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beagle.FourStateBeagleImpl(3) HMSBEAGLE 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
Reimplemented from beagle.GeneralBeagleImpl.
Author
Generated automatically by Doxygen for HMSBEAGLE from the source code.
Version 1.0.0 Fri May 25 2012 beagle.FourStateBeagleImpl(3)
