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<TITLE>MapAlignmentAlgorithmSpectrumAlignment 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_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a></li> </ul>
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<a href="#nested-classes">Classes</a> |
<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">MapAlignmentAlgorithmSpectrumAlignment Class Reference<div class="ingroups"><a class="el" href="group__MapAlignment.html">MapAlignment</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>A map alignment algorithm based on spectrum similarity (dynamic programming).
<a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#details">More...</a></p>
<p><code>#include <<a class="el" href="MapAlignmentAlgorithmSpectrumAlignment_8h_source.html">OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for MapAlignmentAlgorithmSpectrumAlignment:</div>
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<img src="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.png" usemap="#MapAlignmentAlgorithmSpectrumAlignment_map" alt=""/>
<map id="MapAlignmentAlgorithmSpectrumAlignment_map" name="MapAlignmentAlgorithmSpectrumAlignment_map">
<area href="classOpenMS_1_1MapAlignmentAlgorithm.html" title="Base class for all map-alignment algorithms. " alt="MapAlignmentAlgorithm" shape="rect" coords="131,56,384,80"/>
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,253,24"/>
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="263,0,516,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html">Compare</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">innerclass necessary for using the sort algo. <a href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment_1_1Compare.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a0871a5000159ab5a2f3b79d92760665f"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0871a5000159ab5a2f3b79d92760665f">MapAlignmentAlgorithmSpectrumAlignment</a> ()</td></tr>
<tr class="memdesc:a0871a5000159ab5a2f3b79d92760665f"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a0871a5000159ab5a2f3b79d92760665f">More...</a><br/></td></tr>
<tr class="separator:a0871a5000159ab5a2f3b79d92760665f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4b7f0f53c53352adb66f334fb5dd0a2b"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4b7f0f53c53352adb66f334fb5dd0a2b">~MapAlignmentAlgorithmSpectrumAlignment</a> ()</td></tr>
<tr class="memdesc:a4b7f0f53c53352adb66f334fb5dd0a2b"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a4b7f0f53c53352adb66f334fb5dd0a2b">More...</a><br/></td></tr>
<tr class="separator:a4b7f0f53c53352adb66f334fb5dd0a2b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2038727c06b2e23bf60e1d21d7179815"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a2038727c06b2e23bf60e1d21d7179815">alignPeakMaps</a> (std::vector< <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a2038727c06b2e23bf60e1d21d7179815"><td class="mdescLeft"> </td><td class="mdescRight">Aligns peak maps. <a href="#a2038727c06b2e23bf60e1d21d7179815">More...</a><br/></td></tr>
<tr class="separator:a2038727c06b2e23bf60e1d21d7179815"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1MapAlignmentAlgorithm')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td></tr>
<tr class="memitem:a2323adcbf2f7ef45c0a4c63f0001374a inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2323adcbf2f7ef45c0a4c63f0001374a">MapAlignmentAlgorithm</a> ()</td></tr>
<tr class="memdesc:a2323adcbf2f7ef45c0a4c63f0001374a inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a2323adcbf2f7ef45c0a4c63f0001374a">More...</a><br/></td></tr>
<tr class="separator:a2323adcbf2f7ef45c0a4c63f0001374a inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1423ba5efed91566183b0d264fe0c2fe inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a1423ba5efed91566183b0d264fe0c2fe">~MapAlignmentAlgorithm</a> ()</td></tr>
<tr class="memdesc:a1423ba5efed91566183b0d264fe0c2fe inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a1423ba5efed91566183b0d264fe0c2fe">More...</a><br/></td></tr>
<tr class="separator:a1423ba5efed91566183b0d264fe0c2fe inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9e66a73174d03975d49a7e9b3f8854df inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a9e66a73174d03975d49a7e9b3f8854df">alignCompactFeatureMaps</a> (std::vector< std::vector< <a class="el" href="classOpenMS_1_1Peak2D.html">Peak2D</a> > > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a9e66a73174d03975d49a7e9b3f8854df inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns vectors of 2D peaks (memory efficient version of <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a>) <a href="#a9e66a73174d03975d49a7e9b3f8854df">More...</a><br/></td></tr>
<tr class="separator:a9e66a73174d03975d49a7e9b3f8854df inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a32c9e0577b4455dbc2d3493079ef1c81 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a32c9e0577b4455dbc2d3493079ef1c81">alignFeatureMaps</a> (std::vector< <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a32c9e0577b4455dbc2d3493079ef1c81 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns feature maps. <a href="#a32c9e0577b4455dbc2d3493079ef1c81">More...</a><br/></td></tr>
<tr class="separator:a32c9e0577b4455dbc2d3493079ef1c81 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7385e8b646ae9d282c3c06abf1620083 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7385e8b646ae9d282c3c06abf1620083">alignConsensusMaps</a> (std::vector< <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a7385e8b646ae9d282c3c06abf1620083 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns consensus maps. <a href="#a7385e8b646ae9d282c3c06abf1620083">More...</a><br/></td></tr>
<tr class="separator:a7385e8b646ae9d282c3c06abf1620083 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4f223602464cbafef563871036b5dfc1 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a4f223602464cbafef563871036b5dfc1">alignPeptideIdentifications</a> (std::vector< std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > > &, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &)</td></tr>
<tr class="memdesc:a4f223602464cbafef563871036b5dfc1 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Aligns peptide identifications. <a href="#a4f223602464cbafef563871036b5dfc1">More...</a><br/></td></tr>
