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<HTML>
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<TITLE>OptimizePeakDeconvolution Class Reference</TITLE>
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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_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a></li> </ul>
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<div class="title">OptimizePeakDeconvolution Class Reference</div> </div>
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<p>This class provides the deconvolution of peak regions using non-linear optimization.
<a href="classOpenMS_1_1OptimizePeakDeconvolution.html#details">More...</a></p>
<p><code>#include <<a class="el" href="OptimizePeakDeconvolution_8h_source.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePeakDeconvolution.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for OptimizePeakDeconvolution:</div>
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<div class="center">
<img src="classOpenMS_1_1OptimizePeakDeconvolution.png" usemap="#OptimizePeakDeconvolution_map" alt=""/>
<map id="OptimizePeakDeconvolution_map" name="OptimizePeakDeconvolution_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,169,24"/>
</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_1OptimizePeakDeconvolution_1_1Data.html">Data</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Class containing the data needed for optimization. <a href="structOpenMS_1_1OptimizePeakDeconvolution_1_1Data.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">Type definitions</div></td></tr>
<tr class="memitem:a1b5cab7fcfe8ad040fb7363dd14913f1"><td class="memItemLeft" align="right" valign="top">typedef std::vector< <a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a1b5cab7fcfe8ad040fb7363dd14913f1">RawDataVector</a></td></tr>
<tr class="separator:a1b5cab7fcfe8ad040fb7363dd14913f1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a335cff277df421bfa0ce8d2412f02134"><td class="memItemLeft" align="right" valign="top">typedef RawDataVector::iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a></td></tr>
<tr class="separator:a335cff277df421bfa0ce8d2412f02134"><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:a2e9182f18e5991d738350b4059348809"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a2e9182f18e5991d738350b4059348809">optimize</a> (std::vector< <a class="el" href="structOpenMS_1_1PeakShape.html">PeakShape</a> > &peaks, <a class="el" href="structOpenMS_1_1OptimizePeakDeconvolution_1_1Data.html">Data</a> &data)</td></tr>
<tr class="memdesc:a2e9182f18e5991d738350b4059348809"><td class="mdescLeft"> </td><td class="mdescRight">Performs a nonlinear optimization of the peaks that belong to the current isotope pattern. <a href="#a2e9182f18e5991d738350b4059348809">More...</a><br/></td></tr>
<tr class="separator:a2e9182f18e5991d738350b4059348809"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Constructors and Destructor</div></td></tr>
<tr class="memitem:af342c1b96805f2c40241f89ca4255e12"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#af342c1b96805f2c40241f89ca4255e12">OptimizePeakDeconvolution</a> ()</td></tr>
<tr class="memdesc:af342c1b96805f2c40241f89ca4255e12"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#af342c1b96805f2c40241f89ca4255e12">More...</a><br/></td></tr>
<tr class="separator:af342c1b96805f2c40241f89ca4255e12"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abe68f0aa92663252670bc7a5808e81ca"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#abe68f0aa92663252670bc7a5808e81ca">OptimizePeakDeconvolution</a> (const <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a> &opt)</td></tr>
<tr class="memdesc:abe68f0aa92663252670bc7a5808e81ca"><td class="mdescLeft"> </td><td class="mdescRight">Copy-Constructor. <a href="#abe68f0aa92663252670bc7a5808e81ca">More...</a><br/></td></tr>
<tr class="separator:abe68f0aa92663252670bc7a5808e81ca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a803db9e793cd258f1054656c30d812b3"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a803db9e793cd258f1054656c30d812b3">~OptimizePeakDeconvolution</a> ()</td></tr>
<tr class="memdesc:a803db9e793cd258f1054656c30d812b3"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a803db9e793cd258f1054656c30d812b3">More...</a><br/></td></tr>
<tr class="separator:a803db9e793cd258f1054656c30d812b3"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Assignment</div></td></tr>
<tr class="memitem:a33ab7b0d22fa42979de8b9f849ba882f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a33ab7b0d22fa42979de8b9f849ba882f">operator=</a> (const <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a> &opt)</td></tr>
<tr class="separator:a33ab7b0d22fa42979de8b9f849ba882f"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader"></div></td></tr>
<tr class="memitem:aacb90f036a8fff25704290ac0c34364c"><td class="memItemLeft" align="right" valign="top">const <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#aacb90f036a8fff25704290ac0c34364c">getPenalties</a> () const </td></tr>
<tr class="memdesc:aacb90f036a8fff25704290ac0c34364c"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the penalty parameter. <a href="#aacb90f036a8fff25704290ac0c34364c">More...</a><br/></td></tr>
<tr class="separator:aacb90f036a8fff25704290ac0c34364c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acf2242ca0f5bb625f5c3da3dc54c7483"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#acf2242ca0f5bb625f5c3da3dc54c7483">setPenalties</a> (const <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> &penalties)</td></tr>
<tr class="memdesc:acf2242ca0f5bb625f5c3da3dc54c7483"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the penalty parameter. <a href="#acf2242ca0f5bb625f5c3da3dc54c7483">More...</a><br/></td></tr>
<tr class="separator:acf2242ca0f5bb625f5c3da3dc54c7483"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab91109da6782d902c745c771aa85d03d"><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_1OptimizePeakDeconvolution.html#ab91109da6782d902c745c771aa85d03d">getCharge</a> () const </td></tr>
<tr class="memdesc:ab91109da6782d902c745c771aa85d03d"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the charge. <a href="#ab91109da6782d902c745c771aa85d03d">More...</a><br/></td></tr>
<tr class="separator:ab91109da6782d902c745c771aa85d03d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab7a0db6241792d8ce94f3426ad3666a1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#ab7a0db6241792d8ce94f3426ad3666a1">setCharge</a> (const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge)</td></tr>
<tr class="memdesc:ab7a0db6241792d8ce94f3426ad3666a1"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the charge. <a href="#ab7a0db6241792d8ce94f3426ad3666a1">More...</a><br/></td></tr>
<tr class="separator:ab7a0db6241792d8ce94f3426ad3666a1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a8e98639eedf10735c6665597367d8525"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a8e98639eedf10735c6665597367d8525">getNumberOfPeaks_</a> (<a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge, std::vector< <a class="el" href="structOpenMS_1_1PeakShape.html">PeakShape</a> > &temp_shapes, <a class="el" href="structOpenMS_1_1OptimizePeakDeconvolution_1_1Data.html">Data</a> &data)</td></tr>
<tr class="memdesc:a8e98639eedf10735c6665597367d8525"><td class="mdescLeft"> </td><td class="mdescRight">A function to determine the number of peaks that lie in the current m/z interval given the distance between the peaks by the current charge state. <a href="#a8e98639eedf10735c6665597367d8525">More...</a><br/></td></tr>
<tr class="separator:a8e98639eedf10735c6665597367d8525"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af047ae562a0d8e6d44e39d056a5c57ed"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#af047ae562a0d8e6d44e39d056a5c57ed">checkFWHM_</a> (std::vector< <a class="el" href="structOpenMS_1_1PeakShape.html">PeakShape</a> > &peaks, gsl_multifit_fdfsolver *&fit)</td></tr>
<tr class="separator:af047ae562a0d8e6d44e39d056a5c57ed"><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_1OptimizePeakDeconvolution.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a1491750eda19a5fae8d6aa0deafb60ce"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a1491750eda19a5fae8d6aa0deafb60ce">penalties_</a></td></tr>
<tr class="separator:a1491750eda19a5fae8d6aa0deafb60ce"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af71274961d8487036283991f2ba652a1"><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_1OptimizePeakDeconvolution.html#af71274961d8487036283991f2ba652a1">charge_</a></td></tr>
<tr class="memdesc:af71274961d8487036283991f2ba652a1"><td class="mdescLeft"> </td><td class="mdescRight">Charge state of the current isotope pattern. <a href="#af71274961d8487036283991f2ba652a1">More...</a><br/></td></tr>
<tr class="separator:af71274961d8487036283991f2ba652a1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-static-attribs"></a>
Static Protected Attributes</h2></td></tr>
<tr class="memitem:ad722acdb0b7a0cff0c6ce4db69654d3c"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#ad722acdb0b7a0cff0c6ce4db69654d3c">dist_</a></td></tr>
<tr class="memdesc:ad722acdb0b7a0cff0c6ce4db69654d3c"><td class="mdescLeft"> </td><td class="mdescRight">distance between two isotopic peaks <a href="#ad722acdb0b7a0cff0c6ce4db69654d3c">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>This class provides the deconvolution of peak regions using non-linear optimization. </p>
<p>Given a vector of peak shapes, this class optimizes all peak shapes parameters using a non-linear optimization. For the non-linear optimization we use the Levenberg-Marquardt algorithm provided by the gsl. There are a few constraints for the parameters: the positions are equidistant according to the peptide mass rule, e.g. two consecutive isotopic peaks are 1.003/charge away from each other. Besides the peaks have all the same left and right width, respectively.</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>
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<td style="vertical-align:top"><b>max_iteration</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal number of iterations for the fitting step</td>
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<td style="vertical-align:top"><i>eps_abs</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.0001</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">if the absolute error gets smaller than this value the fitting is stopped</td>
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<td style="vertical-align:top"><i>eps_rel</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.0001</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">if the relative error gets smaller than this value the fitting is stopped</td>
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<tr>
<td style="vertical-align:top"><b>fwhm_threshold</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">If a peaks is broader than fwhm_threshold, it is assumed that it contains another peaks and an additional peak is added.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:left_width</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">penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:right_width</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">penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:height</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">penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.</td>
</tr>
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<td style="vertical-align:top"><b>penalties:position</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">penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule.</td>
</tr>
</table>
<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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<td class="memname">typedef RawDataVector::iterator <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a335cff277df421bfa0ce8d2412f02134">PeakIterator</a></td>
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</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="a1b5cab7fcfe8ad040fb7363dd14913f1"></a>
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<td class="memname">typedef std::vector<<a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a>> <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a1b5cab7fcfe8ad040fb7363dd14913f1">RawDataVector</a></td>
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</div><div class="memdoc">
</div>
</div>
<h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a class="anchor" id="af342c1b96805f2c40241f89ca4255e12"></a>
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<td class="memname"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
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</div><div class="memdoc">
<p>Constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a> </td>
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<p>Copy-Constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a> </td>
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<p>Destructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">bool checkFWHM_ </td>
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<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1PeakShape.html">PeakShape</a> > & </td>
<td class="paramname"><em>peaks</em>, </td>
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<p>Non-mutable access to the charge. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> getNumberOfPeaks_ </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td>
<td class="paramname"><em>charge</em>, </td>
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<p>A function to determine the number of peaks that lie in the current m/z interval given the distance between the peaks by the current charge state. </p>
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<td class="memname">const <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a>& getPenalties </td>
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<p>Non-mutable access to the penalty parameter. </p>
<p>Accessors </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html">OptimizePeakDeconvolution</a>& operator= </td>
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<p>References <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#af71274961d8487036283991f2ba652a1">OptimizePeakDeconvolution::charge_</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">DefaultParamHandler::operator=()</a>, and <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a1491750eda19a5fae8d6aa0deafb60ce">OptimizePeakDeconvolution::penalties_</a>.</p>
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<td class="memname">bool optimize </td>
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<p>Performs a nonlinear optimization of the peaks that belong to the current isotope pattern. </p>
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<td class="memname">void setCharge </td>
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<p>Mutable access to the charge. </p>
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<td class="memname">void setPenalties </td>
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<td class="paramname"><em>penalties</em></td><td>)</td>
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<p>Mutable access to the penalty parameter. </p>
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<td class="memname">void updateMembers_ </td>
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<p>This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. </p>
<p>Also call it at the end of the derived classes' copy constructor and assignment operator.</p>
<p>The default implementation is empty. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge_</td>
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<p>Charge state of the current isotope pattern. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a33ab7b0d22fa42979de8b9f849ba882f">OptimizePeakDeconvolution::operator=()</a>.</p>
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<td class="memname">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> dist_</td>
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<p>distance between two isotopic peaks </p>
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<td class="memname"><a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> penalties_</td>
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<p>Referenced by <a class="el" href="classOpenMS_1_1OptimizePeakDeconvolution.html#a33ab7b0d22fa42979de8b9f849ba882f">OptimizePeakDeconvolution::operator=()</a>.</p>
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