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<HTML>
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<TITLE>FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType > 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_1FeatureFinderAlgorithmIsotopeWavelet.html">FeatureFinderAlgorithmIsotopeWavelet</a></li> </ul>
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<a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType > Class Template Reference<div class="ingroups"><a class="el" href="group__FeatureFinder.html">FeatureFinder</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>Implements the isotope wavelet feature finder.
<a href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#details">More...</a></p>
<p><code>#include <<a class="el" href="FeatureFinderAlgorithmIsotopeWavelet_8h_source.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmIsotopeWavelet.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.png" usemap="#FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >_map" alt=""/>
<map id="FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >_map" name="FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >_map">
<area href="classOpenMS_1_1FeatureFinderAlgorithm.html" title="Abstract base class for FeatureFinder algorithms. " alt="FeatureFinderAlgorithm< PeakType, FeatureType >" shape="rect" coords="0,56,392,80"/>
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,392,24"/>
</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_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html">BoxElement</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Internally used data structure for the sweep line algorithm. <a href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.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 class="memitem:a7837c64b8bc2ae095bf949d6ea9fe2d5"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><br class="typebreak"/>
< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a7837c64b8bc2ae095bf949d6ea9fe2d5">Base</a></td></tr>
<tr class="separator:a7837c64b8bc2ae095bf949d6ea9fe2d5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1FeatureFinderAlgorithm')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm< PeakType, FeatureType ></a></td></tr>
<tr class="memitem:adf6f376e844058d129ce8ba868276643 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a></td></tr>
<tr class="memdesc:adf6f376e844058d129ce8ba868276643 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Input map type. <a href="#adf6f376e844058d129ce8ba868276643">More...</a><br/></td></tr>
<tr class="separator:adf6f376e844058d129ce8ba868276643 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6ccfa631b2715c7d67fb491ebb6c422 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html#a181486a43da338e31f089df7661f50bb">MapType::CoordinateType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ae6ccfa631b2715c7d67fb491ebb6c422">CoordinateType</a></td></tr>
<tr class="memdesc:ae6ccfa631b2715c7d67fb491ebb6c422 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Coordinate/Position type of peaks. <a href="#ae6ccfa631b2715c7d67fb491ebb6c422">More...</a><br/></td></tr>
<tr class="separator:ae6ccfa631b2715c7d67fb491ebb6c422 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad697cf4c925820f74c876c10d0cb5570 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html#a221361082f641c3fccc58e9bc66aeee1">MapType::IntensityType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ad697cf4c925820f74c876c10d0cb5570">IntensityType</a></td></tr>
<tr class="memdesc:ad697cf4c925820f74c876c10d0cb5570 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Intensity type of peaks. <a href="#ad697cf4c925820f74c876c10d0cb5570">More...</a><br/></td></tr>
<tr class="separator:ad697cf4c925820f74c876c10d0cb5570 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a21ea3968c35235b6b3cd78a2190280d9 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>< FeatureType > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a></td></tr>
<tr class="memdesc:a21ea3968c35235b6b3cd78a2190280d9 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Output feature type. <a href="#a21ea3968c35235b6b3cd78a2190280d9">More...</a><br/></td></tr>
<tr class="separator:a21ea3968c35235b6b3cd78a2190280d9 inherit pub_types_classOpenMS_1_1FeatureFinderAlgorithm"><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:a3ee942662a8e6bbd9a705201a1896666"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3ee942662a8e6bbd9a705201a1896666">FeatureFinderAlgorithmIsotopeWavelet</a> ()</td></tr>
<tr class="memdesc:a3ee942662a8e6bbd9a705201a1896666"><td class="mdescLeft"> </td><td class="mdescRight">Default Constructor. <a href="#a3ee942662a8e6bbd9a705201a1896666">More...</a><br/></td></tr>
<tr class="separator:a3ee942662a8e6bbd9a705201a1896666"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a522648bd9fecc67681ffdbf0a15b3139"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a522648bd9fecc67681ffdbf0a15b3139">~FeatureFinderAlgorithmIsotopeWavelet</a> ()</td></tr>
<tr class="memdesc:a522648bd9fecc67681ffdbf0a15b3139"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a522648bd9fecc67681ffdbf0a15b3139">More...</a><br/></td></tr>
<tr class="separator:a522648bd9fecc67681ffdbf0a15b3139"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a512f34fae6d03198dea390c33e52e75d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1IsotopeWaveletTransform.html">IsotopeWaveletTransform</a><br class="typebreak"/>
< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> >::TransSpectrum * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a512f34fae6d03198dea390c33e52e75d">prepareHRDataCuda</a> (const <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> i, <a class="el" href="classOpenMS_1_1IsotopeWaveletTransform.html">IsotopeWaveletTransform</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > *iwt)</td></tr>
<tr class="separator:a512f34fae6d03198dea390c33e52e75d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a80a937e9a0dd8e9426bd2e0051ecaa33"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33">createHRData</a> (const <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> i)</td></tr>
