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BeagleResource(3)						     HMSBEAGLE							 BeagleResource(3)

NAME
BeagleResource - Description of a hardware resource. SYNOPSIS
#include <libhmsbeagle/beagle.h> Public Attributes char * name char * description long supportFlags long requiredFlags Detailed Description Description of a hardware resource. Member Data Documentation char* BeagleResource::description Description of resource as a NULL-terminated character string char* BeagleResource::name Name of resource as a NULL-terminated character string long BeagleResource::requiredFlags Bit-flags that identify resource type long BeagleResource::supportFlags Bit-flags of supported capabilities on resource Author Generated automatically by Doxygen for HMSBEAGLE from the source code. Version 1.0.0 Fri May 25 2012 BeagleResource(3)

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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)
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