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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_1MSSim.html">MSSim</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
<a href="#pro-methods">Protected Member Functions</a> |
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<div class="title">MSSim Class Reference<div class="ingroups"><a class="el" href="group__Simulation.html">Simulation</a></div></div> </div>
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<p>Central class for simulation of mass spectrometry experiments.
<a href="classOpenMS_1_1MSSim.html#details">More...</a></p>
<p><code>#include <<a class="el" href="MSSim_8h_source.html">OpenMS/SIMULATION/MSSim.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for MSSim:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1MSSim.png" usemap="#MSSim_map" alt=""/>
<map id="MSSim_map" name="MSSim_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,133,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="143,0,276,24"/>
</map>
</div></div>
<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:a17ed13f970933c372d59a01d28e8f088"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a17ed13f970933c372d59a01d28e8f088">simulate</a> (const <a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &rnd_gen, <a class="el" href="classOpenMS_1_1SampleChannels.html">SampleChannels</a> &peptides)</td></tr>
<tr class="memdesc:a17ed13f970933c372d59a01d28e8f088"><td class="mdescLeft"> </td><td class="mdescRight">General purpose function to simulate a mass spectrometry run. <a href="#a17ed13f970933c372d59a01d28e8f088">More...</a><br/></td></tr>
<tr class="separator:a17ed13f970933c372d59a01d28e8f088"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3b17f7b490e42ed1ae610983dd703e20"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a3b17f7b490e42ed1ae610983dd703e20">getExperiment</a> () const </td></tr>
<tr class="memdesc:a3b17f7b490e42ed1ae610983dd703e20"><td class="mdescLeft"> </td><td class="mdescRight">Access the simulated experiment. <a href="#a3b17f7b490e42ed1ae610983dd703e20">More...</a><br/></td></tr>
<tr class="separator:a3b17f7b490e42ed1ae610983dd703e20"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6e925d5b69cbc6ea51a94f39ae11766f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a6e925d5b69cbc6ea51a94f39ae11766f">getSimulatedFeatures</a> () const </td></tr>
<tr class="memdesc:a6e925d5b69cbc6ea51a94f39ae11766f"><td class="mdescLeft"> </td><td class="mdescRight">Access the simulated features. <a href="#a6e925d5b69cbc6ea51a94f39ae11766f">More...</a><br/></td></tr>
<tr class="separator:a6e925d5b69cbc6ea51a94f39ae11766f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a22d35cb0ae2a4d19e44f6ac8cd4f57c9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a22d35cb0ae2a4d19e44f6ac8cd4f57c9">getChargeConsensus</a> ()</td></tr>
<tr class="memdesc:a22d35cb0ae2a4d19e44f6ac8cd4f57c9"><td class="mdescLeft"> </td><td class="mdescRight">Access the charge consensus map of simulated features. <a href="#a22d35cb0ae2a4d19e44f6ac8cd4f57c9">More...</a><br/></td></tr>
<tr class="separator:a22d35cb0ae2a4d19e44f6ac8cd4f57c9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab19747dafba8e0da8bed29b553a1e056"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#ab19747dafba8e0da8bed29b553a1e056">getContaminants</a> () const </td></tr>
<tr class="memdesc:ab19747dafba8e0da8bed29b553a1e056"><td class="mdescLeft"> </td><td class="mdescRight">Access the contaminants feature map of simulated features. <a href="#ab19747dafba8e0da8bed29b553a1e056">More...</a><br/></td></tr>
<tr class="separator:ab19747dafba8e0da8bed29b553a1e056"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aac38d440d2e98f886eb076696c8c507b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#aac38d440d2e98f886eb076696c8c507b">getLabelingConsensus</a> ()</td></tr>
<tr class="memdesc:aac38d440d2e98f886eb076696c8c507b"><td class="mdescLeft"> </td><td class="mdescRight">Access the labeling consensus map of simulated features. <a href="#aac38d440d2e98f886eb076696c8c507b">More...</a><br/></td></tr>
<tr class="separator:aac38d440d2e98f886eb076696c8c507b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5af1a8d358b9719623b9850903856a6b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> const & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a5af1a8d358b9719623b9850903856a6b">getPeakMap</a> () const </td></tr>
<tr class="memdesc:a5af1a8d358b9719623b9850903856a6b"><td class="mdescLeft"> </td><td class="mdescRight">Access the labeling consensus map of simulated features. <a href="#a5af1a8d358b9719623b9850903856a6b">More...</a><br/></td></tr>
<tr class="separator:a5af1a8d358b9719623b9850903856a6b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:add731c5c3c45ce275597b6fefbed136b"><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_1MSSim.html#add731c5c3c45ce275597b6fefbed136b">getParameters</a> () const </td></tr>
<tr class="memdesc:add731c5c3c45ce275597b6fefbed136b"><td class="mdescLeft"> </td><td class="mdescRight">Returns the default parameters for simulation including the labeling technique with name <code>labeling_name</code>. <a href="#add731c5c3c45ce275597b6fefbed136b">More...</a><br/></td></tr>
<tr class="separator:add731c5c3c45ce275597b6fefbed136b"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors and Destructors</div></td></tr>
<tr class="memitem:a063de8c0272b877c59781b899546e057"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a063de8c0272b877c59781b899546e057">MSSim</a> ()</td></tr>
<tr class="memdesc:a063de8c0272b877c59781b899546e057"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a063de8c0272b877c59781b899546e057">More...</a><br/></td></tr>
<tr class="separator:a063de8c0272b877c59781b899546e057"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8bc8886f081bb9bd5989e50564b4f3f9"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a8bc8886f081bb9bd5989e50564b4f3f9">~MSSim</a> ()</td></tr>
<tr class="memdesc:a8bc8886f081bb9bd5989e50564b4f3f9"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a8bc8886f081bb9bd5989e50564b4f3f9">More...</a><br/></td></tr>
<tr class="separator:a8bc8886f081bb9bd5989e50564b4f3f9"><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>
<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE! <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of progress log being used. <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the progress display. <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the current progress. <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Ends the progress display. <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><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:a63efff66245e023f272fa69fee0631fe"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a63efff66245e023f272fa69fee0631fe">syncParams_</a> (<a class="el" href="classOpenMS_1_1Param.html">Param</a> &p, bool to_outer)</td></tr>
