beagle.BeagleJNIWrapper(3)					     HMSBEAGLE						beagle.BeagleJNIWrapper(3)

NAME

       beagle.BeagleJNIWrapper -

SYNOPSIS

   Public Member Functions
       native ResourceDetails[] getResourceList ()
       native int createInstance (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, InstanceDetails returnInfo)
       native int finalize (int instance)
       native int setPatternWeights (int instance, final double[] patternWeights)
       native int setTipStates (int instance, int tipIndex, final int[] inStates)
       native int getTipStates (int instance, int tipIndex, final int[] inStates)
       native int setTipPartials (int instance, int tipIndex, final double[] inPartials)
       native int setPartials (int instance, int bufferIndex, final double[] inPartials)
       native int getPartials (int instance, int bufferIndex, int scaleIndex, final double[] outPartials)
       native int setEigenDecomposition (int instance, int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final
	   double[] eigenValues)
       native int setStateFrequencies (int instance, int stateFrequenciesIndex, final double[] stateFrequencies)
       native int setCategoryWeights (int instance, int categoryWeightsIndex, final double[] categoryWeights)
       native int setCategoryRates (int instance, final double[] inCategoryRates)
       native int setTransitionMatrix (int instance, int matrixIndex, final double[] inMatrix, double paddedValue)
       native int getTransitionMatrix (int instance, int matrixIndex, final double[] outMatrix)
       native int updateTransitionMatrices (int instance, int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices,
	   final int[] secondDervativeIndices, final double[] edgeLengths, int count)
       native int updatePartials (final int instance, final int[] operations, int operationCount, int cumulativeScalingIndex)
       native int waitForPartials (final int instance, final int[] destinationPartials, int destinationPartialsCount)
       native int accumulateScaleFactors (final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex)
       native int removeScaleFactors (final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex)
       native int resetScaleFactors (final int instance, final int cumulativeScalingIndex)
       native int copyScaleFactors (final int instance, final int destScalingIndex, final int srcScalingIndex)
       native int calculateRootLogLikelihoods (int instance, final int[] bufferIndices, final int[] categoryWeightsIndices, final int[]
	   stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood)
       native int calculateEdgeLogLikelihoods (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)
       native int getSiteLogLikelihoods (final int instance, final double[] outLogLikelihoods)

   Static Public Member Functions
       static void loadBeagleLibrary ()  throws UnsatisfiedLinkError

   Static Public Attributes
       static final String LIBRARY_NAME = getPlatformSpecificLibraryName()
       static BeagleJNIWrapper INSTANCE

Author
       Generated automatically by Doxygen for HMSBEAGLE from the source code.

Version 1.0.0							  Fri May 25 2012					beagle.BeagleJNIWrapper(3)