broad.core.siphy.EvolutionaryModel Class Reference

Collaboration diagram for broad.core.siphy.EvolutionaryModel:

Classes
class	NodeLikelihoodParameters
class	OmegaFit
class	PiFit

Public Member Functions
	EvolutionaryModel (EvolutionaryModelParameters parameters)
void	setOmega (double omega)
void	RPIDecomposition ()
Map< String, Short >	sample ()
Map< String, Short >	sample (PhylogenyNode node, short parentState)
PiFit	fitPI (Map< String, Matrix > alignmentColumn, Phylogeny tree)
OmegaFit	fitOmega (Map< String, Matrix > leafValues, Phylogeny tree, int window)
PiFit	piEMIteration (Map< String, Matrix > column, PhylogenyNode root, Matrix newPI) throws UnableToFitException
double[]	omegaEMIteration (Map< String, Matrix > leafValues, PhylogenyNode root, double newOmega, int window)
double	computeLikelihood (Map< String, Matrix > leafValues, PhylogenyNode root, int site)
double	pruneAndPeel (Map< String, Matrix > leafValues, PhylogenyNode root, int site)
void	computeJMatrix (PhylogenyNode node)
Map< Integer, NodeLikelihoodParameters >	getNodeLikelihoodParameterMap ()
Matrix	computeTransitions (double branchLength)
void	setModelParameters (EvolutionaryModelParameters parameters) throws IllegalArgumentException
EvolutionaryModelParameters	getModelParameters ()
Phylogeny	getTree ()
void	setOmegaDistByTreeLength (String neutralOmegaDistributionByTreeLengthFile) throws IOException
double	getPVal (OmegaFit fit, boolean useLogOddsLikelihood)
void	setNeutralOmegaDistribution (String neutralOmegaFile) throws IOException
void	resetPI ()
EvolutionaryModel	copy ()
EvolutionaryModelParameters	getParameters ()
void	setParameters (EvolutionaryModelParameters parameters)
int	getAlphabetSize ()
void	setAlphabetSize (int alphabetSize)
Matrix	getPi ()
void	setPi (Matrix pi)
void	pruneTree (List< String > ignoreList)
Phylogeny	evolve (String sequence)
void	changeBackground (double pA, double pC, double pG, double pT)
void	changeBackground (Matrix newPi)

Protected Member Functions
Matrix	getRateMatrix ()

Detailed Description

Represents an Markovian Evolutionary Model

Author

mgarber

Constructor & Destructor Documentation

broad.core.siphy.EvolutionaryModel.EvolutionaryModel

(

EvolutionaryModelParameters

parameters

)

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Member Function Documentation

void broad.core.siphy.EvolutionaryModel.changeBackground	(	double	pA,
		double	pC,
		double	pG,
		double	pT
	)

void broad.core.siphy.EvolutionaryModel.changeBackground

(

Matrix

newPi

)

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void broad.core.siphy.EvolutionaryModel.computeJMatrix

(

PhylogenyNode

node

)

double broad.core.siphy.EvolutionaryModel.computeLikelihood	(	Map< String, Matrix >	leafValues,
		PhylogenyNode	root,
		int	site
	)

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Matrix broad.core.siphy.EvolutionaryModel.computeTransitions

(

double

branchLength

)

Computes the vector of transition probabilities for the given branch length and value of the end state.

Parameters

branchLenght

distance to the end state.

Returns

P the transition probabilities matrix for the given branch length.

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EvolutionaryModel broad.core.siphy.EvolutionaryModel.copy

(

)

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Phylogeny broad.core.siphy.EvolutionaryModel.evolve

(

String

sequence

)

Assumes the given sequence as ancestral, the runs the markov process forward to generate sequences at ach node.

Parameters

sequence

- ancestral sequence

Returns

Phylogeny - with the same topology as the model's but its node names have been replaced with the evolved sequence.

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OmegaFit broad.core.siphy.EvolutionaryModel.fitOmega	(	Map< String, Matrix >	leafValues,
		Phylogeny	tree,
		int	window
	)

Implementation of Felsenstein's prunning algorithm to compute the likelihood given this model.

Parameters

observedData

Returns

Exceptions

MathException

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PiFit broad.core.siphy.EvolutionaryModel.fitPI	(	Map< String, Matrix >	alignmentColumn,
		Phylogeny	tree
	)

Implementation of the EM algorithm to fit the base distribution rho at a site assuming omega is constant.

Exceptions

UnableToFitException

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int broad.core.siphy.EvolutionaryModel.getAlphabetSize

(

)

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EvolutionaryModelParameters broad.core.siphy.EvolutionaryModel.getModelParameters

(

)

Map<Integer,NodeLikelihoodParameters> broad.core.siphy.EvolutionaryModel.getNodeLikelihoodParameterMap

(

)

EvolutionaryModelParameters broad.core.siphy.EvolutionaryModel.getParameters

(

)

Matrix broad.core.siphy.EvolutionaryModel.getPi

(

)

double broad.core.siphy.EvolutionaryModel.getPVal	(	OmegaFit	fit,
		boolean	useLogOddsLikelihood
	)

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

protected

Computes current model's rate matrix. If the model is Q = R*rho then it computes Q, otherwise it returns the rate matrix in the Model Parameters

Returns

An update rate matrix.

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Phylogeny broad.core.siphy.EvolutionaryModel.getTree

(

)

double [] broad.core.siphy.EvolutionaryModel.omegaEMIteration	(	Map< String, Matrix >	leafValues,
		PhylogenyNode	root,
		double	newOmega,
		int	window
	)

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PiFit broad.core.siphy.EvolutionaryModel.piEMIteration	(	Map< String, Matrix >	column,
		PhylogenyNode	root,
		Matrix	newPI
	)		throws UnableToFitException

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double broad.core.siphy.EvolutionaryModel.pruneAndPeel	(	Map< String, Matrix >	leafValues,
		PhylogenyNode	root,
		int	site
	)

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void broad.core.siphy.EvolutionaryModel.pruneTree

(

List< String >

ignoreList

)

void broad.core.siphy.EvolutionaryModel.resetPI

(

)

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void broad.core.siphy.EvolutionaryModel.RPIDecomposition

(

)

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Map<String, Short> broad.core.siphy.EvolutionaryModel.sample

(

)

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Map<String,Short> broad.core.siphy.EvolutionaryModel.sample	(	PhylogenyNode	node,
		short	parentState
	)

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void broad.core.siphy.EvolutionaryModel.setAlphabetSize

(

int

alphabetSize

)

void broad.core.siphy.EvolutionaryModel.setModelParameters

(

EvolutionaryModelParameters

parameters

)

throws IllegalArgumentException

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void broad.core.siphy.EvolutionaryModel.setNeutralOmegaDistribution

(

String

neutralOmegaFile

)

throws IOException

void broad.core.siphy.EvolutionaryModel.setOmega

(

double

omega

)

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void broad.core.siphy.EvolutionaryModel.setOmegaDistByTreeLength

(

String

neutralOmegaDistributionByTreeLengthFile

)

throws IOException

void broad.core.siphy.EvolutionaryModel.setParameters

(

EvolutionaryModelParameters

parameters

)

void broad.core.siphy.EvolutionaryModel.setPi

(

Matrix

pi

)

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

• java/broad/core/siphy/EvolutionaryModel.java