<tr class="memdesc:a63efff66245e023f272fa69fee0631fe"><td class="mdescLeft"> </td><td class="mdescRight">handle global params <a href="#a63efff66245e023f272fa69fee0631fe">More...</a><br/></td></tr>
<tr class="separator:a63efff66245e023f272fa69fee0631fe"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5310d1bcc2e2f011b66168535805efa4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a5310d1bcc2e2f011b66168535805efa4">createFeatureMap_</a> (const <a class="el" href="classOpenMS_1_1SampleProteins.html">SampleProteins</a> &peptides, <a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &features, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> map_index)</td></tr>
<tr class="memdesc:a5310d1bcc2e2f011b66168535805efa4"><td class="mdescLeft"> </td><td class="mdescRight">Convert a list of peptides with given abundance values into a <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>. <a href="#a5310d1bcc2e2f011b66168535805efa4">More...</a><br/></td></tr>
<tr class="separator:a5310d1bcc2e2f011b66168535805efa4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.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>
</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:a950bc488db2bf59a683c15ce7f0c56d1"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#a950bc488db2bf59a683c15ce7f0c56d1">experiment_</a></td></tr>
<tr class="separator:a950bc488db2bf59a683c15ce7f0c56d1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa071bc9b9f1a930addc72519b4c31d39"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#aa071bc9b9f1a930addc72519b4c31d39">peak_map_</a></td></tr>
<tr class="separator:aa071bc9b9f1a930addc72519b4c31d39"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afe06eb57fde086ce8eb4a4c5ef6bc1dc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MSSim.html#afe06eb57fde086ce8eb4a4c5ef6bc1dc">feature_maps_</a></td></tr>
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<tr class="memdesc:a813cce92a0e34c5f83c0798cae8a61ae"><td class="mdescLeft"> </td><td class="mdescRight">Labeling functionality. <a href="#a813cce92a0e34c5f83c0798cae8a61ae">More...</a><br/></td></tr>
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</table><table class="memberdecls">
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Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
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}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
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<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
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<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
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<tr class="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>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
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<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
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<tr class="memitem:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td></tr>
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<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
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<tr class="memitem:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">time_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
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<tr class="inherit_header pro_static_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
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</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Central class for simulation of mass spectrometry experiments. </p>
<p>This implementation is an extended and rewritten version of the concepts and ideas presented in:<br/>
</p>
<p>Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gropl, Oliver Kohlbacher, and Knut Reinert.<br/>
LC-MSsim - A simulation software for liquid chromatography mass spectrometry data.<br/>
<em>BMC Bioinformatics</em> 9:423, 2008. </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>Digestion:enzyme</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">Trypsin</td>
<td style="vertical-align:top">Trypsin, none</td><td style="vertical-align:top">Enzyme to use for digestion (select 'none' to skip digestion)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Digestion:model</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">naive</td>
<td style="vertical-align:top">trained, naive</td><td style="vertical-align:top">The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Digestion:min_peptide_length</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Minimum peptide length after digestion (shorter ones will be discarded)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Digestion:model_trained:threshold</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: -2 max: 4</td><td style="vertical-align:top">Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Digestion:model_naive:missed_cleavages</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Maximum number of missed cleavages considered. All possible resulting peptides will be created.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT:<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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT:<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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT:<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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RT: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>RT: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>RT: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>RT: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>RT: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>RT: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>RT: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>RT: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>RT: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>
<tr>
<td style="vertical-align:top"><b>Detectability:dt_simulation_on</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">Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Detectability:min_detect</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Minimum peptide detectability accepted. Peptides with a lower score will be removed</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Detectability:dt_model_file</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">examples/simulation/DTPredict.model</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">SVM model for peptide detectability prediction</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Ionization:esi:ionized_residues</b></td>
