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<TITLE>FeatureFinderAlgorithmPicked< 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_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a></li> </ul>
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<div class="title">FeatureFinderAlgorithmPicked< 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><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html" title="Abstract base class for FeatureFinder algorithms. ">FeatureFinderAlgorithm</a> for picked peaks.
<a href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#details">More...</a></p>
<p><code>#include <<a class="el" href="FeatureFinderAlgorithmPicked_8h_source.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for FeatureFinderAlgorithmPicked< PeakType, FeatureType >:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1FeatureFinderAlgorithmPicked.png" usemap="#FeatureFinderAlgorithmPicked< PeakType, FeatureType >_map" alt=""/>
<map id="FeatureFinderAlgorithmPicked< PeakType, FeatureType >_map" name="FeatureFinderAlgorithmPicked< PeakType, FeatureType >_map">
<area href="classOpenMS_1_1FeatureFinderAlgorithm.html" title="Abstract base class for FeatureFinder algorithms. " alt="FeatureFinderAlgorithm< PeakType, FeatureType >" shape="rect" coords="0,56,345,80"/>
<area href="structOpenMS_1_1FeatureFinderDefs.html" title="The purpose of this struct is to provide definitions of classes and typedefs which are used throughou..." alt="FeatureFinderDefs" shape="rect" coords="355,56,700,80"/>
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,345,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">Type definitions</div></td></tr>
<tr class="memitem:a2f89be2feec82f5414aedc09e488420b"><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 ><br class="typebreak"/>
::<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f89be2feec82f5414aedc09e488420b">MapType</a></td></tr>
<tr class="separator:a2f89be2feec82f5414aedc09e488420b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abb9911ee4d024e85861f29bbbd0a63ef"><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 ><br class="typebreak"/>
::<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abb9911ee4d024e85861f29bbbd0a63ef">FeatureMapType</a></td></tr>
<tr class="separator:abb9911ee4d024e85861f29bbbd0a63ef"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae4e0f0c176662a323a6a64d29ff986dd"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html#a066042ae14211da37d4fa66d466bfa3e">MapType::SpectrumType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a></td></tr>
<tr class="separator:ae4e0f0c176662a323a6a64d29ff986dd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4097a067534171488208ac7b101b5c0c"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1MSSpectrum.html#ae2fc906f686ab141e88c57655afd1774">SpectrumType::FloatDataArrays</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">FloatDataArrays</a></td></tr>
<tr class="separator:a4097a067534171488208ac7b101b5c0c"><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>
<tr class="inherit_header pub_types_structOpenMS_1_1FeatureFinderDefs"><td colspan="2" onclick="javascript:toggleInherit('pub_types_structOpenMS_1_1FeatureFinderDefs')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html">FeatureFinderDefs</a></td></tr>
<tr class="memitem:a3f3de3e0d751949b8d0b60ffb302944a inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">Flag</a> { <a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aaa09b651ef326a9d8efcee5cc5b720ab4">UNUSED</a>,
<a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944aa1e780c62cb3fd2edcac39f739bbe6f6c">USED</a>
}</td></tr>
<tr class="memdesc:a3f3de3e0d751949b8d0b60ffb302944a"><td class="mdescLeft"> </td><td class="mdescRight">Flags that indicate if a peak is already used in a feature. <a href="structOpenMS_1_1FeatureFinderDefs.html#a3f3de3e0d751949b8d0b60ffb302944a">More...</a><br/></td></tr>
<tr class="separator:a3f3de3e0d751949b8d0b60ffb302944a inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0bfd850887fdc58115cead9e9b8b9 inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">IsotopeCluster::IndexPair</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#aaee0bfd850887fdc58115cead9e9b8b9">IndexPair</a></td></tr>
<tr class="memdesc:aaee0bfd850887fdc58115cead9e9b8b9 inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="mdescLeft"> </td><td class="mdescRight">Index to peak consisting of two UInts (scan index / peak index) <a href="#aaee0bfd850887fdc58115cead9e9b8b9">More...</a><br/></td></tr>
<tr class="separator:aaee0bfd850887fdc58115cead9e9b8b9 inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af01a99958d0b18999737158daf8820ac inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html">IsotopeCluster::ChargedIndexSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#af01a99958d0b18999737158daf8820ac">ChargedIndexSet</a></td></tr>
<tr class="memdesc:af01a99958d0b18999737158daf8820ac inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="mdescLeft"> </td><td class="mdescRight">Index to peak consisting of two UInts (scan index / peak index) with charge information. <a href="#af01a99958d0b18999737158daf8820ac">More...</a><br/></td></tr>
<tr class="separator:af01a99958d0b18999737158daf8820ac inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af7439235b89a75354a2e87350e36834f inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="structOpenMS_1_1IsotopeCluster.html#aed4049efd4228c847ab300ac4c466eca">IsotopeCluster::IndexSet</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1FeatureFinderDefs.html#af7439235b89a75354a2e87350e36834f">IndexSet</a></td></tr>
<tr class="memdesc:af7439235b89a75354a2e87350e36834f inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><td class="mdescLeft"> </td><td class="mdescRight">A set of peak indices. <a href="#af7439235b89a75354a2e87350e36834f">More...</a><br/></td></tr>
<tr class="separator:af7439235b89a75354a2e87350e36834f inherit pub_types_structOpenMS_1_1FeatureFinderDefs"><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:aea2bb0ee05df783538f89be9649dc3a6"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">FeatureFinderAlgorithmPicked</a> ()</td></tr>
<tr class="memdesc:aea2bb0ee05df783538f89be9649dc3a6"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#aea2bb0ee05df783538f89be9649dc3a6">More...</a><br/></td></tr>
<tr class="separator:aea2bb0ee05df783538f89be9649dc3a6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a683154793bbb12ab5d16db81209606b0"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a683154793bbb12ab5d16db81209606b0">setSeeds</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> &seeds)</td></tr>
<tr class="memdesc:a683154793bbb12ab5d16db81209606b0"><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"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a72fcb26a14f6beb1c3fbace9ab3e7dbb"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">run</a> ()</td></tr>
<tr class="memdesc:a72fcb26a14f6beb1c3fbace9ab3e7dbb"><td class="mdescLeft"> </td><td class="mdescRight">Main method for actual <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>. <a href="#a72fcb26a14f6beb1c3fbace9ab3e7dbb">More...</a><br/></td></tr>
<tr class="separator:a72fcb26a14f6beb1c3fbace9ab3e7dbb"><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="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: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_1FeatureFinderAlgorithmPicked.html#a81483ea6deb5aa7b6e11d0c3c871f532">create</a> ()</td></tr>
<tr class="separator:a81483ea6deb5aa7b6e11d0c3c871f532"><td class="memSeparator" colspan="2"> </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_1FeatureFinderAlgorithmPicked.html#af73fd15708e50e77665070023a09cc87">getProductName</a> ()</td></tr>
<tr class="separator:af73fd15708e50e77665070023a09cc87"><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:ac02da3d017367d854cb162983679aadc"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">FeatureFinderAlgorithmPickedHelperStructs::Seed</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a></td></tr>
<tr class="separator:ac02da3d017367d854cb162983679aadc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa6c9b584cfcb710d0fce1c647086faaa"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a><br class="typebreak"/>
< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">MassTrace</a></td></tr>
<tr class="separator:aa6c9b584cfcb710d0fce1c647086faaa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af8a4ff323b3f9b72d77f56f9974d5aff"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a><br class="typebreak"/>
< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a></td></tr>
<tr class="separator:af8a4ff323b3f9b72d77f56f9974d5aff"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adb93f7d18f3a19b45d1a05e7c29dbeaa"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a></td></tr>
<tr class="separator:adb93f7d18f3a19b45d1a05e7c29dbeaa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3e0a91daf1d288f768c9683e317488f4"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a></td></tr>
<tr class="separator:a3e0a91daf1d288f768c9683e317488f4"><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:a776f7572fc4f466e9527ca233471920d"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.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:a5eeb26578a9f2313c4fff108fb2d9d7b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">abort_</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a> &seed, const <a class="el" href="classOpenMS_1_1String.html">String</a> &reason)</td></tr>
<tr class="memdesc:a5eeb26578a9f2313c4fff108fb2d9d7b"><td class="mdescLeft"> </td><td class="mdescRight">Writes the abort reason to the log file and counts occurrences for each reason. <a href="#a5eeb26578a9f2313c4fff108fb2d9d7b">More...</a><br/></td></tr>
<tr class="separator:a5eeb26578a9f2313c4fff108fb2d9d7b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc97fb931afc9e8f86fe9e40683a5a6c"><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_1FeatureFinderAlgorithmPicked.html#acc97fb931afc9e8f86fe9e40683a5a6c">intersection_</a> (const <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &f1, const <a class="el" href="classOpenMS_1_1Feature.html">Feature</a> &f2) const </td></tr>
<tr class="separator:acc97fb931afc9e8f86fe9e40683a5a6c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9227a818c19cefa0d29f2940d87de2c6"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">getIsotopeDistribution_</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mass) const </td></tr>
<tr class="memdesc:a9227a818c19cefa0d29f2940d87de2c6"><td class="mdescLeft"> </td><td class="mdescRight">Returns the isotope distribution for a certain mass window. <a href="#a9227a818c19cefa0d29f2940d87de2c6">More...</a><br/></td></tr>
<tr class="separator:a9227a818c19cefa0d29f2940d87de2c6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad47e8e2093326bd3a2476713d538dd9e"><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_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">findBestIsotopeFit_</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a> &center, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> charge, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> &best_pattern) const </td></tr>
<tr class="memdesc:ad47e8e2093326bd3a2476713d538dd9e"><td class="mdescLeft"> </td><td class="mdescRight">Finds the best fitting position of the isotopic pattern estimate defined by <code>center</code>. <a href="#ad47e8e2093326bd3a2476713d538dd9e">More...</a><br/></td></tr>
