📄 sparsematrix.html
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mutable multiply this matrix (A) with M : A * M'</TD>
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<CODE> <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></CODE></FONT></TD>
<TD><CODE><B>SparseMatrix.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html#transpose()">transpose</A></B>()</CODE>
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immutable transpose.</TD>
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<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../../../net/sf/javaml/clustering/mcl/package-summary.html">net.sf.javaml.clustering.mcl</A> with parameters of type <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></FONT></TH>
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<CODE> <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></CODE></FONT></TD>
<TD><CODE><B>MarkovClustering.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/MarkovClustering.html#expand(net.sf.javaml.clustering.mcl.SparseMatrix)">expand</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> m)</CODE>
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expand stochastic quadratic matrix by sqaring it with itself: result = m * m.</TD>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
<TD><CODE><B>SparseMatrix.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html#hadamardProduct(net.sf.javaml.clustering.mcl.SparseMatrix)">hadamardProduct</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> m)</CODE>
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mutable Hadamard product</TD>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> double</CODE></FONT></TD>
<TD><CODE><B>MarkovClustering.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/MarkovClustering.html#inflate(net.sf.javaml.clustering.mcl.SparseMatrix, double, double)">inflate</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> m,
double p,
double zeromax)</CODE>
<BR>
inflate stochastic matrix by Hadamard (elementwise) exponentiation, pruning and normalisation : result = Gamma ( m, p ) = normalise ( prune ( m .^ p ) ).</TD>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></CODE></FONT></TD>
<TD><CODE><B>SparseMatrix.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html#matrixTimes(net.sf.javaml.clustering.mcl.SparseMatrix)">matrixTimes</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> m)</CODE>
<BR>
immutable multiply matrix M with this (A) : M * A</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></CODE></FONT></TD>
<TD><CODE><B>MarkovClustering.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/MarkovClustering.html#run(net.sf.javaml.clustering.mcl.SparseMatrix, double, double, double, double)">run</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> a,
double maxResidual,
double pGamma,
double loopGain,
double maxZero)</CODE>
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run the MCL process.</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></CODE></FONT></TD>
<TD><CODE><B>SparseMatrix.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html#times(net.sf.javaml.clustering.mcl.SparseMatrix)">times</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> m)</CODE>
<BR>
immutable multiply this matrix (A) with M : A * M</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></CODE></FONT></TD>
<TD><CODE><B>SparseMatrix.</B><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html#timesTransposed(net.sf.javaml.clustering.mcl.SparseMatrix)">timesTransposed</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> m)</CODE>
<BR>
mutable multiply this matrix (A) with M : A * M'</TD>
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<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../../../net/sf/javaml/clustering/mcl/package-summary.html">net.sf.javaml.clustering.mcl</A> with parameters of type <A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A></FONT></TH>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html#SparseMatrix(net.sf.javaml.clustering.mcl.SparseMatrix)">SparseMatrix</A></B>(<A HREF="../../../../../../net/sf/javaml/clustering/mcl/SparseMatrix.html" title="class in net.sf.javaml.clustering.mcl">SparseMatrix</A> matrix)</CODE>
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copy contructor</TD>
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