beagle_FourStateBeagleImpl(3)

NAME

beagle.FourStateBeagleImpl -

SYNOPSIS

Inherits beagle.GeneralBeagleImpl.

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)

Static Public Attributes

static final boolean DEBUG = false

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

Member Function Documentation

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

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

Reimplemented from beagle.GeneralBeagleImpl.

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

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

Returns:

the larges absolute exponent