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.