<tr class="separator:a80a937e9a0dd8e9426bd2e0051ecaa33"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a13a43e6d814de94978c515cb084873b1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">run</a> ()</td></tr>
<tr class="memdesc:a13a43e6d814de94978c515cb084873b1"><td class="mdescLeft"> </td><td class="mdescRight">The working horse of this class. <a href="#a13a43e6d814de94978c515cb084873b1">More...</a><br/></td></tr>
<tr class="separator:a13a43e6d814de94978c515cb084873b1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1FeatureFinderAlgorithm')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm< PeakType, FeatureType ></a></td></tr>
<tr class="memitem:ab3f8cbcd66e98d658af1c794192988a8 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#ab3f8cbcd66e98d658af1c794192988a8">FeatureFinderAlgorithm</a> ()</td></tr>
<tr class="memdesc:ab3f8cbcd66e98d658af1c794192988a8 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#ab3f8cbcd66e98d658af1c794192988a8">More...</a><br/></td></tr>
<tr class="separator:ab3f8cbcd66e98d658af1c794192988a8 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a636289874783c1efc7df5cb0359007d5 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a636289874783c1efc7df5cb0359007d5">~FeatureFinderAlgorithm</a> ()</td></tr>
<tr class="memdesc:a636289874783c1efc7df5cb0359007d5 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a636289874783c1efc7df5cb0359007d5">More...</a><br/></td></tr>
<tr class="separator:a636289874783c1efc7df5cb0359007d5 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abe2fce5095efeecbcd815817430058e0 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#abe2fce5095efeecbcd815817430058e0">getDefaultParameters</a> () const </td></tr>
<tr class="memdesc:abe2fce5095efeecbcd815817430058e0 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Returns the default parameters. Reimplment. <a href="#abe2fce5095efeecbcd815817430058e0">More...</a><br/></td></tr>
<tr class="separator:abe2fce5095efeecbcd815817430058e0 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7e594645b8460e600602bb64a8403537 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a7e594645b8460e600602bb64a8403537">setData</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a> &map, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> &features, <a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> &ff)</td></tr>
<tr class="memdesc:a7e594645b8460e600602bb64a8403537 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Sets a reference to the calling <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>. <a href="#a7e594645b8460e600602bb64a8403537">More...</a><br/></td></tr>
<tr class="separator:a7e594645b8460e600602bb64a8403537 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a683154793bbb12ab5d16db81209606b0 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">setSeeds</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> &seeds)</td></tr>
<tr class="memdesc:a683154793bbb12ab5d16db81209606b0 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Sets a reference to the calling <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>. <a href="#a683154793bbb12ab5d16db81209606b0">More...</a><br/></td></tr>
<tr class="separator:a683154793bbb12ab5d16db81209606b0 inherit pub_methods_classOpenMS_1_1FeatureFinderAlgorithm"><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="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:af73fd15708e50e77665070023a09cc87"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af73fd15708e50e77665070023a09cc87">getProductName</a> ()</td></tr>
<tr class="separator:af73fd15708e50e77665070023a09cc87"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a81483ea6deb5aa7b6e11d0c3c871f532"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><br class="typebreak"/>
< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType > * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a81483ea6deb5aa7b6e11d0c3c871f532">create</a> ()</td></tr>
<tr class="separator:a81483ea6deb5aa7b6e11d0c3c871f532"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_static_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1FeatureFinderAlgorithm')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm< PeakType, FeatureType ></a></td></tr>
<tr class="memitem:a0619c54ebc0b33a02eb71f942bb00111 inherit pub_static_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a0619c54ebc0b33a02eb71f942bb00111">registerChildren</a> ()</td></tr>
<tr class="memdesc:a0619c54ebc0b33a02eb71f942bb00111 inherit pub_static_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">register all derived classes here (see <a class="el" href="FeatureFinderAlgorithm__impl_8h.html">FeatureFinderAlgorithm_impl.h</a>) <a href="#a0619c54ebc0b33a02eb71f942bb00111">More...</a><br/></td></tr>
<tr class="separator:a0619c54ebc0b33a02eb71f942bb00111 inherit pub_static_methods_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-types"></a>
Protected Types</h2></td></tr>
<tr class="memitem:ae0878340ed972926f2d75b7196ac65c9"><td class="memItemLeft" align="right" valign="top">typedef std::map< <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>, <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html">BoxElement</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae0878340ed972926f2d75b7196ac65c9">Box</a></td></tr>
<tr class="memdesc:ae0878340ed972926f2d75b7196ac65c9"><td class="mdescLeft"> </td><td class="mdescRight">Key: RT (index), value: <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html" title="Internally used data structure for the sweep line algorithm. ">BoxElement</a>. <a href="#ae0878340ed972926f2d75b7196ac65c9">More...</a><br/></td></tr>
<tr class="separator:ae0878340ed972926f2d75b7196ac65c9"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.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:a32280019a7d0e19a07e0c3fd44aee972"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a32280019a7d0e19a07e0c3fd44aee972">max_charge_</a></td></tr>
