HMSBEAGLE  1.0.0
beagle.BeagleJNIImpl Member List

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

accumulateScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex)beagle.BeagleJNIImplinline
BeagleJNIImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, final int[] resourceList, long preferenceFlags, long requirementFlags) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
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, int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
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, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
beagle::Beagle.calculateRootLogLikelihoods(int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood)beagle.Beagle
copyScaleFactors(int destScalingIndex, int srcScalingIndex)beagle.BeagleJNIImplinline
finalize()beagle.BeagleJNIImplinline
getDetails()beagle.BeagleJNIImplinline
getPartials(int bufferIndex, int scaleIndex, final double[]outPartials)beagle.BeagleJNIImplinline
getSiteLogLikelihoods(final double[] outLogLikelihoods) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
beagle::Beagle.getSiteLogLikelihoods(double[] outLogLikelihoods)beagle.Beagle
getTipStates(int tipIndex, final int[] states)beagle.BeagleJNIImplinline
getTransitionMatrix(int matrixIndex, final double[] outMatrix) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
beagle::Beagle.getTransitionMatrix(int matrixIndex, double[] outMatrix)beagle.Beagle
NONE (defined in beagle.Beagle)beagle.Beaglestatic
OPERATION_TUPLE_SIZE (defined in beagle.Beagle)beagle.Beaglestatic
removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
beagle::Beagle.removeScaleFactors(final int[] scaleIndices, final int count, final int cumulativeScaleIndex)beagle.Beagle
resetScaleFactors(int cumulativeScaleIndex)beagle.BeagleJNIImplinline
setCategoryRates(double[] inCategoryRates) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
beagle::Beagle.setCategoryRates(final double[] inCategoryRates)beagle.Beagle
setCategoryWeights(int categoryWeightsIndex, final double[] categoryWeights)beagle.BeagleJNIImplinline
setEigenDecomposition(int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final double[] eigenValues)beagle.BeagleJNIImplinline
setPartials(int bufferIndex, final double[] partials)beagle.BeagleJNIImplinline
setPatternWeights(final double[] patternWeights)beagle.BeagleJNIImplinline
setStateFrequencies(int stateFrequenciesIndex, final double[] stateFrequencies)beagle.BeagleJNIImplinline
setTipPartials(int tipIndex, final double[] partials)beagle.BeagleJNIImplinline
setTipStates(int tipIndex, final int[] states)beagle.BeagleJNIImplinline
setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue)beagle.BeagleJNIImplinline
updatePartials(final int[] operations, final int operationCount, final int cumulativeScaleIndex) (defined in beagle.BeagleJNIImpl)beagle.BeagleJNIImplinline
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.BeagleJNIImplinline