<td style="vertical-align:top">string list</td><td style="vertical-align:top">[Arg, Lys, His]</td>
<td style="vertical-align:top">Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Sec, Ser, Thr, Val, Trp, Tyr</td><td style="vertical-align:top">List of residues (as three letter code) that will be considered during ES ionization. The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Ionization:esi:charge_impurity</b></td>
<td style="vertical-align:top">string list</td><td style="vertical-align:top">[H+:1]</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally), e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])</td>
</tr>
<tr>
<td style="vertical-align:top"><i>Ionization:esi:max_impurity_set_size</i></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">Maximal @#combinations of charge impurities allowed (each generating one feature) per charge state. E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Ionization:esi:ionization_probability</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.8</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Probability for the binomial distribution of the ESI charge states</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Ionization:maldi:ionization_probabilities</b></td>
<td style="vertical-align:top">float list</td><td style="vertical-align:top">[0.9, 0.1]</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Ionization:mz:lower_measurement_limit</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">200</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Lower m/z detector limit.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>Ionization:mz:upper_measurement_limit</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2500</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Upper m/z detector limit.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:enabled</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">Enable RAW signal simulation? (select 'false' if you only need feature-maps)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:peak_shape</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">Gaussian</td>
<td style="vertical-align:top">Gaussian, Lorentzian</td><td style="vertical-align:top">Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:resolution:value</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">50000</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Instrument resolution at 400 Th.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:resolution:type</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">linear</td>
<td style="vertical-align:top">constant, linear, sqrt</td><td style="vertical-align:top">How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Baseline modeling for MALDI ionization">baseline</span>:scaling</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Scale of baseline. Set to 0 to disable simulation of baseline.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Baseline modeling for MALDI ionization">baseline</span>:shape</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:mz:sampling_points</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 2</td><td style="vertical-align:top">Number of raw data points per FWHM of the peak.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:contaminants:file</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">examples/simulation/contaminants.csv</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Contaminants file with sum formula and absolute RT interval. See 'OpenMS/examples/simulation/contaminants.txt' for details.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Random components that simulate biological and technical variations of the simulated data.">variation</span>:<span title="Shifts in mass to charge dimension of the simulated signals.">mz</span>:error_stddev</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Random components that simulate biological and technical variations of the simulated data.">variation</span>:<span title="Shifts in mass to charge dimension of the simulated signals.">mz</span>:error_mean</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Average systematic m/z error (Da)</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Random components that simulate biological and technical variations of the simulated data.">variation</span>:<span title="Variations in intensity to model randomness in feature intensity.">intensity</span>:scale</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Random components that simulate biological and technical variations of the simulated data.">variation</span>:<span title="Variations in intensity to model randomness in feature intensity.">intensity</span>:scale_stddev</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Parameters modeling noise in mass spectrometry measurements.">noise</span>:<span title="Parameters of Poisson and Exponential for shot noise modeling (set :rate OR :mean = 0 to disable).">shot</span>:rate</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Poisson rate of shot noise per unit m/z. Set this to 0 to disable simulation of shot noise.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Parameters modeling noise in mass spectrometry measurements.">noise</span>:<span title="Parameters of Poisson and Exponential for shot noise modeling (set :rate OR :mean = 0 to disable).">shot</span>:intensity-mean</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">Shot noise intensity mean (exponentially distributed with given mean).</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Parameters modeling noise in mass spectrometry measurements.">noise</span>:<span title="Parameters of Gaussian distribution for white noise modeling (set :mean AND :stddev = 0 to disable).">white</span>:mean</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Mean value of white noise being added to each measured signal.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Parameters modeling noise in mass spectrometry measurements.">noise</span>:<span title="Parameters of Gaussian distribution for white noise modeling (set :mean AND :stddev = 0 to disable).">white</span>:stddev</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Standard deviation of white noise being added to each measured signal.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Parameters modeling noise in mass spectrometry measurements.">noise</span>:<span title="Parameters of Gaussian distribution for detector noise modeling (set :mean AND :stddev = 0 to disable).">detector</span>:mean</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Mean value of the detector noise being added to the complete measurement.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawSignal:<span title="Parameters modeling noise in mass spectrometry measurements.">noise</span>:<span title="Parameters of Gaussian distribution for detector noise modeling (set :mean AND :stddev = 0 to disable).">detector</span>:stddev</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">Standard deviation of the detector noise being added to the complete measurement.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:status</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">disabled</td>
