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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_1RawMSSignalSimulation.html">RawMSSignalSimulation</a></li> </ul>
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<a href="#nested-classes">Classes</a> |
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<div class="title">RawMSSignalSimulation Class Reference<div class="ingroups"><a class="el" href="group__Simulation.html">Simulation</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>Simulates MS signals for a given set of peptides.
<a href="classOpenMS_1_1RawMSSignalSimulation.html#details">More...</a></p>
<p><code>#include <<a class="el" href="RawMSSignalSimulation_8h_source.html">OpenMS/SIMULATION/RawMSSignalSimulation.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for RawMSSignalSimulation:</div>
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<img src="classOpenMS_1_1RawMSSignalSimulation.png" usemap="#RawMSSignalSimulation_map" alt=""/>
<map id="RawMSSignalSimulation_map" name="RawMSSignalSimulation_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,147,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="157,0,304,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html">ContaminantInfo</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ab6281d9d6d4475e15590b56f0b89477e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ab6281d9d6d4475e15590b56f0b89477e">operator=</a> (const <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> &source)</td></tr>
<tr class="separator:ab6281d9d6d4475e15590b56f0b89477e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a75d9558f2de7df62f1eb06390a1d988b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a75d9558f2de7df62f1eb06390a1d988b">loadContaminants</a> ()</td></tr>
<tr class="separator:a75d9558f2de7df62f1eb06390a1d988b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5b2771c7678b4b148088f23b8504186d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a5b2771c7678b4b148088f23b8504186d">generateRawSignals</a> (<a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &features, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment_ct, <a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &contaminants)</td></tr>
<tr class="memdesc:a5b2771c7678b4b148088f23b8504186d"><td class="mdescLeft"> </td><td class="mdescRight">fill experiment with signals and noise <a href="#a5b2771c7678b4b148088f23b8504186d">More...</a><br/></td></tr>
<tr class="separator:a5b2771c7678b4b148088f23b8504186d"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors and Destructors</div></td></tr>
<tr class="memitem:a1bed7cf19b2d607e4731971259142990"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a1bed7cf19b2d607e4731971259142990">RawMSSignalSimulation</a> (const <a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> &rng)</td></tr>
<tr class="memdesc:a1bed7cf19b2d607e4731971259142990"><td class="mdescLeft"> </td><td class="mdescRight">Constructor taking a random generator. <a href="#a1bed7cf19b2d607e4731971259142990">More...</a><br/></td></tr>
<tr class="separator:a1bed7cf19b2d607e4731971259142990"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac5e428ca406da656438952532ce5ff00"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ac5e428ca406da656438952532ce5ff00">RawMSSignalSimulation</a> (const <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> &source)</td></tr>
<tr class="memdesc:ac5e428ca406da656438952532ce5ff00"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#ac5e428ca406da656438952532ce5ff00">More...</a><br/></td></tr>
<tr class="separator:ac5e428ca406da656438952532ce5ff00"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a179ef922a7d5fcf9b33e8395d3a912b7"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a179ef922a7d5fcf9b33e8395d3a912b7">~RawMSSignalSimulation</a> ()</td></tr>
<tr class="memdesc:a179ef922a7d5fcf9b33e8395d3a912b7"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a179ef922a7d5fcf9b33e8395d3a912b7">More...</a><br/></td></tr>
<tr class="separator:a179ef922a7d5fcf9b33e8395d3a912b7"><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-types"></a>
Protected Types</h2></td></tr>
<tr class="memitem:a35d6cf42451e70ae0298555699c807c4"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4">IONIZATIONMETHOD</a> { <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4ae274f3a9dcb993aad7a9b29f932914a6">IM_ESI</a> = 0,
<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4afc48a664f96df3ef817f991bc1b00a32">IM_MALDI</a> = 1,
<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4a9f57de51b887fa0ee31c24108f15c71c">IM_ALL</a> = 2
}</td></tr>
<tr class="separator:a35d6cf42451e70ae0298555699c807c4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a118b7b87c79b44b10112206841e9fa99"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99">PROFILESHAPE</a> { <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99ae950ac3b5ed4f0c15e08535f6f61defc">RT_RECTANGULAR</a>,
<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99ab7fc9e3ba569fdda4990834af71eba55">RT_GAUSSIAN</a>
}</td></tr>
<tr class="separator:a118b7b87c79b44b10112206841e9fa99"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad2e04a1a86912fd63b00661e2348d3b1"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> { <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1ab578920fa0bc05e9decd5952d94c3385">RES_CONSTANT</a>,
<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1a10d18d53cdd2c7a96a6c7bc4830fa59b">RES_LINEAR</a>,
<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1adf61a4cf87044581b77d97e85428ce9c">RES_SQRT</a>
}</td></tr>
<tr class="separator:ad2e04a1a86912fd63b00661e2348d3b1"><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:a891e44560d1411236224315770eb2a56"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a891e44560d1411236224315770eb2a56">RawMSSignalSimulation</a> ()</td></tr>
<tr class="memdesc:a891e44560d1411236224315770eb2a56"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a891e44560d1411236224315770eb2a56">More...</a><br/></td></tr>
<tr class="separator:a891e44560d1411236224315770eb2a56"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.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="memitem:a592956c92badca126cec3abd62da8d67"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.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:a6c9a6c5489b1e8d745d0ea9ac439161e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a6c9a6c5489b1e8d745d0ea9ac439161e">add1DSignal_</a> (<a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &feature, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment_ct)</td></tr>
<tr class="memdesc:a6c9a6c5489b1e8d745d0ea9ac439161e"><td class="mdescLeft"> </td><td class="mdescRight">Add a 1D signal for a single feature. <a href="#a6c9a6c5489b1e8d745d0ea9ac439161e">More...</a><br/></td></tr>
<tr class="separator:a6c9a6c5489b1e8d745d0ea9ac439161e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a211e45de4d29779d4e6ba3da564bec39"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a211e45de4d29779d4e6ba3da564bec39">add2DSignal_</a> (<a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &feature, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment_ct)</td></tr>
<tr class="memdesc:a211e45de4d29779d4e6ba3da564bec39"><td class="mdescLeft"> </td><td class="mdescRight">Add a 2D signal for a single feature. <a href="#a211e45de4d29779d4e6ba3da564bec39">More...</a><br/></td></tr>
<tr class="separator:a211e45de4d29779d4e6ba3da564bec39"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a49d86f146514f9b56b708ecb4d1ab9fe"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a49d86f146514f9b56b708ecb4d1ab9fe">samplePeptideModel1D_</a> (const <a class="el" href="classOpenMS_1_1IsotopeModel.html">IsotopeModel</a> &iso, const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_start, const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_end, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment_ct, <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &activeFeature)</td></tr>
<tr class="memdesc:a49d86f146514f9b56b708ecb4d1ab9fe"><td class="mdescLeft"> </td><td class="mdescRight">Samples signals for the given 1D model. <a href="#a49d86f146514f9b56b708ecb4d1ab9fe">More...</a><br/></td></tr>
<tr class="separator:a49d86f146514f9b56b708ecb4d1ab9fe"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a16ebd8b86c015dc51ba4b39cf74d7cdc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a16ebd8b86c015dc51ba4b39cf74d7cdc">samplePeptideModel2D_</a> (const <a class="el" href="classOpenMS_1_1ProductModel.html">ProductModel</a>< 2 > &pm, const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_start, const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_end, <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> rt_start, <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> rt_end, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment_ct, <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &activeFeature)</td></tr>
<tr class="memdesc:a16ebd8b86c015dc51ba4b39cf74d7cdc"><td class="mdescLeft"> </td><td class="mdescRight">Samples signals for the given 2D model. <a href="#a16ebd8b86c015dc51ba4b39cf74d7cdc">More...</a><br/></td></tr>
<tr class="separator:a16ebd8b86c015dc51ba4b39cf74d7cdc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7a01ecba081141d30e617eec0bfbff03"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a7a01ecba081141d30e617eec0bfbff03">chooseElutionProfile_</a> (<a class="el" href="classOpenMS_1_1EGHModel.html">EGHModel</a> *const elutionmodel, <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &feature, const <a class="el" href="classdouble.html">double</a> scale, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> rt_sampling_rate, const <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment)</td></tr>
