.TH "KernelLauncher" 3 "Fri May 25 2012" "Version 1.0.0" "HMSBEAGLE" \" -*- nroff -*-
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.SH NAME
KernelLauncher \- 
.SH SYNOPSIS
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.PP
.SS "Public Member Functions"

.in +1c
.ti -1c
.RI "\fBKernelLauncher\fP (\fBGPUInterface\fP *inGpu)"
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.ti -1c
.RI "void \fBGetTransitionProbabilitiesSquare\fP (GPUPtr dPtr, GPUPtr dEvec, GPUPtr dIevc, GPUPtr dEigenValues, GPUPtr distanceQueue, unsigned int totalMatrix, unsigned int index)"
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.ti -1c
.RI "void \fBPartialsPartialsPruningDynamicCheckScaling\fP (GPUPtr partials1, GPUPtr partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, int writeScalingIndex, int readScalingIndex, int cumulativeScalingIndex, GPUPtr *dScalingFactors, GPUPtr *dScalingFactorsMaster, unsigned int patternCount, unsigned int categoryCount, int doRescaling, int *hRescalingTrigger, GPUPtr dRescalingTrigger, int sizeReal)"
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.ti -1c
.RI "void \fBPartialsPartialsPruningDynamicScaling\fP (GPUPtr partials1, GPUPtr partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, int doRescaling)"
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.ti -1c
.RI "void \fBStatesPartialsPruningDynamicScaling\fP (GPUPtr states1, GPUPtr partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, int doRescaling)"
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.ti -1c
.RI "void \fBStatesStatesPruningDynamicScaling\fP (GPUPtr states1, GPUPtr states2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, int doRescaling)"
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.ti -1c
.RI "void \fBIntegrateLikelihoodsDynamicScaling\fP (GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBIntegrateLikelihoodsAutoScaling\fP (GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBIntegrateLikelihoodsDynamicScalingSecondDeriv\fP (GPUPtr dResult, GPUPtr dFirstDerivResult, GPUPtr dSecondDerivResult, GPUPtr dRootPartials, GPUPtr dRootFirstDeriv, GPUPtr dRootSecondDeriv, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBPartialsPartialsEdgeLikelihoods\fP (GPUPtr dPartialsTmp, GPUPtr dParentPartials, GPUPtr dChildParials, GPUPtr dTransMatrix, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBPartialsPartialsEdgeLikelihoodsSecondDeriv\fP (GPUPtr dPartialsTmp, GPUPtr dFirstDerivTmp, GPUPtr dSecondDerivTmp, GPUPtr dParentPartials, GPUPtr dChildParials, GPUPtr dTransMatrix, GPUPtr dFirstDerivMatrix, GPUPtr dSecondDerivMatrix, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBStatesPartialsEdgeLikelihoods\fP (GPUPtr dPartialsTmp, GPUPtr dParentPartials, GPUPtr dChildStates, GPUPtr dTransMatrix, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBStatesPartialsEdgeLikelihoodsSecondDeriv\fP (GPUPtr dPartialsTmp, GPUPtr dFirstDerivTmp, GPUPtr dSecondDerivTmp, GPUPtr dParentPartials, GPUPtr dChildStates, GPUPtr dTransMatrix, GPUPtr dFirstDerivMatrix, GPUPtr dSecondDerivMatrix, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBAccumulateFactorsDynamicScaling\fP (GPUPtr dScalingFactors, GPUPtr dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned int patternCount)"
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.ti -1c
.RI "void \fBAccumulateFactorsAutoScaling\fP (GPUPtr dScalingFactors, GPUPtr dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned int patternCount, unsigned int scaleBufferSize)"
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.ti -1c
.RI "void \fBRemoveFactorsDynamicScaling\fP (GPUPtr dScalingFactors, GPUPtr dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned int patternCount)"
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.ti -1c
.RI "void \fBRescalePartials\fP (GPUPtr partials3, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, unsigned int fillWithOnes)"
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.ti -1c
.RI "void \fBIntegrateLikelihoods\fP (GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBIntegrateLikelihoodsSecondDeriv\fP (GPUPtr dResult, GPUPtr dFirstDerivResult, GPUPtr dSecondDerivResult, GPUPtr dRootPartials, GPUPtr dRootFirstDeriv, GPUPtr dRootSecondDeriv, GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int categoryCount)"
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.ti -1c
.RI "void \fBIntegrateLikelihoodsMulti\fP (GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int categoryCount, unsigned int takeLog)"
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.ti -1c
.RI "void \fBIntegrateLikelihoodsFixedScaleMulti\fP (GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dScalingFactors, GPUPtr dPtrQueue, GPUPtr dMaxScalingFactors, GPUPtr dIndexMaxScalingFactors, unsigned int patternCount, unsigned int categoryCount, unsigned int subsetCount, unsigned int subsetIndex)"
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.ti -1c
.RI "void \fBSumSites1\fP (GPUPtr dArray1, GPUPtr dSum1, GPUPtr dPatternWeights, unsigned int patternCount)"
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.ti -1c
.RI "void \fBSumSites2\fP (GPUPtr dArray1, GPUPtr dSum1, GPUPtr dArray2, GPUPtr dSum2, GPUPtr dPatternWeights, unsigned int patternCount)"
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.ti -1c
.RI "void \fBSumSites3\fP (GPUPtr dArray1, GPUPtr dSum1, GPUPtr dArray2, GPUPtr dSum2, GPUPtr dArray3, GPUPtr dSum3, GPUPtr dPatternWeights, unsigned int patternCount)"
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.ti -1c
.RI "void \fBSetupKernelBlocksAndGrids\fP ()"
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.in -1c
.SS "Protected Member Functions"

.in +1c
.ti -1c
.RI "void \fBLoadKernels\fP ()"
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.in -1c

.SH "Author"
.PP 
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