<td style="vertical-align:top">disabled, precursor, MS^E</td><td style="vertical-align:top">Create Tandem-MS scans?</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:tandem_mode</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top">min: 0 max: 2</td><td style="vertical-align:top">Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity <BR></td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:svm_model_set_file</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">examples/simulation/SvmModelSet.model</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">File containing the filenames of SVM Models for different charge variants</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ms2_spectra_per_rt_bin</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Number of allowed MS/MS spectra in a retention time bin.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:min_peak_distance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The minimal distance (in Da) of two peaks in one spectrum so that they can be selected.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:selection_window</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:exclude_overlapping_peaks</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 true overlapping or nearby peaks (within min_peak_distance) are excluded for selection.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:charge_filter</b></td>
<td style="vertical-align:top">int list</td><td style="vertical-align:top">[2, 3]</td>
<td style="vertical-align:top">min: 1 max: 5</td><td style="vertical-align:top">Charges considered for MS2 fragmentation.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion</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 true dynamic exclusion is applied.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:Exclusion:exclusion_time</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The time (in seconds) a feature is excluded.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1000</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">The maximal number of precursors in the inclusion list.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">960</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Minimal rt in seconds.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">3840</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Maximal rt in seconds.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">30</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">rt step size in seconds.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">rt window size in seconds.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.95</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimal protein probability for a protein to be considered identified.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight</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">Minimal pt weight of a precursor</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz</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">Minimal mz to be considered in protein based LP formulation.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">5000</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Minimal mz to be considered in protein based LP formulation.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule</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">Use peptide rule instead of minimal protein id probability</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.95</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:MS_E:add_single_spectra</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 true, the MS2 spectra for each peptide signal are included in the output (might be a lot). They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_losses</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">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>RawTandemSignal:TandemSim:Simple:add_precursor_peaks</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 peaks of the precursor to the spectrum, which happen to occur sometimes</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_abundant_immonium_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 most abundant immonium ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_y_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Add peaks of y-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_b_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Add peaks of b-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_a_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Add peaks of a-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_c_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Add peaks of c-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_x_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Add peaks of x-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:add_z_ions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Add peaks of z-ions to the spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple: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>RawTandemSignal:TandemSim:Simple: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>RawTandemSignal:TandemSim:Simple: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>RawTandemSignal:TandemSim:Simple: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>RawTandemSignal:TandemSim:Simple: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>RawTandemSignal:TandemSim:Simple: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>RawTandemSignal:TandemSim:Simple: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>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:precursor_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 precursor peak</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:precursor_H2O_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 H2O loss peak of the precursor</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:Simple:precursor_NH3_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 NH3 loss peak of the precursor</td>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:SVM: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:SVM: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:SVM: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:SVM: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:SVM: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>
