table of contents
other versions
- wheezy 1.0-6
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)
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)
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)
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: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)
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)
void beagle.BeagleJNIImpl.resetScaleFactors (intcumulativeScaleIndex) [inline]¶
Reset scalefactors This function resets a cumulative scale buffer. Parameters:cumulativeScaleIndex Index number of
cumulative scaleBuffer (input)
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
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
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)
void beagle.BeagleJNIImpl.setPatternWeights (final double[]patternWeights) [inline]¶
Set the weights for each pattern Parameters:patternWeights Array containing
patternCount weights
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)
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)
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)
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)
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
Author¶
Generated automatically by Doxygen for HMSBEAGLE from the source code.Fri May 25 2012 | Version 1.0.0 |