Inheritance diagram for beagle::cpu::BeagleCPUSSEImpl:
Additional Inherited Members | |
 Public Member Functions inherited from beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| 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 inherited from beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| 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 inherited from beagle::cpu::BeagleCPUImpl< BEAGLE_CPU_GENERIC > | |
| 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 |
The documentation for this class was generated from the following file:
- libhmsbeagle/CPU/BeagleCPUSSEImpl.h
