beagle_beagleimpl(3) [debian man page]
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)
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beagle::gpu::BeagleGPUImpl(3) HMSBEAGLE beagle::gpu::BeagleGPUImpl(3) NAME
beagle::gpu::BeagleGPUImpl - SYNOPSIS
Inherits beagle::BeagleImpl. Public Member Functions int createInstance (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) int getInstanceDetails (BeagleInstanceDetails *retunInfo) int setTipStates (int tipIndex, const int *inStates) int setTipPartials (int tipIndex, const double *inPartials) int setPartials (int bufferIndex, const double *inPartials) int getPartials (int bufferIndex, int scaleIndex, double *outPartials) int setEigenDecomposition (int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) int setStateFrequencies (int stateFrequenciesIndex, const double *inStateFrequencies) int setCategoryWeights (int categoryWeightsIndex, const double *inCategoryWeights) int setPatternWeights (const double *inPatternWeights) int setCategoryRates (const double *inCategoryRates) int setTransitionMatrix (int matrixIndex, const double *inMatrix, double paddedValue) int setTransitionMatrices (const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) int getTransitionMatrix (int matrixIndex, double *outMatrix) int updateTransitionMatrices (int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) int updatePartials (const int *operations, int operationCount, int cumulativeScalingIndex) int waitForPartials (const int *destinationPartials, int destinationPartialsCount) int accumulateScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex) int removeScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex) int resetScaleFactors (int cumulativeScalingIndex) int copyScaleFactors (int destScalingIndex, int srcScalingIndex) int calculateRootLogLikelihoods (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) 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 *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) int getSiteLogLikelihoods (double *outLogLikelihoods) int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives) template<> int getSiteLogLikelihoods (double *outLogLikelihoods) template<> int getSiteLogLikelihoods (double *outLogLikelihoods) template<> int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives) template<> int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives) Additional Inherited Members Author Generated automatically by Doxygen for HMSBEAGLE from the source code. Version 1.0.0 Fri May 25 2012 beagle::gpu::BeagleGPUImpl(3)