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<HTML>
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<TITLE>SILACAnalyzer 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_1SILACAnalyzer.html">SILACAnalyzer</a></li>  </ul>
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  <div class="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pub-static-methods">Static Public Member Functions</a> &#124;
<a href="#pri-types">Private Types</a> &#124;
<a href="#pri-methods">Private Member Functions</a> &#124;
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<div class="title">SILACAnalyzer Class Reference</div>  </div>
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<p>Algorithm to use for SILACAnalysis.  
 <a href="classOpenMS_1_1SILACAnalyzer.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="SILACAnalyzer_8h_source.html">OpenMS/FILTERING/DATAREDUCTION/SILACAnalyzer.h</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for SILACAnalyzer:</div>
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  <img src="classOpenMS_1_1SILACAnalyzer.png" usemap="#SILACAnalyzer_map" alt=""/>
  <map id="SILACAnalyzer_map" name="SILACAnalyzer_map">
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="0,0,103,24"/>
</map>
 </div></div>
<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:a3ca615fc4cf75e66d68fdb94df4b94e9"><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a3ca615fc4cf75e66d68fdb94df4b94e9">SILACAnalyzer</a> ()</td></tr>
<tr class="separator:a3ca615fc4cf75e66d68fdb94df4b94e9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3df0796837f7699916b4e26fdb328b04"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a3df0796837f7699916b4e26fdb328b04">initialize</a> (<a class="el" href="classOpenMS_1_1String.html">String</a> selected_labels_, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> charge_min_, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> charge_max_, <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> missed_cleavages_, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> isotopes_per_peptide_min_, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> isotopes_per_peptide_max_, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> rt_threshold_, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> rt_min_, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_cutoff_, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> intensity_correlation_, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> model_deviation_, bool allow_missing_peaks_, std::map&lt; <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &gt; label_identifiers)</td></tr>
<tr class="memdesc:a3df0796837f7699916b4e26fdb328b04"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initializes the algorithm with parameters.  <a href="#a3df0796837f7699916b4e26fdb328b04">More...</a><br/></td></tr>
<tr class="separator:a3df0796837f7699916b4e26fdb328b04"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa9f0460bec4f7066c754fc37a7dcc9eb"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#aa9f0460bec4f7066c754fc37a7dcc9eb">calculateLabelsAndMassShifts</a> (std::map&lt; <a class="el" href="classOpenMS_1_1String.html">String</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &gt; label_identifiers)</td></tr>
<tr class="memdesc:aa9f0460bec4f7066c754fc37a7dcc9eb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Calculate the internal massShift and label datastructures from a map of identifiers and mass shifts (e.g. "Arg6" =&gt; 6.0201290268).  <a href="#aa9f0460bec4f7066c754fc37a7dcc9eb">More...</a><br/></td></tr>
<tr class="separator:aa9f0460bec4f7066c754fc37a7dcc9eb"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a63ca5fae46c85b6bc06a1dc801c7467f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a63ca5fae46c85b6bc06a1dc801c7467f">run_all</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt; <a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a> &gt; &amp;exp, <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;out_map)</td></tr>
<tr class="separator:a63ca5fae46c85b6bc06a1dc801c7467f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7e6a6e0ba384cb31ea0c21c8fbda51cd"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a7e6a6e0ba384cb31ea0c21c8fbda51cd">estimatePeakWidth</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt; <a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a> &gt; &amp;exp)</td></tr>
<tr class="memdesc:a7e6a6e0ba384cb31ea0c21c8fbda51cd"><td class="mdescLeft">&#160;</td><td class="mdescRight">Peak width estimation.  <a href="#a7e6a6e0ba384cb31ea0c21c8fbda51cd">More...</a><br/></td></tr>
<tr class="separator:a7e6a6e0ba384cb31ea0c21c8fbda51cd"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a77bce383632422b42ddb5a3142f2549b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a77bce383632422b42ddb5a3142f2549b">filterData</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt; <a class="el" href="classOpenMS_1_1Peak1D.html">Peak1D</a> &gt; &amp;exp, const <a class="el" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> &amp;peak_width, std::vector&lt; std::vector&lt; <a class="el" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &gt; &gt; &amp;data)</td></tr>
<tr class="memdesc:a77bce383632422b42ddb5a3142f2549b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Filtering.  <a href="#a77bce383632422b42ddb5a3142f2549b">More...</a><br/></td></tr>
<tr class="separator:a77bce383632422b42ddb5a3142f2549b"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1bb2cec563e265f21c96a116b6b3abf8"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a1bb2cec563e265f21c96a116b6b3abf8">clusterData</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>&lt;&gt; &amp;, const <a class="el" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> &amp;, std::vector&lt; <a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a> * &gt; &amp;, std::vector&lt; std::vector&lt; <a class="el" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &gt; &gt; &amp;data)</td></tr>
<tr class="memdesc:a1bb2cec563e265f21c96a116b6b3abf8"><td class="mdescLeft">&#160;</td><td class="mdescRight">Clustering.  <a href="#a1bb2cec563e265f21c96a116b6b3abf8">More...</a><br/></td></tr>
<tr class="separator:a1bb2cec563e265f21c96a116b6b3abf8"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a76a3c66df61210b400938317c735098a"><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::vector<br class="typebreak"/>
&lt; <a class="el" href="classOpenMS_1_1String.html">String</a> &gt; &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a76a3c66df61210b400938317c735098a">getSILAClabels</a> ()</td></tr>
<tr class="memdesc:a76a3c66df61210b400938317c735098a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" =&gt; SILAClabels[0][1]="Arg6".  <a href="#a76a3c66df61210b400938317c735098a">More...</a><br/></td></tr>
<tr class="separator:a76a3c66df61210b400938317c735098a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab0a5d682b988df4438f71140a2e68275"><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::vector<br class="typebreak"/>
&lt; <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> &gt; &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab0a5d682b988df4438f71140a2e68275">getMassShifts</a> ()</td></tr>
<tr class="memdesc:ab0a5d682b988df4438f71140a2e68275"><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the list of mass shifts calcualted.  <a href="#ab0a5d682b988df4438f71140a2e68275">More...</a><br/></td></tr>
<tr class="separator:ab0a5d682b988df4438f71140a2e68275"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8ce8c3ff796302a2bbe9061ec47324b9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a8ce8c3ff796302a2bbe9061ec47324b9">generateClusterConsensusByCluster</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, const <a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a> &amp;) const </td></tr>
<tr class="memdesc:a8ce8c3ff796302a2bbe9061ec47324b9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> from clustering result.  <a href="#a8ce8c3ff796302a2bbe9061ec47324b9">More...</a><br/></td></tr>
<tr class="separator:a8ce8c3ff796302a2bbe9061ec47324b9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7f5a7aaf11bd3bf4b30881d30addfcc9"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a7f5a7aaf11bd3bf4b30881d30addfcc9">generateClusterConsensusByPattern</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, const <a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a> &amp;, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> &amp;cluster_id) const </td></tr>
<tr class="memdesc:a7f5a7aaf11bd3bf4b30881d30addfcc9"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> from clustering result, one consensus per pattern.  <a href="#a7f5a7aaf11bd3bf4b30881d30addfcc9">More...</a><br/></td></tr>
<tr class="separator:a7f5a7aaf11bd3bf4b30881d30addfcc9"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab15433b7b9febd77f6c9fd7aa77e94a2"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab15433b7b9febd77f6c9fd7aa77e94a2">generateClusterDebug</a> (std::ostream &amp;<a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab64766cccc4f8fdf5c87b8bcc9493c4a">out</a>, const <a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a> &amp;clustering, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> &amp;cluster_id) const </td></tr>
<tr class="memdesc:ab15433b7b9febd77f6c9fd7aa77e94a2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate debug output from clustering result.  <a href="#ab15433b7b9febd77f6c9fd7aa77e94a2">More...</a><br/></td></tr>
<tr class="separator:ab15433b7b9febd77f6c9fd7aa77e94a2"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a973d67f591c11ed83454c5eb30080733"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a973d67f591c11ed83454c5eb30080733">generateFilterConsensusByPattern</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, const std::vector&lt; <a class="el" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &gt; &amp;) const </td></tr>
<tr class="memdesc:a973d67f591c11ed83454c5eb30080733"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> from filter result.  <a href="#a973d67f591c11ed83454c5eb30080733">More...</a><br/></td></tr>
<tr class="separator:a973d67f591c11ed83454c5eb30080733"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab7669f90315a785ae91b3642503ffae4"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab7669f90315a785ae91b3642503ffae4">generateClusterFeatureByCluster</a> (<a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;, const <a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a> &amp;) const </td></tr>
<tr class="memdesc:ab7669f90315a785ae91b3642503ffae4"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> from clustering result.  <a href="#ab7669f90315a785ae91b3642503ffae4">More...</a><br/></td></tr>
<tr class="separator:ab7669f90315a785ae91b3642503ffae4"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a1ac17e48c8b64dd12b240bbf41c75501"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a1ac17e48c8b64dd12b240bbf41c75501">readFilterConsensusByPattern</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;, std::vector&lt; std::vector&lt; <a class="el" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &gt; &gt; &amp;)</td></tr>
<tr class="memdesc:a1ac17e48c8b64dd12b240bbf41c75501"><td class="mdescLeft">&#160;</td><td class="mdescRight">Read filter result from <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a>.  <a href="#a1ac17e48c8b64dd12b240bbf41c75501">More...</a><br/></td></tr>
<tr class="separator:a1ac17e48c8b64dd12b240bbf41c75501"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae930eb8197c8961725cdc3aacc6a1c09"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ae930eb8197c8961725cdc3aacc6a1c09">readConsensus</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;<a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a19a2651887fa4d874edfe6a94b54b2d5">in</a>) const </td></tr>
<tr class="memdesc:ae930eb8197c8961725cdc3aacc6a1c09"><td class="mdescLeft">&#160;</td><td class="mdescRight">Read consensusXML from file to <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a>.  <a href="#ae930eb8197c8961725cdc3aacc6a1c09">More...</a><br/></td></tr>
<tr class="separator:ae930eb8197c8961725cdc3aacc6a1c09"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae14ec0b9fd095ebe54c1e8cc75338548"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ae14ec0b9fd095ebe54c1e8cc75338548">writeConsensus</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;<a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab64766cccc4f8fdf5c87b8bcc9493c4a">out</a>) const </td></tr>
<tr class="memdesc:ae14ec0b9fd095ebe54c1e8cc75338548"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write consensusXML from <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> to file.  <a href="#ae14ec0b9fd095ebe54c1e8cc75338548">More...</a><br/></td></tr>
<tr class="separator:ae14ec0b9fd095ebe54c1e8cc75338548"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7d9066a1cc3461a21d32188728049cde"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a7d9066a1cc3461a21d32188728049cde">writeMzQuantML</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, <a class="el" href="classOpenMS_1_1MSQuantifications.html">MSQuantifications</a> &amp;<a class="el" href="classOpenMS_1_1SILACAnalyzer.html#aa924369b7a4efee5ac3ab55a7501c983">msq</a>) const </td></tr>
<tr class="memdesc:a7d9066a1cc3461a21d32188728049cde"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write MzQuantML from <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> to file.  <a href="#a7d9066a1cc3461a21d32188728049cde">More...</a><br/></td></tr>
<tr class="separator:a7d9066a1cc3461a21d32188728049cde"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ade305f744c909667f3c6f4e2fed3262b"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ade305f744c909667f3c6f4e2fed3262b">writeFeatures</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;filename, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a>&lt;&gt; &amp;<a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab64766cccc4f8fdf5c87b8bcc9493c4a">out</a>) const </td></tr>
<tr class="memdesc:ade305f744c909667f3c6f4e2fed3262b"><td class="mdescLeft">&#160;</td><td class="mdescRight">Write featureXML from <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> to file.  <a href="#ade305f744c909667f3c6f4e2fed3262b">More...</a><br/></td></tr>
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<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="-"/>&#160;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">&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</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>&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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> &amp;label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft">&#160;</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">&#160;</td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void&#160;</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">&#160;</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">&#160;</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:a29e0898fe9ab9db3ee0b22cee7a4e9c8"><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classOpenMS_1_1String.html">String</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#a29e0898fe9ab9db3ee0b22cee7a4e9c8">selectColor</a> (<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> nr)</td></tr>
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Private Types</h2></td></tr>
<tr class="memitem:ab82579f850f8826ffe606b8855504348"><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classOpenMS_1_1SILACClustering.html">SILACClustering</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a></td></tr>
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Private Member Functions</h2></td></tr>
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<tr class="memdesc:ae64f4b2329f844481dd2c94c032c0aaa"><td class="mdescLeft">&#160;</td><td class="mdescRight">Generate a consensus entry from a pattern.  <a href="#ae64f4b2329f844481dd2c94c032c0aaa">More...</a><br/></td></tr>
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<tr class="memitem:a60b26944cbd02e52b1e137a7069c6f1a"><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::vector<br class="typebreak"/>
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<tr class="memitem:a2eddf423e5ff345fb99fcfa45116f2f1"><td class="memItemLeft" align="right" valign="top">std::vector&lt; std::vector<br class="typebreak"/>
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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="-"/>&#160;Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
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<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft">&#160;</td><td class="mdescRight">Possible log types.  <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Algorithm to use for SILACAnalysis. </p>
<p>Please initialize before usage using the initialize function. Next, one can estimate the peak width before filtering the data.</p>
<p>In the final step, clusterData will generate the output data.</p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1SILACFiltering.html" title="Filtering for SILAC data. ">SILACFiltering</a> </dd></dl>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
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          <td class="memname">typedef <a class="el" href="classOpenMS_1_1SILACClustering.html">SILACClustering</a> <a class="el" href="classOpenMS_1_1SILACAnalyzer.html#ab82579f850f8826ffe606b8855504348">Clustering</a></td>
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<h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
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<h2 class="groupheader">Member Function Documentation</h2>
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          <td class="memname">void calculateLabelsAndMassShifts </td>
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          <td class="paramname"><em>label_identifiers</em></td><td>)</td>
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<p>Calculate the internal massShift and label datastructures from a map of identifiers and mass shifts (e.g. "Arg6" =&gt; 6.0201290268). </p>
<p>Note that this part is necessary for the algorithm to work and this function is called from the initialize section. The algorithm has to be initialized _first_ with the list of actually used labels (selected_labels) using the initialize_sample call. </p>

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<p>Clustering. </p>

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          <td class="memname"><a class="el" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> estimatePeakWidth </td>
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          <td class="paramname"><em>exp</em></td><td>)</td>
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<p>Peak width estimation. </p>

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          <td class="paramtype">const <a class="el" href="classOpenMS_1_1PeakWidthEstimator_1_1Result.html">PeakWidthEstimator::Result</a> &amp;&#160;</td>
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          <td class="paramtype">std::vector&lt; std::vector&lt; <a class="el" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &gt; &gt; &amp;&#160;</td>
          <td class="paramname"><em>data</em>&#160;</td>
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<p>Filtering. </p>

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<p>Generate <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> from clustering result. </p>

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<p>Generate <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> from clustering result, one consensus per pattern. </p>

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<p>Generate debug output from clustering result. </p>

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<p>Generate <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> from clustering result. </p>

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<p>Generate <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> from filter result. </p>

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          <td class="memname"><a class="el" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> generateSingleConsensusByPattern </td>
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<p>Generate a consensus entry from a pattern. </p>

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<p>Returns the list of mass shifts calcualted. </p>

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<p>Returns the list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" =&gt; SILAClabels[0][1]="Arg6". </p>

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          <td class="paramname"><em>rt_threshold_</em>, </td>
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          <td class="paramname"><em>intensity_cutoff_</em>, </td>
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          <td class="paramname"><em>intensity_correlation_</em>, </td>
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          <td class="paramname"><em>model_deviation_</em>, </td>
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          <td class="paramname"><em>label_identifiers</em>&#160;</td>
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<p>Initializes the algorithm with parameters. </p>
<dl class="params"><dt>Parameters</dt><dd>
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    <tr><td class="paramname">selected_labels_</td><td>Labels used for labelling the sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. The used labels must be described in the label_identifiers parameter </td></tr>
    <tr><td class="paramname">label_identifiers</td><td>a map of labels and corresponding mass shits e.g. "Arg6" =&gt; 6.0201290268 </td></tr>
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          <td class="paramname"><em>filename</em>, </td>
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          <td class="paramtype"><a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &amp;&#160;</td>
          <td class="paramname"><em>in</em>&#160;</td>
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<p>Read consensusXML from file to <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a>. </p>

<p>References <a class="el" href="classOpenMS_1_1ConsensusXMLFile.html#a426f58285a6c7a6b81346bcc4cf58e2a">ConsensusXMLFile::load()</a>.</p>

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          <td class="paramtype">std::vector&lt; std::vector&lt; <a class="el" href="classOpenMS_1_1SILACPattern.html">SILACPattern</a> &gt; &gt; &amp;&#160;</td>
          <td class="paramname">&#160;</td>
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<p>Read filter result from <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a>. </p>

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          <td class="memname">void run_all </td>
          <td>(</td>
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          <td class="memname">void writeConsensus </td>
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<p>Write consensusXML from <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> to file. </p>

<p>References <a class="el" href="classOpenMS_1_1ConsensusMap.html#a2ba4cf095974c86863027d78210dc2fa">ConsensusMap::applyMemberFunction()</a>, <a class="el" href="classOpenMS_1_1ConsensusMap.html#af3fc434b747ad4f686744aca8fe9ef84">ConsensusMap::setExperimentType()</a>, <a class="el" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">UniqueIdInterface::setUniqueId()</a>, <a class="el" href="classOpenMS_1_1ConsensusMap.html#a86f7b200260209865e730a2e4fcaa628">ConsensusMap::sortByPosition()</a>, and <a class="el" href="classOpenMS_1_1ConsensusXMLFile.html#af72f4966d65af7a802025d8640a0e570">ConsensusXMLFile::store()</a>.</p>

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<p>Write featureXML from <a class="el" href="classOpenMS_1_1FeatureMap.html" title="A container for features. ">FeatureMap</a> to file. </p>

<p>References <a class="el" href="classOpenMS_1_1FeatureMap.html#a2ba4cf095974c86863027d78210dc2fa">FeatureMap&lt; FeatureT &gt;::applyMemberFunction()</a>, <a class="el" href="classOpenMS_1_1UniqueIdInterface.html#a9c908a735f82adb8f66a326547a9acf8">UniqueIdInterface::setUniqueId()</a>, <a class="el" href="classOpenMS_1_1FeatureMap.html#a86f7b200260209865e730a2e4fcaa628">FeatureMap&lt; FeatureT &gt;::sortByPosition()</a>, and <a class="el" href="classOpenMS_1_1FeatureXMLFile.html#ae05e70281bd2c24b9cfa431200669858">FeatureXMLFile::store()</a>.</p>

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<p>Write MzQuantML from <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> to file. </p>

<p>References <a class="el" href="classOpenMS_1_1MzQuantMLFile.html#aafe60b67d30415c197f1ebfd10bf01c6">MzQuantMLFile::store()</a>.</p>

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<h2 class="groupheader">Member Data Documentation</h2>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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