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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_1ClusterAnalyzer.html">ClusterAnalyzer</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">ClusterAnalyzer Class Reference<div class="ingroups"><a class="el" href="group__SpectraClustering.html">Clustering</a></div></div> </div>
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<p>Bundles analyzing tools for a clustering (given as sequence of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s)
<a href="classOpenMS_1_1ClusterAnalyzer.html#details">More...</a></p>
<p><code>#include <<a class="el" href="ClusterAnalyzer_8h_source.html">OpenMS/COMPARISON/CLUSTERING/ClusterAnalyzer.h</a>></code></p>
<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:ace9f4a6b43173de5ec5264c3b17b8839"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#ace9f4a6b43173de5ec5264c3b17b8839">ClusterAnalyzer</a> ()</td></tr>
<tr class="memdesc:ace9f4a6b43173de5ec5264c3b17b8839"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#ace9f4a6b43173de5ec5264c3b17b8839">More...</a><br/></td></tr>
<tr class="separator:ace9f4a6b43173de5ec5264c3b17b8839"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a63800e1b364cc7683cf6c39581a57c6f"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#a63800e1b364cc7683cf6c39581a57c6f">ClusterAnalyzer</a> (const <a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> &source)</td></tr>
<tr class="memdesc:a63800e1b364cc7683cf6c39581a57c6f"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a63800e1b364cc7683cf6c39581a57c6f">More...</a><br/></td></tr>
<tr class="separator:a63800e1b364cc7683cf6c39581a57c6f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5b12731bfcd44e23a39faca1e2a72796"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#a5b12731bfcd44e23a39faca1e2a72796">~ClusterAnalyzer</a> ()</td></tr>
<tr class="memdesc:a5b12731bfcd44e23a39faca1e2a72796"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a5b12731bfcd44e23a39faca1e2a72796">More...</a><br/></td></tr>
<tr class="separator:a5b12731bfcd44e23a39faca1e2a72796"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a65875b284ab1d8b9c346998d5630ae47"><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_1ClusterAnalyzer.html#a65875b284ab1d8b9c346998d5630ae47">averageSilhouetteWidth</a> (const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &tree, const <a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > &original)</td></tr>
<tr class="memdesc:a65875b284ab1d8b9c346998d5630ae47"><td class="mdescLeft"> </td><td class="mdescRight">Method to calculate the average silhouette widths for a clustering. <a href="#a65875b284ab1d8b9c346998d5630ae47">More...</a><br/></td></tr>
<tr class="separator:a65875b284ab1d8b9c346998d5630ae47"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab6842fb78cfcd90d7426528978640f7a"><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_1ClusterAnalyzer.html#ab6842fb78cfcd90d7426528978640f7a">dunnIndices</a> (const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &tree, const <a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > &original, const bool tree_from_singlelinkage=false)</td></tr>
<tr class="memdesc:ab6842fb78cfcd90d7426528978640f7a"><td class="mdescLeft"> </td><td class="mdescRight">Method to calculate Dunns indices for a clustering. <a href="#ab6842fb78cfcd90d7426528978640f7a">More...</a><br/></td></tr>
<tr class="separator:ab6842fb78cfcd90d7426528978640f7a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0d3b1464ce71cbf44e55e068e154c925"><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_1ClusterAnalyzer.html#a0d3b1464ce71cbf44e55e068e154c925">cohesion</a> (const std::vector< std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > > &clusters, const <a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > &original)</td></tr>
<tr class="memdesc:a0d3b1464ce71cbf44e55e068e154c925"><td class="mdescLeft"> </td><td class="mdescRight">Method to calculate the cohesions of a certain partition. <a href="#a0d3b1464ce71cbf44e55e068e154c925">More...</a><br/></td></tr>
<tr class="separator:a0d3b1464ce71cbf44e55e068e154c925"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a299d8214ddc27b9c1dfa59d7ac593ae4"><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_1ClusterAnalyzer.html#a299d8214ddc27b9c1dfa59d7ac593ae4">averagePopulationAberration</a> (<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cluster_quantity, std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &tree)</td></tr>
<tr class="memdesc:a299d8214ddc27b9c1dfa59d7ac593ae4"><td class="mdescLeft"> </td><td class="mdescRight">Method to calculate the average aberration from average population in partition resulting from a certain step in clustering. <a href="#a299d8214ddc27b9c1dfa59d7ac593ae4">More...</a><br/></td></tr>
<tr class="separator:a299d8214ddc27b9c1dfa59d7ac593ae4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1ddae30375fef566e4a1f53fb43baba9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#a1ddae30375fef566e4a1f53fb43baba9">cut</a> (const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cluster_quantity, const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &tree, std::vector< std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > > &clusters)</td></tr>
<tr class="memdesc:a1ddae30375fef566e4a1f53fb43baba9"><td class="mdescLeft"> </td><td class="mdescRight">Method to calculate a partition resulting from a certain step in clustering given by the number of clusters. <a href="#a1ddae30375fef566e4a1f53fb43baba9">More...</a><br/></td></tr>
<tr class="separator:a1ddae30375fef566e4a1f53fb43baba9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aab291e2f97b916d42f3c009385f75c36"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#aab291e2f97b916d42f3c009385f75c36">cut</a> (const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> cluster_quantity, const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &tree, std::vector< std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > > &subtrees)</td></tr>
<tr class="memdesc:aab291e2f97b916d42f3c009385f75c36"><td class="mdescLeft"> </td><td class="mdescRight">Method to calculate subtrees from a given tree resulting from a certain step in clustering given by the number of clusters. <a href="#aab291e2f97b916d42f3c009385f75c36">More...</a><br/></td></tr>
