df0019cfb51d6cd7435448f3efff1">More...</a><br/></td></tr>
<tr class="separator:a826df0019cfb51d6cd7435448f3efff1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa5bbec7cdd72c51a4afe57f37a47dca3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#aa5bbec7cdd72c51a4afe57f37a47dca3">getGradientTime</a> () const </td></tr>
<tr class="separator:aa5bbec7cdd72c51a4afe57f37a47dca3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2a79764f03f61629914d871d908d7550"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a2a79764f03f61629914d871d908d7550">createExperiment</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment)</td></tr>
<tr class="memdesc:a2a79764f03f61629914d871d908d7550"><td class="mdescLeft"> </td><td class="mdescRight">Size experiment and assign retention time grid. <a href="#a2a79764f03f61629914d871d908d7550">More...</a><br/></td></tr>
<tr class="separator:a2a79764f03f61629914d871d908d7550"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors and Destructors</div></td></tr>
<tr class="memitem:afa1336d88c4835129380be4566582d81"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#afa1336d88c4835129380be4566582d81">RTSimulation</a> (const <a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &random_generator)</td></tr>
<tr class="memdesc:afa1336d88c4835129380be4566582d81"><td class="mdescLeft"> </td><td class="mdescRight">Constructor taking a random generator. <a href="#afa1336d88c4835129380be4566582d81">More...</a><br/></td></tr>
<tr class="separator:afa1336d88c4835129380be4566582d81"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a14b187e23f1d6f1198426924771d75"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a4a14b187e23f1d6f1198426924771d75">RTSimulation</a> (const <a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a> &source)</td></tr>
<tr class="memdesc:a4a14b187e23f1d6f1198426924771d75"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a4a14b187e23f1d6f1198426924771d75">More...</a><br/></td></tr>
<tr class="separator:a4a14b187e23f1d6f1198426924771d75"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8721f72666b5a0fcc6274a5c2481f455"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a8721f72666b5a0fcc6274a5c2481f455">~RTSimulation</a> ()</td></tr>
<tr class="memdesc:a8721f72666b5a0fcc6274a5c2481f455"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a8721f72666b5a0fcc6274a5c2481f455">More...</a><br/></td></tr>
<tr class="separator:a8721f72666b5a0fcc6274a5c2481f455"><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:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">Synchronize members with param class. <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-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a1755a34bd4d88feb6a87a209273177eb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> const * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a1755a34bd4d88feb6a87a209273177eb">rnd_gen_</a></td></tr>
<tr class="memdesc:a1755a34bd4d88feb6a87a209273177eb"><td class="mdescLeft"> </td><td class="mdescRight">Random number generator. <a href="#a1755a34bd4d88feb6a87a209273177eb">More...</a><br/></td></tr>
<tr class="separator:a1755a34bd4d88feb6a87a209273177eb"><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="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a2318631d862ec8e34f7ffefa4706c503"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a2318631d862ec8e34f7ffefa4706c503">RTSimulation</a> ()</td></tr>
<tr class="memdesc:a2318631d862ec8e34f7ffefa4706c503"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a2318631d862ec8e34f7ffefa4706c503">More...</a><br/></td></tr>
<tr class="separator:a2318631d862ec8e34f7ffefa4706c503"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a592956c92badca126cec3abd62da8d67"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a592956c92badca126cec3abd62da8d67">setDefaultParams_</a> ()</td></tr>
<tr class="memdesc:a592956c92badca126cec3abd62da8d67"><td class="mdescLeft"> </td><td class="mdescRight">Set default parameters. <a href="#a592956c92badca126cec3abd62da8d67">More...</a><br/></td></tr>
<tr class="separator:a592956c92badca126cec3abd62da8d67"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af8d4e3deed965d52f90f788ce339c831"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#af8d4e3deed965d52f90f788ce339c831">noRTColumn_</a> (<a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &)</td></tr>
<tr class="memdesc:af8d4e3deed965d52f90f788ce339c831"><td class="mdescLeft"> </td><td class="mdescRight">Simply set all retention times to -1. <a href="#af8d4e3deed965d52f90f788ce339c831">More...</a><br/></td></tr>
<tr class="separator:af8d4e3deed965d52f90f788ce339c831"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af85a4b66f77e184b1f46ec180a8bced1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#af85a4b66f77e184b1f46ec180a8bced1">smoothRTDistortion_</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment)</td></tr>
<tr class="memdesc:af85a4b66f77e184b1f46ec180a8bced1"><td class="mdescLeft"> </td><td class="mdescRight">smoothes the simulated distortion for the elution profiles with a moving average filter of size 3 <a href="#af85a4b66f77e184b1f46ec180a8bced1">More...</a><br/></td></tr>
<tr class="separator:af85a4b66f77e184b1f46ec180a8bced1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae771da7f17dc446c06274e2f068ba8df"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#ae771da7f17dc446c06274e2f068ba8df">calculateMT_</a> (<a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &features, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &predicted_retention_times)</td></tr>
<tr class="separator:ae771da7f17dc446c06274e2f068ba8df"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae388da65872d2621cff43e34bebd4924"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#ae388da65872d2621cff43e34bebd4924">getChargeContribution_</a> (<a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classdouble.html">double</a> > &q_cterm, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classdouble.html">double</a> > &q_nterm, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classdouble.html">double</a> > &q_aa_basic, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="classdouble.html">double</a> > &q_aa_acidic)</td></tr>
<tr class="separator:ae388da65872d2621cff43e34bebd4924"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:a2ca80ee9bf721feebb4f9db372633a08"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a2ca80ee9bf721feebb4f9db372633a08">rt_model_file_</a></td></tr>
<tr class="separator:a2ca80ee9bf721feebb4f9db372633a08"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aad41a72aba947f4f94385e180f304ea0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#aad41a72aba947f4f94385e180f304ea0">total_gradient_time_</a></td></tr>