<tr class="separator:ad47e8e2093326bd3a2476713d538dd9e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a00f443c46b1d9f3485ef02d844b2433d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">extendMassTraces_</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> &pattern, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> &traces, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> meta_index_overall) const </td></tr>
<tr class="separator:a00f443c46b1d9f3485ef02d844b2433d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa839121d4666e45d2b5b6d6eab010c5f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">extendMassTrace_</a> (<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">MassTrace</a> &trace, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> spectrum_index, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mz, bool increase_rt, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> meta_index_overall, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> min_rt=0.0, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_rt=0.0) const </td></tr>
<tr class="memdesc:aa839121d4666e45d2b5b6d6eab010c5f"><td class="mdescLeft"> </td><td class="mdescRight">Extends a single mass trace in one RT direction. <a href="#aa839121d4666e45d2b5b6d6eab010c5f">More...</a><br/></td></tr>
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<tr class="memitem:a5c38e77e9286e4faf58e56afce913ee2"><td class="memTemplParams" colspan="2">template<typename SpectrumType > </td></tr>
<tr class="memitem:a5c38e77e9286e4faf58e56afce913ee2"><td class="memTemplItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5c38e77e9286e4faf58e56afce913ee2">nearest_</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> pos, const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a> &spec, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> start) const </td></tr>
<tr class="memdesc:a5c38e77e9286e4faf58e56afce913ee2"><td class="mdescLeft"> </td><td class="mdescRight">Returns the index of the peak nearest to m/z <code>pos</code> in spectrum <code>spec</code> (linear search starting from index <code>start</code>) <a href="#a5c38e77e9286e4faf58e56afce913ee2">More...</a><br/></td></tr>
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<tr class="memitem:a48c8332d7771967946379f577ca3d973"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">findIsotope_</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> pos, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum_index, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> &pattern, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> pattern_index, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &peak_index) const </td></tr>
<tr class="memdesc:a48c8332d7771967946379f577ca3d973"><td class="mdescLeft"> </td><td class="mdescRight">Searches for an isotopic peak in the current spectrum and the adjacent spectra. <a href="#a48c8332d7771967946379f577ca3d973">More...</a><br/></td></tr>
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<tr class="memitem:a37daff803c85d8fa7e2ba173b3138d60"><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_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">positionScore_</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> pos1, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> pos2, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> allowed_deviation) const </td></tr>
<tr class="memdesc:a37daff803c85d8fa7e2ba173b3138d60"><td class="mdescLeft"> </td><td class="mdescRight">Calculates a score between 0 and 1 for the m/z deviation of two peaks. <a href="#a37daff803c85d8fa7e2ba173b3138d60">More...</a><br/></td></tr>
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<tr class="memitem:a55abad1b592c5e19bfaddfc9f9c4a43e"><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_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">isotopeScore_</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a> &isotopes, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> &pattern, bool consider_mz_distances) const </td></tr>
<tr class="memdesc:a55abad1b592c5e19bfaddfc9f9c4a43e"><td class="mdescLeft"> </td><td class="mdescRight">Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern. <a href="#a55abad1b592c5e19bfaddfc9f9c4a43e">More...</a><br/></td></tr>
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<tr class="memitem:a5ae84d207afd136419c46d9ec811bb97"><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_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">intensityScore_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak) const </td></tr>
<tr class="memdesc:a5ae84d207afd136419c46d9ec811bb97"><td class="mdescLeft"> </td><td class="mdescRight">Compute the intensity score for the peak <code>peak</code> in spectrum <code>spectrum</code>. <a href="#a5ae84d207afd136419c46d9ec811bb97">More...</a><br/></td></tr>
<tr class="separator:a5ae84d207afd136419c46d9ec811bb97"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad832d6128e519d1c6a7fefd89158c37e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad832d6128e519d1c6a7fefd89158c37e">chooseTraceFitter_</a> (<a class="el" href="classdouble.html">double</a> &tau)</td></tr>
<tr class="memdesc:ad832d6128e519d1c6a7fefd89158c37e"><td class="mdescLeft"> </td><td class="mdescRight">Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric, asymmetric) or based on an inspection of the mass trace (auto) <a href="#ad832d6128e519d1c6a7fefd89158c37e">More...</a><br/></td></tr>
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<tr class="memitem:a3430a3cac3d46d0420ab99024264359f"><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_1FeatureFinderAlgorithmPicked.html#a3430a3cac3d46d0420ab99024264359f">intensityScore_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> rt_bin, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> mz_bin, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity) const </td></tr>
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<tr><td colspan="2"><div class="groupHeader">Handling of fitted mass traces</div></td></tr>
<tr><td colspan="2"><div class="groupText"><p>Methods to handle the results of the mass trace fitting process. </p>
</div></td></tr>
<tr class="memitem:a1f44db8f9a5426ed4be51833385f5d6a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">cropFeature_</a> (<a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > *fitter, const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> &traces, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> &new_traces)</td></tr>
<tr class="memdesc:a1f44db8f9a5426ed4be51833385f5d6a"><td class="mdescLeft"> </td><td class="mdescRight">Creates new mass traces <code>new_traces</code> based on the fitting result and the original traces <code>traces</code>. <a href="#a1f44db8f9a5426ed4be51833385f5d6a">More...</a><br/></td></tr>
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<tr class="memitem:aef59aef1baf90c9ea2376d677c9bf79d"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">checkFeatureQuality_</a> (<a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > *fitter, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> &feature_traces, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &seed_mz, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &min_feature_score, <a class="el" href="classOpenMS_1_1String.html">String</a> &error_msg, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &fit_score, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &correlation, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &final_score)</td></tr>
<tr class="memdesc:aef59aef1baf90c9ea2376d677c9bf79d"><td class="mdescLeft"> </td><td class="mdescRight">Checks the feature based on different score thresholds and model constraints. <a href="#aef59aef1baf90c9ea2376d677c9bf79d">More...</a><br/></td></tr>
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<tr class="memitem:ad608d4f3d2a370fe2c1672c7818146b4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad608d4f3d2a370fe2c1672c7818146b4">writeFeatureDebugInfo_</a> (<a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > *fitter, const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> &traces, const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> &new_traces, bool feature_ok, const <a class="el" href="classOpenMS_1_1String.html">String</a> error_msg, const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> final_score, const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> plot_nr, const <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> &peak, const <a class="el" href="classOpenMS_1_1String.html">String</a> path="debug/features/")</td></tr>
<tr class="memdesc:ad608d4f3d2a370fe2c1672c7818146b4"><td class="mdescLeft"> </td><td class="mdescRight">Creates several files containing plots and viewable data of the fitted mass trace. <a href="#ad608d4f3d2a370fe2c1672c7818146b4">More...</a><br/></td></tr>
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<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:a0b28abb9db6a809eec07048c69fdfaab"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">map_</a></td></tr>
<tr class="memdesc:a0b28abb9db6a809eec07048c69fdfaab"><td class="mdescLeft"> </td><td class="mdescRight">editable copy of the map <a href="#a0b28abb9db6a809eec07048c69fdfaab">More...</a><br/></td></tr>
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<tr class="memitem:a1fd714af1f19177741eb0b4f6eb43e35"><td class="memItemLeft" align="right" valign="top">std::ofstream </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">log_</a></td></tr>
<tr class="memdesc:a1fd714af1f19177741eb0b4f6eb43e35"><td class="mdescLeft"> </td><td class="mdescRight">Output stream for log/debug info. <a href="#a1fd714af1f19177741eb0b4f6eb43e35">More...</a><br/></td></tr>
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<tr class="memitem:afa3f4fa08a8a3b675e2dab06e29412a1"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a></td></tr>
<tr class="memdesc:afa3f4fa08a8a3b675e2dab06e29412a1"><td class="mdescLeft"> </td><td class="mdescRight">debug flag <a href="#afa3f4fa08a8a3b675e2dab06e29412a1">More...</a><br/></td></tr>
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<tr class="memitem:afebc8acd9f3b44ba2936d842469f47e4"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">aborts_</a></td></tr>
<tr class="memdesc:afebc8acd9f3b44ba2936d842469f47e4"><td class="mdescLeft"> </td><td class="mdescRight">Array of abort reasons. <a href="#afebc8acd9f3b44ba2936d842469f47e4">More...</a><br/></td></tr>
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<tr class="memitem:a290ced0989c9db9d895a6a3435360f47"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a>, <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">abort_reasons_</a></td></tr>
<tr class="memdesc:a290ced0989c9db9d895a6a3435360f47"><td class="mdescLeft"> </td><td class="mdescRight">Array of abort reasons. <a href="#a290ced0989c9db9d895a6a3435360f47">More...</a><br/></td></tr>
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<tr class="memitem:a2f4fb91382abc4c1b9f767630d978f4d"><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_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">seeds_</a></td></tr>
<tr class="memdesc:a2f4fb91382abc4c1b9f767630d978f4d"><td class="mdescLeft"> </td><td class="mdescRight">User-specified seed list. <a href="#a2f4fb91382abc4c1b9f767630d978f4d">More...</a><br/></td></tr>
<tr class="separator:a2f4fb91382abc4c1b9f767630d978f4d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afd3d2147a4dba98319002b876781f9ee"><td class="memItemLeft" align="right" valign="top">std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">isotope_distributions_</a></td></tr>
<tr class="memdesc:afd3d2147a4dba98319002b876781f9ee"><td class="mdescLeft"> </td><td class="mdescRight">Vector of precalculated isotope distributions for several mass windows. <a href="#afd3d2147a4dba98319002b876781f9ee">More...</a><br/></td></tr>