<tr class="memdesc:a7a01ecba081141d30e617eec0bfbff03"><td class="mdescLeft"> </td><td class="mdescRight">Add the correct Elution profile to the passed <a class="el" href="classOpenMS_1_1ProductModel.html" title="Class for product models i.e. models with D independent dimensions. ">ProductModel</a>. <a href="#a7a01ecba081141d30e617eec0bfbff03">More...</a><br/></td></tr>
<tr class="separator:a7a01ecba081141d30e617eec0bfbff03"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a457f6bf07d5139fb1089f24ff3192a5c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a457f6bf07d5139fb1089f24ff3192a5c">createContaminants_</a> (<a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> &contaminants, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &exp, <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &exp_ct)</td></tr>
<tr class="memdesc:a457f6bf07d5139fb1089f24ff3192a5c"><td class="mdescLeft"> </td><td class="mdescRight">build contaminant feature map <a href="#a457f6bf07d5139fb1089f24ff3192a5c">More...</a><br/></td></tr>
<tr class="separator:a457f6bf07d5139fb1089f24ff3192a5c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a563cc26d3df581dc1fbf6af58c7f9589"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a563cc26d3df581dc1fbf6af58c7f9589">addShotNoise_</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> minimal_mz_measurement_limit, <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> maximal_mz_measurement_limit)</td></tr>
<tr class="memdesc:a563cc26d3df581dc1fbf6af58c7f9589"><td class="mdescLeft"> </td><td class="mdescRight">Add shot noise to the experiment. <a href="#a563cc26d3df581dc1fbf6af58c7f9589">More...</a><br/></td></tr>
<tr class="separator:a563cc26d3df581dc1fbf6af58c7f9589"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a195e83f9d501e58a9b2ca18ae27768c9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a195e83f9d501e58a9b2ca18ae27768c9">addWhiteNoise_</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment)</td></tr>
<tr class="memdesc:a195e83f9d501e58a9b2ca18ae27768c9"><td class="mdescLeft"> </td><td class="mdescRight">Add white noise to the experiment. <a href="#a195e83f9d501e58a9b2ca18ae27768c9">More...</a><br/></td></tr>
<tr class="separator:a195e83f9d501e58a9b2ca18ae27768c9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a860237be42592676bb9a7f9da6e50fd5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a860237be42592676bb9a7f9da6e50fd5">addDetectorNoise_</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment)</td></tr>
<tr class="memdesc:a860237be42592676bb9a7f9da6e50fd5"><td class="mdescLeft"> </td><td class="mdescRight">Add detector noise to the experiment. <a href="#a860237be42592676bb9a7f9da6e50fd5">More...</a><br/></td></tr>
<tr class="separator:a860237be42592676bb9a7f9da6e50fd5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac264d116286d6f4264b024ec0941cf7f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ac264d116286d6f4264b024ec0941cf7f">addBaseLine_</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment, <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> minimal_mz_measurement_limit)</td></tr>
<tr class="memdesc:ac264d116286d6f4264b024ec0941cf7f"><td class="mdescLeft"> </td><td class="mdescRight">Add a base line to the experiment. <a href="#ac264d116286d6f4264b024ec0941cf7f">More...</a><br/></td></tr>
<tr class="separator:ac264d116286d6f4264b024ec0941cf7f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a63ec44835b1a04db83ddff952d5883bb"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a63ec44835b1a04db83ddff952d5883bb">getSamplingGrid_</a> (std::vector< <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> > &grid, const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_min, const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_max, const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> step_Da)</td></tr>
<tr class="memdesc:a63ec44835b1a04db83ddff952d5883bb"><td class="mdescLeft"> </td><td class="mdescRight">get the mz grid where all m/z values will be mapped to <a href="#a63ec44835b1a04db83ddff952d5883bb">More...</a><br/></td></tr>
<tr class="separator:a63ec44835b1a04db83ddff952d5883bb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afada593e0917529b65351e6bbb0f2449"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#afada593e0917529b65351e6bbb0f2449">compressSignals_</a> (<a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> &experiment)</td></tr>
<tr class="memdesc:afada593e0917529b65351e6bbb0f2449"><td class="mdescLeft"> </td><td class="mdescRight">Compress signales in a single RT scan (to merge signals which were sampled overlapping) <a href="#afada593e0917529b65351e6bbb0f2449">More...</a><br/></td></tr>
<tr class="separator:afada593e0917529b65351e6bbb0f2449"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acd422f7fdbf440c958eff7a0f47ef8d0"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#acd422f7fdbf440c958eff7a0f47ef8d0">getFeatureScaledIntensity_</a> (const <a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> feature_intensity, const <a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> natural_scaling_factor)</td></tr>
