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

List of all members.

Public Member Functions

 FourStateBeagleImpl (final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount)
void calculateRootLogLikelihoods (final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood)

Static Public Attributes

static final boolean DEBUG = false

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)

Member Function Documentation

int beagle.FourStateBeagleImpl.updateStatesPartials ( int  bufferIndex1,
int  matrixIndex1,
int  bufferIndex2,
int  matrixIndex2,
int  bufferIndex3 
) [inline, protected]

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

Reimplemented from beagle.GeneralBeagleImpl.

int beagle.FourStateBeagleImpl.updateStatesStates ( int  bufferIndex1,
int  matrixIndex1,
int  bufferIndex2,
int  matrixIndex2,
int  bufferIndex3 
) [inline, protected]

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

Returns:
the larges absolute exponent

Reimplemented from beagle.GeneralBeagleImpl.


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