<tr class="separator:afd3d2147a4dba98319002b876781f9ee"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Members for parameters often needed in methods</div></td></tr>
<tr class="memitem:ae8eb5ec37d3582ac0963d06ea624ab48"><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_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">pattern_tolerance_</a></td></tr>
<tr class="memdesc:ae8eb5ec37d3582ac0963d06ea624ab48"><td class="mdescLeft"> </td><td class="mdescRight">Stores mass_trace:mz_tolerance. <a href="#ae8eb5ec37d3582ac0963d06ea624ab48">More...</a><br/></td></tr>
<tr class="separator:ae8eb5ec37d3582ac0963d06ea624ab48"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a41848085aa61f5c00fc88e683945adf7"><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_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">trace_tolerance_</a></td></tr>
<tr class="memdesc:a41848085aa61f5c00fc88e683945adf7"><td class="mdescLeft"> </td><td class="mdescRight">Stores isotopic_pattern:mz_tolerance. <a href="#a41848085aa61f5c00fc88e683945adf7">More...</a><br/></td></tr>
<tr class="separator:a41848085aa61f5c00fc88e683945adf7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5fcb56e069842a53246cb6f063e99f22"><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_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">min_spectra_</a></td></tr>
<tr class="memdesc:a5fcb56e069842a53246cb6f063e99f22"><td class="mdescLeft"> </td><td class="mdescRight">Number of spectra that have to show the same mass (for finding a mass trace) <a href="#a5fcb56e069842a53246cb6f063e99f22">More...</a><br/></td></tr>
<tr class="separator:a5fcb56e069842a53246cb6f063e99f22"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4c3291ae9ef170e82168ccf10eaece4b"><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_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">max_missing_trace_peaks_</a></td></tr>
<tr class="memdesc:a4c3291ae9ef170e82168ccf10eaece4b"><td class="mdescLeft"> </td><td class="mdescRight">Stores mass_trace:max_missing. <a href="#a4c3291ae9ef170e82168ccf10eaece4b">More...</a><br/></td></tr>
<tr class="separator:a4c3291ae9ef170e82168ccf10eaece4b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b1ec7d53602252d1f4d7cd0331fc917"><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_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">slope_bound_</a></td></tr>
<tr class="memdesc:a6b1ec7d53602252d1f4d7cd0331fc917"><td class="mdescLeft"> </td><td class="mdescRight">Max slope of mass trace intensities. <a href="#a6b1ec7d53602252d1f4d7cd0331fc917">More...</a><br/></td></tr>
<tr class="separator:a6b1ec7d53602252d1f4d7cd0331fc917"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa2835fd8d8621a7ff9effbf85801917d"><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_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">intensity_percentage_</a></td></tr>
<tr class="memdesc:aa2835fd8d8621a7ff9effbf85801917d"><td class="mdescLeft"> </td><td class="mdescRight">Isotope pattern intensity contribution of required peaks. <a href="#aa2835fd8d8621a7ff9effbf85801917d">More...</a><br/></td></tr>
<tr class="separator:aa2835fd8d8621a7ff9effbf85801917d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afea7a0615504af04bc1b922416f702f7"><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_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">intensity_percentage_optional_</a></td></tr>
<tr class="memdesc:afea7a0615504af04bc1b922416f702f7"><td class="mdescLeft"> </td><td class="mdescRight">Isotope pattern intensity contribution of optional peaks. <a href="#afea7a0615504af04bc1b922416f702f7">More...</a><br/></td></tr>
<tr class="separator:afea7a0615504af04bc1b922416f702f7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a26002e622e0cb7f544d7d364be7c274a"><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_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">optional_fit_improvement_</a></td></tr>
<tr class="memdesc:a26002e622e0cb7f544d7d364be7c274a"><td class="mdescLeft"> </td><td class="mdescRight">Minimal imrovment for leaving out optional isotope. <a href="#a26002e622e0cb7f544d7d364be7c274a">More...</a><br/></td></tr>
<tr class="separator:a26002e622e0cb7f544d7d364be7c274a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac58a0fa7d6013c1855f905dbaa13c22f"><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_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">mass_window_width_</a></td></tr>
<tr class="memdesc:ac58a0fa7d6013c1855f905dbaa13c22f"><td class="mdescLeft"> </td><td class="mdescRight">Width of the isotope pattern mass bins. <a href="#ac58a0fa7d6013c1855f905dbaa13c22f">More...</a><br/></td></tr>
<tr class="separator:ac58a0fa7d6013c1855f905dbaa13c22f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1b9ec9e0082be83ffb6db38de5d6a59e"><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_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">intensity_bins_</a></td></tr>
<tr class="memdesc:a1b9ec9e0082be83ffb6db38de5d6a59e"><td class="mdescLeft"> </td><td class="mdescRight">Number of bins (in RT and MZ) for intensity significance estimation. <a href="#a1b9ec9e0082be83ffb6db38de5d6a59e">More...</a><br/></td></tr>
<tr class="separator:a1b9ec9e0082be83ffb6db38de5d6a59e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a99b8e7ca327a789a40e0b03d4a280ca5"><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_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">min_isotope_fit_</a></td></tr>
<tr class="memdesc:a99b8e7ca327a789a40e0b03d4a280ca5"><td class="mdescLeft"> </td><td class="mdescRight">Mimimum isotope pattern fit for a feature. <a href="#a99b8e7ca327a789a40e0b03d4a280ca5">More...</a><br/></td></tr>
<tr class="separator:a99b8e7ca327a789a40e0b03d4a280ca5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae9d0a125b344c7315dd63aed9b6871fc"><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_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">min_trace_score_</a></td></tr>
<tr class="memdesc:ae9d0a125b344c7315dd63aed9b6871fc"><td class="mdescLeft"> </td><td class="mdescRight">Minimum quality of a traces. <a href="#ae9d0a125b344c7315dd63aed9b6871fc">More...</a><br/></td></tr>
<tr class="separator:ae9d0a125b344c7315dd63aed9b6871fc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abe26e024e3bac78f99e2a6d487cfe007"><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_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">min_rt_span_</a></td></tr>
<tr class="memdesc:abe26e024e3bac78f99e2a6d487cfe007"><td class="mdescLeft"> </td><td class="mdescRight">Minimum RT range that has to be left after the fit. <a href="#abe26e024e3bac78f99e2a6d487cfe007">More...</a><br/></td></tr>
<tr class="separator:abe26e024e3bac78f99e2a6d487cfe007"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a301b8bd9f8b8404ffd2bf375b1f0cf2b"><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_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">max_rt_span_</a></td></tr>
<tr class="memdesc:a301b8bd9f8b8404ffd2bf375b1f0cf2b"><td class="mdescLeft"> </td><td class="mdescRight">Maximum RT range the model is allowed to span. <a href="#a301b8bd9f8b8404ffd2bf375b1f0cf2b">More...</a><br/></td></tr>
<tr class="separator:a301b8bd9f8b8404ffd2bf375b1f0cf2b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac7db097c6fa88dec6877edd3b7638b00"><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_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">max_feature_intersection_</a></td></tr>
<tr class="memdesc:ac7db097c6fa88dec6877edd3b7638b00"><td class="mdescLeft"> </td><td class="mdescRight">Maximum allowed feature intersection (if larger, that one of the feature is removed) <a href="#ac7db097c6fa88dec6877edd3b7638b00">More...</a><br/></td></tr>
<tr class="separator:ac7db097c6fa88dec6877edd3b7638b00"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae464adecb765a4c2b9c35b374620454e"><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_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">reported_mz_</a></td></tr>
<tr class="memdesc:ae464adecb765a4c2b9c35b374620454e"><td class="mdescLeft"> </td><td class="mdescRight">The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model. <a href="#ae464adecb765a4c2b9c35b374620454e">More...</a><br/></td></tr>
<tr class="separator:ae464adecb765a4c2b9c35b374620454e"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Members for intensity significance estimation</div></td></tr>
<tr class="memitem:ac3ad3885811bdd008ebad6dc58424303"><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_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">intensity_rt_step_</a></td></tr>
<tr class="memdesc:ac3ad3885811bdd008ebad6dc58424303"><td class="mdescLeft"> </td><td class="mdescRight">RT bin width. <a href="#ac3ad3885811bdd008ebad6dc58424303">More...</a><br/></td></tr>
<tr class="separator:ac3ad3885811bdd008ebad6dc58424303"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5bce00011821a31f9344547c20c91e89"><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_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">intensity_mz_step_</a></td></tr>
<tr class="memdesc:a5bce00011821a31f9344547c20c91e89"><td class="mdescLeft"> </td><td class="mdescRight">m/z bin width <a href="#a5bce00011821a31f9344547c20c91e89">More...</a><br/></td></tr>
<tr class="separator:a5bce00011821a31f9344547c20c91e89"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7678e0cd827e8669246943be392bd8d0"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector<br class="typebreak"/>
< std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">intensity_thresholds_</a></td></tr>
<tr class="memdesc:a7678e0cd827e8669246943be392bd8d0"><td class="mdescLeft"> </td><td class="mdescRight">Precalculated intensity 20-quantiles (binned) <a href="#a7678e0cd827e8669246943be392bd8d0">More...</a><br/></td></tr>
<tr class="separator:a7678e0cd827e8669246943be392bd8d0"><td class="memSeparator" colspan="2"> </td></tr>
<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>
<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>
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<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:ab76605572e7deccf4898a4398aa30d91"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ab76605572e7deccf4898a4398aa30d91">operator=</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a> &)</td></tr>
<tr class="memdesc:ab76605572e7deccf4898a4398aa30d91"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#ab76605572e7deccf4898a4398aa30d91">More...</a><br/></td></tr>
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<tr class="memitem:add0d0618a5fcb50e31d55e698a8aa4ad"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#add0d0618a5fcb50e31d55e698a8aa4ad">FeatureFinderAlgorithmPicked</a> (const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a> &)</td></tr>
<tr class="memdesc:add0d0618a5fcb50e31d55e698a8aa4ad"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#add0d0618a5fcb50e31d55e698a8aa4ad">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<class PeakType, class FeatureType><br/>
class OpenMS::FeatureFinderAlgorithmPicked< PeakType, FeatureType ></h3>
<p><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html" title="Abstract base class for FeatureFinder algorithms. ">FeatureFinderAlgorithm</a> for picked peaks. </p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><b>debug</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">When debug mode is activated, several files with intermediate results are written to the folder 'debug' (do not use in parallel mode).</td>
</tr>