<tr class="memdesc:acd422f7fdbf440c958eff7a0f47ef8d0"><td class="mdescLeft"> </td><td class="mdescRight">Computes a rescaled feature intensity based on the set parameters for feature intensity scaling and the passed parameter <code>natural_scaling_factor</code>. <a href="#acd422f7fdbf440c958eff7a0f47ef8d0">More...</a><br/></td></tr>
<tr class="separator:acd422f7fdbf440c958eff7a0f47ef8d0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8c6dfb7bec9ef0f17c9ff984d4b953f9"><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_1RawMSSignalSimulation.html#a8c6dfb7bec9ef0f17c9ff984d4b953f9">getResolution_</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> query_mz, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> resolution, const <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> model) const </td></tr>
<tr class="memdesc:a8c6dfb7bec9ef0f17c9ff984d4b953f9"><td class="mdescLeft"> </td><td class="mdescRight">Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z. <a href="#a8c6dfb7bec9ef0f17c9ff984d4b953f9">More...</a><br/></td></tr>
<tr class="separator:a8c6dfb7bec9ef0f17c9ff984d4b953f9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad8eb6b369dbd92ca1bc538dfee062061"><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_1RawMSSignalSimulation.html#ad8eb6b369dbd92ca1bc538dfee062061">getPeakWidth_</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz, const bool is_gaussian) const </td></tr>
<tr class="memdesc:ad8eb6b369dbd92ca1bc538dfee062061"><td class="mdescLeft"> </td><td class="mdescRight">compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used) <a href="#ad8eb6b369dbd92ca1bc538dfee062061">More...</a><br/></td></tr>
<tr class="separator:ad8eb6b369dbd92ca1bc538dfee062061"><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:aa5172269ee939c487130758cadcd4cfb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#aa5172269ee939c487130758cadcd4cfb">sampling_points_per_FWHM_</a></td></tr>
<tr class="memdesc:aa5172269ee939c487130758cadcd4cfb"><td class="mdescLeft"> </td><td class="mdescRight">number of points sampled per peak's FWHM <a href="#aa5172269ee939c487130758cadcd4cfb">More...</a><br/></td></tr>
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<tr class="memitem:a9230fb31da1a74d4242603f43ec837d2"><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_1RawMSSignalSimulation.html#a9230fb31da1a74d4242603f43ec837d2">mz_error_mean_</a></td></tr>
<tr class="memdesc:a9230fb31da1a74d4242603f43ec837d2"><td class="mdescLeft"> </td><td class="mdescRight">Mean of peak m/z error. <a href="#a9230fb31da1a74d4242603f43ec837d2">More...</a><br/></td></tr>
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<tr class="memitem:a6f24877bfac4bb851db844d4d64bc70b"><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_1RawMSSignalSimulation.html#a6f24877bfac4bb851db844d4d64bc70b">mz_error_stddev_</a></td></tr>
<tr class="memdesc:a6f24877bfac4bb851db844d4d64bc70b"><td class="mdescLeft"> </td><td class="mdescRight">Standard deviation of peak m/z error. <a href="#a6f24877bfac4bb851db844d4d64bc70b">More...</a><br/></td></tr>
<tr class="separator:a6f24877bfac4bb851db844d4d64bc70b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6779ed53a1a1cea178001f2e6a6d19c8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a6779ed53a1a1cea178001f2e6a6d19c8">intensity_scale_</a></td></tr>
<tr class="memdesc:a6779ed53a1a1cea178001f2e6a6d19c8"><td class="mdescLeft"> </td><td class="mdescRight">Scaling factor of peak intensities. <a href="#a6779ed53a1a1cea178001f2e6a6d19c8">More...</a><br/></td></tr>
<tr class="separator:a6779ed53a1a1cea178001f2e6a6d19c8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6e56e3a5bdaa0417bb08f9687b79b3da"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a6e56e3a5bdaa0417bb08f9687b79b3da">intensity_scale_stddev_</a></td></tr>
<tr class="memdesc:a6e56e3a5bdaa0417bb08f9687b79b3da"><td class="mdescLeft"> </td><td class="mdescRight">Standard deviation of peak intensity scaling. <a href="#a6e56e3a5bdaa0417bb08f9687b79b3da">More...</a><br/></td></tr>
<tr class="separator:a6e56e3a5bdaa0417bb08f9687b79b3da"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3f60891f90436d076f7219221ff2b963"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a3f60891f90436d076f7219221ff2b963">res_model_</a></td></tr>
<tr class="memdesc:a3f60891f90436d076f7219221ff2b963"><td class="mdescLeft"> </td><td class="mdescRight">model of how resolution behaves with increasing m/z <a href="#a3f60891f90436d076f7219221ff2b963">More...</a><br/></td></tr>
<tr class="separator:a3f60891f90436d076f7219221ff2b963"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adbfbec82b64e1711adf583d967462c6a"><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_1RawMSSignalSimulation.html#adbfbec82b64e1711adf583d967462c6a">res_base_</a></td></tr>
