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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_1ClusterFunctor.html">ClusterFunctor</a></li> </ul>
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<div class="title">ClusterFunctor Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__SpectraClustering.html">Clustering</a></div></div> </div>
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<p>Base class for cluster functors.
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<p><code>#include <<a class="el" href="ClusterFunctor_8h_source.html">OpenMS/COMPARISON/CLUSTERING/ClusterFunctor.h</a>></code></p>
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Inheritance diagram for ClusterFunctor:</div>
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<img src="classOpenMS_1_1ClusterFunctor.png" usemap="#ClusterFunctor_map" alt=""/>
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<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight"><a class="el" href="namespaceOpenMS_1_1Exception.html" title="Exception namespace ">Exception</a> thrown if not enough data (<2) is used. <a href="classOpenMS_1_1ClusterFunctor_1_1InsufficientInput.html#details">More...</a><br/></td></tr>
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Public Member Functions</h2></td></tr>
<tr class="memitem:af2422628fd52348a0f64d0f5a2df9975"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterFunctor.html#af2422628fd52348a0f64d0f5a2df9975">ClusterFunctor</a> ()</td></tr>
<tr class="memdesc:af2422628fd52348a0f64d0f5a2df9975"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#af2422628fd52348a0f64d0f5a2df9975">More...</a><br/></td></tr>
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<tr class="memitem:a1b126f049b60a895a02769ae246be3d3"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterFunctor.html#a1b126f049b60a895a02769ae246be3d3">ClusterFunctor</a> (const <a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> &source)</td></tr>
<tr class="memdesc:a1b126f049b60a895a02769ae246be3d3"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a1b126f049b60a895a02769ae246be3d3">More...</a><br/></td></tr>
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<tr class="memitem:a1deb8d4beff7b61fea04ef6bc372759b"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterFunctor.html#a1deb8d4beff7b61fea04ef6bc372759b">~ClusterFunctor</a> ()</td></tr>
<tr class="memdesc:a1deb8d4beff7b61fea04ef6bc372759b"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a1deb8d4beff7b61fea04ef6bc372759b">More...</a><br/></td></tr>
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<tr class="memitem:a7bd743ed3bb05541320a9443b469693f"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterFunctor.html#a7bd743ed3bb05541320a9443b469693f">operator=</a> (const <a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> &source)</td></tr>
<tr class="memdesc:a7bd743ed3bb05541320a9443b469693f"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a7bd743ed3bb05541320a9443b469693f">More...</a><br/></td></tr>
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<tr class="memitem:a762295d1d68d2e4a1d6b1fe717f5bece"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterFunctor.html#a762295d1d68d2e4a1d6b1fe717f5bece">operator()</a> (<a class="el" href="classOpenMS_1_1DistanceMatrix.html">DistanceMatrix</a>< <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> > &original_distance, std::vector< <a class="el" href="classOpenMS_1_1BinaryTreeNode.html">BinaryTreeNode</a> > &cluster_tree, const <a class="el" href="group__Concept.html#gab685845059e8a2c92743427d9a698c70">Real</a> threshold=1) const =0</td></tr>
<tr class="memdesc:a762295d1d68d2e4a1d6b1fe717f5bece"><td class="mdescLeft"> </td><td class="mdescRight">abstract for clustering the indices according to their respective element distances <a href="#a762295d1d68d2e4a1d6b1fe717f5bece">More...</a><br/></td></tr>
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Static Public Member Functions</h2></td></tr>
<tr class="memitem:a7899dbe105534dc1f81971dd71a26ff0"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ClusterFunctor.html#a7899dbe105534dc1f81971dd71a26ff0">registerChildren</a> ()</td></tr>
<tr class="memdesc:a7899dbe105534dc1f81971dd71a26ff0"><td class="mdescLeft"> </td><td class="mdescRight">registers all derived products <a href="#a7899dbe105534dc1f81971dd71a26ff0">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>Base class for cluster functors. </p>
<p>Each cluster functor employs a different method for stepwise merging clusters up to a given threshold, starting from the most elementary partition of data. Elements are represented by indices of a given distance matrix, which also should represent the order of input. </p>
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<p>default constructor </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> & </td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> </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">virtual void operator() </td>
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<td class="paramtype"><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_distance</em>, </td>
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<td class="paramname"><em>threshold</em> = <code>1</code> </td>
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<p>abstract for clustering the indices according to their respective element distances </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">original_distance</td><td>DistanceMatrix<Real> containing the distances of the elements to be clustered, will be changed during clustering process, make sure to have a copy or be able to redo </td></tr>
<tr><td class="paramname">cluster_tree</td><td>vector< BinaryTreeNode >, represents the clustering, each node contains the next merged clusters (not element indices) and their distance, strict order is kept: left_child < right_child, </td></tr>
<tr><td class="paramname">threshold</td><td>Real value, the minimal distance from which on cluster merging is considered unrealistic. By default set to 1, i.e. complete clustering until only one cluster remains</td></tr>
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<p><code>original_distance</code> is considered mirrored at the main diagonal, so only entrys up the main diagonal are used. The <code>threshold</code> can be taken from the maximal distance of two elements considered related and adapted in a way corresponding to the employed clustering method. The results are represented by <code>cluster_tree</code>, to get the actual clustering (with element indices) from a certain step of the clustering </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> , <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> </dd></dl>
<p>Implemented in <a class="el" href="classOpenMS_1_1AverageLinkage.html#a7acf823d809b7d2056caed7c6783ba95">AverageLinkage</a>, <a class="el" href="classOpenMS_1_1CompleteLinkage.html#a7acf823d809b7d2056caed7c6783ba95">CompleteLinkage</a>, and <a class="el" href="classOpenMS_1_1SingleLinkage.html#a7acf823d809b7d2056caed7c6783ba95">SingleLinkage</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ClusterFunctor.html">ClusterFunctor</a> & </td>
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<p>assignment operator </p>
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<td class="memname">static void registerChildren </td>
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<p>registers all derived products </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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