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<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak's intensity is significant in the local environment (between 0 and 1)">intensity</span>:bins</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Number of bins per dimension (RT and m/z). The higher this value, the more local the intensity significance score is.<BR>This parameter should be decreased, if the algorithm is used on small regions of a map.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">mass_trace</span>:mz_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.03</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Tolerated m/z deviation of peaks belonging to the same mass trace.<BR>It should be larger than the m/z resolution of the instument.<BR>This value must be smaller than that 1/charge_high!</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">mass_trace</span>:min_spectra</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Number of spectra that have to show a similar peak mass in a mass trace.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">mass_trace</span>:max_missing</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Number of consecutive spectra where a high mass deviation or missing peak is acceptable.<BR>This parameter should be well below 'min_spectra'!</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a mass trace (between 0 and 1).">mass_trace</span>:slope_bound</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">The maximum slope of mass trace intensities when extending from the highest peak.<BR>This parameter is important to seperate overlapping elution peaks.<BR>It should be increased if feature elution profiles fluctuate a lot.</td>
</tr>
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<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:charge_low</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Lowest charge to search for.</td>
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<tr>
<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:charge_high</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">4</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Highest charge to search for.</td>
</tr>
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<td style="vertical-align:top"><b><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:mz_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.03</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Tolerated m/z deviation from the theoretical isotopic pattern.<BR>It should be larger than the m/z resolution of the instument.<BR>This value must be smaller than that 1/charge_high!</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:intensity_percentage</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top">min: 0 max: 100</td><td style="vertical-align:top">Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present.</td>
</tr>
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<td style="vertical-align:top"><i><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:intensity_percentage_optional</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.1</td>
<td style="vertical-align:top">min: 0 max: 100</td><td style="vertical-align:top">Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing.</td>
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<td style="vertical-align:top"><i><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:optional_fit_improvement</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2</td>
<td style="vertical-align:top">min: 0 max: 100</td><td style="vertical-align:top">Minimal percental improvement of isotope fit to allow leaving out an optional peak.</td>
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<tr>
<td style="vertical-align:top"><i><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:mass_window_width</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">25</td>
<td style="vertical-align:top">min: 1 max: 200</td><td style="vertical-align:top">Window width in Dalton for precalculation of estimated isotope distributions.</td>
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<tr>
<td style="vertical-align:top"><i><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:abundance_12C</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">98.93</td>
<td style="vertical-align:top">min: 0 max: 100</td><td style="vertical-align:top">Rel. abundance of the light carbon. Modify if labeled.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the calculation of a score indicating if a peak is part of a isotopic pattern (between 0 and 1).">isotopic_pattern</span>:abundance_14N</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">99.632</td>
<td style="vertical-align:top">min: 0 max: 100</td><td style="vertical-align:top">Rel. abundance of the light nitrogen. Modify if labeled.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings that determine which peaks are considered a seed">seed</span>:min_score</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.8</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimum seed score a peak has to reach to be used as seed.<BR>The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score.<BR>If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score.</td>
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<tr>
<td style="vertical-align:top"><i><span title="Settings for the model fitting">fit</span>:epsilon_abs</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.0001</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Absolute epsilon used for convergence of the fit.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the model fitting">fit</span>:epsilon_rel</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.0001</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Relative epsilon used for convergence of the fit.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the model fitting">fit</span>:max_iterations</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">500</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Maximum number of iterations of the fit.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:min_score</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.7</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Feature score threshold for a feature to be reported.<BR>The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:min_isotope_fit</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.8</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimum isotope fit of the feature before model fitting.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:min_trace_score</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Trace score threshold.<BR>Traces below this threshold are removed after the model fitting.<BR>This parameter is important for features that overlap in m/z dimension.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:min_rt_span</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.333</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Minimum RT span in relation to extended area that has to remain after model fitting.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:max_rt_span</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2.5</td>
<td style="vertical-align:top">min: 0.5</td><td style="vertical-align:top">Maximum RT span in relation to extended area that the model is allowed to have.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:rt_shape</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">symmetric</td>
<td style="vertical-align:top">symmetric, asymmetric</td><td style="vertical-align:top">Choose model used for RT profile fitting. If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used.</td>
</tr>
<tr>
<td style="vertical-align:top"><i><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:max_intersection</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.35</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Maximum allowed intersection of features.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for the features (intensity, quality assessment, ...)">feature</span>:reported_mz</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">monoisotopic</td>
<td style="vertical-align:top">maximum, average, monoisotopic</td><td style="vertical-align:top">The mass type that is reported for features.<BR>'maximum' returns the m/z value of the highest mass trace.<BR>'average' returns the intensity-weighted average m/z value of all contained peaks.<BR>'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for user-specified seeds.">user-seed</span>:rt_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Allowed RT deviation of seeds from the user-specified seed position.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for user-specified seeds.">user-seed</span>:mz_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1.1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top">Allowed m/z deviation of seeds from the user-specified seed position.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Settings for user-specified seeds.">user-seed</span>:min_score</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: 0 max: 1</td><td style="vertical-align:top">Overwrites 'seed:min_score' for user-specified seeds. The cutoff is typically a bit lower in this case.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>debug:pseudo_rt_shift</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">500</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Pseudo RT shift used when .</td>
</tr>
</table>
<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
<dl class="improvement"><dt><b><a class="el" href="improvement.html#_improvement000010">Improvement:</a></b></dt><dd><p class="startdd">RT model with tailing/fronting (Marc) </p>
<p class="enddd">More general MZ model - e.g. based on co-elution or with sulfur-averagines (Marc)</p>
</dd></dl>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000020">Todo:</a></b></dt><dd><p class="startdd">Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc) </p>
<p class="enddd">Implement user-specified seed lists support (Marc)</p>
</dd></dl>
</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_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1MSSpectrum.html#ae2fc906f686ab141e88c57655afd1774">SpectrumType::FloatDataArrays</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4097a067534171488208ac7b101b5c0c">FloatDataArrays</a></td>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a></td>
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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_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a></td>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html">FeatureFinderAlgorithmPickedHelperStructs::MassTrace</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">MassTrace</a></td>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html">FeatureFinderAlgorithmPickedHelperStructs::MassTraces</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a></td>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html">FeatureFinderAlgorithmPickedHelperStructs::Seed</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1MSExperiment.html#a066042ae14211da37d4fa66d466bfa3e">MapType::SpectrumType</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a></td>
