.TH "beagle::cpu::BeagleCPUImpl" 3 "Fri May 25 2012" "Version 1.0.0" "HMSBEAGLE" \" -*- nroff -*-
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.SH NAME
beagle::cpu::BeagleCPUImpl \- 
.SH SYNOPSIS
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.PP
.PP
Inherits \fBbeagle::BeagleImpl\fP\&.
.SS "Public Member Functions"

.in +1c
.ti -1c
.RI "int \fBcreateInstance\fP (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags)"
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.ti -1c
.RI "int \fBgetInstanceDetails\fP (\fBBeagleInstanceDetails\fP *returnInfo)"
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.ti -1c
.RI "int \fBsetTipStates\fP (int tipIndex, const int *inStates)"
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.ti -1c
.RI "int \fBsetTipPartials\fP (int tipIndex, const double *inPartials)"
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.ti -1c
.RI "int \fBsetPartials\fP (int bufferIndex, const double *inPartials)"
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.ti -1c
.RI "int \fBgetPartials\fP (int bufferIndex, int scaleBuffer, double *outPartials)"
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.ti -1c
.RI "int \fBsetEigenDecomposition\fP (int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)"
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.ti -1c
.RI "int \fBsetStateFrequencies\fP (int stateFrequenciesIndex, const double *inStateFrequencies)"
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.ti -1c
.RI "int \fBsetCategoryWeights\fP (int categoryWeightsIndex, const double *inCategoryWeights)"
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.ti -1c
.RI "int \fBsetPatternWeights\fP (const double *inPatternWeights)"
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.ti -1c
.RI "int \fBsetCategoryRates\fP (const double *inCategoryRates)"
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.ti -1c
.RI "int \fBsetTransitionMatrix\fP (int matrixIndex, const double *inMatrix, double paddedValue)"
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.ti -1c
.RI "int \fBsetTransitionMatrices\fP (const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)"
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.ti -1c
.RI "int \fBgetTransitionMatrix\fP (int matrixIndex, double *outMatrix)"
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.ti -1c
.RI "int \fBupdateTransitionMatrices\fP (int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)"
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.ti -1c
.RI "int \fBupdatePartials\fP (const int *operations, int operationCount, int cumulativeScalingIndex)"
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.ti -1c
.RI "int \fBwaitForPartials\fP (const int *destinationPartials, int destinationPartialsCount)"
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.ti -1c
.RI "int \fBaccumulateScaleFactors\fP (const int *scalingIndices, int count, int cumulativeScalingIndex)"
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.ti -1c
.RI "int \fBremoveScaleFactors\fP (const int *scalingIndices, int count, int cumulativeScalingIndex)"
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.ti -1c
.RI "int \fBresetScaleFactors\fP (int cumulativeScalingIndex)"
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.ti -1c
.RI "int \fBcopyScaleFactors\fP (int destScalingIndex, int srcScalingIndex)"
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.ti -1c
.RI "int \fBcalculateRootLogLikelihoods\fP (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood)"
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.ti -1c
.RI "int \fBcalculateEdgeLogLikelihoods\fP (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)"
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.ti -1c
.RI "int \fBgetSiteLogLikelihoods\fP (double *outLogLikelihoods)"
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.ti -1c
.RI "int \fBgetSiteDerivatives\fP (double *outFirstDerivatives, double *outSecondDerivatives)"
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.ti -1c
.RI "int \fBblock\fP (void)"
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.ti -1c
.RI "virtual const char * \fBgetName\fP ()"
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.ti -1c
.RI "virtual const long \fBgetFlags\fP ()"
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.in -1c
.SS "Protected Member Functions"

.in +1c
.ti -1c
.RI "virtual void \fBcalcStatesStates\fP (REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2)"
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.ti -1c
.RI "virtual void \fBcalcStatesPartials\fP (REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2)"
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.ti -1c
.RI "virtual void \fBcalcPartialsPartials\fP (REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2)"
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.ti -1c
.RI "virtual int \fBcalcRootLogLikelihoods\fP (const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood)"
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.ti -1c
.RI "virtual int \fBcalcRootLogLikelihoodsMulti\fP (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood)"
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.ti -1c
.RI "virtual int \fBcalcEdgeLogLikelihoods\fP (const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood)"
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.ti -1c
.RI "virtual int \fBcalcEdgeLogLikelihoodsMulti\fP (const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)"
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.ti -1c
.RI "virtual int \fBcalcEdgeLogLikelihoodsFirstDeriv\fP (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)"
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.ti -1c
.RI "virtual int \fBcalcEdgeLogLikelihoodsSecondDeriv\fP (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)"
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.ti -1c
.RI "virtual void \fBcalcStatesStatesFixedScaling\fP (REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors)"
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.ti -1c
.RI "virtual void \fBcalcStatesPartialsFixedScaling\fP (REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors)"
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.ti -1c
.RI "virtual void \fBcalcPartialsPartialsFixedScaling\fP (REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors)"
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.ti -1c
.RI "virtual void \fBcalcPartialsPartialsAutoScaling\fP (REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling)"
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.ti -1c
.RI "virtual void \fBrescalePartials\fP (REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes)"
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.ti -1c
.RI "virtual void \fBautoRescalePartials\fP (REALTYPE *destP, signed short *scaleFactors)"
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.ti -1c
.RI "virtual int \fBgetPaddedPatternsModulus\fP ()"
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.ti -1c
.RI "void * \fBmallocAligned\fP (size_t size)"
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.in -1c
.SS "Protected Attributes"

