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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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