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HMSBEAGLE
1.0.0
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This is the complete list of members for beagle.Beagle, including all inherited members.
| accumulateScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) | 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, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood) | beagle.Beagle | |
| copyScaleFactors(int destScalingIndex, int srcScalingIndex) | beagle.Beagle | |
| finalize() | beagle.Beagle | |
| getDetails() | beagle.Beagle | |
| getPartials(int bufferIndex, int scaleIndex, final double[]outPartials) | beagle.Beagle | |
| getSiteLogLikelihoods(double[] outLogLikelihoods) | beagle.Beagle | |
| getTipStates(int tipIndex, final int[] outStates) | 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(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) | beagle.Beagle | |
| resetScaleFactors(int cumulativeScaleIndex) | beagle.Beagle | |
| setCategoryRates(final double[] inCategoryRates) | beagle.Beagle | |
| setCategoryWeights(int categoryWeightsIndex, final double[] categoryWeights) | beagle.Beagle | |
| setEigenDecomposition(int eigenIndex, final double[] inEigenVectors, final double[] inInverseEigenVectors, final double[] inEigenValues) | beagle.Beagle | |
| setPartials(int bufferIndex, final double[] inPartials) | beagle.Beagle | |
| setPatternWeights(final double[] patternWeights) | beagle.Beagle | |
| setStateFrequencies(int stateFrequenciesIndex, final double[] stateFrequencies) | beagle.Beagle | |
| setTipPartials(int tipIndex, final double[] inPartials) | beagle.Beagle | |
| setTipStates(int tipIndex, final int[] inStates) | beagle.Beagle | |
| setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue) | 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.Beagle |
1.8.1