HMSBEAGLE  1.0.0
beagle::BeagleImpl Member List

This is the complete list of members for beagle::BeagleImpl, including all inherited members.

accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
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 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
copyScaleFactors(int destScalingIndex, int srcScalingIndex)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
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 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
getInstanceDetails(BeagleInstanceDetails *returnInfo)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
getPartials(int bufferIndex, int scaleIndex, double *outPartials)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
getSiteLogLikelihoods(double *outLogLikelihoods)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
getTransitionMatrix(int matrixIndex, double *outMatrix)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
resetScaleFactors(int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
resourceNumber (defined in beagle::BeagleImpl)beagle::BeagleImpl
setCategoryRates(const double *inCategoryRates)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setPartials(int bufferIndex, const double *inPartials)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setPatternWeights(const double *inPatternWeights)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setTipPartials(int tipIndex, const double *inPartials)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setTipStates(int tipIndex, const int *inStates)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
waitForPartials(const int *destinationPartials, int destinationPartialsCount)=0 (defined in beagle::BeagleImpl)beagle::BeagleImplpure virtual
~BeagleImpl() (defined in beagle::BeagleImpl)beagle::BeagleImplinlinevirtual