HMSBEAGLE
1.0.0
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This is the complete list of members for beagle.GeneralBeagleImpl, including all inherited members.
accumulateScaleFactors(int[] scaleIndices, int count, int outScaleIndex) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.accumulateScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) | beagle.Beagle | |
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) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | 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(final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.calculateRootLogLikelihoods(int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood) | beagle.Beagle | |
categoryCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
categoryRates (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
categoryWeights (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
cMatrices (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
compactBufferCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
copyScaleFactors(int destScalingIndex, int srcScalingIndex) | beagle.GeneralBeagleImpl | inline |
DEBUG (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | static |
eigenBufferCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
eigenValues (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
finalize() | beagle.GeneralBeagleImpl | inline |
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) | beagle.GeneralBeagleImpl | inline |
getDetails() | beagle.GeneralBeagleImpl | inline |
getPartials(final int bufferIndex, final int scaleIndex, final double[] partials) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.getPartials(int bufferIndex, int scaleIndex, final double[]outPartials) | beagle.Beagle | |
getSiteLogLikelihoods(final double[] outLogLikelihoods) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.getSiteLogLikelihoods(double[] outLogLikelihoods) | beagle.Beagle | |
getTipStates(int tipIndex, int[] states) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.getTipStates(int tipIndex, final int[] outStates) | beagle.Beagle | |
getTransitionMatrix(final int matrixIndex, final double[] outMatrix) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.getTransitionMatrix(int matrixIndex, double[] outMatrix) | beagle.Beagle | |
logScalingFactors (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
matrices (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
matrixBufferCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
matrixSize (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
NONE (defined in beagle.Beagle) | beagle.Beagle | static |
OPERATION_TUPLE_SIZE (defined in beagle.Beagle) | beagle.Beagle | static |
partials (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
partialsBufferCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
partialsSize (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
patternCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
patternWeights (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.removeScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex) | beagle.Beagle | |
resetScaleFactors(int cumulativeScaleIndex) | beagle.GeneralBeagleImpl | inline |
SCALING (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | static |
SCALING_FACTOR_COUNT (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | static |
SCALING_FACTOR_OFFSET (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | static |
scalingFactorCounts (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
scalingFactors (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
setCategoryRates(double[] categoryRates) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setCategoryRates(final double[] inCategoryRates) | beagle.Beagle | |
setCategoryWeights(final int categoryWeightsIndex, final double[] categoryWeights) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setCategoryWeights(int categoryWeightsIndex, final double[] categoryWeights) | beagle.Beagle | |
setEigenDecomposition(int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setEigenDecomposition(int eigenIndex, final double[] inEigenVectors, final double[] inInverseEigenVectors, final double[] inEigenValues) | beagle.Beagle | |
setPartials(final int bufferIndex, final double[] partials) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setPartials(int bufferIndex, final double[] inPartials) | beagle.Beagle | |
setPatternWeights(final double[] patternWeights) | beagle.GeneralBeagleImpl | inline |
setStateFrequencies(final int stateFrequenciesIndex, final double[] stateFrequencies) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setStateFrequencies(int stateFrequenciesIndex, final double[] stateFrequencies) | beagle.Beagle | |
setTipPartials(int tipIndex, double[] inPartials) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setTipPartials(int tipIndex, final double[] inPartials) | beagle.Beagle | |
setTipStates(int tipIndex, int[] states) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setTipStates(int tipIndex, final int[] inStates) | beagle.Beagle | |
setTransitionMatrix(final int matrixIndex, final double[] inMatrix, final double paddedValue) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue) | beagle.Beagle | |
stateCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
stateFrequencies (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
tipCount (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
tipStates (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | protected |
updatePartials(final int[] operations, final int operationCount, final int cumulativeScaleIndex) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.updatePartials(final int[] operations, int operationCount, int cumulativeScaleIndex) | beagle.Beagle | |
updatePartialsPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inlineprotected |
updateStatesPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3) | beagle.GeneralBeagleImpl | inlineprotected |
updateStatesStates(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3) | beagle.GeneralBeagleImpl | inlineprotected |
updateTransitionMatrices(final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count) (defined in beagle.GeneralBeagleImpl) | beagle.GeneralBeagleImpl | inline |
beagle::Beagle.updateTransitionMatrices(int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count) | beagle.Beagle |