Uses of Class
org.knowceans.mcl.SparseMatrix

Uses of SparseMatrix in org.knowceans.mcl

Methods in org.knowceans.mcl that return SparseMatrix

SparseMatrix	SparseMatrix.copy() copy the matrix and its elements
SparseMatrix	MarkovClustering.expand(SparseMatrix m) expand stochastic quadratic matrix by sqaring it with itself: result = m * m.
static SparseMatrix	MatrixLoader.loadSparse(java.lang.String file) read a graph with line format labelfrom labelto weight
SparseMatrix	SparseMatrix.matrixTimes(SparseMatrix m) immutable multiply matrix M with this (A) : M * A
SparseMatrix	MarkovClustering.run(SparseMatrix a, double maxResidual, double pGamma, double loopGain, double maxZero) run the MCL process.
SparseMatrix	SparseMatrix.times(SparseMatrix m) immutable multiply this matrix (A) with M : A * M
SparseMatrix	SparseMatrix.timesTransposed(SparseMatrix m) mutable multiply this matrix (A) with M : A * M'
SparseMatrix	SparseMatrix.transpose() immutable transpose.

Methods in org.knowceans.mcl with parameters of type SparseMatrix

private void	MarkovClustering.addLoops(SparseMatrix a, double loopGain) add loops with specific energy, which corresponds to adding loopGain to the diagonal elements.
SparseMatrix	MarkovClustering.expand(SparseMatrix m) expand stochastic quadratic matrix by sqaring it with itself: result = m * m.
void	SparseMatrix.hadamardProduct(SparseMatrix m) mutable Hadamard product
double	MarkovClustering.inflate(SparseMatrix m, double p, double zeromax) inflate stochastic matrix by Hadamard (elementwise) exponentiation, pruning and normalisation : result = Gamma ( m, p ) = normalise ( prune ( m .^ p ) ).
SparseMatrix	SparseMatrix.matrixTimes(SparseMatrix m) immutable multiply matrix M with this (A) : M * A
private static void	MarkovClustering.print(SparseMatrix a, java.lang.String label)
SparseMatrix	MarkovClustering.run(SparseMatrix a, double maxResidual, double pGamma, double loopGain, double maxZero) run the MCL process.
SparseMatrix	SparseMatrix.times(SparseMatrix m) immutable multiply this matrix (A) with M : A * M
SparseMatrix	SparseMatrix.timesTransposed(SparseMatrix m) mutable multiply this matrix (A) with M : A * M'

Constructors in org.knowceans.mcl with parameters of type SparseMatrix

SparseMatrix(SparseMatrix matrix)
copy contructor