NAME
beagle.GeneralBeagleImpl -
SYNOPSIS
Inherits beagle.Beagle.
Inherited by beagle.DependencyAwareBeagleImpl, and beagle.FourStateBeagleImpl.
Public Member Functions
GeneralBeagleImpl (final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int stateCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount)
void finalize () throws Throwable
void setPatternWeights (final double[] patternWeights)
void setTipStates (int tipIndex, int[] states)
void getTipStates (int tipIndex, int[] states)
void setTipPartials (int tipIndex, double[] inPartials)
void setPartials (final int bufferIndex, final double[] partials)
void getPartials (final int bufferIndex, final int scaleIndex, final double[] partials)
void setEigenDecomposition (int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues)
void setStateFrequencies (final int stateFrequenciesIndex, final double[] stateFrequencies)
void setCategoryWeights (final int categoryWeightsIndex, final double[] categoryWeights)
void setCategoryRates (double[] categoryRates)
void setTransitionMatrix (final int matrixIndex, final double[] inMatrix, final double paddedValue)
void getTransitionMatrix (final int matrixIndex, final double[] outMatrix)
void updateTransitionMatrices (final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count)
void updatePartials (final int[] operations, final int operationCount, final int cumulativeScaleIndex)
void accumulateScaleFactors (int[] scaleIndices, int count, int outScaleIndex)
void removeScaleFactors (int[] scaleIndices, int count, int cumulativeScaleIndex)
void copyScaleFactors (int destScalingIndex, int srcScalingIndex)
void resetScaleFactors (int cumulativeScaleIndex)
void calculateRootLogLikelihoods (final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final 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, final int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative)
void getSiteLogLikelihoods (final double[] outLogLikelihoods)
InstanceDetails getDetails ()
Static Public Attributes
static final boolean DEBUG = false
static final boolean SCALING = true
static final int SCALING_FACTOR_COUNT = 254
static final int SCALING_FACTOR_OFFSET = 126
Protected Member Functions
int updateStatesStates (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)
int updateStatesPartials (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)
int updatePartialsPartials (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)
Protected Attributes
final int tipCount
final int partialsBufferCount
final int compactBufferCount
final int stateCount
final int patternCount
final int eigenBufferCount
final int matrixBufferCount
final int categoryCount
int partialsSize
int matrixSize
double[][] cMatrices
double[][] eigenValues
double[][] stateFrequencies
double[] categoryRates
double[][] categoryWeights
double[] patternWeights
double[][] partials
int[][] scalingFactorCounts
int[][] tipStates
double[][] matrices
double[] scalingFactors
double[] logScalingFactors
Constructor & Destructor Documentation
beagle.GeneralBeagleImpl.GeneralBeagleImpl (final inttipCount, final intpartialsBufferCount, final intcompactBufferCount, final intstateCount, final intpatternCount, final inteigenBufferCount, final intmatrixBufferCount, final intcategoryCount, final intscaleBufferCount) [inline]
Constructor
Parameters:
stateCount number of states
Member Function Documentation
void beagle.GeneralBeagleImpl.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.GeneralBeagleImpl.finalize () throws Throwable [inline]
Finalize this instance
This function finalizes the instance by releasing allocated memory
Implements beagle.Beagle.
InstanceDetails beagle.GeneralBeagleImpl.getDetails () [inline]
Get a details class for this instance
Returns:
Implements beagle.Beagle.
void beagle.GeneralBeagleImpl.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.GeneralBeagleImpl.setPatternWeights (final double[]patternWeights) [inline]
Set the weights for each pattern
Parameters:
patternWeights Array containing patternCount weights
Implements beagle.Beagle.
void beagle.GeneralBeagleImpl.setTipStates (inttipIndex, int[]states) [inline]
Sets partials for a tip - these are numbered from 0 and remain constant throughout the run.
Parameters:
tipIndex the tip index
states an array of patternCount state indices
void beagle.GeneralBeagleImpl.updatePartials (final int[]operations, final intoperationCount, final intcumulativeScaleIndex) [inline]
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}
int beagle.GeneralBeagleImpl.updateStatesPartials (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3) [inline], [protected]
Calculates partial likelihoods at a node when one child has states and one has partials.
Reimplemented in beagle.FourStateBeagleImpl.
int beagle.GeneralBeagleImpl.updateStatesStates (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3) [inline], [protected]
Calculates partial likelihoods at a node when both children have states.
Returns:
the larges absolute exponent
Reimplemented in beagle.FourStateBeagleImpl.
Author
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