---
name: "beagle_BeagleJNIWrapper"
section: "3"
platform: "linux"
package: "libhmsbeagle-dev"
version: "1.0-6"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/beagle_BeagleJNIWrapper"
---

# 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.