beagle.FourStateBeagleImpl Class Reference

Inheritance diagram for beagle.FourStateBeagleImpl:

List of all members.

Public Member Functions
	FourStateBeagleImpl (final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount)
void	calculateRootLogLikelihoods (final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood)
Public Member Functions inherited from beagle.GeneralBeagleImpl
	GeneralBeagleImpl (final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int stateCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount)
void	finalize () throws Throwable
void	setPatternWeights (final double[] patternWeights)
void	setTipStates (int tipIndex, int[] states)
void	getTipStates (int tipIndex, int[] states)
void	setTipPartials (int tipIndex, double[] inPartials)
void	setPartials (final int bufferIndex, final double[] partials)
void	getPartials (final int bufferIndex, final int scaleIndex, final double[] partials)
void	setEigenDecomposition (int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues)
void	setStateFrequencies (final int stateFrequenciesIndex, final double[] stateFrequencies)
void	setCategoryWeights (final int categoryWeightsIndex, final double[] categoryWeights)
void	setCategoryRates (double[] categoryRates)
void	setTransitionMatrix (final int matrixIndex, final double[] inMatrix, final double paddedValue)
void	getTransitionMatrix (final int matrixIndex, final double[] outMatrix)
void	updateTransitionMatrices (final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count)
void	updatePartials (final int[] operations, final int operationCount, final int cumulativeScaleIndex)
void	accumulateScaleFactors (int[] scaleIndices, int count, int outScaleIndex)
void	removeScaleFactors (int[] scaleIndices, int count, int cumulativeScaleIndex)
void	copyScaleFactors (int destScalingIndex, int srcScalingIndex)
void	resetScaleFactors (int cumulativeScaleIndex)
void	calculateEdgeLogLikelihoods (final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative)
void	getSiteLogLikelihoods (final double[] outLogLikelihoods)
InstanceDetails	getDetails ()
Public Member Functions inherited from beagle.Beagle
void	setTipStates (int tipIndex, final int[] inStates)
void	getTipStates (int tipIndex, final int[] outStates)
void	setTipPartials (int tipIndex, final double[] inPartials)
void	setPartials (int bufferIndex, final double[] inPartials)
void	getPartials (int bufferIndex, int scaleIndex, final double[]outPartials)
void	setEigenDecomposition (int eigenIndex, final double[] inEigenVectors, final double[] inInverseEigenVectors, final double[] inEigenValues)
void	setStateFrequencies (int stateFrequenciesIndex, final double[] stateFrequencies)
void	setCategoryWeights (int categoryWeightsIndex, final double[] categoryWeights)
void	setCategoryRates (final double[] inCategoryRates)
void	updateTransitionMatrices (int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count)
void	setTransitionMatrix (int matrixIndex, final double[] inMatrix, double paddedValue)
void	getTransitionMatrix (int matrixIndex, double[] outMatrix)
void	updatePartials (final int[] operations, int operationCount, int cumulativeScaleIndex)
void	accumulateScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex)
void	removeScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex)
void	calculateRootLogLikelihoods (int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood)
void	calculateEdgeLogLikelihoods (int[] parentBufferIndices, int[] childBufferIndices, int[] probabilityIndices, int[] firstDerivativeIndices, int[] secondDerivativeIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood, double[] outSumFirstDerivative, double[] outSumSecondDerivative)
void	getSiteLogLikelihoods (double[] outLogLikelihoods)

Static Public Attributes
static final boolean	DEBUG = false
Static Public Attributes inherited from beagle.GeneralBeagleImpl
static final boolean	SCALING = true
static final int	SCALING_FACTOR_COUNT = 254
static final int	SCALING_FACTOR_OFFSET = 126
Static Public Attributes inherited from beagle.Beagle
static int	OPERATION_TUPLE_SIZE = 7
static int	NONE = -1

Protected Member Functions
int	updateStatesStates (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)
int	updateStatesPartials (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)
int	updatePartialsPartials (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)

Additional Inherited Members
Protected Attributes inherited from beagle.GeneralBeagleImpl
final int	tipCount
final int	partialsBufferCount
final int	compactBufferCount
final int	stateCount
final int	patternCount
final int	eigenBufferCount
final int	matrixBufferCount
final int	categoryCount
int	partialsSize
int	matrixSize
double[][]	cMatrices
double[][]	eigenValues
double[][]	stateFrequencies
double[]	categoryRates
double[][]	categoryWeights
double[]	patternWeights
double[][]	partials
int[][]	scalingFactorCounts
int[][]	tipStates
double[][]	matrices
double[]	scalingFactors
double[]	logScalingFactors

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Member Function Documentation

int beagle.FourStateBeagleImpl.updateStatesPartials ( int  bufferIndex1, int  matrixIndex1, int  bufferIndex2, int  matrixIndex2, int  bufferIndex3  )

inlineprotected

Calculates partial likelihoods at a node when one child has states and one has partials.

Reimplemented from beagle.GeneralBeagleImpl.

int beagle.FourStateBeagleImpl.updateStatesStates ( int  bufferIndex1, int  matrixIndex1, int  bufferIndex2, int  matrixIndex2, int  bufferIndex3  )

inlineprotected

Calculates partial likelihoods at a node when both children have states.

Returns:

the larges absolute exponent

Reimplemented from beagle.GeneralBeagleImpl.

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

• java/beagle/FourStateBeagleImpl.java