<tr class="separator:aab291e2f97b916d42f3c009385f75c36"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac228371cea18f2d7413fa9587af138a4"><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_1ClusterAnalyzer.html#ac228371cea18f2d7413fa9587af138a4">newickTree</a> (const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &tree, const bool include_distance=false)</td></tr>
<tr class="memdesc:ac228371cea18f2d7413fa9587af138a4"><td class="mdescLeft"> </td><td class="mdescRight">Returns the hierarchy described by a clustering tree as Newick-String. <a href="#ac228371cea18f2d7413fa9587af138a4">More...</a><br/></td></tr>
<tr class="separator:ac228371cea18f2d7413fa9587af138a4"><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:a408835ff6fbad757825d8600e0662937"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#a408835ff6fbad757825d8600e0662937">operator=</a> (const <a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> &source)</td></tr>
<tr class="memdesc:a408835ff6fbad757825d8600e0662937"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a408835ff6fbad757825d8600e0662937">More...</a><br/></td></tr>
<tr class="separator:a408835ff6fbad757825d8600e0662937"><td class="memSeparator" colspan="2"> </td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Bundles analyzing tools for a clustering (given as sequence of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s) </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> </td>
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<p>default constructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> </td>
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<span class="mlabels"><span class="mlabel">virtual</span></span> </td>
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<p>destructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname"><a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> averagePopulationAberration </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>cluster_quantity</em>, </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > & </td>
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<p>Method to calculate the average aberration from average population in partition resulting from a certain step in clustering. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">cluster_quantity</td><td>desired partition Size analogue to <a class="el" href="classOpenMS_1_1ClusterAnalyzer.html#a1ddae30375fef566e4a1f53fb43baba9" title="Method to calculate a partition resulting from a certain step in clustering given by the number of cl...">ClusterAnalyzer::cut</a> </td></tr>
<tr><td class="paramname">tree</td><td>vector of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s representing the clustering </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
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<tr><td class="paramname">invalid_parameter</td><td>if desired clustering is invalid </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>the average aberration from the average cluster population (number of elements/cluster_quantity) at cluster_quantity </dd></dl>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a> </dd></dl>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> averageSilhouetteWidth </td>
<td>(</td>
<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > & </td>
<td class="paramname"><em>tree</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > & </td>
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<p>Method to calculate the average silhouette widths for a clustering. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">tree</td><td>vector of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s representing the clustering </td></tr>
<tr><td class="paramname">original</td><td><a class="el" href="classOpenMS_1_1DistanceMatrix.html" title="A two-dimensional distance matrix, similar to OpenMS::Matrix. ">DistanceMatrix</a> for all clustered elements started from </td></tr>
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</dd>
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<dl class="section return"><dt>Returns</dt><dd>a vector filled with the average silhouette widths for each clusterstep</dd></dl>
<p>The average silhouette width will becalculated for each clustering step beginning with the first step(n-1 cluster) ending with the last (1 cluster, average silhouette width is 0 by definition). </p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a> </dd></dl>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> cohesion </td>
<td>(</td>
<td class="paramtype">const std::vector< std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > > & </td>
<td class="paramname"><em>clusters</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > & </td>
<td class="paramname"><em>original</em> </td>
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<p>Method to calculate the cohesions of a certain partition. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">clusters</td><td>vector of vectors holding the clusters (with indices to the actual elements) </td></tr>
<tr><td class="paramname">original</td><td><a class="el" href="classOpenMS_1_1DistanceMatrix.html" title="A two-dimensional distance matrix, similar to OpenMS::Matrix. ">DistanceMatrix</a> for all clustered elements started from </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>a vector that holds the cohesions of each cluster given with <code>clusters</code> (order corresponds to <code>clusters</code>) </dd></dl>
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<td class="memname">void cut </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>cluster_quantity</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > & </td>
<td class="paramname"><em>tree</em>, </td>
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<td class="paramtype">std::vector< std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > > & </td>
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<p>Method to calculate a partition resulting from a certain step in clustering given by the number of clusters. </p>
