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beagle::cpu::BeagleCPUImpl(3) HMSBEAGLE beagle::cpu::BeagleCPUImpl(3)

NAME

beagle::cpu::BeagleCPUImpl -

SYNOPSIS

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 accumulateScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex)
 
int removeScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex)
 
int resetScaleFactors (int cumulativeScalingIndex)
 
int copyScaleFactors (int destScalingIndex, int srcScalingIndex)
 
int calculateRootLogLikelihoods (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood)
 
int 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)
 
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 calcRootLogLikelihoodsMulti (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, 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 calcEdgeLogLikelihoodsMulti (const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, 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
 
(we don't really need this field) int kPatternCount
 
(we don't really need this field, but it is handy) int kPaddedPatternCount
 
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
 
stored for convenience. kPartialsSize = kStateCount*kPatternCount int kInternalPartialsBufferCount
 
stored for convenience. kMatrixSize = kStateCount*(kStateCount + 1) long kFlags
 
REALTYPE realtypeMin
 
int scalingExponentThreshhold
 
EigenDecomposition
 
< BEAGLE_CPU_EIGEN_GENERIC > * gEigenDecomposition"
 
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
 

Additional Inherited Members

Member Data Documentation

int beagle::cpu::BeagleCPUImpl::kPatternCount [protected]

(we don't really need this field, but it is handy) after initialize this will be tipStates.size()

int beagle::cpu::BeagleCPUImpl::kTipCount [protected]

(we don't really need this field) after initialize this will be partials.size()
 

Author

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Fri May 25 2012 Version 1.0.0