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beagle.Beagle(3) | HMSBEAGLE | beagle.Beagle(3) |
NAME¶
beagle.Beagle -SYNOPSIS¶
Inherited by beagle.BeagleJNIImpl, and beagle.GeneralBeagleImpl.Public Member Functions¶
void finalize () throws Throwable
Static Public Attributes¶
static int OPERATION_TUPLE_SIZE = 7
Detailed Description¶
Beagle - An interface exposing the BEAGLE likelihood evaluation library. This interface mirrors the beagle.h API but it for a single instance only. It is intended to be used by JNI wrappers of the BEAGLE library and for Java implementations for testing purposes. BeagleFactory handles the creation of specific istances. Author:Andrew Rambaut
Marc A. Suchard
Version:
$Id:$
Member Function Documentation¶
void beagle.Beagle.accumulateScaleFactors (final int[]scaleIndices, final intcount, final intcumulativeScaleIndex)¶
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.Beagle.calculateEdgeLogLikelihoods (int[]parentBufferIndices, int[]childBufferIndices, int[]probabilityIndices, int[]firstDerivativeIndices, int[]secondDerivativeIndices, int[]categoryWeightsIndices, int[]stateFrequenciesIndices, int[]cumulativeScaleIndices, intcount, double[]outSumLogLikelihood, double[]outSumFirstDerivative, double[]outSumSecondDerivative)¶
Calculate site log likelihoods and derivatives along an edge This function integrates at list of partials at a parent and child node with respect to a set of partials-weights and state frequencies to return the log likelihoods and first and second derivatives for each site Parameters:parentBufferIndices List of indices of
parent partialsBuffers (input)
childBufferIndices List of indices of child partialsBuffers (input)
probabilityIndices List indices of transition probability matrices for
this edge (input)
firstDerivativeIndices List indices of first derivative matrices (input)
secondDerivativeIndices List indices of second derivative matrices
(input)
categoryWeightsIndices List of indices of category weights to apply to
each partialsBuffer (input)
stateFrequenciesIndices List of indices of state frequencies for each
partialsBuffer (input) There should be one set for each of parentBufferIndices
cumulativeScaleIndices List of scalingFactors indices to accumulate over
(input). There There should be one set for each of parentBufferIndices
count Number of partialsBuffers (input)
outSumLogLikelihood Pointer to destination for resulting sum of log
likelihoods (output)
outSumFirstDerivative Pointer to destination for resulting sum of first
derivatives (output)
outSumSecondDerivative Pointer to destination for resulting sum of second
derivatives (output)
void beagle.Beagle.calculateRootLogLikelihoods (int[]bufferIndices, int[]categoryWeightsIndices, int[]stateFrequenciesIndices, int[]cumulativeScaleIndices, intcount, double[]outSumLogLikelihood)¶
Calculate site log likelihoods at a root node This function integrates a list of partials at a node with respect to a set of partials-weights and state frequencies to return the log likelihoods for each site Parameters:bufferIndices List of partialsBuffer
indices to integrate (input)
categoryWeightsIndices List of indices of category weights to apply to
each partialsBuffer (input) should be one categoryCount sized set for each of
parentBufferIndices
stateFrequenciesIndices List of indices of state frequencies for each
partialsBuffer (input) should be one set for each of parentBufferIndices
cumulativeScaleIndices List of scalingFactors indices to accumulate over
(input). There should be one set for each of parentBufferIndices
count Number of partialsBuffer to integrate (input)
outSumLogLikelihood Pointer to destination for resulting sum of log
likelihoods (output)
void beagle.Beagle.copyScaleFactors (intdestScalingIndex, intsrcScalingIndex)¶
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.Beagle.finalize () throws Throwable¶
Finalize this instance This function finalizes the instance by releasing allocated memory Implemented in beagle.GeneralBeagleImpl, and beagle.BeagleJNIImpl.InstanceDetails beagle.Beagle.getDetails ()¶
Get a details class for this instance Returns:void beagle.Beagle.getPartials (intbufferIndex, intscaleIndex, final double[]outPartials)¶
