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

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.RI "virtual int \fBcreateInstance\fP (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags)=0"
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.RI "virtual int \fBgetInstanceDetails\fP (\fBBeagleInstanceDetails\fP *returnInfo)=0"
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.RI "virtual int \fBsetTipStates\fP (int tipIndex, const int *inStates)=0"
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.RI "virtual int \fBsetTipPartials\fP (int tipIndex, const double *inPartials)=0"
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.RI "virtual int \fBsetPartials\fP (int bufferIndex, const double *inPartials)=0"
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.RI "virtual int \fBgetPartials\fP (int bufferIndex, int scaleIndex, double *outPartials)=0"
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.RI "virtual int \fBsetEigenDecomposition\fP (int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)=0"
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.RI "virtual int \fBsetStateFrequencies\fP (int stateFrequenciesIndex, const double *inStateFrequencies)=0"
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.RI "virtual int \fBsetCategoryWeights\fP (int categoryWeightsIndex, const double *inCategoryWeights)=0"
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.RI "virtual int \fBsetPatternWeights\fP (const double *inPatternWeights)=0"
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.RI "virtual int \fBsetCategoryRates\fP (const double *inCategoryRates)=0"
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.RI "virtual int \fBsetTransitionMatrix\fP (int matrixIndex, const double *inMatrix, double paddedValue)=0"
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.RI "virtual int \fBsetTransitionMatrices\fP (const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)=0"
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.RI "virtual int \fBgetTransitionMatrix\fP (int matrixIndex, double *outMatrix)=0"
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.RI "virtual int \fBupdateTransitionMatrices\fP (int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)=0"
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.RI "virtual int \fBupdatePartials\fP (const int *operations, int operationCount, int cumulativeScalingIndex)=0"
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.RI "virtual int \fBwaitForPartials\fP (const int *destinationPartials, int destinationPartialsCount)=0"
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.RI "virtual int \fBaccumulateScaleFactors\fP (const int *scalingIndices, int count, int cumulativeScalingIndex)=0"
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.RI "virtual int \fBremoveScaleFactors\fP (const int *scalingIndices, int count, int cumulativeScalingIndex)=0"
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.RI "virtual int \fBresetScaleFactors\fP (int cumulativeScalingIndex)=0"
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.RI "virtual int \fBcopyScaleFactors\fP (int destScalingIndex, int srcScalingIndex)=0"
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.RI "virtual int \fBcalculateRootLogLikelihoods\fP (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)=0"
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.RI "virtual 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 *scalingFactorsIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative)=0"
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.RI "virtual int \fBgetSiteLogLikelihoods\fP (double *outLogLikelihoods)=0"
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.RI "virtual int \fBgetSiteDerivatives\fP (double *outFirstDerivatives, double *outSecondDerivatives)=0"
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.SS "Public Attributes"

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.RI "int \fBresourceNumber\fP"
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.in -1c

.SH "Author"
.PP 
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