<tr class="separator:a4f223602464cbafef563871036b5dfc1 inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aef01d65c73bbdd9f550309195007622b inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#aef01d65c73bbdd9f550309195007622b">setReference</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> reference_index=0, const <a class="el" href="classOpenMS_1_1String.html">String</a> &reference_file="")</td></tr>
<tr class="memdesc:aef01d65c73bbdd9f550309195007622b inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Defines a reference for the alignment. <a href="#aef01d65c73bbdd9f550309195007622b">More...</a><br/></td></tr>
<tr class="separator:aef01d65c73bbdd9f550309195007622b inherit pub_methods_classOpenMS_1_1MapAlignmentAlgorithm"><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>
<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE! <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of progress log being used. <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the progress display. <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the current progress. <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Ends the progress display. <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><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:a9584ec9238430832ac2c381039513247"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9584ec9238430832ac2c381039513247">create</a> ()</td></tr>
<tr class="memdesc:a9584ec9238430832ac2c381039513247"><td class="mdescLeft"> </td><td class="mdescRight">Creates a new instance of this class (for <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) <a href="#a9584ec9238430832ac2c381039513247">More...</a><br/></td></tr>
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<tr class="memitem:a8d4600093afb26cff7d7db82a1837e9f"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8d4600093afb26cff7d7db82a1837e9f">getProductName</a> ()</td></tr>
<tr class="memdesc:a8d4600093afb26cff7d7db82a1837e9f"><td class="mdescLeft"> </td><td class="mdescRight">Returns the product name (for the <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) <a href="#a8d4600093afb26cff7d7db82a1837e9f">More...</a><br/></td></tr>
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<tr class="inherit_header pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td colspan="2" onclick="javascript:toggleInherit('pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm')"><img src="closed.png" alt="-"/> Static Public Member Functions inherited from <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a></td></tr>
<tr class="memitem:acc270843ebe2525547c6ac01bf341234 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#acc270843ebe2525547c6ac01bf341234">fitModel</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &model_type, const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &params, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &trafos)</td></tr>
<tr class="memdesc:acc270843ebe2525547c6ac01bf341234 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Fits a model with given parameters to the transformations. <a href="#acc270843ebe2525547c6ac01bf341234">More...</a><br/></td></tr>
<tr class="separator:acc270843ebe2525547c6ac01bf341234 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="mdescLeft"> </td><td class="mdescRight">Register all derived classes in this method. <a href="#a7899dbe105534dc1f81971dd71a26ff0">More...</a><br/></td></tr>
<tr class="separator:a7899dbe105534dc1f81971dd71a26ff0 inherit pub_static_methods_classOpenMS_1_1MapAlignmentAlgorithm"><td class="memSeparator" colspan="2"> </td></tr>
</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:a6bc1d6b26465ed9cbf771c2cb0ad4313"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a6bc1d6b26465ed9cbf771c2cb0ad4313">MapAlignmentAlgorithmSpectrumAlignment</a> (const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> &)</td></tr>
<tr class="memdesc:a6bc1d6b26465ed9cbf771c2cb0ad4313"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor is not implemented -> private. <a href="#a6bc1d6b26465ed9cbf771c2cb0ad4313">More...</a><br/></td></tr>
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<tr class="memitem:ac24b9ad324036fbcb50828e3b9268d1e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac24b9ad324036fbcb50828e3b9268d1e">operator=</a> (const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> &)</td></tr>
<tr class="memdesc:ac24b9ad324036fbcb50828e3b9268d1e"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator is not implemented -> private. <a href="#ac24b9ad324036fbcb50828e3b9268d1e">More...</a><br/></td></tr>
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<tr class="memitem:a028b9561e7458f15cc08cba7238118b7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a028b9561e7458f15cc08cba7238118b7">prepareAlign_</a> (const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &pattern, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> &aligned, std::vector< <a class="el" href="classOpenMS_1_1TransformationDescription.html">TransformationDescription</a> > &transformation)</td></tr>
<tr class="memdesc:a028b9561e7458f15cc08cba7238118b7"><td class="mdescLeft"> </td><td class="mdescRight">A function to prepare the sequence for the alignment. It calls intern the main function for the alignment. <a href="#a028b9561e7458f15cc08cba7238118b7">More...</a><br/></td></tr>
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<tr class="memitem:ada98b6ec65437d5660a8bf43e1bc15fc"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ada98b6ec65437d5660a8bf43e1bc15fc">msFilter_</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> &peakmap, std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &spectrum_pointer_container)</td></tr>
<tr class="memdesc:ada98b6ec65437d5660a8bf43e1bc15fc"><td class="mdescLeft"> </td><td class="mdescRight">filtered the MSLevel to gain only MSLevel 1 <a href="#ada98b6ec65437d5660a8bf43e1bc15fc">More...</a><br/></td></tr>
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<tr class="memitem:ad60d86ce26e0eb12d4c4917de4cae236"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ad60d86ce26e0eb12d4c4917de4cae236">fourierActivation_</a> (std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &spectrum_pointer_container)</td></tr>
