HMSBEAGLE  1.0.0
Public Member Functions | Public Attributes
beagle::BeagleImpl Class Reference
Inheritance diagram for beagle::BeagleImpl:
beagle::cpu::BeagleCPUImpl beagle::gpu::BeagleGPUImpl

List of all members.

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

The documentation for this class was generated from the following file: