.TH "beagle::gpu::BeagleGPUImpl" 3 "Fri May 25 2012" "Version 1.0.0" "HMSBEAGLE" \" -*- nroff -*-
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.SH NAME
beagle::gpu::BeagleGPUImpl \- 
.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 *retunInfo)"
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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 scaleIndex, 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 "template<> int \fBgetSiteLogLikelihoods\fP (double *outLogLikelihoods)"
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.ti -1c
.RI "template<> int \fBgetSiteLogLikelihoods\fP (double *outLogLikelihoods)"
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.ti -1c
.RI "template<> int \fBgetSiteDerivatives\fP (double *outFirstDerivatives, double *outSecondDerivatives)"
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.ti -1c
.RI "template<> int \fBgetSiteDerivatives\fP (double *outFirstDerivatives, double *outSecondDerivatives)"
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.in -1c
.SS "Additional Inherited Members"


.SH "Author"
.PP 
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