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

# 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.