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 |