<tr class="memdesc:ad60d86ce26e0eb12d4c4917de4cae236"><td class="mdescLeft"> </td><td class="mdescRight">does the transformation if the Discrete Cosines Fourier Transformation is selected. <a href="#ad60d86ce26e0eb12d4c4917de4cae236">More...</a><br/></td></tr>
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<tr class="memitem:a2bc102affe34d954f253f24a0f1673f4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a2bc102affe34d954f253f24a0f1673f4">transform_</a> (<a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> &spec)</td></tr>
<tr class="memdesc:a2bc102affe34d954f253f24a0f1673f4"><td class="mdescLeft"> </td><td class="mdescRight">calculate the Discrete Cosines Fourier Transformation. <a href="#a2bc102affe34d954f253f24a0f1673f4">More...</a><br/></td></tr>
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<tr class="memitem:a9722326c38c717ec2e0eea7955aed051"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9722326c38c717ec2e0eea7955aed051">insideBand_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> m, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> k_)</td></tr>
<tr class="memdesc:a9722326c38c717ec2e0eea7955aed051"><td class="mdescLeft"> </td><td class="mdescRight">function for the test if cell i,j of the grid is inside the band <a href="#a9722326c38c717ec2e0eea7955aed051">More...</a><br/></td></tr>
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<tr class="memitem:a3b40e068d05ddb744123900a90148d94"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3b40e068d05ddb744123900a90148d94">bestk_</a> (const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &pattern, std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &aligned, std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > &buffer, bool column_row_orientation, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xbegin, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xend, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ybegin, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> yend)</td></tr>
<tr class="memdesc:a3b40e068d05ddb744123900a90148d94"><td class="mdescLeft"> </td><td class="mdescRight">calculate the size of the band for the alignment for two given Sequence <a href="#a3b40e068d05ddb744123900a90148d94">More...</a><br/></td></tr>
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<tr class="memitem:a7be42d61be33e31f1725bc3a4e84935c"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a7be42d61be33e31f1725bc3a4e84935c">scoreCalculation_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> patternbegin, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> alignbegin, const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &pattern, std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &aligned, std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > &buffer, bool column_row_orientation)</td></tr>
<tr class="memdesc:a7be42d61be33e31f1725bc3a4e84935c"><td class="mdescLeft"> </td><td class="mdescRight">calculate the score of two given MSSpectrums calls intern scoring_ <a href="#a7be42d61be33e31f1725bc3a4e84935c">More...</a><br/></td></tr>
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<tr class="memitem:a33e063cd96aaa8be717605e697029a54"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a33e063cd96aaa8be717605e697029a54">scoring_</a> (const <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> &a, <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> &b)</td></tr>
<tr class="memdesc:a33e063cd96aaa8be717605e697029a54"><td class="mdescLeft"> </td><td class="mdescRight">return the score of two given MSSpectrums by calling the scorefunction <a href="#a33e063cd96aaa8be717605e697029a54">More...</a><br/></td></tr>
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<tr class="memitem:a7141ee1dd0cfb6b893aa77cb2a29bd9e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a7141ee1dd0cfb6b893aa77cb2a29bd9e">affineGapalign_</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xbegin, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ybegin, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> xend, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> yend, const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &pattern, std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &aligned, std::vector< int > &xcoordinate, std::vector< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > &ycoordinate, std::vector< int > &xcoordinatepattern)</td></tr>
<tr class="memdesc:a7141ee1dd0cfb6b893aa77cb2a29bd9e"><td class="mdescLeft"> </td><td class="mdescRight">affine gap cost Alignment <a href="#a7141ee1dd0cfb6b893aa77cb2a29bd9e">More...</a><br/></td></tr>
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<tr class="memitem:a1a04c61f71e0325273f9e89cdc1c5a67"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a1a04c61f71e0325273f9e89cdc1c5a67">bucketFilter_</a> (const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &pattern, std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &aligned, std::vector< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> > &xcoordinate, std::vector< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > &ycoordinate, std::vector< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> > &xcoordinatepattern)</td></tr>
<tr class="memdesc:a1a04c61f71e0325273f9e89cdc1c5a67"><td class="mdescLeft"> </td><td class="mdescRight">preparation function of data points to construct later the spline function. <a href="#a1a04c61f71e0325273f9e89cdc1c5a67">More...</a><br/></td></tr>
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<tr class="memitem:af6a7c231cbbebdb557a892af1c22b146"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af6a7c231cbbebdb557a892af1c22b146">debugFileCreator_</a> (const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &pattern, std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &aligned)</td></tr>
<tr class="memdesc:af6a7c231cbbebdb557a892af1c22b146"><td class="mdescLeft"> </td><td class="mdescRight">Creates files for the debugging. <a href="#af6a7c231cbbebdb557a892af1c22b146">More...</a><br/></td></tr>
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<tr class="memitem:ad39786131abad2728aeada5bd882c264"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ad39786131abad2728aeada5bd882c264">eraseFloatDataArrayEntry_</a> (std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > &spectrum_pointer_container)</td></tr>
<tr class="memdesc:ad39786131abad2728aeada5bd882c264"><td class="mdescLeft"> </td><td class="mdescRight">Delete entries of the FloatDataArray which was made from <a class="el" href="classOpenMS_1_1CompareFouriertransform.html" title="Compare Discrete Cosines value from a Fourier transformation, also known as Discrete Cosines Transfor...">CompareFouriertransform</a>. <a href="#ad39786131abad2728aeada5bd882c264">More...</a><br/></td></tr>
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<tr class="memitem:a1809434361710cb8459386366900d35a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a1809434361710cb8459386366900d35a">debugscoreDistributionCalculation_</a> (<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> score)</td></tr>
<tr class="memdesc:a1809434361710cb8459386366900d35a"><td class="mdescLeft"> </td><td class="mdescRight">Rounding the score of two spectras, only necessary for debugging. <a href="#a1809434361710cb8459386366900d35a">More...</a><br/></td></tr>
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<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
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</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:a0bfda7af52aef129dd99f8664efd3da8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0bfda7af52aef129dd99f8664efd3da8">gap_</a></td></tr>
<tr class="memdesc:a0bfda7af52aef129dd99f8664efd3da8"><td class="mdescLeft"> </td><td class="mdescRight">Represent the gap cost for opening o closing a gap in the alignment. <a href="#a0bfda7af52aef129dd99f8664efd3da8">More...</a><br/></td></tr>
<tr class="separator:a0bfda7af52aef129dd99f8664efd3da8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5f4343fd568e4980066be6af2eef3351"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a5f4343fd568e4980066be6af2eef3351">e_</a></td></tr>
<tr class="memdesc:a5f4343fd568e4980066be6af2eef3351"><td class="mdescLeft"> </td><td class="mdescRight">Extension cost after a gap ist open. <a href="#a5f4343fd568e4980066be6af2eef3351">More...</a><br/></td></tr>
<tr class="separator:a5f4343fd568e4980066be6af2eef3351"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab890c00034eaf606dcd4438319dac090"><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_1MapAlignmentAlgorithmSpectrumAlignment.html#ab890c00034eaf606dcd4438319dac090">c1_</a></td></tr>
<tr class="memdesc:ab890c00034eaf606dcd4438319dac090"><td class="mdescLeft"> </td><td class="mdescRight">Pointer holds the scoringfunction, which can be selected. <a href="#ab890c00034eaf606dcd4438319dac090">More...</a><br/></td></tr>
<tr class="separator:ab890c00034eaf606dcd4438319dac090"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab194d52a2d0143fcdb17c626ebaaf588"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ab194d52a2d0143fcdb17c626ebaaf588">cutoffScore_</a></td></tr>
<tr class="memdesc:ab194d52a2d0143fcdb17c626ebaaf588"><td class="mdescLeft"> </td><td class="mdescRight">This is the minimal score to be count as a mismatch(range 0.0 - 1.0) <a href="#ab194d52a2d0143fcdb17c626ebaaf588">More...</a><br/></td></tr>
<tr class="separator:ab194d52a2d0143fcdb17c626ebaaf588"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a23c2cf21022e3e7bf4e9b82919dba1b8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a23c2cf21022e3e7bf4e9b82919dba1b8">bucketsize_</a></td></tr>
<tr class="memdesc:a23c2cf21022e3e7bf4e9b82919dba1b8"><td class="mdescLeft"> </td><td class="mdescRight">Defines the size of one bucket. <a href="#a23c2cf21022e3e7bf4e9b82919dba1b8">More...</a><br/></td></tr>
<tr class="separator:a23c2cf21022e3e7bf4e9b82919dba1b8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4e8ad8a7db1b7e3ee65134b631931a1a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a4e8ad8a7db1b7e3ee65134b631931a1a">anchorPoints_</a></td></tr>
<tr class="memdesc:a4e8ad8a7db1b7e3ee65134b631931a1a"><td class="mdescLeft"> </td><td class="mdescRight">Defines the amount of ankerpoints which are selected within one bucket. <a href="#a4e8ad8a7db1b7e3ee65134b631931a1a">More...</a><br/></td></tr>
<tr class="separator:a4e8ad8a7db1b7e3ee65134b631931a1a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afa3f4fa08a8a3b675e2dab06e29412a1"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#afa3f4fa08a8a3b675e2dab06e29412a1">debug_</a></td></tr>
<tr class="memdesc:afa3f4fa08a8a3b675e2dab06e29412a1"><td class="mdescLeft"> </td><td class="mdescRight">Debug mode flag default: False. <a href="#afa3f4fa08a8a3b675e2dab06e29412a1">More...</a><br/></td></tr>
<tr class="separator:afa3f4fa08a8a3b675e2dab06e29412a1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af300c42aaa79482d8acadf3470835ab8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#af300c42aaa79482d8acadf3470835ab8">mismatchscore_</a></td></tr>
<tr class="memdesc:af300c42aaa79482d8acadf3470835ab8"><td class="mdescLeft"> </td><td class="mdescRight">Represent the cost of a mismath in the alignment. <a href="#af300c42aaa79482d8acadf3470835ab8">More...</a><br/></td></tr>
<tr class="separator:af300c42aaa79482d8acadf3470835ab8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9b1cc0d5756927db86ca7ef37148b812"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a9b1cc0d5756927db86ca7ef37148b812">threshold_</a></td></tr>
<tr class="memdesc:a9b1cc0d5756927db86ca7ef37148b812"><td class="mdescLeft"> </td><td class="mdescRight">This is the minimum score for counting as a match(1-cutoffScore_) <a href="#a9b1cc0d5756927db86ca7ef37148b812">More...</a><br/></td></tr>
<tr class="separator:a9b1cc0d5756927db86ca7ef37148b812"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0a9eefab469443f2ac99f95d3ffa167f"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a0a9eefab469443f2ac99f95d3ffa167f">debugmatrix_</a></td></tr>
<tr class="memdesc:a0a9eefab469443f2ac99f95d3ffa167f"><td class="mdescLeft"> </td><td class="mdescRight">Container holding the score of the matchmatrix and also the insertmatrix. <a href="#a0a9eefab469443f2ac99f95d3ffa167f">More...</a><br/></td></tr>
<tr class="separator:a0a9eefab469443f2ac99f95d3ffa167f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3d66c4ad95892c40bce2188850fb36d8"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a3d66c4ad95892c40bce2188850fb36d8">debugscorematrix_</a></td></tr>
