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<TITLE>SpectraSTSimilarityScore Class Reference</TITLE>
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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pub-static-methods">Static Public Member Functions</a> |
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<a href="classOpenMS_1_1SpectraSTSimilarityScore-members.html">List of all members</a> </div>
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<div class="headertitle">
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<div class="title">SpectraSTSimilarityScore Class Reference<div class="ingroups"><a class="el" href="group__SpectraComparison.html">Spectrum Comparison</a></div></div> </div>
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<div class="contents">
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<p>Similarity score of SpectraST.
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<a href="classOpenMS_1_1SpectraSTSimilarityScore.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="SpectraSTSimilarityScore_8h_source.html">OpenMS/COMPARISON/SPECTRA/SpectraSTSimilarityScore.h</a>></code></p>
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<div class="dynheader">
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Inheritance diagram for SpectraSTSimilarityScore:</div>
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<div class="dyncontent">
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<img src="classOpenMS_1_1SpectraSTSimilarityScore.png" usemap="#SpectraSTSimilarityScore_map" alt=""/>
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<map id="SpectraSTSimilarityScore_map" name="SpectraSTSimilarityScore_map">
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<area href="classOpenMS_1_1PeakSpectrumCompareFunctor.html" title="Base class for compare functors of spectra, that return a similiarity value for two spectra..." alt="PeakSpectrumCompareFunctor" shape="rect" coords="0,56,188,80"/>
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<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,188,24"/>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr class="memitem:a1e5d0a185dbd030756fdc495801808fc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#a1e5d0a185dbd030756fdc495801808fc">operator=</a> (const <a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> &source)</td></tr>
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<tr class="memdesc:a1e5d0a185dbd030756fdc495801808fc"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a1e5d0a185dbd030756fdc495801808fc">More...</a><br/></td></tr>
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<tr class="separator:a1e5d0a185dbd030756fdc495801808fc"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a18a43af59537ec0e9415461e7b47979e"><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_1SpectraSTSimilarityScore.html#a18a43af59537ec0e9415461e7b47979e">operator()</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec1, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec2) const </td></tr>
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<tr class="memdesc:a18a43af59537ec0e9415461e7b47979e"><td class="mdescLeft"> </td><td class="mdescRight">: calculates the dot product of the two spectra <a href="#a18a43af59537ec0e9415461e7b47979e">More...</a><br/></td></tr>
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<tr class="separator:a18a43af59537ec0e9415461e7b47979e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3a69baa896c33a5c50d17b534d675e79"><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_1SpectraSTSimilarityScore.html#a3a69baa896c33a5c50d17b534d675e79">operator()</a> (const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> &bin1, const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> &bin2) const </td></tr>
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<tr class="memdesc:a3a69baa896c33a5c50d17b534d675e79"><td class="mdescLeft"> </td><td class="mdescRight">: calculates the dot product of the two spectra <a href="#a3a69baa896c33a5c50d17b534d675e79">More...</a><br/></td></tr>
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<tr class="separator:a3a69baa896c33a5c50d17b534d675e79"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:acf573025185d987b7df2656221ef494d"><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_1SpectraSTSimilarityScore.html#acf573025185d987b7df2656221ef494d">operator()</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec) const </td></tr>
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<tr class="memdesc:acf573025185d987b7df2656221ef494d"><td class="mdescLeft"> </td><td class="mdescRight">: calculates the dot product of itself <a href="#acf573025185d987b7df2656221ef494d">More...</a><br/></td></tr>
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<tr class="separator:acf573025185d987b7df2656221ef494d"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a13d13d8f85b36a4b74e56ce84dea187f"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#a13d13d8f85b36a4b74e56ce84dea187f">preprocess</a> (<a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec, <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> remove_peak_intensity_threshold=2.01, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> cut_peaks_below=1000, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> min_peak_number=5, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> max_peak_number=150)</td></tr>
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<tr class="memdesc:a13d13d8f85b36a4b74e56ce84dea187f"><td class="mdescLeft"> </td><td class="mdescRight">Preprocesses the spectrum. <a href="#a13d13d8f85b36a4b74e56ce84dea187f">More...</a><br/></td></tr>
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<tr class="separator:a13d13d8f85b36a4b74e56ce84dea187f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae9d9239eb98ec2a2c043472a0a4ce5cb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#ae9d9239eb98ec2a2c043472a0a4ce5cb">transform</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec)</td></tr>
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<tr class="memdesc:ae9d9239eb98ec2a2c043472a0a4ce5cb"><td class="mdescLeft"> </td><td class="mdescRight">spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized. <a href="#ae9d9239eb98ec2a2c043472a0a4ce5cb">More...</a><br/></td></tr>
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<tr class="separator:ae9d9239eb98ec2a2c043472a0a4ce5cb"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aae58ce401bbbd351af85dd5dd1cdf486"><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_1SpectraSTSimilarityScore.html#aae58ce401bbbd351af85dd5dd1cdf486">dot_bias</a> (const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> &bin1, const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> &bin2, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> dot_product=-1) const </td></tr>
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<tr class="memdesc:aae58ce401bbbd351af85dd5dd1cdf486"><td class="mdescLeft"> </td><td class="mdescRight">Calculates how much of the dot prudct is dominated by a few peaks. <a href="#aae58ce401bbbd351af85dd5dd1cdf486">More...</a><br/></td></tr>
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<tr class="separator:aae58ce401bbbd351af85dd5dd1cdf486"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:abbbb7d2a2dc6759c5e9e81fd3abb00d7"><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_1SpectraSTSimilarityScore.html#abbbb7d2a2dc6759c5e9e81fd3abb00d7">delta_D</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> top_hit, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> runner_up)</td></tr>
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<tr class="memdesc:abbbb7d2a2dc6759c5e9e81fd3abb00d7"><td class="mdescLeft"> </td><td class="mdescRight">calculates the normalized distance between top_hit and runner_up. <a href="#abbbb7d2a2dc6759c5e9e81fd3abb00d7">More...</a><br/></td></tr>
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<tr class="separator:abbbb7d2a2dc6759c5e9e81fd3abb00d7"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a882fcc4ec17e4f88b669344dde015d73"><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_1SpectraSTSimilarityScore.html#a882fcc4ec17e4f88b669344dde015d73">compute_F</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> dot_product, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> <a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#abbbb7d2a2dc6759c5e9e81fd3abb00d7">delta_D</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> <a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#aae58ce401bbbd351af85dd5dd1cdf486">dot_bias</a>)</td></tr>
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<tr class="memdesc:a882fcc4ec17e4f88b669344dde015d73"><td class="mdescLeft"> </td><td class="mdescRight">: computes the overall all score <a href="#a882fcc4ec17e4f88b669344dde015d73">More...</a><br/></td></tr>
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<tr class="separator:a882fcc4ec17e4f88b669344dde015d73"><td class="memSeparator" colspan="2"> </td></tr>
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<tr><td colspan="2"><div class="groupHeader"></div></td></tr>
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<tr class="memitem:a79cb327ac3a4f5c289dfadf7ade6bb99"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#a79cb327ac3a4f5c289dfadf7ade6bb99">SpectraSTSimilarityScore</a> ()</td></tr>
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<tr class="memdesc:a79cb327ac3a4f5c289dfadf7ade6bb99"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#a79cb327ac3a4f5c289dfadf7ade6bb99">More...</a><br/></td></tr>
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<tr class="separator:a79cb327ac3a4f5c289dfadf7ade6bb99"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac33d56f2688c15280d5dad6577562823"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#ac33d56f2688c15280d5dad6577562823">SpectraSTSimilarityScore</a> (const <a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> &source)</td></tr>
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<tr class="memdesc:ac33d56f2688c15280d5dad6577562823"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#ac33d56f2688c15280d5dad6577562823">More...</a><br/></td></tr>
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<tr class="separator:ac33d56f2688c15280d5dad6577562823"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa7af6293ece6ce3b7bdaacc094a24949"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#aa7af6293ece6ce3b7bdaacc094a24949">~SpectraSTSimilarityScore</a> ()</td></tr>
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<tr class="memdesc:aa7af6293ece6ce3b7bdaacc094a24949"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#aa7af6293ece6ce3b7bdaacc094a24949">More...</a><br/></td></tr>
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<tr class="separator:aa7af6293ece6ce3b7bdaacc094a24949"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a></td></tr>
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<tr class="memitem:aa94067fde55bc9222f8743b27e32b3f1 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#aa94067fde55bc9222f8743b27e32b3f1">PeakSpectrumCompareFunctor</a> ()</td></tr>
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<tr class="memdesc:aa94067fde55bc9222f8743b27e32b3f1 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#aa94067fde55bc9222f8743b27e32b3f1">More...</a><br/></td></tr>
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<tr class="separator:aa94067fde55bc9222f8743b27e32b3f1 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3d6a3451fd30c5edc780cee37cef38c9 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#a3d6a3451fd30c5edc780cee37cef38c9">PeakSpectrumCompareFunctor</a> (const <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a> &source)</td></tr>
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<tr class="memdesc:a3d6a3451fd30c5edc780cee37cef38c9 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a3d6a3451fd30c5edc780cee37cef38c9">More...</a><br/></td></tr>
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<tr class="separator:a3d6a3451fd30c5edc780cee37cef38c9 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a695d3eee5bc48c6168e9df8c81e8e1f3 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#a695d3eee5bc48c6168e9df8c81e8e1f3">~PeakSpectrumCompareFunctor</a> ()</td></tr>
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<tr class="memdesc:a695d3eee5bc48c6168e9df8c81e8e1f3 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a695d3eee5bc48c6168e9df8c81e8e1f3">More...</a><br/></td></tr>
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<tr class="separator:a695d3eee5bc48c6168e9df8c81e8e1f3 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a0e88bb1b164535dcfbc1eb5d872af850 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#a0e88bb1b164535dcfbc1eb5d872af850">operator=</a> (const <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a> &source)</td></tr>
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<tr class="memdesc:a0e88bb1b164535dcfbc1eb5d872af850 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a0e88bb1b164535dcfbc1eb5d872af850">More...</a><br/></td></tr>
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<tr class="separator:a0e88bb1b164535dcfbc1eb5d872af850 inherit pub_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<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>
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<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<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>
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<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>
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<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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Static Public Member Functions</h2></td></tr>
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<tr class="memitem:aea33b1d3b12fac714a9b5a9489d9ce10"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html#aea33b1d3b12fac714a9b5a9489d9ce10">create</a> ()</td></tr>
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<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_1SpectraSTSimilarityScore.html#af73fd15708e50e77665070023a09cc87">getProductName</a> ()</td></tr>
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<tr class="memdesc:af73fd15708e50e77665070023a09cc87"><td class="mdescLeft"> </td><td class="mdescRight">Reimplemented from <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html" title="Base class for compare functors of spectra, that return a similiarity value for two spectra...">PeakSpectrumCompareFunctor</a>. <a href="#af73fd15708e50e77665070023a09cc87">More...</a><br/></td></tr>
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<tr class="inherit_header pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a></td></tr>
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<tr class="memitem:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
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<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="mdescLeft"> </td><td class="mdescRight">registers all derived products <a href="#a7899dbe105534dc1f81971dd71a26ff0">More...</a><br/></td></tr>
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<tr class="separator:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:af73fd15708e50e77665070023a09cc87 inherit pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><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_1PeakSpectrumCompareFunctor.html#af73fd15708e50e77665070023a09cc87">getProductName</a> ()</td></tr>
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<tr class="separator:af73fd15708e50e77665070023a09cc87 inherit pub_static_methods_classOpenMS_1_1PeakSpectrumCompareFunctor"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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Additional Inherited Members</h2></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>
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<tr class="memitem:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
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<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><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>
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<tr class="separator:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<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>
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<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>
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<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
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<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
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<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
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<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>
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<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="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </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>
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<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>
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<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Similarity score of SpectraST. </p>
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<p>Unlike the other similarity scores this score is used for matching a spectrum against a whole library, although the dot poduct seems to be an effective method for scoring on its own. For calculating the Spectrast score, first preprocess the spectra if not already done. Transform them and calculate the dot product and the dot bias. Afterwards get the best two hits and calculate delta_D. Now for every spectrum from the library you can calculate the final score.</p>
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<p>The details of the score can be found in: H. Lam et al., Development and validation of a spectral library searching method for peptide identification from MS/MS, Proteomics, 7 , 655-667, 2007 </p>
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> </td>
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<td class="paramname"></td><td>)</td>
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<p>default constructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> & </td>
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<td class="paramname"><em>source</em></td><td>)</td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> </td>
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<td class="paramname"></td><td>)</td>
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<td class="mlabels-right">
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> compute_F </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>dot_product</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>delta_D</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>dot_bias</em> </td>
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<p>: computes the overall all score </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">dot_product</td><td>of a match </td></tr>
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<tr><td class="paramname">delta_D</td><td>should be calculated after all dot products for a unidentified spectrum are computed </td></tr>
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<tr><td class="paramname">dot_bias</td><td></td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the SpectraST similarity score </dd></dl>
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<td class="memname">static <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a>* create </td>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> delta_D </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>top_hit</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>runner_up</em> </td>
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<p>calculates the normalized distance between top_hit and runner_up. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">top_hit</td><td>is the best score for a given match. </td></tr>
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<tr><td class="paramname">runner_up</td><td>a match with a worse score than top_hit. e.g. the second best score.</td></tr>
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<dl class="section return"><dt>Returns</dt><dd>normalized distance </dd></dl>
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<tr><td class="paramname">DividedByZero</td><td>exception if top_hit is 0.</td></tr>
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<dl class="section note"><dt>Note</dt><dd>Range of the dot products is between 0 and 1. </dd></dl>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> dot_bias </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> & </td>
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<td class="paramname"><em>bin1</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> & </td>
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<td class="paramname"><em>bin2</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
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<td class="paramname"><em>dot_product</em> = <code>-1</code> </td>
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<td></td><td> const</td>
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<p>Calculates how much of the dot prudct is dominated by a few peaks. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">dot_product</td><td>if -1 this value will be calculated as well. </td></tr>
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<tr><td class="paramname">bin1</td><td>first spectrum in binned representation </td></tr>
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<tr><td class="paramname">bin2</td><td>second spectrum in binned representation </td></tr>
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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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<p>Reimplemented from <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html" title="Base class for compare functors of spectra, that return a similiarity value for two spectra...">PeakSpectrumCompareFunctor</a>. </p>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
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<td class="paramname"><em>spec1</em>, </td>
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<p>: calculates the dot product of the two spectra </p>
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<p>Implements <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#a1bdb502bb510e9a61ad5762ff98d5edc">PeakSpectrumCompareFunctor</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> operator() </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> & </td>
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<td class="paramname"><em>bin1</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> & </td>
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<td class="paramname"><em>bin2</em> </td>
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<td></td><td> const</td>
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<p>: calculates the dot product of the two spectra </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> operator() </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
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<td class="paramname"><em>spec</em></td><td>)</td>
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<p>: calculates the dot product of itself </p>
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<p>Implements <a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html#a59481527ad716059d361e32eb1ed5cb3">PeakSpectrumCompareFunctor</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1SpectraSTSimilarityScore.html">SpectraSTSimilarityScore</a> & </td>
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<td class="paramname"><em>source</em></td><td>)</td>
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<p>assignment operator </p>
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<td class="memname">bool preprocess </td>
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<td class="paramtype"><a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
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<td class="paramname"><em>spec</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td>
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<td class="paramname"><em>remove_peak_intensity_threshold</em> = <code>2.01</code>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
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<td class="paramname"><em>cut_peaks_below</em> = <code>1000</code>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
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<td class="paramname"><em>min_peak_number</em> = <code>5</code>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
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<td class="paramname"><em>max_peak_number</em> = <code>150</code> </td>
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<p>Preprocesses the spectrum. </p>
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<p>The preprocessing removes peak below a intensity threshold, reject spectra that does not have enough peaks, and cuts peaks exceeding the max_peak_number most intense peaks.</p>
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<dl class="section return"><dt>Returns</dt><dd>true if spectrum passes filtering </dd></dl>
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<td class="memname"><a class="el" href="classOpenMS_1_1BinnedSpectrum.html">BinnedSpectrum</a> transform </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
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<td class="paramname"><em>spec</em></td><td>)</td>
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<p>spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized. </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5</font></TD>
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