beagle::BeagleImpl(3) HMSBEAGLE beagle::BeagleImpl(3)
NAME
beagle::BeagleImpl -
SYNOPSIS
Inherited by beagle::cpu::BeagleCPUImpl, and beagle::gpu::BeagleGPUImpl.
Public Member Functions
virtual int createInstance (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int
eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long
requirementFlags)=0
virtual int getInstanceDetails (BeagleInstanceDetails *returnInfo)=0
virtual int setTipStates (int tipIndex, const int *inStates)=0
virtual int setTipPartials (int tipIndex, const double *inPartials)=0
virtual int setPartials (int bufferIndex, const double *inPartials)=0
virtual int getPartials (int bufferIndex, int scaleIndex, double *outPartials)=0
virtual int setEigenDecomposition (int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double
*inEigenValues)=0
virtual int setStateFrequencies (int stateFrequenciesIndex, const double *inStateFrequencies)=0
virtual int setCategoryWeights (int categoryWeightsIndex, const double *inCategoryWeights)=0
virtual int setPatternWeights (const double *inPatternWeights)=0
virtual int setCategoryRates (const double *inCategoryRates)=0
virtual int setTransitionMatrix (int matrixIndex, const double *inMatrix, double paddedValue)=0
virtual int setTransitionMatrices (const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)=0
virtual int getTransitionMatrix (int matrixIndex, double *outMatrix)=0
virtual int updateTransitionMatrices (int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int
*secondDerivativeIndices, const double *edgeLengths, int count)=0
virtual int updatePartials (const int *operations, int operationCount, int cumulativeScalingIndex)=0
virtual int waitForPartials (const int *destinationPartials, int destinationPartialsCount)=0
virtual int accumulateScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex)=0
virtual int removeScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex)=0
virtual int resetScaleFactors (int cumulativeScalingIndex)=0
virtual int copyScaleFactors (int destScalingIndex, int srcScalingIndex)=0
virtual int calculateRootLogLikelihoods (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices,
const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)=0
virtual int calculateEdgeLogLikelihoods (const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices,
const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int
*stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative,
double *outSumSecondDerivative)=0
virtual int getSiteLogLikelihoods (double *outLogLikelihoods)=0
virtual int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives)=0
Public Attributes
int resourceNumber
Author
Generated automatically by Doxygen for HMSBEAGLE from the source code.
Version 1.0.0 Fri May 25 2012 beagle::BeagleImpl(3)