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern</a> <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</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>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">DefaultParamHandler::defaultsToParam_()</a>, <a class="el" href="classOpenMS_1_1Param.html#a6b40506fffbae670045d065c354bb9b8">Param::setMaxFloat()</a>, <a class="el" href="classOpenMS_1_1Param.html#aadc7a8536eb15f8c6fa05eefca0e25be">Param::setMinFloat()</a>, <a class="el" href="classOpenMS_1_1Param.html#a3a23089ec40eeed796efe7b69ecb02ac">Param::setMinInt()</a>, <a class="el" href="classOpenMS_1_1Param.html#a7dae78ea20f5b33125f50c6ee27b1a60">Param::setSectionDescription()</a>, <a class="el" href="classOpenMS_1_1Param.html#a10933782584a46cded91c40574027ee2">Param::setValidStrings()</a>, and <a class="el" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">Param::setValue()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a81483ea6deb5aa7b6e11d0c3c871f532">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::create()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType > & </td>
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<p>Not implemented. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void abort_ </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a> & </td>
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<p>Writes the abort reason to the log file and counts occurrences for each reason. </p>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_reasons_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::aborts_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</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">bool checkFeatureQuality_ </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > * </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> & </td>
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<p>Checks the feature based on different score thresholds and model constraints. </p>
<p><a class="el" href="classOpenMS_1_1Feature.html" title="An LC-MS feature. ">Feature</a> can get invalid for following reasons: </p>
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Invalid fit: Fitted model is bigger than 'max_rt_span' </li>
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Invalid feature after fit - too few traces or peaks left </li>
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Invalid fit: Center outside of feature bounds </li>
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Invalid fit: Less than 'min_rt_span' left after fit </li>
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<a class="el" href="classOpenMS_1_1Feature.html" title="An LC-MS feature. ">Feature</a> quality too low after fit </li>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">fitter</td><td>The <a class="el" href="classOpenMS_1_1TraceFitter.html" title="Abstract fitter for RT profile fitting. ">TraceFitter</a> containing the results from the rt profile fitting step. </td></tr>
<tr><td class="paramname">feature_traces</td><td>Cropped feature mass traces. </td></tr>
<tr><td class="paramname">seed_mz</td><td>Mz of the seed </td></tr>
<tr><td class="paramname">min_feature_score</td><td>Minimal required feature score </td></tr>
<tr><td class="paramname">error_msg</td><td>Will be filled with the error message, if the feature is invalid </td></tr>
<tr><td class="paramname">fit_score</td><td>Will be filled with the fit score </td></tr>
<tr><td class="paramname">correlation</td><td>Will be filled with correlation between feature and model </td></tr>
<tr><td class="paramname">final_score</td><td>Will be filled with the final score</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>true if the feature is valid </dd></dl>
<p>References <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#af72d2c9ae5ecbd8b8d4605fbbef613cc">TraceFitter< PeakType >::checkMaximalRTSpan()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a2190523e8d48946faff97a41131fcf92">TraceFitter< PeakType >::checkMinimalRTSpan()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">TraceFitter< PeakType >::computeTheoretical()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">TraceFitter< PeakType >::getCenter()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getPeakCount()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#adee689cac2b64d7164dbfc3d48110d91">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getRTBounds()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a7e409d85407a4cfbc76fdc4aac06f185">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::isValid()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_rt_span_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_rt_span_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks</a>, <a class="el" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">OpenMS::Math::pearsonCorrelationCoefficient()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_</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"><a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a><<a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>>* chooseTraceFitter_ </td>
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<p>Choose a the best trace fitter for the current mass traces based on the user parameter (symmetric, asymmetric) or based on an inspection of the mass trace (auto) </p>
<dl class="section return"><dt>Returns</dt><dd>A pointer to the trace fitter that should be used. </dd></dl>
<p>References <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a>, and <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</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">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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<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aea2bb0ee05df783538f89be9649dc3a6">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::FeatureFinderAlgorithmPicked()</a>.</p>
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<td class="memname">void cropFeature_ </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> & </td>
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<p>Creates new mass traces <code>new_traces</code> based on the fitting result and the original traces <code>traces</code>. </p>
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<tr><td class="paramname">traces</td><td>Original mass traces found in the experiment. </td></tr>
<tr><td class="paramname">new_traces</td><td>Mass traces created by cropping the original mass traces. </td></tr>
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</dd>
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<p>References <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a65120f4f127d69944775cd5aae06709f">TraceFitter< PeakType >::computeTheoretical()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a10ddb3b8cc795c598f76db017b9ca322">TraceFitter< PeakType >::getLowerRTBound()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a0ab9bd668829f0fc9608bd56560ac1ae">TraceFitter< PeakType >::getUpperRTBound()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#aac1b70a2ed67ead038c4d3f5ac4d8a81">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::isValid()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::max_trace</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_trace_score_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks</a>, <a class="el" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">OpenMS::Math::pearsonCorrelationCoefficient()</a>, and <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a7db81fa54d4743c867872ac5b0938247">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::theoretical_int</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">void extendMassTrace_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa6c9b584cfcb710d0fce1c647086faaa">MassTrace</a> & </td>
<td class="paramname"><em>trace</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td>
<td class="paramname"><em>spectrum_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>mz</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>increase_rt</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>meta_index_overall</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>min_rt</em> = <code>0.0</code>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>max_rt</em> = <code>0.0</code> </td>
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<td></td>
<td>)</td>
<td></td><td> const</td>
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<p>Extends a single mass trace in one RT direction. </p>
<p>How to use this method:</p>
<ul>
<li>Add the starting peak to the <code>trace</code> </li>
<li>Indicate using <code>increase_rt</code> whether to extend in downstream or upstream direction</li>
</ul>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">trace</td><td>The trace that should be extended </td></tr>
<tr><td class="paramname">spectrum_index</td><td>The index of the spectrum from which on the mass trace should be extended </td></tr>
<tr><td class="paramname">mz</td><td>The mz location (center) of the trace </td></tr>
<tr><td class="paramname">increase_rt</td><td>Indicator whether the extension is done in forward or backward direction (with respect to the current spectrum) </td></tr>
<tr><td class="paramname">meta_index_overall</td><td>The index of the overall score </td></tr>
<tr><td class="paramname">min_rt</td><td>The rt minimum up to which the trace will be extended. </td></tr>
<tr><td class="paramname">max_rt</td><td>The rt maximum up to which the trace will be extended.</td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>This method assumes that it extends from a local maximum. </dd>
<dd>
If <code>min_rt</code> or <code>max_rt</code> are set to 0.0 no boundary is assumed in the respective direction. </dd></dl>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_missing_trace_peaks_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::slope_bound_</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>.</p>
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<td class="memname">void extendMassTraces_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> & </td>
<td class="paramname"><em>pattern</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> & </td>
<td class="paramname"><em>traces</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>meta_index_overall</em> </td>
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<td></td>
<td>)</td>
<td></td><td> const</td>
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<p>Extends all mass traces of an isotope pattern in one step</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pattern</td><td>The IsotopePattern that should be extended. </td></tr>
<tr><td class="paramname">traces</td><td>The MassTraces datastructure where the extended mass traces will be stored in. </td></tr>
<tr><td class="paramname">meta_index_overall</td><td>The index of the data array where the qualtiy scores for the given charge are stored. </td></tr>
</table>
</dd>
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<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">Peak2D::getIntensity()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">Peak2D::getMZ()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#a2bf8eeb17dafb3d8ed1b08810fba2440">FeatureFinderAlgorithmPickedHelperStructs::Seed::intensity</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#aac1b70a2ed67ead038c4d3f5ac4d8a81">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::isValid()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_missing_trace_peaks_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::max_trace</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::pattern_tolerance_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">FeatureFinderAlgorithmPickedHelperStructs::Seed::peak</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTrace.html#a45696e11061da82e7cfd8a0ee88f5d8e">FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >::peaks</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum</a>, and <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern</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"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> findBestIsotopeFit_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a> & </td>
