beagle.BeagleJNIImpl(3) HMSBEAGLE beagle.BeagleJNIImpl(3)
NAME
beagle.BeagleJNIImpl -
SYNOPSIS
Inherits beagle.Beagle.
Public Member Functions
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)
void finalize () throws Throwable
void setPatternWeights (final double[] patternWeights)
void setTipStates (int tipIndex, final int[] states)
void getTipStates (int tipIndex, final int[] states)
void setTipPartials (int tipIndex, final double[] partials)
void setPartials (int bufferIndex, final double[] partials)
void getPartials (int bufferIndex, int scaleIndex, final double[]outPartials)
void setEigenDecomposition (int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final double[] eigenValues)
void setStateFrequencies (int stateFrequenciesIndex, final double[] stateFrequencies)
void setCategoryWeights (int categoryWeightsIndex, final double[] categoryWeights)
void setCategoryRates (double[] inCategoryRates)
void setTransitionMatrix (int matrixIndex, final double[] inMatrix, double paddedValue)
void getTransitionMatrix (int matrixIndex, final double[] outMatrix)
void updateTransitionMatrices (int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[]
secondDervativeIndices, final double[] edgeLengths, int count)
void updatePartials (final int[] operations, final int operationCount, final int cumulativeScaleIndex)
void accumulateScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex)
void removeScaleFactors (int[] scaleIndices, int count, int cumulativeScaleIndex)
void copyScaleFactors (int destScalingIndex, int srcScalingIndex)
void resetScaleFactors (int cumulativeScaleIndex)
void calculateRootLogLikelihoods (int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[]
cumulativeScaleIndices, int count, final double[] outSumLogLikelihood)
void 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)
void getSiteLogLikelihoods (final double[] outLogLikelihoods)
InstanceDetails getDetails ()
Additional Inherited Members
Member Function Documentation
void beagle.BeagleJNIImpl.accumulateScaleFactors (final int[]scaleIndices, final intcount, final intcumulativeScaleIndex) [inline]
Accumulate scale factors
This function adds (log) scale factors from a list of scaleBuffers to a cumulative scale buffer. It is used to calculate the marginal
scaling at a specific node for each site.
Parameters:
scaleIndices List of scaleBuffers to add (input)
count Number of scaleBuffers in list (input)
cumulativeScaleIndex Index number of scaleBuffer to accumulate factors into (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.copyScaleFactors (intdestScalingIndex, intsrcScalingIndex) [inline]
Copy scale factors
This function copies scale factors from one buffer to another.
Parameters:
instance Instance number (input)
destScalingIndex Destination scaleBuffer (input)
srcScalingIndex Source scaleBuffer (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.finalize () throws Throwable [inline]
Finalize this instance
This function finalizes the instance by releasing allocated memory
Implements beagle.Beagle.
InstanceDetails beagle.BeagleJNIImpl.getDetails () [inline]
Get a details class for this instance
Returns:
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.getPartials (intbufferIndex, intscaleIndex, final double[]outPartials) [inline]
Get partials from an instance buffer
This function copies an array of partials from an instance buffer. The inPartials array should be stateCount * patternCount * categoryCount
in length.
Parameters:
bufferIndex Index of destination partialsBuffer (input)
scaleIndex Index of scaleBuffer to apply to partials (input)
outPartials Pointer to which to receive partialsBuffer (output)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.getTipStates (inttipIndex, final int[]outStates) [inline]
Get the compressed state representation for tip node
This function copies a compact state representation from an instance buffer. Compact state representation is an array of states: 0 to
stateCount - 1 (missing = stateCount). The inStates array should be patternCount in length (replication across categoryCount is not
required).
Parameters:
tipIndex Index of destination partialsBuffer (input)
outStates Pointer to compressed states (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.resetScaleFactors (intcumulativeScaleIndex) [inline]
Reset scalefactors
This function resets a cumulative scale buffer.
Parameters:
cumulativeScaleIndex Index number of cumulative scaleBuffer (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setCategoryWeights (intcategoryWeightsIndex, final double[]categoryWeights) [inline]
Set a set of category weights. These will probably correspond to an eigen-system.
