.TH "beagle.BeagleJNIWrapper" 3 "Fri May 25 2012" "Version 1.0.0" "HMSBEAGLE" \" -*- nroff -*-
.ad l
.nh
.SH NAME
beagle.BeagleJNIWrapper \- 
.SH SYNOPSIS
.br
.PP
.SS "Public Member Functions"

.in +1c
.ti -1c
.RI "native \fBResourceDetails\fP[] \fBgetResourceList\fP ()"
.br
.ti -1c
.RI "native int \fBcreateInstance\fP (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, final int[] resourceList, int resourceCount, long preferenceFlags, long requirementFlags, \fBInstanceDetails\fP returnInfo)"
.br
.ti -1c
.RI "native int \fBfinalize\fP (int instance)"
.br
.ti -1c
.RI "native int \fBsetPatternWeights\fP (int instance, final double[] patternWeights)"
.br
.ti -1c
.RI "native int \fBsetTipStates\fP (int instance, int tipIndex, final int[] inStates)"
.br
.ti -1c
.RI "native int \fBgetTipStates\fP (int instance, int tipIndex, final int[] inStates)"
.br
.ti -1c
.RI "native int \fBsetTipPartials\fP (int instance, int tipIndex, final double[] inPartials)"
.br
.ti -1c
.RI "native int \fBsetPartials\fP (int instance, int bufferIndex, final double[] inPartials)"
.br
.ti -1c
.RI "native int \fBgetPartials\fP (int instance, int bufferIndex, int scaleIndex, final double[] outPartials)"
.br
.ti -1c
.RI "native int \fBsetEigenDecomposition\fP (int instance, int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final double[] eigenValues)"
.br
.ti -1c
.RI "native int \fBsetStateFrequencies\fP (int instance, int stateFrequenciesIndex, final double[] stateFrequencies)"
.br
.ti -1c
.RI "native int \fBsetCategoryWeights\fP (int instance, int categoryWeightsIndex, final double[] categoryWeights)"
.br
.ti -1c
.RI "native int \fBsetCategoryRates\fP (int instance, final double[] inCategoryRates)"
.br
.ti -1c
.RI "native int \fBsetTransitionMatrix\fP (int instance, int matrixIndex, final double[] inMatrix, double paddedValue)"
.br
.ti -1c
.RI "native int \fBgetTransitionMatrix\fP (int instance, int matrixIndex, final double[] outMatrix)"
.br
.ti -1c
.RI "native int \fBupdateTransitionMatrices\fP (int instance, int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count)"
.br
.ti -1c
.RI "native int \fBupdatePartials\fP (final int instance, final int[] operations, int operationCount, int cumulativeScalingIndex)"
.br
.ti -1c
.RI "native int \fBwaitForPartials\fP (final int instance, final int[] destinationPartials, int destinationPartialsCount)"
.br
.ti -1c
.RI "native int \fBaccumulateScaleFactors\fP (final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex)"
.br
.ti -1c
.RI "native int \fBremoveScaleFactors\fP (final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex)"
.br
.ti -1c
.RI "native int \fBresetScaleFactors\fP (final int instance, final int cumulativeScalingIndex)"
.br
.ti -1c
.RI "native int \fBcopyScaleFactors\fP (final int instance, final int destScalingIndex, final int srcScalingIndex)"
.br
.ti -1c
.RI "native int \fBcalculateRootLogLikelihoods\fP (int instance, final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood)"
.br
.ti -1c
.RI "native int \fBcalculateEdgeLogLikelihoods\fP (int instance, final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] scalingFactorsIndices, int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative)"
.br
.ti -1c
.RI "native int \fBgetSiteLogLikelihoods\fP (final int instance, final double[] outLogLikelihoods)"
.br
.in -1c
.SS "Static Public Member Functions"

.in +1c
.ti -1c
.RI "static void \fBloadBeagleLibrary\fP ()  throws UnsatisfiedLinkError "
.br
.in -1c
.SS "Static Public Attributes"

.in +1c
.ti -1c
.RI "static final String \fBLIBRARY_NAME\fP = getPlatformSpecificLibraryName()"
.br
.ti -1c
.RI "static \fBBeagleJNIWrapper\fP \fBINSTANCE\fP"
.br
.in -1c

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