.in +1c
.ti -1c
.RI "int \fBkBufferCount\fP"
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.ti -1c
.RI "int \fBkTipCount\fP"
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.RI "\fI(we don't really need this field) \fP"
.ti -1c
.RI "int \fBkPatternCount\fP"
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.RI "\fI(we don't really need this field, but it is handy) \fP"
.ti -1c
.RI "int \fBkPaddedPatternCount\fP"
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.RI "\fIthe number of data patterns in each partial and tipStates element \fP"
.ti -1c
.RI "int \fBkExtraPatterns\fP"
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.RI "\fIthe number of data patterns padded to be a multiple of 2 or 4 \fP"
.ti -1c
.RI "int \fBkMatrixCount\fP"
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.RI "\fIkPaddedPatternCount - kPatternCount \fP"
.ti -1c
.RI "int \fBkStateCount\fP"
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.RI "\fIthe number of transition matrices to alloc and store \fP"
.ti -1c
.RI "int \fBkTransPaddedStateCount\fP"
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.RI "\fIthe number of states \fP"
.ti -1c
.RI "int \fBkPartialsPaddedStateCount\fP"
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.ti -1c
.RI "int \fBkEigenDecompCount\fP"
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.ti -1c
.RI "int \fBkCategoryCount\fP"
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.RI "\fIthe number of eigen solutions to alloc and store \fP"
.ti -1c
.RI "int \fBkScaleBufferCount\fP"
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.ti -1c
.RI "int \fBkPartialsSize\fP"
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.ti -1c
.RI "int \fBkMatrixSize\fP"
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.RI "\fIstored for convenience\&. kPartialsSize = kStateCount*kPatternCount \fP"
.ti -1c
.RI "int \fBkInternalPartialsBufferCount\fP"
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.RI "\fIstored for convenience\&. kMatrixSize = kStateCount*(kStateCount + 1) \fP"
.ti -1c
.RI "long \fBkFlags\fP"
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.ti -1c
.RI "REALTYPE \fBrealtypeMin\fP"
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.ti -1c
.RI "int \fBscalingExponentThreshhold\fP"
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.ti -1c
.RI "\fBEigenDecomposition\fP
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< BEAGLE_CPU_EIGEN_GENERIC > * \fBgEigenDecomposition\fP"
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.ti -1c
.RI "double * \fBgCategoryRates\fP"
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.ti -1c
.RI "double * \fBgPatternWeights\fP"
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.ti -1c
.RI "REALTYPE ** \fBgCategoryWeights\fP"
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.ti -1c
.RI "REALTYPE ** \fBgStateFrequencies\fP"
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.ti -1c
.RI "REALTYPE ** \fBgPartials\fP"
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.ti -1c
.RI "int ** \fBgTipStates\fP"
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.ti -1c
.RI "REALTYPE ** \fBgScaleBuffers\fP"
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.ti -1c
.RI "signed short ** \fBgAutoScaleBuffers\fP"
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.ti -1c
.RI "int * \fBgActiveScalingFactors\fP"
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.ti -1c
.RI "REALTYPE ** \fBgTransitionMatrices\fP"
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.ti -1c
.RI "REALTYPE * \fBintegrationTmp\fP"
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.ti -1c
.RI "REALTYPE * \fBfirstDerivTmp\fP"
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.ti -1c
.RI "REALTYPE * \fBsecondDerivTmp\fP"
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.ti -1c
.RI "REALTYPE * \fBoutLogLikelihoodsTmp\fP"
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.ti -1c
.RI "REALTYPE * \fBoutFirstDerivativesTmp\fP"
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.ti -1c
.RI "REALTYPE * \fBoutSecondDerivativesTmp\fP"
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.ti -1c
.RI "REALTYPE * \fBones\fP"
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.ti -1c
.RI "REALTYPE * \fBzeros\fP"
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.in -1c
.SS "Additional Inherited Members"
.SH "Member Data Documentation"
.PP 
.SS "int beagle::cpu::BeagleCPUImpl::kPatternCount\fC [protected]\fP"

.PP
(we don't really need this field, but it is handy) after initialize this will be tipStates\&.size() 
.SS "int beagle::cpu::BeagleCPUImpl::kTipCount\fC [protected]\fP"

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

.SH "Author"
.PP 
Generated automatically by Doxygen for HMSBEAGLE from the source code\&.