broad.pda.geneexpression.clustering.Kmeans Class Reference

Collaboration diagram for broad.pda.geneexpression.clustering.Kmeans:

Classes
class	KmeansInfo
class	SilhouetteInfo

Public Member Functions
	Kmeans (MatrixWithHeaders mat, MatrixWithHeaders initCentroids, int numOfClusters, String distanceMetric)
void	runKmeans ()
void	calcSilhouette ()
void	calcLightSilhouette ()
double	getSilhouette ()
void	writeClusters (BufferedWriter bw) throws IOException
void	writeClustersCentroids (BufferedWriter bw) throws IOException
void	writeDistanceFromCentroids (BufferedWriter bw) throws IOException
void	writeDistanceFromInputCentroids (BufferedWriter bw) throws IOException
KmeansInfo	getClusterInfo ()
void	writeDistanceFromInputCentroids (MatrixWithHeaders centroids, BufferedWriter bw) throws IOException
void	writeSilhouetteRes (int currK, BufferedWriter bwGeneS, BufferedWriter bwAllS, BufferedWriter bwClusterS) throws IOException

Static Public Member Functions
static double	distance (double[] a, double[] b, String metric)

Constructor & Destructor Documentation

broad.pda.geneexpression.clustering.Kmeans.Kmeans	(	MatrixWithHeaders	mat,
		MatrixWithHeaders	initCentroids,
		int	numOfClusters,
		String	distanceMetric
	)

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Member Function Documentation

void broad.pda.geneexpression.clustering.Kmeans.calcLightSilhouette

(

)

void broad.pda.geneexpression.clustering.Kmeans.calcSilhouette

(

)

static double broad.pda.geneexpression.clustering.Kmeans.distance ( double[]  a, double[]  b, String  metric  )

static

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KmeansInfo broad.pda.geneexpression.clustering.Kmeans.getClusterInfo

(

)

double broad.pda.geneexpression.clustering.Kmeans.getSilhouette

(

)

void broad.pda.geneexpression.clustering.Kmeans.runKmeans

(

)

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void broad.pda.geneexpression.clustering.Kmeans.writeClusters

(

BufferedWriter

bw

)

throws IOException

void broad.pda.geneexpression.clustering.Kmeans.writeClustersCentroids

(

BufferedWriter

bw

)

throws IOException

void broad.pda.geneexpression.clustering.Kmeans.writeDistanceFromCentroids

(

BufferedWriter

bw

)

throws IOException

void broad.pda.geneexpression.clustering.Kmeans.writeDistanceFromInputCentroids

(

BufferedWriter

bw

)

throws IOException

void broad.pda.geneexpression.clustering.Kmeans.writeDistanceFromInputCentroids	(	MatrixWithHeaders	centroids,
		BufferedWriter	bw
	)		throws IOException

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void broad.pda.geneexpression.clustering.Kmeans.writeSilhouetteRes	(	int	currK,
		BufferedWriter	bwGeneS,
		BufferedWriter	bwAllS,
		BufferedWriter	bwClusterS
	)		throws IOException

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The documentation for this class was generated from the following file:

• java/broad/pda/geneexpression/clustering/Kmeans.java