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HMSBEAGLE
1.0.0
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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::BeagleImpl | pure 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::BeagleImpl | pure virtual |
| calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| copyScaleFactors(int destScalingIndex, int srcScalingIndex)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure 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::BeagleImpl | pure virtual |
| getInstanceDetails(BeagleInstanceDetails *returnInfo)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| getPartials(int bufferIndex, int scaleIndex, double *outPartials)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| getSiteLogLikelihoods(double *outLogLikelihoods)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| getTransitionMatrix(int matrixIndex, double *outMatrix)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| resetScaleFactors(int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| resourceNumber (defined in beagle::BeagleImpl) | beagle::BeagleImpl | |
| setCategoryRates(const double *inCategoryRates)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setPartials(int bufferIndex, const double *inPartials)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setPatternWeights(const double *inPatternWeights)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setTipPartials(int tipIndex, const double *inPartials)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setTipStates(int tipIndex, const int *inStates)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| waitForPartials(const int *destinationPartials, int destinationPartialsCount)=0 (defined in beagle::BeagleImpl) | beagle::BeagleImpl | pure virtual |
| ~BeagleImpl() (defined in beagle::BeagleImpl) | beagle::BeagleImpl | inlinevirtual |
1.8.1