beagle_cpu_beaglecpu4stateimpl(3) [debian man page]
beagle::cpu::BeagleCPU4StateImpl(3) HMSBEAGLE beagle::cpu::BeagleCPU4StateImpl(3) NAME
beagle::cpu::BeagleCPU4StateImpl - SYNOPSIS
Inherits beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC >. Public Member Functions virtual const char * getName () 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 scalingFactorsIndex, 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 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 *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) virtual void calcPartialsPartialsAutoScaling (REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) int integrateOutStatesAndScale (const REALTYPE *integrationTmp, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) virtual void rescalePartials (REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) Additional Inherited Members Author Generated automatically by Doxygen for HMSBEAGLE from the source code. Version 1.0.0 Fri May 25 2012 beagle::cpu::BeagleCPU4StateImpl(3)
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beagle::gpu::BeagleGPUImpl(3) HMSBEAGLE beagle::gpu::BeagleGPUImpl(3) NAME
beagle::gpu::BeagleGPUImpl - 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 *retunInfo) 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 scaleIndex, 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) template<> int getSiteLogLikelihoods (double *outLogLikelihoods) template<> int getSiteLogLikelihoods (double *outLogLikelihoods) template<> int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives) template<> int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives) Additional Inherited Members Author Generated automatically by Doxygen for HMSBEAGLE from the source code. Version 1.0.0 Fri May 25 2012 beagle::gpu::BeagleGPUImpl(3)