HMSBEAGLE  1.0.0
beagle.BeagleJNIWrapper Member List

This is the complete list of members for beagle.BeagleJNIWrapper, including all inherited members.

accumulateScaleFactors(final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
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) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
calculateRootLogLikelihoods(int instance, final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
copyScaleFactors(final int instance, final int destScalingIndex, final int srcScalingIndex) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
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) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
finalize(int instance) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
getPartials(int instance, int bufferIndex, int scaleIndex, final double[] outPartials) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
getResourceList() (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
getSiteLogLikelihoods(final int instance, final double[] outLogLikelihoods) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
getTipStates(int instance, int tipIndex, final int[] inStates) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
getTransitionMatrix(int instance, int matrixIndex, final double[] outMatrix) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
INSTANCE (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapperstatic
LIBRARY_NAME (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapperstatic
loadBeagleLibrary() (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapperinlinestatic
removeScaleFactors(final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
resetScaleFactors(final int instance, final int cumulativeScalingIndex) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setCategoryRates(int instance, final double[] inCategoryRates) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setCategoryWeights(int instance, int categoryWeightsIndex, final double[] categoryWeights) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setEigenDecomposition(int instance, int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final double[] eigenValues) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setPartials(int instance, int bufferIndex, final double[] inPartials) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setPatternWeights(int instance, final double[] patternWeights) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setStateFrequencies(int instance, int stateFrequenciesIndex, final double[] stateFrequencies) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setTipPartials(int instance, int tipIndex, final double[] inPartials) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setTipStates(int instance, int tipIndex, final int[] inStates) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
setTransitionMatrix(int instance, int matrixIndex, final double[] inMatrix, double paddedValue) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
updatePartials(final int instance, final int[] operations, int operationCount, int cumulativeScalingIndex) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
updateTransitionMatrices(int instance, int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper
waitForPartials(final int instance, final int[] destinationPartials, int destinationPartialsCount) (defined in beagle.BeagleJNIWrapper)beagle.BeagleJNIWrapper