<tr class="memdesc:adbfbec82b64e1711adf583d967462c6a"><td class="mdescLeft"> </td><td class="mdescRight">base resolution at 400 Th <a href="#adbfbec82b64e1711adf583d967462c6a">More...</a><br/></td></tr>
<tr class="separator:adbfbec82b64e1711adf583d967462c6a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae65a24617ce997568df4171fb42332a3"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ae65a24617ce997568df4171fb42332a3">grid_</a></td></tr>
<tr class="memdesc:ae65a24617ce997568df4171fb42332a3"><td class="mdescLeft"> </td><td class="mdescRight">m/z sampling grid for all signals <a href="#ae65a24617ce997568df4171fb42332a3">More...</a><br/></td></tr>
<tr class="separator:ae65a24617ce997568df4171fb42332a3"><td class="memSeparator" colspan="2"> </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_1RawMSSignalSimulation.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="memitem:a5d74c3f1b030f8633a63cc9cbd1e255c"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html">ContaminantInfo</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a5d74c3f1b030f8633a63cc9cbd1e255c">contaminants_</a></td></tr>
<tr class="separator:a5d74c3f1b030f8633a63cc9cbd1e255c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0ab3b2ea50a415b711d57ef6c888da8e"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector<br class="typebreak"/>
< <a class="el" href="classdouble.html">double</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a0ab3b2ea50a415b711d57ef6c888da8e">threaded_random_numbers_</a></td></tr>
<tr class="separator:a0ab3b2ea50a415b711d57ef6c888da8e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a515ff53e001edd54753be797f9da72aa"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a515ff53e001edd54753be797f9da72aa">threaded_random_numbers_index_</a></td></tr>
<tr class="separator:a515ff53e001edd54753be797f9da72aa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6dbbe280d54cf3dd4962dd7c3e5cb059"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a6dbbe280d54cf3dd4962dd7c3e5cb059">contaminants_loaded_</a></td></tr>
<tr class="separator:a6dbbe280d54cf3dd4962dd7c3e5cb059"><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>
<tr class="inherit_header pro_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<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>
<tr class="separator:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<tr class="separator:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0c749bf4e621699b7a5c45ae22c2fa90 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#a0c749bf4e621699b7a5c45ae22c2fa90">end_</a></td></tr>
<tr class="separator:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<tr class="separator:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<tr class="separator:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StopWatch.html">StopWatch</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a6d9750520313ea7f843d7a49cb2e9e5f">stop_watch_</a></td></tr>
<tr class="separator:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<tr class="separator:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_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-static-attribs"></a>
Static Protected Attributes</h2></td></tr>
<tr class="memitem:ab49500496d9f3af2a1d4c0ced31118ff"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ab49500496d9f3af2a1d4c0ced31118ff">THREADED_RANDOM_NUMBER_POOL_SIZE_</a> = 500</td></tr>
<tr class="separator:ab49500496d9f3af2a1d4c0ced31118ff"><td class="memSeparator" colspan="2"> </td></tr>
<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><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_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>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</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>
<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Simulates MS signals for a given set of peptides. </p>
<p>Simulates MS signals for a given set of peptides, with charge annotation, given detectabilities, predicted retention times and charge values.</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>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>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>
<tr>
<td style="vertical-align:top"><b>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>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>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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b>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>
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<td style="vertical-align:top"><b>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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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<td style="vertical-align:top"><b><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>
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</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.