Parameters:
categoryWeightsIndex the index of the buffer
categoryWeights the array of weights
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setEigenDecomposition (inteigenIndex, final double[]inEigenVectors, final double[]inInverseEigenVectors, final
double[]inEigenValues) [inline]
Set an eigen-decomposition buffer
This function copies an eigen-decomposition into a instance buffer.
Parameters:
eigenIndex Index of eigen-decomposition buffer (input)
inEigenVectors Flattened matrix (stateCount x stateCount) of eigen-vectors (input)
inInverseEigenVectors Flattened matrix (stateCount x stateCount) of inverse-eigen-vectors (input)
inEigenValues Vector of eigenvalues
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setPartials (intbufferIndex, final double[]inPartials) [inline]
Set an instance partials buffer
This function copies an array of partials into an instance buffer. The inPartials array should be stateCount * patternCount * categoryCount
in length.
Parameters:
bufferIndex Index of destination partialsBuffer (input)
inPartials Pointer to partials values to set (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setPatternWeights (final double[]patternWeights) [inline]
Set the weights for each pattern
Parameters:
patternWeights Array containing patternCount weights
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setStateFrequencies (intstateFrequenciesIndex, final double[]stateFrequencies) [inline]
Set a set of state frequences. These will probably correspond to an eigen-system.
Parameters:
stateFrequenciesIndex the index of the frequency buffer
stateFrequencies the array of frequences (stateCount)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setTipPartials (inttipIndex, final double[]inPartials) [inline]
Set an instance partials buffer
This function copies an array of partials into an instance buffer. The inPartials array should be stateCount * patternCount in length. For
most applications this will be used to set the partial likelihoods for the observed states. Internally, the partials will be copied
categoryCount times.
Parameters:
tipIndex Index of destination partialsBuffer (input)
inPartials Pointer to partials values to set (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setTipStates (inttipIndex, final int[]inStates) [inline]
Set the compressed state representation for tip node
This function copies a compact state representation into an instance buffer. Compact state representation is an array of states: 0 to
stateCount - 1 (missing = stateCount). The inStates array should be patternCount in length (replication across categoryCount is not
required).
Parameters:
tipIndex Index of destination partialsBuffer (input)
inStates Pointer to compressed states (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.setTransitionMatrix (intmatrixIndex, final double[]inMatrix, doublepaddedValue) [inline]
This function copies a finite-time transition probability matrix into a matrix buffer. This function is used when the application wishes to
explicitly set the transition probability matrix rather than using the setEigenDecomposition and updateTransitionMatrices functions. The
inMatrix array should be of size stateCount * stateCount * categoryCount and will contain one matrix for each rate category.
This function copies a finite-time transition probability matrix into a matrix buffer.
Parameters:
matrixIndex Index of matrix buffer (input)
inMatrix Pointer to source transition probability matrix (input)
paddedValue Value to be used for padding for ambiguous states (e.g. 1 for probability matrices, 0 for derivative matrices) (input)
Implements beagle.Beagle.
void beagle.BeagleJNIImpl.updateTransitionMatrices (inteigenIndex, final int[]probabilityIndices, final int[]firstDerivativeIndices, final
int[]secondDervativeIndices, final double[]edgeLengths, intcount) [inline]
Calculate a list of transition probability matrices
This function calculates a list of transition probabilities matrices and their first and second derivatives (if requested).
Parameters:
eigenIndex Index of eigen-decomposition buffer (input)
probabilityIndices List of indices of transition probability matrices to update (input)
firstDerivativeIndices List of indices of first derivative matrices to update (input, NULL implies no calculation)
secondDervativeIndices List of indices of second derivative matrices to update (input, NULL implies no calculation)
edgeLengths List of edge lengths with which to perform calculations (input)
count Length of lists
Implements beagle.Beagle.
Author
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Version 1.0.0 Fri May 25 2012 beagle.BeagleJNIImpl(3)