, including all inherited members.
accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
block(void) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | |
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::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, 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::BeagleCPUImpl | [protected, virtual] |
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::BeagleCPUImpl | [protected, virtual] |
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::BeagleCPUImpl | [protected, virtual] |
calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, 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::BeagleCPUImpl | [virtual] |
calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
copyScaleFactors(int destScalingIndex, int srcScalingIndex) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
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::BeagleCPUImpl | [virtual] |
firstDerivTmp (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gActiveScalingFactors (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gAutoScaleBuffers (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gCategoryRates (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gCategoryWeights (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gEigenDecomposition (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
getFlags() (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
getInstanceDetails(BeagleInstanceDetails *returnInfo) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
getName() (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
getPaddedPatternsModulus() (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
getSiteLogLikelihoods(double *outLogLikelihoods) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
getTransitionMatrix(int matrixIndex, double *outMatrix) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
gPartials (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gPatternWeights (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gScaleBuffers (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gStateFrequencies (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gTipStates (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
gTransitionMatrices (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
integrationTmp (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kBufferCount (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kCategoryCount | beagle::cpu::BeagleCPUImpl | [protected] |
kEigenDecompCount (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kExtraPatterns | beagle::cpu::BeagleCPUImpl | [protected] |
kFlags (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kInternalPartialsBufferCount | beagle::cpu::BeagleCPUImpl | [protected] |
kMatrixCount | beagle::cpu::BeagleCPUImpl | [protected] |
kMatrixSize | beagle::cpu::BeagleCPUImpl | [protected] |
kPaddedPatternCount | beagle::cpu::BeagleCPUImpl | [protected] |
kPartialsPaddedStateCount (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kPartialsSize (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kPatternCount | beagle::cpu::BeagleCPUImpl | [protected] |
kScaleBufferCount (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
kStateCount | beagle::cpu::BeagleCPUImpl | [protected] |
kTipCount | beagle::cpu::BeagleCPUImpl | [protected] |
kTransPaddedStateCount | beagle::cpu::BeagleCPUImpl | [protected] |
mallocAligned(size_t size) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
ones (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
outFirstDerivativesTmp (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
outLogLikelihoodsTmp (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
outSecondDerivativesTmp (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
realtypeMin (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected, virtual] |
resetScaleFactors(int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
resourceNumber (defined in beagle::BeagleImpl) | beagle::BeagleImpl | |
scalingExponentThreshhold (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
secondDerivTmp (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
setCategoryRates(const double *inCategoryRates) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setPartials(int bufferIndex, const double *inPartials) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setPatternWeights(const double *inPatternWeights) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setTipPartials(int tipIndex, const double *inPartials) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setTipStates(int tipIndex, const int *inStates) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
waitForPartials(const int *destinationPartials, int destinationPartialsCount) (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
zeros (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [protected] |
~BeagleCPUImpl() (defined in beagle::cpu::BeagleCPUImpl) | beagle::cpu::BeagleCPUImpl | [virtual] |
~BeagleImpl() (defined in beagle::BeagleImpl) | beagle::BeagleImpl | [inline, virtual] |