beagle.GeneralBeagleImpl(3)					     HMSBEAGLE					       beagle.GeneralBeagleImpl(3)

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
       Generated automatically by Doxygen for HMSBEAGLE from the source code.

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