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HMSBEAGLE
1.0.0
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This is the complete list of members for beagle.BeagleJNIImpl, including all inherited members.
| accumulateScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) | beagle.BeagleJNIImpl | inline |
| BeagleJNIImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, final int[] resourceList, long preferenceFlags, long requirementFlags) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| calculateEdgeLogLikelihoods(final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.calculateEdgeLogLikelihoods(int[] parentBufferIndices, int[] childBufferIndices, int[] probabilityIndices, int[] firstDerivativeIndices, int[] secondDerivativeIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood, double[] outSumFirstDerivative, double[] outSumSecondDerivative) | beagle.Beagle | |
| calculateRootLogLikelihoods(int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.calculateRootLogLikelihoods(int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood) | beagle.Beagle | |
| copyScaleFactors(int destScalingIndex, int srcScalingIndex) | beagle.BeagleJNIImpl | inline |
| finalize() | beagle.BeagleJNIImpl | inline |
| getDetails() | beagle.BeagleJNIImpl | inline |
| getPartials(int bufferIndex, int scaleIndex, final double[]outPartials) | beagle.BeagleJNIImpl | inline |
| getSiteLogLikelihoods(final double[] outLogLikelihoods) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.getSiteLogLikelihoods(double[] outLogLikelihoods) | beagle.Beagle | |
| getTipStates(int tipIndex, final int[] states) | beagle.BeagleJNIImpl | inline |
| getTransitionMatrix(int matrixIndex, final double[] outMatrix) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.getTransitionMatrix(int matrixIndex, double[] outMatrix) | beagle.Beagle | |
| NONE (defined in beagle.Beagle) | beagle.Beagle | static |
| OPERATION_TUPLE_SIZE (defined in beagle.Beagle) | beagle.Beagle | static |
| removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.removeScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) | beagle.Beagle | |
| resetScaleFactors(int cumulativeScaleIndex) | beagle.BeagleJNIImpl | inline |
| setCategoryRates(double[] inCategoryRates) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.setCategoryRates(final double[] inCategoryRates) | beagle.Beagle | |
| setCategoryWeights(int categoryWeightsIndex, final double[] categoryWeights) | beagle.BeagleJNIImpl | inline |
| setEigenDecomposition(int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final double[] eigenValues) | beagle.BeagleJNIImpl | inline |
| setPartials(int bufferIndex, final double[] partials) | beagle.BeagleJNIImpl | inline |
| setPatternWeights(final double[] patternWeights) | beagle.BeagleJNIImpl | inline |
| setStateFrequencies(int stateFrequenciesIndex, final double[] stateFrequencies) | beagle.BeagleJNIImpl | inline |
| setTipPartials(int tipIndex, final double[] partials) | beagle.BeagleJNIImpl | inline |
| setTipStates(int tipIndex, final int[] states) | beagle.BeagleJNIImpl | inline |
| setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue) | beagle.BeagleJNIImpl | inline |
| updatePartials(final int[] operations, final int operationCount, final int cumulativeScaleIndex) (defined in beagle.BeagleJNIImpl) | beagle.BeagleJNIImpl | inline |
| beagle::Beagle.updatePartials(final int[] operations, int operationCount, int cumulativeScaleIndex) | beagle.Beagle | |
| updateTransitionMatrices(int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count) | beagle.BeagleJNIImpl | inline |
1.8.1