Public Member Functions |
| GeneralBeagleImpl (final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int stateCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount) |
void | finalize () throws Throwable |
void | setPatternWeights (final double[] patternWeights) |
void | setTipStates (int tipIndex, int[] states) |
void | getTipStates (int tipIndex, int[] states) |
void | setTipPartials (int tipIndex, double[] inPartials) |
void | setPartials (final int bufferIndex, final double[] partials) |
void | getPartials (final int bufferIndex, final int scaleIndex, final double[] partials) |
void | setEigenDecomposition (int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues) |
void | setStateFrequencies (final int stateFrequenciesIndex, final double[] stateFrequencies) |
void | setCategoryWeights (final int categoryWeightsIndex, final double[] categoryWeights) |
void | setCategoryRates (double[] categoryRates) |
void | setTransitionMatrix (final int matrixIndex, final double[] inMatrix, final double paddedValue) |
void | getTransitionMatrix (final int matrixIndex, final double[] outMatrix) |
void | updateTransitionMatrices (final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count) |
void | updatePartials (final int[] operations, final int operationCount, final int cumulativeScaleIndex) |
void | accumulateScaleFactors (int[] scaleIndices, int count, int outScaleIndex) |
void | removeScaleFactors (int[] scaleIndices, int count, int cumulativeScaleIndex) |
void | copyScaleFactors (int destScalingIndex, int srcScalingIndex) |
void | resetScaleFactors (int cumulativeScaleIndex) |
void | calculateRootLogLikelihoods (final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood) |
void | 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, final int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) |
void | getSiteLogLikelihoods (final double[] outLogLikelihoods) |
InstanceDetails | getDetails () |
void | setTipStates (int tipIndex, final int[] inStates) |
void | getTipStates (int tipIndex, final int[] outStates) |
void | setTipPartials (int tipIndex, final double[] inPartials) |
void | setPartials (int bufferIndex, final double[] inPartials) |
void | getPartials (int bufferIndex, int scaleIndex, final double[]outPartials) |
void | setEigenDecomposition (int eigenIndex, final double[] inEigenVectors, final double[] inInverseEigenVectors, final double[] inEigenValues) |
void | setStateFrequencies (int stateFrequenciesIndex, final double[] stateFrequencies) |
void | setCategoryWeights (int categoryWeightsIndex, final double[] categoryWeights) |
void | setCategoryRates (final double[] inCategoryRates) |
void | updateTransitionMatrices (int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count) |
void | setTransitionMatrix (int matrixIndex, final double[] inMatrix, double paddedValue) |
void | getTransitionMatrix (int matrixIndex, double[] outMatrix) |
void | updatePartials (final int[] operations, int operationCount, int cumulativeScaleIndex) |
void | accumulateScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex) |
void | removeScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex) |
void | calculateRootLogLikelihoods (int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood) |
void | 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) |
void | getSiteLogLikelihoods (double[] outLogLikelihoods) |