HMSBEAGLE
1.0.0
|
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) |
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.
Reimplemented from beagle.GeneralBeagleImpl.