<p>If you want to fetch all clusters which were created with a threshold, you simply count the number of tree-nodes which are not -1, and substract that from the number of leafes, to get the number of clusters formed , i.e. cluster_quantity = data.size() - real_leaf_count;</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">cluster_quantity</td><td>Size giving the number of clusters (i.e. starting elements - cluster_quantity = cluster step) </td></tr>
<tr><td class="paramname">tree</td><td>vector of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s representing the clustering </td></tr>
<tr><td class="paramname">clusters</td><td>vector of vectors holding the clusters (with indices to the actual elements) </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">invalid_parameter</td><td>if desired clusterstep is invalid </td></tr>
</table>
</dd>
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<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a></dd></dl>
<p>after call of this method the argument clusters is filled corresponding to the given <code>cluster_quantity</code> with the indices of the elements clustered </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1SpectraMerger.html#a600d56293a3a35b7ef362d788c35eb99">SpectraMerger::mergeSpectraPrecursors()</a>.</p>
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<td class="memname">void cut </td>
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<td class="paramtype">const <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>cluster_quantity</em>, </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > & </td>
<td class="paramname"><em>tree</em>, </td>
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<td class="paramtype">std::vector< std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > > & </td>
<td class="paramname"><em>subtrees</em> </td>
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<p>Method to calculate subtrees from a given tree resulting from a certain step in clustering given by the number of clusters. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">cluster_quantity</td><td>Size giving the number of clusters (i.e. starting elements - cluster_quantity = cluster step) </td></tr>
<tr><td class="paramname">tree</td><td>vector of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s representing the clustering </td></tr>
<tr><td class="paramname">subtrees</td><td>vector of trees holding the trees, tree is composed of cut at given size </td></tr>
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<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname">invalid_parameter</td><td>if desired clusterstep is invalid </td></tr>
</table>
</dd>
</dl>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a></dd></dl>
<p>after call of this method the argument clusters is filled corresponding to the given <code>cluster_quantity</code> with the indices of the elements clustered </p>
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<td class="memname">std::vector<<a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a>> dunnIndices </td>
<td>(</td>
<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > & </td>
<td class="paramname"><em>tree</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > & </td>
<td class="paramname"><em>original</em>, </td>
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<td class="paramtype">const bool </td>
<td class="paramname"><em>tree_from_singlelinkage</em> = <code>false</code> </td>
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<p>Method to calculate Dunns indices for a clustering. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">tree</td><td>vector of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s representing the clustering </td></tr>
<tr><td class="paramname">original</td><td><a class="el" href="classOpenMS_1_1DistanceMatrix.html" title="A two-dimensional distance matrix, similar to OpenMS::Matrix. ">DistanceMatrix</a> for all clustered elements started from </td></tr>
<tr><td class="paramname">tree_from_singlelinkage</td><td>true if tree was created by <a class="el" href="classOpenMS_1_1SingleLinkage.html" title="SingleLinkage ClusterMethod. ">SingleLinkage</a>, i.e. the distances are the minimal distances in increasing order and can be used to speed up the calculation </td></tr>
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<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a> </dd></dl>
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<td class="memname"><a class="el" href="classOpenMS_1_1String.html">String</a> newickTree </td>
<td>(</td>
<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > & </td>
<td class="paramname"><em>tree</em>, </td>
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<td class="paramtype">const bool </td>
<td class="paramname"><em>include_distance</em> = <code>false</code> </td>
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<p>Returns the hierarchy described by a clustering tree as Newick-String. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">tree</td><td>vector of <a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a>'s representing the clustering </td></tr>
<tr><td class="paramname">include_distance</td><td>bool value indicating whether the distance shall be included to the string </td></tr>
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<dl class="section see"><dt>See Also</dt><dd><a class="el" href="classOpenMS_1_1BinaryTreeNode.html" title="Elements of a binary tree used to represent a hierarchical clustering process. ">BinaryTreeNode</a> </dd></dl>
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<td class="memname"><a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a>& operator= </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1ClusterAnalyzer.html">ClusterAnalyzer</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<span class="mlabels"><span class="mlabel">private</span></span> </td>
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<p>assignment operator </p>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5</font></TD>
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