Public Member Functions
	EvolutionaryModelParameters (Phylogeny tree, double kappa, double mu, Matrix Q, Matrix pi)

	EvolutionaryModelParameters (File sourceFile) throws IOException, ParseException

EvolutionaryModelParameters	copy ()

	EvolutionaryModelParameters (double kappa, double[] bg, double mu)

void	generateHKYQMatrix (double kappa, double scalingFactor)

void	write (BufferedWriter bw) throws IOException

String	toString ()

double[]	getBackgroundNucleotideFreqs ()

Matrix	getRateMatrix ()

Phylogeny	getTree ()

void	setTree (Phylogeny tree)

void	setRateMatrix (Matrix Q)

void	setBackgroundNucleotideFreqs (Matrix dist)

Constructor & Destructor Documentation

broad.core.siphy.EvolutionaryModelParameters.EvolutionaryModelParameters	(	Phylogeny	tree,
		double	kappa,
		double	mu,
		Matrix	Q,
		Matrix	pi
	)

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broad.core.siphy.EvolutionaryModelParameters.EvolutionaryModelParameters ( File sourceFile ) throws IOException, ParseException

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broad.core.siphy.EvolutionaryModelParameters.EvolutionaryModelParameters	(	double	kappa,
		double[]	bg,
		double	mu
	)

Member Function Documentation

EvolutionaryModelParameters broad.core.siphy.EvolutionaryModelParameters.copy ( )

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void broad.core.siphy.EvolutionaryModelParameters.generateHKYQMatrix	(	double	kappa,
		double	scalingFactor
	)

double [] broad.core.siphy.EvolutionaryModelParameters.getBackgroundNucleotideFreqs ( )

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Matrix broad.core.siphy.EvolutionaryModelParameters.getRateMatrix ( )

Phylogeny broad.core.siphy.EvolutionaryModelParameters.getTree ( )

void broad.core.siphy.EvolutionaryModelParameters.setBackgroundNucleotideFreqs ( Matrix dist )

void broad.core.siphy.EvolutionaryModelParameters.setRateMatrix ( Matrix Q )

void broad.core.siphy.EvolutionaryModelParameters.setTree ( Phylogeny tree )

String broad.core.siphy.EvolutionaryModelParameters.toString ( )

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void broad.core.siphy.EvolutionaryModelParameters.write ( BufferedWriter bw ) throws IOException

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