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HMSBEAGLE
1.0.0
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This is the complete list of members for beagle::cpu::BeagleCPU4StateImpl, including all inherited members.
| accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protectedvirtual |
| block(void) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| calcEdgeLogLikelihoods(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcEdgeLogLikelihoodsFirstDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protectedvirtual |
| calcEdgeLogLikelihoodsMulti(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protectedvirtual |
| calcEdgeLogLikelihoodsSecondDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int secondDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protectedvirtual |
| calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | 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 *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| copyScaleFactors(int destScalingIndex, int srcScalingIndex) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| firstDerivTmp (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gActiveScalingFactors (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gAutoScaleBuffers (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gCategoryRates (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gCategoryWeights (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gEigenDecomposition (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| getFlags() (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | virtual |
| getInstanceDetails(BeagleInstanceDetails *returnInfo) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| getName() (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| getPaddedPatternsModulus() (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protectedvirtual |
| getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| getSiteLogLikelihoods(double *outLogLikelihoods) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| getTransitionMatrix(int matrixIndex, double *outMatrix) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| gPartials (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gPatternWeights (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gScaleBuffers (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gStateFrequencies (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gTipStates (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| gTransitionMatrices (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| integrateOutStatesAndScale(const REALTYPE *integrationTmp, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | inline |
| integrationTmp (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kBufferCount (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kCategoryCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kEigenDecompCount (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kExtraPatterns | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kFlags (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kInternalPartialsBufferCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kMatrixCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kMatrixSize | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kPaddedPatternCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kPartialsPaddedStateCount (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kPartialsSize (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kPatternCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kScaleBufferCount (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kStateCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kTipCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| kTransPaddedStateCount | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| mallocAligned(size_t size) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| ones (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| outFirstDerivativesTmp (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| outLogLikelihoodsTmp (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| outSecondDerivativesTmp (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| realtypeMin (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| resetScaleFactors(int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| scalingExponentThreshhold (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| secondDerivTmp (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| setCategoryRates(const double *inCategoryRates) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setPartials(int bufferIndex, const double *inPartials) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setPatternWeights(const double *inPatternWeights) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setTipPartials(int tipIndex, const double *inPartials) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setTipStates(int tipIndex, const int *inStates) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| waitForPartials(const int *destinationPartials, int destinationPartialsCount) (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| zeros (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | protected |
| ~BeagleCPU4StateImpl() (defined in beagle::cpu::BeagleCPU4StateImpl) | beagle::cpu::BeagleCPU4StateImpl | virtual |
| ~BeagleCPUImpl() (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >) | beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | virtual |
1.8.1