NAME¶

beagle.GeneralBeagleImpl -

SYNOPSIS¶

Inherits beagle.Beagle. Inherited by beagle.DependencyAwareBeagleImpl, and beagle.FourStateBeagleImpl.

Public Member Functions¶

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 calculateRootLogLikelihoods (final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood) 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 ()

Static Public Attributes¶

static final boolean DEBUG = false static final boolean SCALING = true static final int SCALING_FACTOR_COUNT = 254 static final int SCALING_FACTOR_OFFSET = 126

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)

Protected Attributes¶

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

Constructor & Destructor Documentation¶

beagle.GeneralBeagleImpl.GeneralBeagleImpl (final inttipCount, final intpartialsBufferCount, final intcompactBufferCount, final intstateCount, final intpatternCount, final inteigenBufferCount, final intmatrixBufferCount, final intcategoryCount, final intscaleBufferCount) [inline]¶

Constructor Parameters:

Member Function Documentation¶

void beagle.GeneralBeagleImpl.copyScaleFactors (intdestScalingIndex, intsrcScalingIndex) [inline]¶

Copy scale factors This function copies scale factors from one buffer to another. Parameters: Implements beagle.Beagle.

void beagle.GeneralBeagleImpl.finalize () throws Throwable [inline]¶

Finalize this instance This function finalizes the instance by releasing allocated memory Implements beagle.Beagle.

InstanceDetails beagle.GeneralBeagleImpl.getDetails () [inline]¶

Get a details class for this instance Returns: Implements beagle.Beagle.

void beagle.GeneralBeagleImpl.resetScaleFactors (intcumulativeScaleIndex) [inline]¶

Reset scalefactors This function resets a cumulative scale buffer. Parameters: Implements beagle.Beagle.

void beagle.GeneralBeagleImpl.setPatternWeights (final double[]patternWeights) [inline]¶

Set the weights for each pattern Parameters: Implements beagle.Beagle.

void beagle.GeneralBeagleImpl.setTipStates (inttipIndex, int[]states) [inline]¶

Sets partials for a tip - these are numbered from 0 and remain constant throughout the run. Parameters:

void beagle.GeneralBeagleImpl.updatePartials (final int[]operations, final intoperationCount, final intcumulativeScaleIndex) [inline]¶

Operations list is a list of 7-tuple integer indices, with one 7-tuple per operation. Format of 7-tuple operation: {destinationPartials, destinationScaleWrite, destinationScaleRead, child1Partials, child1TransitionMatrix, child2Partials, child2TransitionMatrix}

int beagle.GeneralBeagleImpl.updateStatesPartials (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3) [inline], [protected]¶

Calculates partial likelihoods at a node when one child has states and one has partials. Reimplemented in beagle.FourStateBeagleImpl.

int beagle.GeneralBeagleImpl.updateStatesStates (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3) [inline], [protected]¶

Calculates partial likelihoods at a node when both children have states. Returns: Reimplemented in beagle.FourStateBeagleImpl.

Author¶

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