HMSBEAGLE
1.0.0
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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.BeagleJNIWrapper | static |
LIBRARY_NAME (defined in beagle.BeagleJNIWrapper) | beagle.BeagleJNIWrapper | static |
loadBeagleLibrary() (defined in beagle.BeagleJNIWrapper) | beagle.BeagleJNIWrapper | inlinestatic |
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 |