<td class="paramname"><em>center</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>charge</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> & </td>
<td class="paramname"><em>best_pattern</em> </td>
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<td></td>
<td>)</td>
<td></td><td> const</td>
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<p>Finds the best fitting position of the isotopic pattern estimate defined by <code>center</code>. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">center</td><td>the maximum peak of the isotope distribution (contains charge as well) </td></tr>
<tr><td class="paramname">charge</td><td>The charge of the pattern </td></tr>
<tr><td class="paramname">best_pattern</td><td>Returns the indices of the isotopic peaks. If a isopopic peak is missing -1 is returned. </td></tr>
</table>
</dd>
</dl>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">FeatureFinderAlgorithmPickedHelperStructs::Seed::peak</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum</a>, and <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern</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">void findIsotope_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>pos</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>spectrum_index</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> & </td>
<td class="paramname"><em>pattern</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>pattern_index</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> & </td>
<td class="paramname"><em>peak_index</em> </td>
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<td></td>
<td>)</td>
<td></td><td> const</td>
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<p>Searches for an isotopic peak in the current spectrum and the adjacent spectra. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pos</td><td>m/z position of the searched for peak </td></tr>
<tr><td class="paramname">spectrum_index</td><td>index of the central spectrum </td></tr>
<tr><td class="paramname">pattern</td><td>IsotopePattern to store found peaks </td></tr>
<tr><td class="paramname">pattern_index</td><td>index of the isotope in the pattern </td></tr>
<tr><td class="paramname">peak_index</td><td>starting index of the search (to avoid multiple binary searches) </td></tr>
</table>
</dd>
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<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#a830e58a22131827d85007a70e3069a5f">MSSpectrum< PeakT >::findNearest()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::intensity</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::mz_score</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5c38e77e9286e4faf58e56afce913ee2">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::nearest_()</a>, <a class="el" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::pattern_tolerance_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5ffc5efccefcdddcb7606303d72fa148">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::spectrum</a>, and <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a7d03330cd21316709f10c3e9ca55f95c">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_mz</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a>& getIsotopeDistribution_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>mass</em></td><td>)</td>
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<p>Returns the isotope distribution for a certain mass window. </p>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotope_distributions_</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::mass_window_width_</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">static const <a class="el" href="classOpenMS_1_1String.html">String</a> getProductName </td>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensityScore_ </td>
<td>(</td>
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<td class="paramname"><em>spectrum</em>, </td>
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<td class="paramname"><em>peak</em> </td>
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<p>Compute the intensity score for the peak <code>peak</code> in spectrum <code>spectrum</code>. </p>
<p>The intensity score is computed by interpolating the score between the 4 nearest intensity bins. The scores from the different bins are weighted by the distance of the bin center to the peak.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">spectrum</td><td>Index of the spectrum we are currently looking at </td></tr>
<tr><td class="paramname">peak</td><td>Index of the peak that should be scored inside the spectrum <code>spectrum</code> </td></tr>
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<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d8aab759e082ef93475344071fb7809">MSExperiment< PeakT, ChromatogramPeakT >::getMinMZ()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9244f3b9aefde24a9b246a8396c3bb84">MSExperiment< PeakT, ChromatogramPeakT >::getMinRT()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_bins_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_mz_step_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_rt_step_</a>, <a class="el" href="group__MathFunctionsMisc.html#gadaeb3f406822442307da5b2b94c40885">OpenMS::Math::isOdd()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_</a>, and <a class="el" href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</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"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensityScore_ </td>
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<td class="paramname"><em>rt_bin</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>mz_bin</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>intensity</em> </td>
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<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_thresholds_</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intersection_ </td>
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<td class="paramname"><em>f1</em>, </td>
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<p>Calculates the intersection between features. The value is normalized by the size of the smaller feature, so it ranges from 0 to 1. </p>
<p>References <a class="el" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">Feature::getConvexHulls()</a>, <a class="el" href="classOpenMS_1_1DBoundingBox.html#af99d7503ed85cda7c0ccc2217f36cee1">DBoundingBox< D >::intersects()</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#ac093fc547d9a49aef9950f6cd92b5588">DIntervalBase< D >::maxPosition()</a>, <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a84873a73e9e222a574dccff3bc2d860e">DIntervalBase< D >::minPosition()</a>, and <a class="el" href="classOpenMS_1_1Internal_1_1DIntervalBase.html#a1d3473af083e9dd668d782424aa2da05">DIntervalBase< D >::width()</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"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> isotopeScore_ </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a> & </td>
<td class="paramname"><em>isotopes</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3e0a91daf1d288f768c9683e317488f4">IsotopePattern</a> & </td>
<td class="paramname"><em>pattern</em>, </td>
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<p>Calculates a score between 0 and 1 for the correlation between theoretical and found isotope pattern. </p>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::intensity</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_isotope_fit_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a4671707ce0fc9ba23aa8319f67afa141">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::mz_score</a>, <a class="el" href="group__Conditions.html#gad781993fbeead99f7a76a5b0c67b70e1">OPENMS_POSTCONDITION</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#af2e76e2f5a4b1549e43a4dac9a3c35c2">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::optional_begin</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a511873304a043cc9222285de3a2c2913">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::optional_end</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::optional_fit_improvement_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak</a>, <a class="el" href="group__MathFunctionsStatistics.html#gac7a454e1847d508ba6635d47f49fbe8c">OpenMS::Math::pearsonCorrelationCoefficient()</a>, and <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> nearest_ </td>
<td>(</td>
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<td class="paramname"><em>pos</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae4e0f0c176662a323a6a64d29ff986dd">SpectrumType</a> & </td>
<td class="paramname"><em>spec</em>, </td>
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<td class="paramname"><em>start</em> </td>
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<p>Returns the index of the peak nearest to m/z <code>pos</code> in spectrum <code>spec</code> (linear search starting from index <code>start</code>) </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html">FeatureFinderAlgorithmPicked</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>, FeatureType > & </td>
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<p>Not implemented. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> positionScore_ </td>
<td>(</td>
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<td class="paramname"><em>pos1</em>, </td>
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<p>Calculates a score between 0 and 1 for the m/z deviation of two peaks. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">virtual void run </td>
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<p>Main method for actual <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>. </p>