<tr class="memdesc:a3d66c4ad95892c40bce2188850fb36d8"><td class="mdescLeft"> </td><td class="mdescRight">Container holding the only the score of Spectrums. <a href="#a3d66c4ad95892c40bce2188850fb36d8">More...</a><br/></td></tr>
<tr class="separator:a3d66c4ad95892c40bce2188850fb36d8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac7c42fdddecd7a8212baa9bfa43ff958"><td class="memItemLeft" align="right" valign="top">std::vector< std::pair< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>, <br class="typebreak"/>
<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#ac7c42fdddecd7a8212baa9bfa43ff958">debugtraceback_</a></td></tr>
<tr class="memdesc:ac7c42fdddecd7a8212baa9bfa43ff958"><td class="mdescLeft"> </td><td class="mdescRight">Container holding the path of the traceback. <a href="#ac7c42fdddecd7a8212baa9bfa43ff958">More...</a><br/></td></tr>
<tr class="separator:ac7c42fdddecd7a8212baa9bfa43ff958"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8e7a8926f87a4a4709278d537577e4f8"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html#a8e7a8926f87a4a4709278d537577e4f8">scoredistribution_</a></td></tr>
<tr class="memdesc:a8e7a8926f87a4a4709278d537577e4f8"><td class="mdescLeft"> </td><td class="mdescRight">Container holding the score of each cell(matchmatrix,insertmatrix, traceback) <a href="#a8e7a8926f87a4a4709278d537577e4f8">More...</a><br/></td></tr>
<tr class="separator:a8e7a8926f87a4a4709278d537577e4f8"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
<tr class="separator:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
<tr class="separator:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a0c749bf4e621699b7a5c45ae22c2fa90">end_</a></td></tr>
<tr class="separator:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td></tr>
<tr class="separator:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
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<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>A map alignment algorithm based on spectrum similarity (dynamic programming). </p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
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<td style="vertical-align:top"><b>gapcost</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top"> This Parameter stands for the cost of opining a gap in the Alignment. A Gap means that one Spectrum can not be aligned directly to another Spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagen as a insert or delete of the spectrum in the map. The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and has to be punished a bit, so such only in case it 's a good choice to open a gap, if the score is bad enough. The Parameter is to giving as a positive number, the implementation convert it to a negative number.</td>
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<td style="vertical-align:top"><b>affinegapcost</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.5</td>
<td style="vertical-align:top">min: 0</td><td style="vertical-align:top"> This Parameter controls the cost of extension a already open gap. The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure gap match gap match. There for the punishment for the extension of a gap has to be lower than the normal gapcost. If the the result of the aligmnet show high compression, it is a good idea to lower the affine gapcost or the normal gapcost.</td>
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<td style="vertical-align:top"><i>cutoff_score</i></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">The Parameter defines the threshold which filtered Spectra, these Spectra are high potential candidate for deciding the interval of a sub-alignment. Only those pair of Spectra are selected, which has a score higher or same of the threshold.</td>
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<td style="vertical-align:top"><i>bucketsize</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top">min: 1</td><td style="vertical-align:top">Defines the numbers of buckets. It is a quantize of the interval of those points, which defines the main alignment(match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve.</td>
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<td style="vertical-align:top"><i>anchorpoints</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top">min: 1 max: 100</td><td style="vertical-align:top">Defines the percent of numbers of match points which a selected from one bucket. The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve.</td>
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<td style="vertical-align:top"><i>debug</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">active the debug mode, there a files written starting with debug prefix.</td>
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<td style="vertical-align:top"><i>mismatchscore</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">-5</td>
<td style="vertical-align:top">max: 0</td><td style="vertical-align:top">Defines the score of two Spectra if they have no similarity to each other. </td>
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<td style="vertical-align:top"><b>scorefunction</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">SteinScottImproveScore</td>
<td style="vertical-align:top">SteinScottImproveScore, ZhangSimilarityScore</td><td style="vertical-align:top"> The score function is the core of an alignment. The success of an alignment depends mostly of the elected score function. The score function return the similarity of two Spectrum back. The score influence defines later the way of possible traceback. There exist many way of algorithm to calculate the score.</td>
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<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
<dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000001">Experimental classes:</a></b></dt><dd>This algorithm is work in progress and might change.</dd></dl>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> </td>
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<p>Default constructor. </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> </td>
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<p>Destructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> & </td>
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<p>Copy constructor is not implemented -> private. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void affineGapalign_ </td>
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<td class="paramtype">std::vector< int > & </td>
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<td class="paramtype">std::vector< int > & </td>
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<p>affine gap cost Alignment </p>
<p>This Alignment is based on the Needleman Wunsch Algorithm. To improve the time complexity a banded version was implemented, known as k - alignment. To save some space, the alignment is going to be calculated by position xbegin to xend of one sequence and ybegin and yend by another given sequence. The result of the alignment is stored in the second argument. The first sequence is used as a template for the alignment.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">xbegin</td><td>cordinate for the beginning of the template sequence. </td></tr>
<tr><td class="paramname">ybegin</td><td>cordinate for the beginning of the aligend sequence . </td></tr>
<tr><td class="paramname">xend</td><td>cordinate for the end of the template sequence. </td></tr>
<tr><td class="paramname">yend</td><td>cordinate for the end of the aligend sequence. </td></tr>
<tr><td class="paramname">pattern</td><td>template map. </td></tr>
<tr><td class="paramname">aligned</td><td>map to be aligned. </td></tr>
<tr><td class="paramname">xcoordinate</td><td>save the postion of ankerpoints </td></tr>
<tr><td class="paramname">ycoordinate</td><td>save the retentiontimes of an ankerpoints </td></tr>
<tr><td class="paramname">xcoordinatepattern</td><td>save the reference position of the ankerpoints from the pattern</td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1OutOfRange.html" title="Out of range exception. ">Exception::OutOfRange</a></td><td>if a out of bound appear <code>pattern</code> or <code>aligned</code> </td></tr>
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<td class="memname">virtual void alignPeakMaps </td>
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<p>Aligns peak maps. </p>
<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1NotImplemented.html" title="Not implemented exception. ">Exception::NotImplemented</a></td><td>is thrown if an algorithm cannot align peak maps </td></tr>
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<p>Reimplemented from <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html#a2038727c06b2e23bf60e1d21d7179815">MapAlignmentAlgorithm</a>.</p>
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<td class="memname"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> bestk_ </td>
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<td class="paramtype">std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > & </td>
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<p>calculate the size of the band for the alignment for two given Sequence </p>
<p>This function calculates the size of the band for the alignment. It takes three samples from the aligned sequence and tries to find the highscore pairs(matching against the template sequence). The highscore pair with the worst distance is to be chosen as the size of k.</p>
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<tr><td class="paramname">pattern</td><td>vector of pointers of the template sequence </td></tr>
<tr><td class="paramname">aligned</td><td>vector of pointers of the aligned sequence </td></tr>
<tr><td class="paramname">buffer</td><td>holds the calculated score of index i,j. </td></tr>
<tr><td class="paramname">column_row_orientation</td><td>indicate the order of the matrix </td></tr>
<tr><td class="paramname">xbegin</td><td>indicate the beginning of the template sequence </td></tr>
<tr><td class="paramname">xend</td><td>indicate the end of the template sequence </td></tr>
<tr><td class="paramname">ybegin</td><td>indicate the beginning of the aligned sequence </td></tr>
<tr><td class="paramname">yend</td><td>indicate the end of the aligned sequence </td></tr>
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<td class="memname">void bucketFilter_ </td>
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<p>preparation function of data points to construct later the spline function. </p>
<p>This function reduced the amount of data values for the next step. The reduction is done by using a number of buckets, where the data points a selected. Within the buckets, only defined number a selected, to be written back as a data point. The selection within the buckets is done by scoring.</p>
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<tr><td class="paramname">aligned</td><td>map to be aligned. </td></tr>
<tr><td class="paramname">xcoordinate</td><td>save the position of anchor points </td></tr>
<tr><td class="paramname">ycoordinate</td><td>save the retention times of an anchor points </td></tr>
<tr><td class="paramname">xcoordinatepattern</td><td>save the reference position of the anchor points from the pattern </td></tr>
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<td class="memname">static <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithm.html">MapAlignmentAlgorithm</a>* create </td>
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<p>Creates a new instance of this class (for <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) </p>
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<td class="memname">void debugFileCreator_ </td>
<td>(</td>
<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
<td class="paramname"><em>pattern</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
<td class="paramname"><em>aligned</em> </td>
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<td>)</td>
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<p>Creates files for the debugging. </p>
<p>This function is only active if the debugflag ist true. The debugfileCreator creates following files debugtraceback.txt(gnuplotScript), debugscoreheatmap.r and debugRscript. Debugscoreheatmap.r contains the scores of the Spectra to each other from the alignment and also the traceback. DebugRscript is the R script which reads those data. So both files are only working under R. Start R and type main(location of debugscoreheatmap.r). The output will be a heatmap of each sub-alignment. Debugtraceback.txt shows the way of the Traceback by using gnuplot.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pattern</td><td>template map. </td></tr>