<tr class="memdesc:a32280019a7d0e19a07e0c3fd44aee972"><td class="mdescLeft"> </td><td class="mdescRight">The maximal charge state we will consider. <a href="#a32280019a7d0e19a07e0c3fd44aee972">More...</a><br/></td></tr>
<tr class="separator:a32280019a7d0e19a07e0c3fd44aee972"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a792fce9b5d6d0fe62dfd0303b33e557b"><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_1FeatureFinderAlgorithmIsotopeWavelet.html#a792fce9b5d6d0fe62dfd0303b33e557b">intensity_threshold_</a></td></tr>
<tr class="memdesc:a792fce9b5d6d0fe62dfd0303b33e557b"><td class="mdescLeft"> </td><td class="mdescRight">The only parameter of the isotope wavelet. <a href="#a792fce9b5d6d0fe62dfd0303b33e557b">More...</a><br/></td></tr>
<tr class="separator:a792fce9b5d6d0fe62dfd0303b33e557b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3fd609fd7b023618f7f2c5c64e8ed803"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a3fd609fd7b023618f7f2c5c64e8ed803">RT_votes_cutoff_</a></td></tr>
<tr class="separator:a3fd609fd7b023618f7f2c5c64e8ed803"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab9444d66ec037a0f90523b6ac87c9087"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ab9444d66ec037a0f90523b6ac87c9087">real_RT_votes_cutoff_</a></td></tr>
<tr class="separator:ab9444d66ec037a0f90523b6ac87c9087"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0864e2810fe75ef5519f320c957efb1b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a0864e2810fe75ef5519f320c957efb1b">RT_interleave_</a></td></tr>
<tr class="memdesc:a0864e2810fe75ef5519f320c957efb1b"><td class="mdescLeft"> </td><td class="mdescRight">The number of subsequent scans a pattern must cover in order to be considered as signal. <a href="#a0864e2810fe75ef5519f320c957efb1b">More...</a><br/></td></tr>
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<tr class="memitem:a3de08d2b695a532ae39b30bd7c46e68a"><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_1FeatureFinderAlgorithmIsotopeWavelet.html#a3de08d2b695a532ae39b30bd7c46e68a">use_gpus_</a></td></tr>
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<tr class="memitem:a17a0a86ea1bf9a231c53429ea99e086b"><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_1FeatureFinderAlgorithmIsotopeWavelet.html#a17a0a86ea1bf9a231c53429ea99e086b">intensity_type_</a></td></tr>
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<tr class="memitem:a40b4eaf0409b4d2ffff61e83e35aba41"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a40b4eaf0409b4d2ffff61e83e35aba41">use_tbb_</a></td></tr>
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<tr class="memitem:ae8f10b1319ef92b7f0ed3a31aaab93a9"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae8f10b1319ef92b7f0ed3a31aaab93a9">use_cuda_</a></td></tr>
<tr class="separator:ae8f10b1319ef92b7f0ed3a31aaab93a9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac0914e52b60b67388b6ca7648922b447"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ac0914e52b60b67388b6ca7648922b447">check_PPMs_</a></td></tr>
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<tr class="memitem:af082d2d0e78145cb7e949f3e6a4d92a7"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af082d2d0e78145cb7e949f3e6a4d92a7">hr_data_</a></td></tr>
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<tr class="memitem:af8edb64f6f222069d7e8d143d4034213"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#af8edb64f6f222069d7e8d143d4034213">gpu_ids_</a></td></tr>
<tr class="memdesc:af8edb64f6f222069d7e8d143d4034213"><td class="mdescLeft"> </td><td class="mdescRight">A list of all GPU devices that can be used. <a href="#af8edb64f6f222069d7e8d143d4034213">More...</a><br/></td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm< PeakType, FeatureType ></a></td></tr>
<tr class="memitem:a365c5cf67d48519199fe00cb5688d628 inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a365c5cf67d48519199fe00cb5688d628">map_</a></td></tr>
<tr class="memdesc:a365c5cf67d48519199fe00cb5688d628 inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Input data pointer. <a href="#a365c5cf67d48519199fe00cb5688d628">More...</a><br/></td></tr>
<tr class="separator:a365c5cf67d48519199fe00cb5688d628 inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5f09052343ef99616ad653897841ce3e inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">features_</a></td></tr>
<tr class="memdesc:a5f09052343ef99616ad653897841ce3e inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Output data pointer. <a href="#a5f09052343ef99616ad653897841ce3e">More...</a><br/></td></tr>
<tr class="separator:a5f09052343ef99616ad653897841ce3e inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adf68cb378c76b322b2cc4dbb2c145a3e inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeatureFinder.html">FeatureFinder</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">ff_</a></td></tr>
<tr class="memdesc:adf68cb378c76b322b2cc4dbb2c145a3e inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Pointer to the calling <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> that is used to access the feature flags. <a href="#adf68cb378c76b322b2cc4dbb2c145a3e">More...</a><br/></td></tr>
<tr class="separator:adf68cb378c76b322b2cc4dbb2c145a3e inherit pro_attribs_classOpenMS_1_1FeatureFinderAlgorithm"><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>
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<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>
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<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>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><h3>template<typename PeakType, typename FeatureType><br/>
class OpenMS::FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType ></h3>
<p>Implements the isotope wavelet feature finder. </p>