</tr>
<tr>
<td style="vertical-align:top"><b>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>RawTandemSignal:TandemSim:SVM: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>
<tr>
<td style="vertical-align:top"><b>Global:ionization_type</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">ESI</td>
<td style="vertical-align:top">MALDI, ESI</td><td style="vertical-align:top">Type of Ionization (MALDI or ESI)</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>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1DetectabilitySimulation.html" title="Simulates peptide detectability. ">DetectabilitySimulation</a> </dd>
<dd>
<a class="el" href="classOpenMS_1_1DigestSimulation.html" title="Simulates protein digestion. ">DigestSimulation</a> </dd>
<dd>
<a class="el" href="classOpenMS_1_1IonizationSimulation.html" title="Simulates Protein ionization. ">IonizationSimulation</a> </dd>
<dd>
<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html" title="Simulates MS signals for a given set of peptides. ">RawMSSignalSimulation</a> </dd>
<dd>
<a class="el" href="classOpenMS_1_1RTSimulation.html" title="Simulates/Predicts retention times for peptides or peptide separation. ">RTSimulation</a> </dd></dl>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a class="anchor" id="a063de8c0272b877c59781b899546e057"></a>
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<td class="memname"><a class="el" href="classOpenMS_1_1MSSim.html">MSSim</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
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</table>
</div><div class="memdoc">
<p>Default constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1MSSim.html">MSSim</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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</div><div class="memdoc">
<p>Destructor. </p>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void createFeatureMap_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1SampleProteins.html">SampleProteins</a> & </td>
<td class="paramname"><em>peptides</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> & </td>
<td class="paramname"><em>features</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>map_index</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
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</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<p>Convert a list of peptides with given abundance values into a <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>. </p>
</div>
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<td class="memname"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>& getChargeConsensus </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
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<p>Access the charge consensus map of simulated features. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> const& getContaminants </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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</table>
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<p>Access the contaminants feature map of simulated features. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> const& getExperiment </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<p>Access the simulated experiment. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>& getLabelingConsensus </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Access the labeling consensus map of simulated features. </p>
</div>
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<td class="memname"><a class="el" href="classOpenMS_1_1Param.html">Param</a> getParameters </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<p>Returns the default parameters for simulation including the labeling technique with name <code>labeling_name</code>. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> const& getPeakMap </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<p>Access the labeling consensus map of simulated features. </p>
</div>
</div>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> const& getSimulatedFeatures </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
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<p>Access the simulated features. </p>
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<td class="memname">void simulate </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> & </td>
<td class="paramname"><em>rnd_gen</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1SampleChannels.html">SampleChannels</a> & </td>
<td class="paramname"><em>peptides</em> </td>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>General purpose function to simulate a mass spectrometry run. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">rnd_gen</td><td>GSL random number generator which will be passed to the different classes </td></tr>
<tr><td class="paramname">peptides</td><td>List of peptides and abundances that will be simulated </td></tr>
</table>
</dd>
</dl>
</div>
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<td class="memname">void syncParams_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td>
<td class="paramname"><em>p</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>to_outer</em> </td>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>handle global params </p>
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<td class="memname">void updateMembers_ </td>
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<td class="paramname"></td><td>)</td>
<td></td>
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<span class="mlabels"><span class="mlabel">private</span><span class="mlabel">virtual</span></span> </td>
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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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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> consensus_map_</td>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> contaminants_map_</td>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> experiment_</td>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a5377a8d620ef376a0b1eb2503b847e79">FeatureMapSimVector</a> feature_maps_</td>
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<td class="memname"><a class="el" href="classOpenMS_1_1BaseLabeler.html">BaseLabeler</a>* labeler_</td>
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<p>Labeling functionality. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> peak_map_</td>
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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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