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<HTML>
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<TITLE>TraceFitter< PeakType > Class Template 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_1TraceFitter.html">TraceFitter</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">TraceFitter< PeakType > Class Template Reference<span class="mlabels"><span class="mlabel">abstract</span></span></div> </div>
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<p>Abstract fitter for RT profile fitting.
<a href="classOpenMS_1_1TraceFitter.html#details">More...</a></p>
<p><code>#include <<a class="el" href="TraceFitter_8h_source.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/TraceFitter.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for TraceFitter< PeakType >:</div>
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<div class="center">
<img src="classOpenMS_1_1TraceFitter.png" usemap="#TraceFitter< PeakType >_map" alt=""/>
<map id="TraceFitter< PeakType >_map" name="TraceFitter< PeakType >_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="99,0,288,24"/>
<area href="classOpenMS_1_1EGHTraceFitter.html" title="A RT Profile fitter using an Exponential Gaussian Hybrid background model. " alt="EGHTraceFitter< PeakType >" shape="rect" coords="0,112,189,136"/>
<area href="classOpenMS_1_1GaussTraceFitter.html" title="Fitter for RT profiles using a gaussian background model. " alt="GaussTraceFitter< PeakType >" shape="rect" coords="199,112,388,136"/>
</map>
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<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a113c8da1eadad990ed5c5c3fbfd5c2df"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a113c8da1eadad990ed5c5c3fbfd5c2df">TraceFitter</a> ()</td></tr>
<tr class="memdesc:a113c8da1eadad990ed5c5c3fbfd5c2df"><td class="mdescLeft"> </td><td class="mdescRight">default constructor. <a href="#a113c8da1eadad990ed5c5c3fbfd5c2df">More...</a><br/></td></tr>
<tr class="separator:a113c8da1eadad990ed5c5c3fbfd5c2df"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abdd45634136f9a86f16cf14743c903e0"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#abdd45634136f9a86f16cf14743c903e0">TraceFitter</a> (const <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> &source)</td></tr>
<tr class="memdesc:abdd45634136f9a86f16cf14743c903e0"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#abdd45634136f9a86f16cf14743c903e0">More...</a><br/></td></tr>
<tr class="separator:abdd45634136f9a86f16cf14743c903e0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac9fed0a961481c6439dfc3b32422d89c"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">operator=</a> (const <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> &source)</td></tr>
<tr class="memdesc:ac9fed0a961481c6439dfc3b32422d89c"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#ac9fed0a961481c6439dfc3b32422d89c">More...</a><br/></td></tr>
<tr class="separator:ac9fed0a961481c6439dfc3b32422d89c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a73cdd08b53019fc20c8b8a0119222988"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a73cdd08b53019fc20c8b8a0119222988">~TraceFitter</a> ()</td></tr>
<tr class="memdesc:a73cdd08b53019fc20c8b8a0119222988"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a73cdd08b53019fc20c8b8a0119222988">More...</a><br/></td></tr>
<tr class="separator:a73cdd08b53019fc20c8b8a0119222988"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7b2aeb3c8d1a4fd03c5843af07474735"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">fit</a> (<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &traces)=0</td></tr>
<tr class="separator:a7b2aeb3c8d1a4fd03c5843af07474735"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a10ddb3b8cc795c598f76db017b9ca322"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a10ddb3b8cc795c598f76db017b9ca322">getLowerRTBound</a> () const =0</td></tr>
<tr class="separator:a10ddb3b8cc795c598f76db017b9ca322"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0ab9bd668829f0fc9608bd56560ac1ae"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a0ab9bd668829f0fc9608bd56560ac1ae">getUpperRTBound</a> () const =0</td></tr>
<tr class="separator:a0ab9bd668829f0fc9608bd56560ac1ae"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0eac57e7b543d5084b9cdbb940fd031c"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">getHeight</a> () const =0</td></tr>
<tr class="separator:a0eac57e7b543d5084b9cdbb940fd031c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae740893fa17f26ea27e6f2383d72cb40"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">getCenter</a> () const =0</td></tr>
<tr class="separator:ae740893fa17f26ea27e6f2383d72cb40"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa1e7b6cd685312da3c92644d8fe71aac"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#aa1e7b6cd685312da3c92644d8fe71aac">getFWHM</a> () const =0</td></tr>
<tr class="separator:aa1e7b6cd685312da3c92644d8fe71aac"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a65120f4f127d69944775cd5aae06709f"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">computeTheoretical</a> (const <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &trace, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> k)=0</td></tr>
<tr class="separator:a65120f4f127d69944775cd5aae06709f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2190523e8d48946faff97a41131fcf92"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a2190523e8d48946faff97a41131fcf92">checkMinimalRTSpan</a> (const std::pair< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &rt_bounds, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> min_rt_span)=0</td></tr>
<tr class="separator:a2190523e8d48946faff97a41131fcf92"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af72d2c9ae5ecbd8b8d4605fbbef613cc"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#af72d2c9ae5ecbd8b8d4605fbbef613cc">checkMaximalRTSpan</a> (const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_rt_span)=0</td></tr>
<tr class="separator:af72d2c9ae5ecbd8b8d4605fbbef613cc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a642bbbd0de05e84147e701bfeaf188a2"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">getFeatureIntensityContribution</a> ()=0</td></tr>
<tr class="separator:a642bbbd0de05e84147e701bfeaf188a2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab67d38bd9a15db565531cc729df77924"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#ab67d38bd9a15db565531cc729df77924">getGnuplotFormula</a> (<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > const &trace, const char function_name, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> baseline, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> rt_shift)=0</td></tr>
<tr class="separator:ab67d38bd9a15db565531cc729df77924"><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:aa392ac4217e565f35cfe6ec42edd4e19"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#aa392ac4217e565f35cfe6ec42edd4e19">printState_</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> iter, gsl_multifit_fdfsolver *s)=0</td></tr>
<tr class="separator:aa392ac4217e565f35cfe6ec42edd4e19"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a776f7572fc4f466e9527ca233471920d"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
<tr class="memdesc:a776f7572fc4f466e9527ca233471920d"><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="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
<tr class="separator:a776f7572fc4f466e9527ca233471920d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6ce8e085d31fd86c925b6e8805f2facd"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a6ce8e085d31fd86c925b6e8805f2facd">getOptimizedParameters_</a> (gsl_multifit_fdfsolver *s)=0</td></tr>
<tr class="separator:a6ce8e085d31fd86c925b6e8805f2facd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a69d24e3ee5021aebcec9f61015fb5313"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">optimize_</a> (<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > &traces, const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> num_params, <a class="el" href="classdouble.html">double</a> x_init[], <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(*residual)(const gsl_vector *x, void *params, gsl_vector *f), <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(*jacobian)(const gsl_vector *x, void *params, gsl_matrix *J), <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(*evaluate)(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J))</td></tr>
<tr class="separator:a69d24e3ee5021aebcec9f61015fb5313"><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:a7914deb9fb6c8400f80b3532aa2e7b73"><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_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">epsilon_abs_</a></td></tr>
<tr class="memdesc:a7914deb9fb6c8400f80b3532aa2e7b73"><td class="mdescLeft"> </td><td class="mdescRight">Absolute error. <a href="#a7914deb9fb6c8400f80b3532aa2e7b73">More...</a><br/></td></tr>
<tr class="separator:a7914deb9fb6c8400f80b3532aa2e7b73"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5430cfbbe8dd77a2709a1442ca25a9db"><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_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">epsilon_rel_</a></td></tr>
<tr class="memdesc:a5430cfbbe8dd77a2709a1442ca25a9db"><td class="mdescLeft"> </td><td class="mdescRight">Relative error. <a href="#a5430cfbbe8dd77a2709a1442ca25a9db">More...</a><br/></td></tr>
<tr class="separator:a5430cfbbe8dd77a2709a1442ca25a9db"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae81a426a24a2be1e601bb7e8a946d6a6"><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_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">max_iterations_</a></td></tr>
<tr class="memdesc:ae81a426a24a2be1e601bb7e8a946d6a6"><td class="mdescLeft"> </td><td class="mdescRight">Maximum number of iterations. <a href="#ae81a426a24a2be1e601bb7e8a946d6a6">More...</a><br/></td></tr>
<tr class="separator:ae81a426a24a2be1e601bb7e8a946d6a6"><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>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><h3>template<class PeakType><br/>
class OpenMS::TraceFitter< PeakType ></h3>
<p>Abstract fitter for RT profile fitting. </p>
<p>This class provides the basic interface and some functionality to fit multiple mass traces to a given RT shape model using the Levenberg-Marquardt algorithm.</p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000024">Todo:</a></b></dt><dd>docu needs update</dd></dl>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> </td>
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<p>default constructor. </p>
<p>References <a class="el" href="classOpenMS_1_1StringList.html#a5f86b59b547048311dd50df5fb6d3bb5">StringList::create()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">DefaultParamHandler::defaults_</a>, and <a class="el" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">Param::setValue()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</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_1TraceFitter.html">TraceFitter</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">virtual bool checkMaximalRTSpan </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>max_rt_span</em></td><td>)</td>
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<p>Checks if the fitted model is not to big</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">max_rt_span</td><td>Maximum RT span in relation to extended area that the model is allowed to have </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#aecd366afa85dccec2192de9d8dc1e0e0">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#aecd366afa85dccec2192de9d8dc1e0e0">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>.</p>
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<td class="memname">virtual bool checkMinimalRTSpan </td>
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<td class="paramtype">const std::pair< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
<td class="paramname"><em>rt_bounds</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>min_rt_span</em> </td>
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<p>Checks if the fitted model fills out at least 'min_rt_span' of the RT span</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">rt_bounds</td><td>RT boundaries of the fitted model </td></tr>
<tr><td class="paramname">min_rt_span</td><td>Minimum RT span in relation to extended area that has to remain after model fitting </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a29da0a7e5ad702ed2425e8c5244eb61d">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a69c967cdc32e6fd10e80f0b2a31e6bf4">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> computeTheoretical </td>
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<td class="paramname"><em>trace</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>k</em> </td>
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<p>Returns the theoretical value of the fitted model at position k in the passed Mass Trace</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">trace</td><td>the mass trace for which the value should be computed </td></tr>
<tr><td class="paramname">k</td><td>use the position of the k-th peak to compute the value </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#ad4ae88cf98ab9fa0da9bb0da7274bf66">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#ad4ae88cf98ab9fa0da9bb0da7274bf66">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>.</p>
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<td class="memname">virtual void fit </td>
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<td class="paramtype"><a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
<td class="paramname"><em>traces</em></td><td>)</td>
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<p>Main method of the <a class="el" href="classOpenMS_1_1TraceFitter.html" title="Abstract fitter for RT profile fitting. ">TraceFitter</a> which triggers the actual fitting. </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a99d30f96dbdc29d5eb5b9060c3b8113e">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a99d30f96dbdc29d5eb5b9060c3b8113e">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getCenter </td>
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<p>Returns the center position of the fitted model </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#ae8e2fe7e1f0337f36647f5a4ec63411e">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#ae8e2fe7e1f0337f36647f5a4ec63411e">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::writeFeatureDebugInfo_()</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getFeatureIntensityContribution </td>
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<p>??? </p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000025">Todo:</a></b></dt><dd>docu needs update </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a2cee68978c212685ef6db90b63f5551a">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a320145b90cde0b751cdbbdb14b77f2df">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getFWHM </td>
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<p>Returns the mass trace width at half max (FWHM) </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#af78548d2419bdbe09b16dfcb1296c047">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#af78548d2419bdbe09b16dfcb1296c047">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1String.html">String</a> getGnuplotFormula </td>
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<td class="paramtype"><a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > const & </td>
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<p>Returns a textual representation of the fitted model function, that can be plotted using Gnuplot</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">trace</td><td>The <a class="el" href="classOpenMS_1_1MassTrace.html" title="A container type that gathers peaks similar in m/z and moving along retention time. ">MassTrace</a> that should be plotted </td></tr>
<tr><td class="paramname">function_name</td><td>The name of the function (e.g. f(x) -> function_name = f) </td></tr>
<tr><td class="paramname">baseline</td><td>The intensity of the baseline </td></tr>
<tr><td class="paramname">rt_shift</td><td>A shift value, that allows to plot all RT profiles side by side, even if they would overlap in reality. This should be 0 for the first mass trace and increase by a fixed value for each mass trace. </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a6923eb0e13b4eb55a341cdc873220e69">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a30c8ffe521f049061e56fa2ce1b13193">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::writeFeatureDebugInfo_()</a>.</p>
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<p>Returns the height of the fitted model </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a3621a5a688c4ea837892df3fa4a447cf">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a3621a5a688c4ea837892df3fa4a447cf">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getLowerRTBound </td>
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<p>Returns the lower bound of the fitted RT model </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a2070f4fd34410d801bdc74ba13718c9f">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a2070f4fd34410d801bdc74ba13718c9f">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>.</p>
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<td class="memname">virtual void getOptimizedParameters_ </td>
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<p>Updates all member variables to the fitted values stored in the solver.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">s</td><td>The solver containing the fitted parameter values. </td></tr>
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<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#ad38a370e40e67024b5c204701dde62c1">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a78e4534ece0e83b70cf7e26a1c76d7b7">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">TraceFitter< PeakType >::optimize_()</a>.</p>
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<td class="memname">virtual <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getUpperRTBound </td>
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<p>Returns the upper bound of the fitted RT model </p>
<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#ad9c65d4305eece3ec652869f25fea9ab">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#ad9c65d4305eece3ec652869f25fea9ab">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>.</p>
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<td class="memname">virtual <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
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<p>assignment operator </p>
<p>References <a class="el" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">TraceFitter< PeakType >::epsilon_abs_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">TraceFitter< PeakType >::epsilon_rel_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">TraceFitter< PeakType >::max_iterations_</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">DefaultParamHandler::operator=()</a>, and <a class="el" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">TraceFitter< PeakType >::updateMembers_()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a9e327b8627f42e568529686f633a8344">GaussTraceFitter< PeakType >::operator=()</a>, and <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#ad42bdb472837e734816c251d5f6312f9">EGHTraceFitter< PeakType >::operator=()</a>.</p>
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<td class="memname">void optimize_ </td>
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<td class="paramtype"><a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > & </td>
<td class="paramname"><em>traces</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(*)(const gsl_vector *x, void *params, gsl_vector *f) </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(*)(const gsl_vector *x, void *params, gsl_matrix *J) </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(*)(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J) </td>
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<p>Optimize the given parameters using the Levenberg-Marquardt algorithm. </p>
<p>References <a class="el" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">TraceFitter< PeakType >::epsilon_abs_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">TraceFitter< PeakType >::epsilon_rel_</a>, <a class="el" href="namespaceOpenMS_1_1OptimizationFunctions.html#aacf12ce6c8657d87174c792d19c318bf">OpenMS::OptimizationFunctions::evaluate()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a6ce8e085d31fd86c925b6e8805f2facd">TraceFitter< PeakType >::getOptimizedParameters_()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getPeakCount()</a>, <a class="el" href="namespaceOpenMS_1_1OptimizationFunctions.html#a906050fe19898e6bdaad3442b61c7199">OpenMS::OptimizationFunctions::jacobian()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">TraceFitter< PeakType >::max_iterations_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#aa392ac4217e565f35cfe6ec42edd4e19">TraceFitter< PeakType >::printState_()</a>, and <a class="el" href="namespaceOpenMS_1_1OptimizationFunctions.html#a3d21e47729faa48b51b02169c9383902">OpenMS::OptimizationFunctions::residual()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a99d30f96dbdc29d5eb5b9060c3b8113e">GaussTraceFitter< PeakType >::fit()</a>, and <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a99d30f96dbdc29d5eb5b9060c3b8113e">EGHTraceFitter< PeakType >::fit()</a>.</p>
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<td class="memname">virtual void printState_ </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td>
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<p>Prints the state of the current iteration (e.g., values of the parameters)</p>
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<p>Implemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a5a6c5cb5c3bbe8cf2c2b7aa4639667bb">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a5a6c5cb5c3bbe8cf2c2b7aa4639667bb">GaussTraceFitter< PeakType ></a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">TraceFitter< PeakType >::optimize_()</a>.</p>
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<td class="memname">virtual 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>
<p>Reimplemented in <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a776f7572fc4f466e9527ca233471920d">EGHTraceFitter< PeakType ></a>, and <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a776f7572fc4f466e9527ca233471920d">GaussTraceFitter< PeakType ></a>.</p>
<p>References <a class="el" href="classOpenMS_1_1TraceFitter.html#a7914deb9fb6c8400f80b3532aa2e7b73">TraceFitter< PeakType >::epsilon_abs_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a5430cfbbe8dd77a2709a1442ca25a9db">TraceFitter< PeakType >::epsilon_rel_</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ae81a426a24a2be1e601bb7e8a946d6a6">TraceFitter< PeakType >::max_iterations_</a>, and <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">TraceFitter< PeakType >::operator=()</a>, <a class="el" href="classOpenMS_1_1GaussTraceFitter.html#a776f7572fc4f466e9527ca233471920d">GaussTraceFitter< PeakType >::updateMembers_()</a>, and <a class="el" href="classOpenMS_1_1EGHTraceFitter.html#a776f7572fc4f466e9527ca233471920d">EGHTraceFitter< PeakType >::updateMembers_()</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#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> epsilon_abs_</td>
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<p>Absolute error. </p>
<p>Test for the convergence of the sequence by comparing the last iteration step dx with the absolute error epsabs and relative error epsrel to the current position x </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">TraceFitter< PeakType >::operator=()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">TraceFitter< PeakType >::optimize_()</a>, and <a class="el" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">TraceFitter< PeakType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> epsilon_rel_</td>
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<p>Relative error. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">TraceFitter< PeakType >::operator=()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">TraceFitter< PeakType >::optimize_()</a>, and <a class="el" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">TraceFitter< PeakType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> max_iterations_</td>
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<p>Maximum number of iterations. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TraceFitter.html#ac9fed0a961481c6439dfc3b32422d89c">TraceFitter< PeakType >::operator=()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a69d24e3ee5021aebcec9f61015fb5313">TraceFitter< PeakType >::optimize_()</a>, and <a class="el" href="classOpenMS_1_1TraceFitter.html#a776f7572fc4f466e9527ca233471920d">TraceFitter< PeakType >::updateMembers_()</a>.</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 11:19:35 using doxygen 1.8.5</font></TD>
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