HMSBEAGLE  1.0.0
Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes
beagle.GeneralBeagleImpl Class Reference
Inheritance diagram for beagle.GeneralBeagleImpl:
beagle.Beagle beagle.DependencyAwareBeagleImpl beagle.FourStateBeagleImpl

List of all members.

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 ()
- Public Member Functions inherited from beagle.Beagle
void setTipStates (int tipIndex, final int[] inStates)
void getTipStates (int tipIndex, final int[] outStates)
void setTipPartials (int tipIndex, final double[] inPartials)
void setPartials (int bufferIndex, final double[] inPartials)
void getPartials (int bufferIndex, int scaleIndex, final double[]outPartials)
void setEigenDecomposition (int eigenIndex, final double[] inEigenVectors, final double[] inInverseEigenVectors, final double[] inEigenValues)
void setStateFrequencies (int stateFrequenciesIndex, final double[] stateFrequencies)
void setCategoryWeights (int categoryWeightsIndex, final double[] categoryWeights)
void setCategoryRates (final double[] inCategoryRates)
void updateTransitionMatrices (int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count)
void setTransitionMatrix (int matrixIndex, final double[] inMatrix, double paddedValue)
void getTransitionMatrix (int matrixIndex, double[] outMatrix)
void updatePartials (final int[] operations, int operationCount, int cumulativeScaleIndex)
void accumulateScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex)
void removeScaleFactors (final int[] scaleIndices, final int count, final int cumulativeScaleIndex)
void calculateRootLogLikelihoods (int[] bufferIndices, int[] categoryWeightsIndices, int[] stateFrequenciesIndices, int[] cumulativeScaleIndices, int count, double[] outSumLogLikelihood)
void 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)
void getSiteLogLikelihoods (double[] outLogLikelihoods)

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
- Static Public Attributes inherited from beagle.Beagle
static int OPERATION_TUPLE_SIZE = 7
static int NONE = -1

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 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 
)
inline

Constructor

Parameters:
stateCountnumber of states

Member Function Documentation

void beagle.GeneralBeagleImpl.copyScaleFactors ( int  destScalingIndex,
int  srcScalingIndex 
)
inline

Copy scale factors

This function copies scale factors from one buffer to another.

Parameters:
instanceInstance number (input)
destScalingIndexDestination scaleBuffer (input)
srcScalingIndexSource 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 ( int  cumulativeScaleIndex)
inline

Reset scalefactors

This function resets a cumulative scale buffer.

Parameters:
cumulativeScaleIndexIndex number of cumulative scaleBuffer (input)

Implements beagle.Beagle.

void beagle.GeneralBeagleImpl.setPatternWeights ( final double[]  patternWeights)
inline

Set the weights for each pattern

Parameters:
patternWeightsArray containing patternCount weights

Implements beagle.Beagle.

void beagle.GeneralBeagleImpl.setTipStates ( int  tipIndex,
int[]  states 
)
inline

Sets partials for a tip - these are numbered from 0 and remain constant throughout the run.

Parameters:
tipIndexthe tip index
statesan array of patternCount state indices
void beagle.GeneralBeagleImpl.updatePartials ( final int[]  operations,
final int  operationCount,
final int  cumulativeScaleIndex 
)
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 ( int  bufferIndex1,
int  matrixIndex1,
int  bufferIndex2,
int  matrixIndex2,
int  bufferIndex3 
)
inlineprotected

Calculates partial likelihoods at a node when one child has states and one has partials.

Reimplemented in beagle.FourStateBeagleImpl.

int beagle.GeneralBeagleImpl.updateStatesStates ( int  bufferIndex1,
int  matrixIndex1,
int  bufferIndex2,
int  matrixIndex2,
int  bufferIndex3 
)
inlineprotected

Calculates partial likelihoods at a node when both children have states.

Returns:
the larges absolute exponent

Reimplemented in beagle.FourStateBeagleImpl.


The documentation for this class was generated from the following file: