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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_1SeedListGenerator.html">SeedListGenerator</a></li> </ul>
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<p>Generate seed lists for feature detection.
<a href="classOpenMS_1_1SeedListGenerator.html#details">More...</a></p>
<p><code>#include <<a class="el" href="SeedListGenerator_8h_source.html">OpenMS/TRANSFORMATIONS/FEATUREFINDER/SeedListGenerator.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a35c852f1e1c3bbae92fe8b56e305920c"><td class="memItemLeft" align="right" valign="top">typedef std::vector< <a class="el" href="classOpenMS_1_1DPosition.html">DPosition</a>< 2 > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a></td></tr>
<tr class="memdesc:a35c852f1e1c3bbae92fe8b56e305920c"><td class="mdescLeft"> </td><td class="mdescRight">List of seed positions. <a href="#a35c852f1e1c3bbae92fe8b56e305920c">More...</a><br/></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ac2b15c68bc927e2aa5ca913e4911d24d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#ac2b15c68bc927e2aa5ca913e4911d24d">SeedListGenerator</a> ()</td></tr>
<tr class="memdesc:ac2b15c68bc927e2aa5ca913e4911d24d"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#ac2b15c68bc927e2aa5ca913e4911d24d">More...</a><br/></td></tr>
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<tr class="memitem:ad9b568b4d958e1571f316c4ee0c451a7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#ad9b568b4d958e1571f316c4ee0c451a7">generateSeedList</a> (const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> &experiment, <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> &seeds)</td></tr>
<tr class="memdesc:ad9b568b4d958e1571f316c4ee0c451a7"><td class="mdescLeft"> </td><td class="mdescRight">Generate a seed list based on an MS experiment. <a href="#ad9b568b4d958e1571f316c4ee0c451a7">More...</a><br/></td></tr>
<tr class="separator:ad9b568b4d958e1571f316c4ee0c451a7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4456d3176dd2c169760e892ad3b0baa1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#a4456d3176dd2c169760e892ad3b0baa1">generateSeedList</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &peptides, <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> &seeds, bool use_peptide_mass=false)</td></tr>
<tr class="memdesc:a4456d3176dd2c169760e892ad3b0baa1"><td class="mdescLeft"> </td><td class="mdescRight">Generate a seed list based on a list of peptide identifications. <a href="#a4456d3176dd2c169760e892ad3b0baa1">More...</a><br/></td></tr>
<tr class="separator:a4456d3176dd2c169760e892ad3b0baa1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0fa7c579836567cabcb4ea683dd6d17b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#a0fa7c579836567cabcb4ea683dd6d17b">generateSeedLists</a> (const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#ga5162db95dc78bdf2e3a71d73bec703e9">UInt64</a>, <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> > &seed_lists)</td></tr>
<tr class="memdesc:a0fa7c579836567cabcb4ea683dd6d17b"><td class="mdescLeft"> </td><td class="mdescRight">Generate seed lists based on a consensus map. <a href="#a0fa7c579836567cabcb4ea683dd6d17b">More...</a><br/></td></tr>
<tr class="separator:a0fa7c579836567cabcb4ea683dd6d17b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ada845054d1959183aa987e7b3e5cd498"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#ada845054d1959183aa987e7b3e5cd498">convertSeedList</a> (const <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> &seeds, <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &features)</td></tr>
<tr class="memdesc:ada845054d1959183aa987e7b3e5cd498"><td class="mdescLeft"> </td><td class="mdescRight">Convert a list of seed positions to a feature map (expected format for <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>) <a href="#ada845054d1959183aa987e7b3e5cd498">More...</a><br/></td></tr>
<tr class="separator:ada845054d1959183aa987e7b3e5cd498"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adeb23d09ee6e957eff5d225a6b2f5c53"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#adeb23d09ee6e957eff5d225a6b2f5c53">convertSeedList</a> (const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> &features, <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> &seeds)</td></tr>
<tr class="memdesc:adeb23d09ee6e957eff5d225a6b2f5c53"><td class="mdescLeft"> </td><td class="mdescRight">Convert a feature map with seed positions back to a simple list. <a href="#adeb23d09ee6e957eff5d225a6b2f5c53">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>Generate seed lists for feature detection. </p>
<p>Seed lists specify locations in an MS experiment where features are expected. Currently, only the "centroided" <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a> algorithm (class <code><a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmPicked.html" title="FeatureFinderAlgorithm for picked peaks. ">FeatureFinderAlgorithmPicked</a></code>) supports custom seed lists (in featureXML format).</p>
<dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000006">Experimental classes:</a></b></dt><dd>This is a new class that still needs to be tested. </dd></dl>
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<td class="memname">typedef std::vector<<a class="el" href="classOpenMS_1_1DPosition.html">DPosition</a><2> > <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a></td>
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<p>List of seed positions. </p>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<p>Default constructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void convertSeedList </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> & </td>
<td class="paramname"><em>seeds</em>, </td>
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<p>Convert a list of seed positions to a feature map (expected format for <a class="el" href="classOpenMS_1_1FeatureFinder.html" title="The main feature finder class. ">FeatureFinder</a>) </p>
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<td class="memname">void convertSeedList </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FeatureMap.html">FeatureMap</a><> & </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> & </td>
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<p>Convert a feature map with seed positions back to a simple list. </p>
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<td class="memname">void generateSeedList </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> & </td>
<td class="paramname"><em>experiment</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> & </td>
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<p>Generate a seed list based on an MS experiment. </p>
<p>This uses the locations of MS2 precurors as seed positions. </p>
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<td class="memname">void generateSeedList </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
<td class="paramname"><em>peptides</em>, </td>
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<td class="paramname"><em>use_peptide_mass</em> = <code>false</code> </td>
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<p>Generate a seed list based on a list of peptide identifications. </p>
<p>This uses the retention time of the MS2 precursor ("RT" <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> entry) together with either the precursor m/z value ("MZ" <a class="el" href="classOpenMS_1_1MetaInfo.html" title="A Type-Name-Value tuple class. ">MetaInfo</a> entry) or - if <code>use_peptide_mass</code> is true - the monoisotopic mass and charge of the best peptide hit to define the seed position for a peptide identification.</p>
<p>The peptide hits in <code>peptides</code> will be sorted if <code>use_peptide_mass</code> is true. </p>
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<td class="memname">void generateSeedLists </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td>
<td class="paramname"><em>consensus</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#ga5162db95dc78bdf2e3a71d73bec703e9">UInt64</a>, <a class="el" href="classOpenMS_1_1SeedListGenerator.html#a35c852f1e1c3bbae92fe8b56e305920c">SeedList</a> > & </td>
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<p>Generate seed lists based on a consensus map. </p>
<p>This creates one seed list per constituent map of the consensus map. For each constituent map, a seed is generated at the position of each consensus feature that does not contain a sub-feature from this map. (The idea is to fill "holes" in the consensus map by looking for features explicitly at the positions of the "holes".) The seed lists are indexed by the IDs of the constituent maps in the consensus map.</p>
<p>Note that the resulting seed lists use the retention time scale of the consensus map, which might be different from the original time scales of the experiments if e.g. the MapAligner tool was used to perform retention time correction as part of the alignment process. </p>
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