---
name: "beagle_GeneralBeagleImpl"
section: "3"
platform: "linux"
package: "libhmsbeagle-dev"
version: "1.0-6"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/beagle_GeneralBeagleImpl"
---

# 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.