<tr><td class="paramname">aligned</td><td>map to be aligned. </td></tr>
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</dd>
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<td class="memname">void debugscoreDistributionCalculation_ </td>
<td>(</td>
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<td class="paramname"><em>score</em></td><td>)</td>
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<p>Rounding the score of two spectras, only necessary for debugging. </p>
<p>This function rounded the score of two spectras.This is necessary for some function in the Debug-Mode </p>
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<td class="memname">void eraseFloatDataArrayEntry_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
<td class="paramname"><em>spectrum_pointer_container</em></td><td>)</td>
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<p>Delete entries of the FloatDataArray which was made from <a class="el" href="classOpenMS_1_1CompareFouriertransform.html" title="Compare Discrete Cosines value from a Fourier transformation, also known as Discrete Cosines Transfor...">CompareFouriertransform</a>. </p>
<p>This function erase the entries with was done by the <a class="el" href="classOpenMS_1_1CompareFouriertransform.html" title="Compare Discrete Cosines value from a Fourier transformation, also known as Discrete Cosines Transfor...">CompareFouriertransform</a> function. </p>
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<td class="memname">void fourierActivation_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
<td class="paramname"><em>spectrum_pointer_container</em></td><td>)</td>
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<p>does the transformation if the Discrete Cosines Fourier Transformation is selected. </p>
<p>Call internally the function transform, only if the comparison score function Fourier is selected. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">spectrum_pointer_container</td><td>is the sequence which has to be transform </td></tr>
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<td class="memname">static <a class="el" href="classOpenMS_1_1String.html">String</a> getProductName </td>
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<p>Returns the product name (for the <a class="el" href="classOpenMS_1_1Factory.html" title="Returns FactoryProduct* based on the name of the desired concrete FactoryProduct. ...">Factory</a>) </p>
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<td class="memname">bool insideBand_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>i</em>, </td>
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<td class="paramname"><em>m</em>, </td>
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<td class="paramname"><em>k_</em> </td>
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<p>function for the test if cell i,j of the grid is inside the band </p>
<p>The function returns true if the cell underlie these conditions: -k<=i-j<=k+n-m else retun false. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">i</td><td>coordinate i </td></tr>
<tr><td class="paramname">j</td><td>coordinate j </td></tr>
<tr><td class="paramname">n</td><td>size of column </td></tr>
<tr><td class="paramname">m</td><td>size of row </td></tr>
<tr><td class="paramname">k_</td><td>size of k_ </td></tr>
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<td class="memname">void msFilter_ </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> & </td>
<td class="paramname"><em>peakmap</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
<td class="paramname"><em>spectrum_pointer_container</em> </td>
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<p>filtered the MSLevel to gain only MSLevel 1 </p>
<p>The alignment works only on MSLevel 1 data, so a filter has to be run.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">peakmap</td><td>map which has to be filtered </td></tr>
<tr><td class="paramname">spectrum_pointer_container</td><td>output container, where pointers of the <a class="el" href="classOpenMS_1_1MSSpectrum.html" title="The representation of a 1D spectrum. ">MSSpectrum</a> are saved(only with MS level 1)</td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<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 no spectra are contained in <code>peakmap</code> </td></tr>
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<td class="memname"><a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">MapAlignmentAlgorithmSpectrumAlignment</a> & </td>
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<p>Assignment operator is not implemented -> private. </p>
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<td class="memname">void prepareAlign_ </td>
<td>(</td>
<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
<td class="paramname"><em>pattern</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> & </td>
<td class="paramname"><em>aligned</em>, </td>
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<td class="paramname"><em>transformation</em> </td>
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<p>A function to prepare the sequence for the alignment. It calls intern the main function for the alignment. </p>
<p>This function takes two arguments. These argument types are two MSExperiments. The first argument should have been filtered, so that only the type of MSLevel 1 exists in the Sequence. The second argument doesn't have to fulfill this restriction. It's going to be filtered automatically. With these two arguments a precalculation is done to find some corresponding data points(maximum 4) for building alignment blocks. After the alignment a retransformation is done, the new Retention Times appear in the original data.</p>
<p>The parameters are MSExperiments. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pattern</td><td>template map. </td></tr>
<tr><td class="paramname">aligned</td><td>map which has to be aligned. </td></tr>
<tr><td class="paramname">transformation</td><td>container for rebuilding the alignment only by specific data-points </td></tr>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> scoreCalculation_ </td>
<td>(</td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> * > & </td>
