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¶
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