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beagle_fourstatebeagleimpl

beagle.FourStateBeagleImpl(3)					     HMSBEAGLE					     beagle.FourStateBeagleImpl(3)

NAME

       beagle.FourStateBeagleImpl -

SYNOPSIS

       Inherits beagle.GeneralBeagleImpl.

   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)

   Additional Inherited Members
Member Function Documentation
   int beagle.FourStateBeagleImpl.updateStatesPartials (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3)
       [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 (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3)
       [inline],  [protected]
       Calculates partial likelihoods at a node when both children have states.

       Returns:
	   the larges absolute exponent

       Reimplemented from beagle.GeneralBeagleImpl.

Author
       Generated automatically by Doxygen for HMSBEAGLE from the source code.

Version 1.0.0							  Fri May 25 2012				     beagle.FourStateBeagleImpl(3)