beagle_cpu_beaglecpu4stateimplfactory(3) [debian man page]
beagle::cpu::BeagleCPU4StateImplFactory(3) HMSBEAGLE beagle::cpu::BeagleCPU4StateImplFactory(3) NAME
beagle::cpu::BeagleCPU4StateImplFactory - SYNOPSIS
Inherits beagle::BeagleImplFactory. Public Member Functions virtual BeagleImpl * createImpl (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode) virtual const char * getName () virtual const long getFlags () Author Generated automatically by Doxygen for HMSBEAGLE from the source code. Version 1.0.0 Fri May 25 2012 beagle::cpu::BeagleCPU4StateImplFactory(3)
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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 Generated automatically by Doxygen for HMSBEAGLE from the source code. Version 1.0.0 Fri May 25 2012 beagle::cpu::BeagleCPUImpl(3)