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 |