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) |