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<td class="paramtype">std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::map< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > > & </td>
<td class="paramname"><em>buffer</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>column_row_orientation</em> </td>
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<p>calculate the score of two given MSSpectrums calls intern scoring_ </p>
<p>This function calculates the score from two MSSpectrums. These two MSSpectrums are chosen by the coordinates i,j. I,j indicate the index in the matrix. To find the right index on the sequence, each beginning is also given to the function. A flag indicates the labeling of the axes. The buffermatrix stores the result of the scoring. If the band expands only a lookup of known scores is done.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">i</td><td>is a index from the matrix. </td></tr>
<tr><td class="paramname">j</td><td>is a index from the matrix. </td></tr>
<tr><td class="paramname">patternbegin</td><td>indicate the beginning of the template sequence </td></tr>
<tr><td class="paramname">alignbegin</td><td>indicate the beginning of the aligned sequence </td></tr>
<tr><td class="paramname">pattern</td><td>vector of pointers of the template sequence </td></tr>
<tr><td class="paramname">aligned</td><td>vector of pointers of the aligned sequence </td></tr>
<tr><td class="paramname">buffer</td><td>holds the calculated score of index i,j. </td></tr>
<tr><td class="paramname">column_row_orientation</td><td>indicate the order of the matrix </td></tr>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> scoring_ </td>
<td>(</td>
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<td class="paramname"><em>a</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> & </td>
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<p>return the score of two given MSSpectrums by calling the scorefunction </p>
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<td class="memname">void transform_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum</a><> & </td>
<td class="paramname"><em>spec</em></td><td>)</td>
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<p>calculate the Discrete Cosines Fourier Transformation. </p>
<p>This Function transforms a given <a class="el" href="classOpenMS_1_1MSSpectrum.html" title="The representation of a 1D spectrum. ">MSSpectrum</a> to a Discrete Cosines Fourier Transformation. It stores only the part of the cosines of the FFT in the FloatDataArray which is a container from the <a class="el" href="classOpenMS_1_1MSSpectrum.html" title="The representation of a 1D spectrum. ">MSSpectrum</a>. Only call this function, if you are sure there is no other transformation done earlier over the same <a class="el" href="classOpenMS_1_1MSSpectrum.html" title="The representation of a 1D spectrum. ">MSSpectrum</a>, because it isn't checked if there already exists a transformation. </p>
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<td class="memname">void updateMembers_ </td>
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<p>This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. </p>
<p>Also call it at the end of the derived classes' copy constructor and assignment operator.</p>
<p>The default implementation is empty. </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> anchorPoints_</td>
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<p>Defines the amount of ankerpoints which are selected within one bucket. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> bucketsize_</td>
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<p>Defines the size of one bucket. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1PeakSpectrumCompareFunctor.html">PeakSpectrumCompareFunctor</a>* c1_</td>
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<p>Pointer holds the scoringfunction, which can be selected. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> cutoffScore_</td>
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<p>This is the minimal score to be count as a mismatch(range 0.0 - 1.0) </p>
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<td class="memname">bool debug_</td>
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<p>Debug mode flag default: False. </p>
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<td class="memname">std::vector<std::vector<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> > debugmatrix_</td>
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<p>Container holding the score of the matchmatrix and also the insertmatrix. </p>
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<td class="memname">std::vector<std::vector<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> > debugscorematrix_</td>
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<p>Container holding the only the score of Spectrums. </p>
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<td class="memname">std::vector<std::pair<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>, <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> > debugtraceback_</td>
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<p>Container holding the path of the traceback. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> e_</td>
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<p>Extension cost after a gap ist open. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> gap_</td>
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<p>Represent the gap cost for opening o closing a gap in the alignment. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> mismatchscore_</td>
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<p>Represent the cost of a mismath in the alignment. </p>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> scoredistribution_</td>
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<p>Container holding the score of each cell(matchmatrix,insertmatrix, traceback) </p>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> threshold_</td>
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<p>This is the minimum score for counting as a match(1-cutoffScore_) </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 11:19:26 using doxygen 1.8.5</font></TD>
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