<p>Implements <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a18954417d3124a8095783ea13dc6d00b">FeatureFinderAlgorithm< PeakType, FeatureType ></a>.</p>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a290ced0989c9db9d895a6a3435360f47">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_reasons_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afebc8acd9f3b44ba2936d842469f47e4">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::aborts_</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#aa23ed32415e6667bd2737377c24c16fb">MSExperiment< PeakT, ChromatogramPeakT >::areaBeginConst()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a5f9d4faff212e67330d60f958f0ce4bc">MSExperiment< PeakT, ChromatogramPeakT >::areaEndConst()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#a2387033802383edbdc95f9bbb12a707e">IsotopeDistribution::begin()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">OpenMS::Constants::c</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad832d6128e519d1c6a7fefd89158c37e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::chooseTraceFitter_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afa3f4fa08a8a3b675e2dab06e29412a1">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::debug_</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">DefaultParamHandler::defaults_</a>, <a class="el" href="classOpenMS_1_1Feature.html#a57c4a49592647cc2db0dc517ed9a1a02">Feature::encloses()</a>, <a class="el" href="classOpenMS_1_1DBoundingBox.html#ac55b302033b5b9d7c78a223db8cfaffb">DBoundingBox< D >::encloses()</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#ab45dae688fc5d8983727abffa4389003">IsotopeDistribution::end()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">ProgressLogger::endProgress()</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#a2a548700db35cba3fec126772ef27c72">IsotopeDistribution::estimateFromPeptideWeight()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">FeatureFinderAlgorithm< PeakType, FeatureType >::features_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf68cb378c76b322b2cc4dbb2c145a3e">FeatureFinderAlgorithm< PeakType, FeatureType >::ff_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#a830e58a22131827d85007a70e3069a5f">MSSpectrum< PeakT >::findNearest()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a7b2aeb3c8d1a4fd03c5843af07474735">TraceFitter< PeakType >::fit()</a>, <a class="el" href="classOpenMS_1_1ConvexHull2D.html#a88c6186ce22fc5eae73df90899695229">ConvexHull2D::getBoundingBox()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">TraceFitter< PeakType >::getCenter()</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#ac80a487ac41c375532f8bff16871ae15">BaseFeature::getCharge()</a>, <a class="el" href="classOpenMS_1_1Feature.html#ab071fe5bd7b2f969e4f9ed5d7467da1e">Feature::getConvexHull()</a>, <a class="el" href="classOpenMS_1_1Feature.html#ad99bb8ba2103d6c52ee10ae6369b46e7">Feature::getConvexHulls()</a>, <a class="el" href="classOpenMS_1_1ElementDB.html#a62508929fb2f7f12cfbd486272f1b480">ElementDB::getElement()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a642bbbd0de05e84147e701bfeaf188a2">TraceFitter< PeakType >::getFeatureIntensityContribution()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#aa1e7b6cd685312da3c92644d8fe71aac">TraceFitter< PeakType >::getFWHM()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#a0eac57e7b543d5084b9cdbb940fd031c">TraceFitter< PeakType >::getHeight()</a>, <a class="el" href="classOpenMS_1_1ElementDB.html#ae141930c87ab8851ec484bc1fd0ccb90">ElementDB::getInstance()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a09903c7965f8ece31f2c1e07b41ae6dd">Peak2D::getIntensity()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a87d8ffa067f5ee283997ac69b197234f">MSExperiment< PeakT, ChromatogramPeakT >::getMaxMZ()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#af67f955c87166e64d9361815dc3760b5">MSExperiment< PeakT, ChromatogramPeakT >::getMaxRT()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d8aab759e082ef93475344071fb7809">MSExperiment< PeakT, ChromatogramPeakT >::getMinMZ()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9244f3b9aefde24a9b246a8396c3bb84">MSExperiment< PeakT, ChromatogramPeakT >::getMinRT()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">Peak2D::getMZ()</a>, <a class="el" href="classOpenMS_1_1Feature.html#a0adf747960bee685e34bfbbe57a7089b">Feature::getOverallQuality()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">MSSpectrum< PeakT >::getRT()</a>, <a class="el" href="classOpenMS_1_1Feature.html#aaa5e4ac166de2cd5d3e38ccb4157bd77">Feature::getSubordinates()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#abd839e76d16452338866dd6bf6290c72">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getTheoreticalmaxPosition()</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="OpenSwathChromatogramExtractor_8C.html#ad1b6cd7c1daf3c44f94b28a904153b46">IF_MASTERTHREAD</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#a2bf8eeb17dafb3d8ed1b08810fba2440">FeatureFinderAlgorithmPickedHelperStructs::Seed::intensity</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#ac102a03577b6512164d6e4ff3cf78df0">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::intensity</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_bins_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5bce00011821a31f9344547c20c91e89">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_mz_step_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_optional_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac3ad3885811bdd008ebad6dc58424303">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_rt_step_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a7678e0cd827e8669246943be392bd8d0">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_thresholds_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#acc97fb931afc9e8f86fe9e40683a5a6c">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intersection_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afd3d2147a4dba98319002b876781f9ee">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotope_distributions_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a7e409d85407a4cfbc76fdc4aac06f185">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::isValid()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1fd714af1f19177741eb0b4f6eb43e35">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::log_</a>, <a class="el" href="LogStream_8h.html#a6ff63e8955665c4a58b1598f2b07c51a">LOG_DEBUG</a>, <a class="el" href="LogStream_8h.html#aeb4f36db01bd128c7afeac5889dac311">LOG_INFO</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a0b28abb9db6a809eec07048c69fdfaab">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::map_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::mass_window_width_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_feature_intersection_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac71f27c40d35a3658e5753647c3e63ca">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::max_trace</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_isotope_fit_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#af40104dc784144260a2345e53e5f0305">FeatureFinderAlgorithmPickedHelperStructs::Seed::peak</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#aec70588359757e4c6f30670fc74d2ebe">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::peak</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a37daff803c85d8fa7e2ba173b3138d60">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::positionScore_()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a7a25c5ed4c5f83b23ded7014aef42ad4">OpenMS::Constants::PROTON_MASS_U</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::reported_mz_</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac2bc824d6ff2633ec34793c9e918d479">MSExperiment< PeakT, ChromatogramPeakT >::resize()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::seeds_</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#ad66e45f6a7c4a7224810862a41545b1b">IsotopeDistribution::set()</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#ab595724fe9b9eb5d37011f07d90b9e0b">BaseFeature::setCharge()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#ab875c2479c6cd2a0189e4684bfa4f97d">Peak2D::setIntensity()</a>, <a class="el" href="classOpenMS_1_1Element.html#af005f66c79814a28924d954f0150ec44">Element::setIsotopeDistribution()</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#a261a831dc055b354545a8c0e48f57cad">IsotopeDistribution::setMaxIsotope()</a>, <a class="el" href="classOpenMS_1_1MetaInfoInterface.html#a135a7e818125b31198a8a65d9ac7a3d1">MetaInfoInterface::setMetaValue()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a2694f0775c46d9076355cb85d9815425">Peak2D::setMZ()</a>, <a class="el" href="classOpenMS_1_1Feature.html#aeba0cded976431f70fbea5499218ce18">Feature::setOverallQuality()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">DefaultParamHandler::setParameters()</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">ProgressLogger::setProgress()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a396c5ebcac2e70f9b9a478bb2456985b">Peak2D::setRT()</a>, <a class="el" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">UniqueIdInterface::setUniqueId()</a>, <a class="el" href="classOpenMS_1_1Param.html#a432099944e11263aa20aaf8ea1389790">Param::setValue()</a>, <a class="el" href="classOpenMS_1_1BaseFeature.html#a908f7d0328c34d70706d48af082d4751">BaseFeature::setWidth()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#a9d78a687cf2a391198bb3cbc08bc06cb">IsotopeDistribution::size()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#a9d78a687cf2a391198bb3cbc08bc06cb">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::size()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a93f1c9f620403aec160d98e83e125502">FeatureMap< FeatureT >::sortByIntensity()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a604ce6f3380b18acbebda3c1ed14e70c">FeatureMap< FeatureT >::sortByMZ()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1Seed.html#ae90f6d024629703c9ba0dbd5eb5ef4b2">FeatureFinderAlgorithmPickedHelperStructs::Seed::spectrum</a>, <a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">ProgressLogger::startProgress()</a>, <a class="el" href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">FeatureXMLFile::store()</a>, <a class="el" href="classOpenMS_1_1MzMLFile.html#adb795d215478320be7c6130ff7ddf853">MzMLFile::store()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a3554cb60a93215ed6c61b257a67efcc3">FeatureMap< FeatureT >::swapFeaturesOnly()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1IsotopePattern.html#a5dbfbed553b8cf7f9ef1bcb2c4ac94ca">FeatureFinderAlgorithmPickedHelperStructs::IsotopePattern::theoretical_pattern</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#adf5dffb508ec1b791c73f990ff92a3dd">IsotopeDistribution::trimLeft()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1TheoreticalIsotopePattern.html#abe90dc4ba735b87228bfe913b490f9f2">FeatureFinderAlgorithmPickedHelperStructs::TheoreticalIsotopePattern::trimmed_left</a>, <a class="el" href="classOpenMS_1_1IsotopeDistribution.html#a055e732ad7e3eed9cce0d279ae7af3a6">IsotopeDistribution::trimRight()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#ac342b58a6d6d5e6fae39d3300c37178d">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::updateBaseline()</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 void setSeeds </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> & </td>
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<p>Sets a reference to the calling <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>. </p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1IllegalArgument.html" title="A method or algorithm argument contains illegal values. ">Exception::IllegalArgument</a></td><td>is thrown if the algorithm does not support user-specified seed lists </td></tr>
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<p>Reimplemented from <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a683154793bbb12ab5d16db81209606b0">FeatureFinderAlgorithm< PeakType, FeatureType ></a>.</p>