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.Beagle.getSiteLogLikelihoods (double[]outLogLikelihoods)¶
Return the individual log likelihoods for each site pattern. Parameters:outLogLikelihoods an array in which the
likelihoods will be put
void beagle.Beagle.getTipStates (inttipIndex, final int[]outStates)¶
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.Beagle.getTransitionMatrix (intmatrixIndex, double[]outMatrix)¶
Get a finite-time transition probability matrix This function copies a finite-time transition matrix buffer into the array outMatrix. The outMatrix array should be of size stateCount * stateCount * categoryCount and will be filled with one matrix for each rate category. Parameters:matrixIndex Index of matrix buffer
(input)
outMatrix Pointer to destination transition probability matrix
(output)
void beagle.Beagle.removeScaleFactors (final int[]scaleIndices, final intcount, final intcumulativeScaleIndex)¶
Remove scale factors This function removes (log) scale factors from a cumulative scale buffer. The scale factors to be removed are indicated in a list of scaleBuffers. Parameters:scaleIndices List of scaleBuffers to
remove (input)
count Number of scaleBuffers in list (input)
cumulativeScaleIndex Index number of scaleBuffer containing accumulated
factors (input)
void beagle.Beagle.resetScaleFactors (intcumulativeScaleIndex)¶
Reset scalefactors This function resets a cumulative scale buffer. Parameters:cumulativeScaleIndex Index number of
cumulative scaleBuffer (input)
void beagle.Beagle.setCategoryRates (final double[]inCategoryRates)¶
Set category rates This function sets the vector of category rates for an instance. Parameters:inCategoryRates Array containing
categoryCount rate scalers (input)
void beagle.Beagle.setCategoryWeights (intcategoryWeightsIndex, final double[]categoryWeights)¶
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.Beagle.setEigenDecomposition (inteigenIndex, final double[]inEigenVectors, final double[]inInverseEigenVectors, final double[]inEigenValues)¶
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.Beagle.setPartials (intbufferIndex, final double[]inPartials)¶
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.Beagle.setPatternWeights (final double[]patternWeights)¶
Set the weights for each pattern Parameters:patternWeights Array containing
patternCount weights
void beagle.Beagle.setStateFrequencies (intstateFrequenciesIndex, final double[]stateFrequencies)¶
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.Beagle.setTipPartials (inttipIndex, final double[]inPartials)¶
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.Beagle.setTipStates (inttipIndex, final int[]inStates)¶
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.Beagle.setTransitionMatrix (intmatrixIndex, final double[]inMatrix, doublepaddedValue)¶
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)
Parameters:
matrixIndex Index of matrix buffer
(input)
inMatrix Pointer to source transition probability matrix (input)
void beagle.Beagle.updatePartials (final int[]operations, intoperationCount, intcumulativeScaleIndex)¶
Calculate or queue for calculation partials using a list of operations This function either calculates or queues for calculation a list partials. Implementations supporting SYNCH may queue these calculations while other implementations perform these operations immediately. Implementations supporting GPU may perform all operations in the list simultaneously. Operations list is a list of 7-tuple integer indices, with one 7-tuple per operation. Format of 7-tuple operation: {destinationPartials, destinationScaleWrite, destinationScaleRead, child1Partials, child1TransitionMatrix, child2Partials, child2TransitionMatrix} Parameters:operations List of 7-tuples specifying
operations (input)
operationCount Number of operations (input)
cumulativeScaleIndex Index number of scaleBuffer to store accumulated
factors (input)
void beagle.Beagle.updateTransitionMatrices (inteigenIndex, final int[]probabilityIndices, final int[]firstDerivativeIndices, final int[]secondDervativeIndices, final double[]edgeLengths, intcount)¶
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¶
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