beagle_cpu_BeagleCPUImpl3

Inherits beagle::BeagleImpl.

Public Member Functions

int 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)

int getInstanceDetails (BeagleInstanceDetails *returnInfo)

int setTipStates (int tipIndex, const int *inStates)

int setTipPartials (int tipIndex, const double *inPartials)

int setPartials (int bufferIndex, const double *inPartials)

int getPartials (int bufferIndex, int scaleBuffer, double *outPartials)

int setEigenDecomposition (int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)

int setStateFrequencies (int stateFrequenciesIndex, const double *inStateFrequencies)

int setCategoryWeights (int categoryWeightsIndex, const double *inCategoryWeights)

int setPatternWeights (const double *inPatternWeights)

int setCategoryRates (const double *inCategoryRates)

int setTransitionMatrix (int matrixIndex, const double *inMatrix, double paddedValue)

int setTransitionMatrices (const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)

int getTransitionMatrix (int matrixIndex, double *outMatrix)

int updateTransitionMatrices (int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)

int updatePartials (const int *operations, int operationCount, int cumulativeScalingIndex)

int waitForPartials (const int *destinationPartials, int destinationPartialsCount)

int resetScaleFactors (int cumulativeScalingIndex)

int copyScaleFactors (int destScalingIndex, int srcScalingIndex)

int getSiteLogLikelihoods (double *outLogLikelihoods)

int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives)

int block (void)

virtual const char * getName ()

virtual const long getFlags ()

Protected Member Functions

virtual void calcStatesStates (REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2)

virtual void calcStatesPartials (REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2)

virtual void calcPartialsPartials (REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2)

virtual int calcRootLogLikelihoods (const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood)

virtual int calcEdgeLogLikelihoods (const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood)

virtual int 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)

virtual int 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)

virtual void calcStatesStatesFixedScaling (REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors)

virtual void calcStatesPartialsFixedScaling (REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors)

virtual void calcPartialsPartialsFixedScaling (REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors)

virtual void calcPartialsPartialsAutoScaling (REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling)

virtual void rescalePartials (REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes)

virtual void autoRescalePartials (REALTYPE *destP, signed short *scaleFactors)

virtual int getPaddedPatternsModulus ()

void * mallocAligned (size_t size)

Protected Attributes

int kBufferCount

int kTipCount

the number of data patterns in each partial and tipStates element int kExtraPatterns

the number of data patterns padded to be a multiple of 2 or 4 int kMatrixCount

kPaddedPatternCount - kPatternCount int kStateCount

the number of transition matrices to alloc and store int kTransPaddedStateCount

the number of states int kPartialsPaddedStateCount

int kEigenDecompCount

int kCategoryCount

the number of eigen solutions to alloc and store int kScaleBufferCount

int kPartialsSize

int kMatrixSize

REALTYPE realtypeMin

int scalingExponentThreshhold

EigenDecomposition

double * gCategoryRates

double * gPatternWeights

REALTYPE ** gCategoryWeights

REALTYPE ** gStateFrequencies

REALTYPE ** gPartials

int ** gTipStates

REALTYPE ** gScaleBuffers

signed short ** gAutoScaleBuffers

int * gActiveScalingFactors

REALTYPE ** gTransitionMatrices

REALTYPE * integrationTmp

REALTYPE * firstDerivTmp

REALTYPE * secondDerivTmp

REALTYPE * outLogLikelihoodsTmp

REALTYPE * outFirstDerivativesTmp

REALTYPE * outSecondDerivativesTmp

REALTYPE * ones

REALTYPE * zeros