HMSBEAGLE  1.0.0
beagle.FourStateBeagleImpl Member List
This is the complete list of members for beagle.FourStateBeagleImpl, 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.FourStateBeagleImpl)beagle.FourStateBeagleImpl [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.FourStateBeagleImpl)beagle.FourStateBeagleImpl [static]
eigenBufferCount (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImpl [protected]
eigenValues (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImpl [protected]
finalize()beagle.GeneralBeagleImpl [inline]
FourStateBeagleImpl(final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount) (defined in beagle.FourStateBeagleImpl)beagle.FourStateBeagleImpl [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]
tmpPartials (defined in beagle.GeneralBeagleImpl)beagle.GeneralBeagleImpl [package]
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.FourStateBeagleImpl)beagle.FourStateBeagleImpl [inline, protected]
updateStatesPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)beagle.FourStateBeagleImpl [inline, protected]
updateStatesStates(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)beagle.FourStateBeagleImpl [inline, protected]
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