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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Version 1.0.0 Fri May 25 2012 beagle::cpu::BeagleCPUImpl(3)