<p>The <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html" title="Implements the isotope wavelet feature finder. ">FeatureFinderAlgorithmIsotopeWavelet</a> class has been designed for finding features in 1D or 2D MS data sets using the isotope wavelet. In the case of two dimensional data, the class provides additionally the sweep line algorithm. Please note that the algorithm implemented here is only marginally related to the algorithm presented in Schulz-Trieglaff et al. (2007, 2008), as no fitting procedure is applied anymore after the wavelet-based seeding step. The wavelet has been designed to extract even very lowly-abundant features (see Hussong et. al (2007, 2009)), usually featuring a very low signal-to-noise ratio. The wavelet in its current implementation is not able to resolve overlapping patterns (see also Hussong et. al (2009)) and slightly shifts masses to the right due to the construction of the wavelet.</p>
<B>Parameters of this class are:</B><BR><BR>
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<td style="vertical-align:top"><b>max_charge</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">The maximal charge state to be considered.</td>
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<td style="vertical-align:top"><b>intensity_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">The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform. If you set intensity_threshold=-1, t' will be zero.<BR>As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g.</td>
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<td style="vertical-align:top"><i>intensity_type</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">ref</td>
<td style="vertical-align:top">ref, trans, corrected</td><td style="vertical-align:top">Determines the intensity type returned for the identified features. 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet).</td>
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<td style="vertical-align:top"><i>check_ppm</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Enables/disables a ppm test vs. the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied.</td>
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<td style="vertical-align:top"><b>hr_data</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check a single MS scan out of your recording, if you are unsure.</td>
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<td style="vertical-align:top"><i>sweep_line:rt_votes_cutoff</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature.</td>
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<td style="vertical-align:top"><i>sweep_line:rt_interleave</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Defines the maximum number of scans (w.r.t. rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value.</td>
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<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 <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a7837c64b8bc2ae095bf949d6ea9fe2d5">Base</a></td>
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<td class="memname">typedef std::map<<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html">BoxElement</a>> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#ae0878340ed972926f2d75b7196ac65c9">Box</a></td>
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<p>Key: RT (index), value: <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet_1_1BoxElement.html" title="Internally used data structure for the sweep line algorithm. ">BoxElement</a>. </p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html">FeatureFinderAlgorithmIsotopeWavelet</a> </td>
<td>(</td>
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<p>Default Constructor. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a81483ea6deb5aa7b6e11d0c3c871f532">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::create()</a>.</p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html">FeatureFinderAlgorithmIsotopeWavelet</a> </td>
<td>(</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">static <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html">FeatureFinderAlgorithm</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType>* create </td>
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<td class="memname"><a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>>* createHRData </td>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a512f34fae6d03198dea390c33e52e75d">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::prepareHRDataCuda()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>.</p>
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<p>The working horse of this class. </p>
<p>Implements <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a18954417d3124a8095783ea13dc6d00b">FeatureFinderAlgorithm< PeakType, FeatureType ></a>.</p>
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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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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>A list of all GPU devices that can be used. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_threshold_</td>
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<p>The only parameter of the isotope wavelet. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>The maximal charge state we will consider. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a80a937e9a0dd8e9426bd2e0051ecaa33">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::createHRData()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>.</p>
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<p>The number of subsequent scans a pattern must cover in order to be considered as signal. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_()</a>.</p>
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<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#a13a43e6d814de94978c515cb084873b1">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html#aaf258e1a9846d9b238ee4b3005ad3ee9">FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::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 11:19:34 using doxygen 1.8.5</font></TD>
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