HMSBEAGLE  1.0.0
beagle::cpu::BeagleCPU4StateImpl Member List

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::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplvirtual
calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) (defined in beagle::cpu::BeagleCPU4StateImpl)beagle::cpu::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplvirtual
calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPU4StateImpl)beagle::cpu::BeagleCPU4StateImplvirtual
calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (defined in beagle::cpu::BeagleCPU4StateImpl)beagle::cpu::BeagleCPU4StateImplvirtual
calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPU4StateImpl)beagle::cpu::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplvirtual
calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (defined in beagle::cpu::BeagleCPU4StateImpl)beagle::cpu::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplinline
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
kCategoryCountbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kEigenDecompCount (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >)beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kExtraPatternsbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kFlags (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >)beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kInternalPartialsBufferCountbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kMatrixCountbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kMatrixSizebeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kPaddedPatternCountbeagle::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
kPatternCountbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kScaleBufferCount (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >)beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kStateCountbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kTipCountbeagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >protected
kTransPaddedStateCountbeagle::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::BeagleCPU4StateImplvirtual
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::BeagleCPU4StateImplvirtual
~BeagleCPUImpl() (defined in beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >)beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >virtual