<tr class="memdesc:aad41a72aba947f4f94385e180f304ea0"><td class="mdescLeft"> </td><td class="mdescRight">Total gradient time. <a href="#aad41a72aba947f4f94385e180f304ea0">More...</a><br/></td></tr>
<tr class="separator:aad41a72aba947f4f94385e180f304ea0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a41136c7b340c11631ca29175229a4b18"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#a41136c7b340c11631ca29175229a4b18">gradient_min_</a></td></tr>
<tr class="memdesc:a41136c7b340c11631ca29175229a4b18"><td class="mdescLeft"> </td><td class="mdescRight">gradient ranges <a href="#a41136c7b340c11631ca29175229a4b18">More...</a><br/></td></tr>
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<tr class="memdesc:a630005e5d32afe42a191a84ed1307171"><td class="mdescLeft"> </td><td class="mdescRight">Maximal observed gradient time. <a href="#a630005e5d32afe42a191a84ed1307171">More...</a><br/></td></tr>
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<tr class="memdesc:a5070ae6e05eee20e2092127475da3951"><td class="mdescLeft"> </td><td class="mdescRight">bin size in rt dimension <a href="#a5070ae6e05eee20e2092127475da3951">More...</a><br/></td></tr>
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<tr class="memitem:aa23e9628bc5d51649d0f0f6692a51847"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#aa23e9628bc5d51649d0f0f6692a51847">egh_tau_location_</a></td></tr>
<tr class="memdesc:aa23e9628bc5d51649d0f0f6692a51847"><td class="mdescLeft"> </td><td class="mdescRight">EGH tau value. <a href="#aa23e9628bc5d51649d0f0f6692a51847">More...</a><br/></td></tr>
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<tr class="memitem:aff67422b2f91eb7c4b0c07310a21c62b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#aff67422b2f91eb7c4b0c07310a21c62b">egh_tau_scale_</a></td></tr>
<tr class="memdesc:aff67422b2f91eb7c4b0c07310a21c62b"><td class="mdescLeft"> </td><td class="mdescRight">EGH tau scale parameter of the lorentzian variation. <a href="#aff67422b2f91eb7c4b0c07310a21c62b">More...</a><br/></td></tr>
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<tr class="memdesc:a87bc858f8d96b32af415e416942d98b1"><td class="mdescLeft"> </td><td class="mdescRight">EGH sigma value. <a href="#a87bc858f8d96b32af415e416942d98b1">More...</a><br/></td></tr>
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<tr class="memitem:ab05d1f4edb0b7f9c544dd83b61b77b2e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RTSimulation.html#ab05d1f4edb0b7f9c544dd83b61b77b2e">egh_variance_scale_</a></td></tr>
<tr class="memdesc:ab05d1f4edb0b7f9c544dd83b61b77b2e"><td class="mdescLeft"> </td><td class="mdescRight">EGH sigma scale parameter of the lorentzian variation. <a href="#ab05d1f4edb0b7f9c544dd83b61b77b2e">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Simulates/Predicts retention times for peptides or peptide separation. </p>
<p>The retention times for the different peptides are determined based on a SVM model or are all set to -1 in case of simulations without a <a class="el" href="classOpenMS_1_1HPLC.html" title="Representation of a HPLC experiment. ">HPLC</a> column.</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>rt_column</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">HPLC</td>
<td style="vertical-align:top">none, HPLC, CE</td><td style="vertical-align:top">Modelling of an RT or CE column</td>
</tr>
<tr>
<td style="vertical-align:top"><b>auto_scale</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">Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence.</td>
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<tr>
<td style="vertical-align:top"><b>total_gradient_time</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2500</td>
<td style="vertical-align:top">min: 1e-05</td><td style="vertical-align:top">The duration [s] of the gradient.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>sampling_rate</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0.01 max: 60</td><td style="vertical-align:top">Time interval [s] between consecutive scans</td>
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<tr>
<td style="vertical-align:top"><b>scan_window:min</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">500</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Start of RT Scan Window [s]</td>
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<tr>
<td style="vertical-align:top"><b>scan_window:max</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1500</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">End of RT Scan Window [s]</td>
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<tr>
<td style="vertical-align:top"><b><span title="Random component that simulates technical/biological variation">variation</span>:feature_stddev</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">Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)</td>
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<tr>
<td style="vertical-align:top"><b><span title="Random component that simulates technical/biological variation">variation</span>:affine_offset</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Global offset in retention time [s] from predicted model</td>
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<tr>
<td style="vertical-align:top"><b><span title="Random component that simulates technical/biological variation">variation</span>:affine_scale</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">Global scaling in retention time from predicted model</td>
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<tr>
<td style="vertical-align:top"><b>column_condition:distortion</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0 max: 10</td><td style="vertical-align:top">Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4.</td>
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<tr>
<td style="vertical-align:top"><b>profile_shape:<span title="Width of the EGH elution shape, i.e. the sigma^2 parameter, which is computed using 'value' + rnd_cauchy('variance')">width</span>:value</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">9</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s].</td>
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<tr>
<td style="vertical-align:top"><b>profile_shape:<span title="Width of the EGH elution shape, i.e. the sigma^2 parameter, which is computed using 'value' + rnd_cauchy('variance')">width</span>:variance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1.6</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0).</td>
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<tr>
<td style="vertical-align:top"><b>profile_shape:<span title="Skewness of the EGH elution shape, i.e. the tau parameter, which is computed using 'value' + rnd_cauchy('variance')">skewness</span>:value</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">Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>profile_shape:<span title="Skewness of the EGH elution shape, i.e. the tau parameter, which is computed using 'value' + rnd_cauchy('variance')">skewness</span>:variance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.3</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0).</td>
</tr>
<tr>
<td style="vertical-align:top"><b>HPLC:model_file</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">examples/simulation/RTPredict.model</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">SVM model for retention time prediction</td>
</tr>
<tr>
<td style="vertical-align:top"><b>CE:pH</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 0 max: 14</td><td style="vertical-align:top">pH of buffer</td>
</tr>
<tr>
<td style="vertical-align:top"><b>CE:alpha</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Exponent Alpha used to calculate mobility</td>
</tr>
<tr>
<td style="vertical-align:top"><b>CE:mu_eo</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0 max: 5</td><td style="vertical-align:top">Electroosmotic flow</td>
</tr>
<tr>
<td style="vertical-align:top"><b>CE:lenght_d</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">70</td>
<td style="vertical-align:top">min: 0 max: 1000</td><td style="vertical-align:top">Length of capillary [cm] from injection site to MS</td>
</tr>
<tr>
<td style="vertical-align:top"><b>CE:length_total</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">75</td>
<td style="vertical-align:top">min: 0 max: 1000</td><td style="vertical-align:top">Total length of capillary [cm]</td>
</tr>
<tr>
<td style="vertical-align:top"><b>CE:voltage</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1000</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Voltage applied to capillary</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">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> & </td>
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<p>Constructor taking a random generator. </p>
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<p>Copy constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a> </td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a> </td>
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<p>Default constructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void calculateMT_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> & </td>
<td class="paramname"><em>features</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>predicted_retention_times</em> </td>
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<p>Wrapper for the Migration time calculation (CE)</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">features</td><td>will get modified with metavalue "RT_CE_width_factor", describing widening of MT shape. </td></tr>
<tr><td class="paramname">predicted_retention_times</td><td>will contain afterwards the predicted retention times. </td></tr>
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<td class="memname">void createExperiment </td>
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<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em></td><td>)</td>
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<p>Size experiment and assign retention time grid. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> getGradientTime </td>
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<p>Returns true if a RT column was simulated. </p>
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<p>Simply set all retention times to -1. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1RTSimulation.html">RTSimulation</a>& operator= </td>
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<p>Assignment operator. </p>
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<td class="memname">void predictContaminantsRT </td>
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<p>Set retention times randomly for given contaminants. </p>
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<td class="memname">void predictRT </td>
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<p>Predict retention times for given peptide features based for <a class="el" href="classOpenMS_1_1HPLC.html" title="Representation of a HPLC experiment. ">HPLC</a> or CE. </p>
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<p>Set default parameters. </p>
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<td class="paramname"><em>experiment</em></td><td>)</td>
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<p>smoothes the simulated distortion for the elution profiles with a moving average filter of size 3 </p>
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<p>Synchronize members with param class. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<p>Wrapper for the SVM RT Prediction (<a class="el" href="classOpenMS_1_1HPLC.html" title="Representation of a HPLC experiment. ">HPLC</a>) using AASequences. </p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<p>EGH tau value. </p>
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<p>EGH tau scale parameter of the lorentzian variation. </p>
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<p>EGH sigma value. </p>
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<p>EGH sigma scale parameter of the lorentzian variation. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> gradient_max_</td>
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<p>Maximal observed gradient time. </p>
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<p>gradient ranges </p>
<p>Minimal observed gradient time </p>
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<td class="memname"><a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> const* rnd_gen_</td>
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<p>Random number generator. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">OpenMS::String</a> rt_model_file_</td>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> rt_sampling_rate_</td>
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<p>bin size in rt dimension </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> total_gradient_time_</td>
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<p>Total gradient time. </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 11:19:33 using doxygen 1.8.5</font></TD>
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