beagle.Beagle Member List

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

accumulateScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex)	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(int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood)	beagle.Beagle
copyScaleFactors(int destScalingIndex, int srcScalingIndex)	beagle.Beagle
finalize()	beagle.Beagle
getDetails()	beagle.Beagle
getPartials(int bufferIndex, int scaleIndex, final double[]outPartials)	beagle.Beagle
getSiteLogLikelihoods(double[] outLogLikelihoods)	beagle.Beagle
getTipStates(int tipIndex, final int[] outStates)	beagle.Beagle
getTransitionMatrix(int matrixIndex, double[] outMatrix)	beagle.Beagle
NONE (defined in beagle.Beagle)	beagle.Beagle	static
OPERATION_TUPLE_SIZE (defined in beagle.Beagle)	beagle.Beagle	static
removeScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex)	beagle.Beagle
resetScaleFactors(int cumulativeScaleIndex)	beagle.Beagle
setCategoryRates(final double[] inCategoryRates)	beagle.Beagle
setCategoryWeights(int categoryWeightsIndex, final double[] categoryWeights)	beagle.Beagle
setEigenDecomposition(int eigenIndex, final double[] inEigenVectors, final double[] inInverseEigenVectors, final double[] inEigenValues)	beagle.Beagle
setPartials(int bufferIndex, final double[] inPartials)	beagle.Beagle
setPatternWeights(final double[] patternWeights)	beagle.Beagle
setStateFrequencies(int stateFrequenciesIndex, final double[] stateFrequencies)	beagle.Beagle
setTipPartials(int tipIndex, final double[] inPartials)	beagle.Beagle
setTipStates(int tipIndex, final int[] inStates)	beagle.Beagle
setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue)	beagle.Beagle
updatePartials(final int[] operations, int operationCount, int cumulativeScaleIndex)	beagle.Beagle
updateTransitionMatrices(int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count)	beagle.Beagle