HMSBEAGLE  1.0.0
beagle.DependencyAwareBeagleImpl Member List

This is the complete list of members for beagle.DependencyAwareBeagleImpl, including all inherited members.

accumulateScaleFactors(int[] scaleIndices, int count, int outScaleIndex) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
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.GeneralBeagleImplinline
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.GeneralBeagleImplinline
beagle::Beagle.calculateRootLogLikelihoods(int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood)beagle.Beagle
categoryCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
categoryRates (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
categoryWeights (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
cMatrices (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
compactBufferCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
copyScaleFactors(int destScalingIndex, int srcScalingIndex)beagle.GeneralBeagleImplinline
DEBUG (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplstatic
DependencyAwareBeagleImpl(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) (defined in beagle.DependencyAwareBeagleImpl)beagle.DependencyAwareBeagleImplinline
eigenBufferCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
eigenValues (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
finalize()beagle.GeneralBeagleImplinline
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.GeneralBeagleImplinline
getDetails()beagle.GeneralBeagleImplinline
getPartials(final int bufferIndex, final int scaleIndex, final double[] partials) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.getPartials(int bufferIndex, int scaleIndex, final double[]outPartials)beagle.Beagle
getSiteLogLikelihoods(final double[] outLogLikelihoods) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.getSiteLogLikelihoods(double[] outLogLikelihoods)beagle.Beagle
getTipStates(int tipIndex, int[] states) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.getTipStates(int tipIndex, final int[] outStates)beagle.Beagle
getTransitionMatrix(final int matrixIndex, final double[] outMatrix) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.getTransitionMatrix(int matrixIndex, double[] outMatrix)beagle.Beagle
logScalingFactors (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
matrices (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
matrixBufferCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
matrixSize (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
NONE (defined in beagle.Beagle)beagle.Beaglestatic
OPERATION_TUPLE_SIZE (defined in beagle.Beagle)beagle.Beaglestatic
partials (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
partialsBufferCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
partialsSize (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
patternCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
patternWeights (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.removeScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex)beagle.Beagle
resetScaleFactors(int cumulativeScaleIndex)beagle.GeneralBeagleImplinline
SCALING (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplstatic
SCALING_FACTOR_COUNT (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplstatic
SCALING_FACTOR_OFFSET (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplstatic
scalingFactorCounts (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
scalingFactors (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
setCategoryRates(double[] categoryRates) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.setCategoryRates(final double[] inCategoryRates)beagle.Beagle
setCategoryWeights(final int categoryWeightsIndex, final double[] categoryWeights) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.setCategoryWeights(int categoryWeightsIndex, final double[] categoryWeights)beagle.Beagle
setEigenDecomposition(int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
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.GeneralBeagleImplinline
beagle::Beagle.setPartials(int bufferIndex, final double[] inPartials)beagle.Beagle
setPatternWeights(final double[] patternWeights)beagle.GeneralBeagleImplinline
setStateFrequencies(final int stateFrequenciesIndex, final double[] stateFrequencies) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.setStateFrequencies(int stateFrequenciesIndex, final double[] stateFrequencies)beagle.Beagle
setTipPartials(int tipIndex, double[] inPartials) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.setTipPartials(int tipIndex, final double[] inPartials)beagle.Beagle
setTipStates(int tipIndex, int[] states)beagle.GeneralBeagleImplinline
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.GeneralBeagleImplinline
beagle::Beagle.setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue)beagle.Beagle
stateCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
stateFrequencies (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
tipCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
tipStates (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplprotected
updatePartials(final int[] operations, final int operationCount, final int cumulativeScaleIndex)beagle.GeneralBeagleImplinline
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.GeneralBeagleImplinlineprotected
updateStatesPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)beagle.GeneralBeagleImplinlineprotected
updateStatesStates(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)beagle.GeneralBeagleImplinlineprotected
updateTransitionMatrices(final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count) (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImplinline
beagle::Beagle.updateTransitionMatrices(int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count)beagle.Beagle
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