<p>References <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a2f4fb91382abc4c1b9f767630d978f4d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::seeds_</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>References <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1b9ec9e0082be83ffb6db38de5d6a59e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_bins_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa2835fd8d8621a7ff9effbf85801917d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#afea7a0615504af04bc1b922416f702f7">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensity_percentage_optional_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac58a0fa7d6013c1855f905dbaa13c22f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::mass_window_width_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac7db097c6fa88dec6877edd3b7638b00">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_feature_intersection_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a4c3291ae9ef170e82168ccf10eaece4b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_missing_trace_peaks_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a301b8bd9f8b8404ffd2bf375b1f0cf2b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::max_rt_span_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a99b8e7ca327a789a40e0b03d4a280ca5">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_isotope_fit_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#abe26e024e3bac78f99e2a6d487cfe007">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_rt_span_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5fcb56e069842a53246cb6f063e99f22">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_spectra_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae9d0a125b344c7315dd63aed9b6871fc">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::min_trace_score_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a26002e622e0cb7f544d7d364be7c274a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::optional_fit_improvement_</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae8eb5ec37d3582ac0963d06ea624ab48">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::pattern_tolerance_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ae464adecb765a4c2b9c35b374620454e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::reported_mz_</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a6b1ec7d53602252d1f4d7cd0331fc917">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::slope_bound_</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a41848085aa61f5c00fc88e683945adf7">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::trace_tolerance_</a>.</p>
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<td class="memname">void writeFeatureDebugInfo_ </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1TraceFitter.html">TraceFitter</a>< <a class="el" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a> > * </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> & </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#af8a4ff323b3f9b72d77f56f9974d5aff">MassTraces</a> & </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td>
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<td>)</td>
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<p>Creates several files containing plots and viewable data of the fitted mass trace. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">fitter</td><td>The <a class="el" href="classOpenMS_1_1TraceFitter.html" title="Abstract fitter for RT profile fitting. ">TraceFitter</a> containing the results from the rt profile fitting step. </td></tr>
<tr><td class="paramname">traces</td><td>Original mass traces found in the spectra </td></tr>
<tr><td class="paramname">new_traces</td><td>Cropped feature mass traces </td></tr>
<tr><td class="paramname">feature_ok</td><td>Status of the feature </td></tr>
<tr><td class="paramname">error_msg</td><td>If the feature is invalid, <code>error_msg</code> contains the reason </td></tr>
<tr><td class="paramname">final_score</td><td>Final score of the feature </td></tr>
<tr><td class="paramname">plot_nr</td><td>Index of the feature </td></tr>
<tr><td class="paramname">peak</td><td>The Seed Peak </td></tr>
<tr><td class="paramname">path</td><td>The path where to put the debug files (default is debug/features) </td></tr>
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<p>References <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#acb405e09b194cb848140c99da3d6c34b">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::baseline</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a5f09052343ef99616ad653897841ce3e">FeatureFinderAlgorithm< PeakType, FeatureType >::features_</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ae740893fa17f26ea27e6f2383d72cb40">TraceFitter< PeakType >::getCenter()</a>, <a class="el" href="classOpenMS_1_1TraceFitter.html#ab67d38bd9a15db565531cc729df77924">TraceFitter< PeakType >::getGnuplotFormula()</a>, <a class="el" href="classOpenMS_1_1Peak2D.html#a6fefef82aae7a3208e71648e763d5ea4">Peak2D::getMZ()</a>, <a class="el" href="structOpenMS_1_1FeatureFinderAlgorithmPickedHelperStructs_1_1MassTraces.html#a34c827b6d53a8c171b233332bfe4d634">FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >::getPeakCount()</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="classOpenMS_1_1String.html#a5fe4516f447b7b646e39003f6c753ad5">String::number()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, and <a class="el" href="classOpenMS_1_1TextFile.html#a4fb93f999151e70a0f506c4c36f63fd7">TextFile::store()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname">std::map<<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ac02da3d017367d854cb162983679aadc">Seed</a>, <a class="el" href="classOpenMS_1_1String.html">String</a>> abort_reasons_</td>
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<p>Array of abort reasons. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">std::map<<a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>> aborts_</td>
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<p>Array of abort reasons. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">bool debug_</td>
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<p>debug flag </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> intensity_bins_</td>
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<p>Number of bins (in RT and MZ) for intensity significance estimation. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_mz_step_</td>
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<p>m/z bin width </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_percentage_</td>
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<p>Isotope pattern intensity contribution of required peaks. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_percentage_optional_</td>
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<p>Isotope pattern intensity contribution of optional peaks. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_rt_step_</td>
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<p>RT bin width. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">std::vector<std::vector<std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>> > > intensity_thresholds_</td>
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<p>Precalculated intensity 20-quantiles (binned) </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a3430a3cac3d46d0420ab99024264359f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname">std::vector<<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#adb93f7d18f3a19b45d1a05e7c29dbeaa">TheoreticalIsotopePattern</a>> isotope_distributions_</td>
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<p>Vector of precalculated isotope distributions for several mass windows. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<p>Output stream for log/debug info. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5eeb26578a9f2313c4fff108fb2d9d7b">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::abort_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aef59aef1baf90c9ea2376d677c9bf79d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::checkFeatureQuality_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#adf6f376e844058d129ce8ba868276643">MapType</a> map_</td>
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<p>editable copy of the map </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#ad47e8e2093326bd3a2476713d538dd9e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findBestIsotopeFit_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a5ae84d207afd136419c46d9ec811bb97">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::intensityScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mass_window_width_</td>
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<p>Width of the isotope pattern mass bins. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a9227a818c19cefa0d29f2940d87de2c6">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::getIsotopeDistribution_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_feature_intersection_</td>
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<p>Maximum allowed feature intersection (if larger, that one of the feature is removed) </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> max_missing_trace_peaks_</td>
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<p>Stores mass_trace:max_missing. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_rt_span_</td>
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<p>Maximum RT range the model is allowed to span. </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#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> min_isotope_fit_</td>
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<p>Mimimum isotope pattern fit for a feature. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<p>Minimum RT range that has to be left after the fit. </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#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> min_spectra_</td>
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<p>Number of spectra that have to show the same mass (for finding a mass trace) </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> min_trace_score_</td>
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<p>Minimum quality of a traces. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a1f44db8f9a5426ed4be51833385f5d6a">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::cropFeature_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> optional_fit_improvement_</td>
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<p>Minimal imrovment for leaving out optional isotope. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a55abad1b592c5e19bfaddfc9f9c4a43e">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::isotopeScore_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> pattern_tolerance_</td>
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<p>Stores mass_trace:mz_tolerance. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a00f443c46b1d9f3485ef02d844b2433d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a48c8332d7771967946379f577ca3d973">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> reported_mz_</td>
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<p>The mass type that is reported for features. 'maximum' returns the m/z value of the highest mass trace. 'average' returns the intensity-weighted average m/z value of all contained peaks. 'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithm.html#a21ea3968c35235b6b3cd78a2190280d9">FeatureMapType</a> seeds_</td>
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<p>User-specified seed list. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a683154793bbb12ab5d16db81209606b0">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::setSeeds()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> slope_bound_</td>
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<p>Max slope of mass trace intensities. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::updateMembers_()</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> trace_tolerance_</td>
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<p>Stores isotopic_pattern:mz_tolerance. </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#aa839121d4666e45d2b5b6d6eab010c5f">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTrace_()</a>, <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a72fcb26a14f6beb1c3fbace9ab3e7dbb">FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run()</a>, and <a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html#a776f7572fc4f466e9527ca233471920d">FeatureFinderAlgorithmPicked< PeakType, 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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