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</div><h2 class="groupheader">Member Enumeration Documentation</h2>
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<td class="memname">enum <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a35d6cf42451e70ae0298555699c807c4">IONIZATIONMETHOD</a></td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a35d6cf42451e70ae0298555699c807c4ae274f3a9dcb993aad7a9b29f932914a6"></a>IM_ESI</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a35d6cf42451e70ae0298555699c807c4afc48a664f96df3ef817f991bc1b00a32"></a>IM_MALDI</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="a35d6cf42451e70ae0298555699c807c4a9f57de51b887fa0ee31c24108f15c71c"></a>IM_ALL</em> </td><td class="fielddoc">
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<td class="memname">enum <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a118b7b87c79b44b10112206841e9fa99">PROFILESHAPE</a></td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="a118b7b87c79b44b10112206841e9fa99ae950ac3b5ed4f0c15e08535f6f61defc"></a>RT_RECTANGULAR</em> </td><td class="fielddoc">
</td></tr>
<tr><td class="fieldname"><em><a class="anchor" id="a118b7b87c79b44b10112206841e9fa99ab7fc9e3ba569fdda4990834af71eba55"></a>RT_GAUSSIAN</em> </td><td class="fielddoc">
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<td class="memname">enum <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a></td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </td>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><em><a class="anchor" id="ad2e04a1a86912fd63b00661e2348d3b1ab578920fa0bc05e9decd5952d94c3385"></a>RES_CONSTANT</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ad2e04a1a86912fd63b00661e2348d3b1a10d18d53cdd2c7a96a6c7bc4830fa59b"></a>RES_LINEAR</em> </td><td class="fielddoc">
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<tr><td class="fieldname"><em><a class="anchor" id="ad2e04a1a86912fd63b00661e2348d3b1adf61a4cf87044581b77d97e85428ce9c"></a>RES_SQRT</em> </td><td class="fielddoc">
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenMS_1_1SimRandomNumberGenerator.html">SimRandomNumberGenerator</a> & </td>
<td class="paramname"><em>rng</em></td><td>)</td>
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</div><div class="memdoc">
<p>Constructor taking a random generator. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<p>Copy constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
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<span class="mlabels"><span class="mlabel">protected</span></span> </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 add1DSignal_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1Feature.html">Feature</a> & </td>
<td class="paramname"><em>feature</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment_ct</em> </td>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>Add a 1D signal for a single feature. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">feature</td><td>The feature which should be simulated </td></tr>
<tr><td class="paramname">experiment</td><td>The experiment to which the simulated signals should be added </td></tr>
<tr><td class="paramname">experiment_ct</td><td>Ground truth for picked peaks </td></tr>
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</dd>
</dl>
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<td class="memname">void add2DSignal_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1Feature.html">Feature</a> & </td>
<td class="paramname"><em>feature</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment_ct</em> </td>
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<td></td>
<td>)</td>
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<p>Add a 2D signal for a single feature. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">feature</td><td>The feature which should be simulated </td></tr>
<tr><td class="paramname">experiment</td><td>The experiment to which the simulated signals should be added </td></tr>
<tr><td class="paramname">experiment_ct</td><td>Ground truth for picked peaks </td></tr>
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</dd>
</dl>
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<td class="memname">void addBaseLine_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>minimal_mz_measurement_limit</em> </td>
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<td></td>
<td>)</td>
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<p>Add a base line to the experiment. </p>
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<td class="memname">void addDetectorNoise_ </td>
<td>(</td>
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<td class="paramname"><em>experiment</em></td><td>)</td>
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<p>Add detector noise to the experiment. </p>
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<td class="memname">void addShotNoise_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>minimal_mz_measurement_limit</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>maximal_mz_measurement_limit</em> </td>
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<td></td>
<td>)</td>
<td></td><td></td>
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<p>Add shot noise to the experiment. </p>
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<td class="memname">void addWhiteNoise_ </td>
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<td class="paramname"><em>experiment</em></td><td>)</td>
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<p>Add white noise to the experiment. </p>
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<td class="memname">void chooseElutionProfile_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1EGHModel.html">EGHModel</a> *const </td>
<td class="paramname"><em>elutionmodel</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1Feature.html">Feature</a> & </td>
<td class="paramname"><em>feature</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classdouble.html">double</a> </td>
<td class="paramname"><em>scale</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>rt_sampling_rate</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em> </td>
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<td>)</td>
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<p>Add the correct Elution profile to the passed <a class="el" href="classOpenMS_1_1ProductModel.html" title="Class for product models i.e. models with D independent dimensions. ">ProductModel</a>. </p>
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<td class="memname">void compressSignals_ </td>
<td>(</td>
<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>Compress signales in a single RT scan (to merge signals which were sampled overlapping) </p>
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<td class="memname">void createContaminants_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> & </td>
<td class="paramname"><em>contaminants</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>exp</em>, </td>
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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>exp_ct</em> </td>
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<td></td>
<td>)</td>
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<p>build contaminant feature map </p>
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<td class="memname">void generateRawSignals </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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<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment_ct</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a9396dc872898d760f035465bc56585d8">FeatureMapSim</a> & </td>
<td class="paramname"><em>contaminants</em> </td>
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<td>)</td>
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<p>fill experiment with signals and noise </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> getFeatureScaledIntensity_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> </td>
<td class="paramname"><em>feature_intensity</em>, </td>
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<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> </td>
<td class="paramname"><em>natural_scaling_factor</em> </td>
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<p>Computes a rescaled feature intensity based on the set parameters for feature intensity scaling and the passed parameter <code>natural_scaling_factor</code>. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">feature_intensity</td><td>Intensity of the current feature. </td></tr>
<tr><td class="paramname">natural_scaling_factor</td><td>Additional scaling factor used by some of the sampling models.</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>Rescaled feature intensity. </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getPeakWidth_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>mz</em>, </td>
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<td class="paramtype">const bool </td>
<td class="paramname"><em>is_gaussian</em> </td>
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<p>compute the peak's SD (Gaussian) at a given m/z (internally the resolution model is used) </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getResolution_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>query_mz</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>resolution</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> </td>
<td class="paramname"><em>model</em> </td>
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<p>Compute resolution at a given m/z given a base resolution and how it degrades with increasing m/z. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">query_mz</td><td>The m/z value where the resolution should be estimated </td></tr>
<tr><td class="paramname">resolution</td><td>The resolution at 400 Th </td></tr>
<tr><td class="paramname">model</td><td>The model describing how resolution behaves, i.e.<ul>
<li>RES_CONSTANT: resolution does not change with m/z (this will just return <code>resolution</code>)<br/>
</li>
<li>RES_LINEAR: resolution decreases linear with m/z, i.e. at 800 Th, it will have 50% of original<br/>
</li>
<li>RES_SQRT: the resolution decreases with square root of mass, i.e. at 1600 Th, it will have 50% of original (sqrt(400) = sqrt(1600)*0.5) </li>
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<td class="memname">void getSamplingGrid_ </td>
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<td class="paramtype">std::vector< <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> > & </td>
<td class="paramname"><em>grid</em>, </td>
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<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>mz_min</em>, </td>
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<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>mz_max</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td>
<td class="paramname"><em>step_Da</em> </td>
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<p>get the mz grid where all m/z values will be mapped to </p>
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<td class="memname">void loadContaminants </td>
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<p>load the contaminants from contaminants:file param You do not have to call this function before calling <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#a5b2771c7678b4b148088f23b8504186d" title="fill experiment with signals and noise ">generateRawSignals()</a>, but it might be useful to check if the contaminant file is valid </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a>& operator= </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html">RawMSSignalSimulation</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<td class="memname">void samplePeptideModel1D_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1IsotopeModel.html">IsotopeModel</a> & </td>
<td class="paramname"><em>iso</em>, </td>
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<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>mz_start</em>, </td>
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<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>mz_end</em>, </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>
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<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment_ct</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1Feature.html">Feature</a> & </td>
<td class="paramname"><em>activeFeature</em> </td>
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<p>Samples signals for the given 1D model. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">iso</td><td>The isotope model from which the signals will be sampled </td></tr>
<tr><td class="paramname">mz_start</td><td>Start coordinate (in m/z dimension) of the region where the signals will be sampled </td></tr>
<tr><td class="paramname">mz_end</td><td>End coordinate (in m/z dimension) of the region where the signals will be sampled </td></tr>
<tr><td class="paramname">experiment</td><td>Experiment to which the sampled signals will be added </td></tr>
<tr><td class="paramname">experiment_ct</td><td>Experiment to which the centroided Ground Truth sampled signals will be added </td></tr>
<tr><td class="paramname">activeFeature</td><td>The current feature that is simulated </td></tr>
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<td class="memname">void samplePeptideModel2D_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1ProductModel.html">ProductModel</a>< 2 > & </td>
<td class="paramname"><em>pm</em>, </td>
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<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>mz_start</em>, </td>
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<td></td>
<td class="paramtype">const <a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>mz_end</em>, </td>
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<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>rt_start</em>, </td>
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<td class="paramtype"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> </td>
<td class="paramname"><em>rt_end</em>, </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>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="namespaceOpenMS.html#ad8fab082e8d37c2f39ca13d92608d71d">MSSimExperiment</a> & </td>
<td class="paramname"><em>experiment_ct</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1Feature.html">Feature</a> & </td>
<td class="paramname"><em>activeFeature</em> </td>
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<td>)</td>
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<p>Samples signals for the given 2D model. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pm</td><td>The product model from which the signals will be sampled </td></tr>
<tr><td class="paramname">mz_start</td><td>Start coordinate (in m/z dimension) of the region where the signals will be sampled </td></tr>
<tr><td class="paramname">mz_end</td><td>End coordinate (in m/z dimension) of the region where the signals will be sampled </td></tr>
<tr><td class="paramname">rt_start</td><td>Start coordinate (in rt dimension) of the region where the signals will be sampled </td></tr>
<tr><td class="paramname">rt_end</td><td>End coordinate (in rt dimension) of the region where the signals will be sampled </td></tr>
<tr><td class="paramname">experiment</td><td>Experiment to which the sampled signals will be added </td></tr>
<tr><td class="paramname">experiment_ct</td><td>Experiment to which the centroided Ground Truth sampled signals will be added </td></tr>
<tr><td class="paramname">activeFeature</td><td>The current feature that is simulated </td></tr>
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<td class="memname">void setDefaultParams_ </td>
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<p>Set default parameters. </p>
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<td class="memname">void updateMembers_ </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">std::vector<<a class="el" href="structOpenMS_1_1RawMSSignalSimulation_1_1ContaminantInfo.html">ContaminantInfo</a>> contaminants_</td>
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<td class="memname">bool contaminants_loaded_</td>
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<td class="memname">std::vector<<a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a>> grid_</td>
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<p>m/z sampling grid for all signals </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> intensity_scale_</td>
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<p>Scaling factor of peak intensities. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a1c6dc92dcdd8dd005518ab11d341ae5f">SimIntensityType</a> intensity_scale_stddev_</td>
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<p>Standard deviation of peak intensity scaling. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_error_mean_</td>
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<p>Mean of peak m/z error. </p>
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<td class="memname"><a class="el" href="namespaceOpenMS.html#a375f999020e3ba21026a3f0be0c079f6">SimCoordinateType</a> mz_error_stddev_</td>
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<p>Standard deviation of peak m/z error. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> res_base_</td>
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<p>base resolution at 400 Th </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1RawMSSignalSimulation.html#ad2e04a1a86912fd63b00661e2348d3b1">RESOLUTIONMODEL</a> res_model_</td>
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<p>model of how resolution behaves with increasing m/z </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="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> sampling_points_per_FWHM_</td>
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<p>number of points sampled per peak's FWHM </p>
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<td class="memname">const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> THREADED_RANDOM_NUMBER_POOL_SIZE_ = 500</td>
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<td class="memname">std::vector<std::vector<<a class="el" href="classdouble.html">double</a>> > threaded_random_numbers_</td>
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<p><code>threaded_random_numbers</code> keeps a set of random numbers for each thread simulating a feature. </p>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>> threaded_random_numbers_index_</td>
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<p>Indicates which random numbers each thread has used already and if the random number pool should be rebuild. </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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