.TH "beagle.GeneralBeagleImpl" 3 "Fri May 25 2012" "Version 1.0.0" "HMSBEAGLE" \" -*- nroff -*-
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.SH NAME
beagle.GeneralBeagleImpl \- 
.SH SYNOPSIS
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.PP
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Inherits \fBbeagle\&.Beagle\fP\&.
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Inherited by \fBbeagle\&.DependencyAwareBeagleImpl\fP, and \fBbeagle\&.FourStateBeagleImpl\fP\&.
.SS "Public Member Functions"

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.RI "\fBGeneralBeagleImpl\fP (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)"
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.RI "void \fBfinalize\fP ()  throws Throwable "
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.RI "void \fBsetPatternWeights\fP (final double[] patternWeights)"
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.RI "void \fBsetTipStates\fP (int tipIndex, int[] states)"
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.RI "void \fBgetTipStates\fP (int tipIndex, int[] states)"
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.RI "void \fBsetTipPartials\fP (int tipIndex, double[] inPartials)"
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.RI "void \fBsetPartials\fP (final int bufferIndex, final double[] partials)"
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.RI "void \fBgetPartials\fP (final int bufferIndex, final int scaleIndex, final double[] partials)"
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.RI "void \fBsetEigenDecomposition\fP (int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues)"
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.RI "void \fBsetStateFrequencies\fP (final int stateFrequenciesIndex, final double[] stateFrequencies)"
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.RI "void \fBsetCategoryWeights\fP (final int categoryWeightsIndex, final double[] categoryWeights)"
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.RI "void \fBsetCategoryRates\fP (double[] categoryRates)"
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.RI "void \fBsetTransitionMatrix\fP (final int matrixIndex, final double[] inMatrix, final double paddedValue)"
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.RI "void \fBgetTransitionMatrix\fP (final int matrixIndex, final double[] outMatrix)"
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.RI "void \fBupdateTransitionMatrices\fP (final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count)"
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.RI "void \fBupdatePartials\fP (final int[] operations, final int operationCount, final int cumulativeScaleIndex)"
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.RI "void \fBaccumulateScaleFactors\fP (int[] scaleIndices, int count, int outScaleIndex)"
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.RI "void \fBremoveScaleFactors\fP (int[] scaleIndices, int count, int cumulativeScaleIndex)"
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.RI "void \fBcopyScaleFactors\fP (int destScalingIndex, int srcScalingIndex)"
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.RI "void \fBresetScaleFactors\fP (int cumulativeScaleIndex)"
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.RI "void \fBcalculateRootLogLikelihoods\fP (final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood)"
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.RI "void \fBcalculateEdgeLogLikelihoods\fP (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)"
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.RI "void \fBgetSiteLogLikelihoods\fP (final double[] outLogLikelihoods)"
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.RI "\fBInstanceDetails\fP \fBgetDetails\fP ()"
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.SS "Static Public Attributes"

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.RI "static final boolean \fBDEBUG\fP = false"
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.RI "static final boolean \fBSCALING\fP = true"
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.RI "static final int \fBSCALING_FACTOR_COUNT\fP = 254"
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.RI "static final int \fBSCALING_FACTOR_OFFSET\fP = 126"
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.SS "Protected Member Functions"

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.RI "int \fBupdateStatesStates\fP (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)"
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.RI "int \fBupdateStatesPartials\fP (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)"
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.RI "int \fBupdatePartialsPartials\fP (int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3)"
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.SS "Protected Attributes"

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.RI "final int \fBtipCount\fP"
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.RI "final int \fBpartialsBufferCount\fP"
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.RI "final int \fBcompactBufferCount\fP"
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.RI "final int \fBstateCount\fP"
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.RI "final int \fBpatternCount\fP"
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.RI "final int \fBeigenBufferCount\fP"
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.RI "final int \fBmatrixBufferCount\fP"
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.RI "final int \fBcategoryCount\fP"
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.RI "int \fBpartialsSize\fP"
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.RI "int \fBmatrixSize\fP"
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.RI "double[][] \fBcMatrices\fP"
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.RI "double[][] \fBeigenValues\fP"
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.RI "double[][] \fBstateFrequencies\fP"
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.RI "double[] \fBcategoryRates\fP"
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.RI "double[][] \fBcategoryWeights\fP"
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.RI "double[] \fBpatternWeights\fP"
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.RI "double[][] \fBpartials\fP"
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.RI "int[][] \fBscalingFactorCounts\fP"
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.RI "int[][] \fBtipStates\fP"
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.RI "double[][] \fBmatrices\fP"
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.RI "double[] \fBscalingFactors\fP"
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.RI "double[] \fBlogScalingFactors\fP"
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.SH "Constructor & Destructor Documentation"
.PP 
.SS "beagle\&.GeneralBeagleImpl\&.GeneralBeagleImpl (final inttipCount, final intpartialsBufferCount, final intcompactBufferCount, final intstateCount, final intpatternCount, final inteigenBufferCount, final intmatrixBufferCount, final intcategoryCount, final intscaleBufferCount)\fC [inline]\fP"
Constructor
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\fBParameters:\fP
.RS 4
\fIstateCount\fP number of states 
.RE
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.SH "Member Function Documentation"
.PP 
.SS "void beagle\&.GeneralBeagleImpl\&.copyScaleFactors (intdestScalingIndex, intsrcScalingIndex)\fC [inline]\fP"
Copy scale factors
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This function copies scale factors from one buffer to another\&.
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\fBParameters:\fP
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\fIinstance\fP Instance number (input) 
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\fIdestScalingIndex\fP Destination scaleBuffer (input) 
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\fIsrcScalingIndex\fP Source scaleBuffer (input) 
.RE
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Implements \fBbeagle\&.Beagle\fP\&.
.SS "void beagle\&.GeneralBeagleImpl\&.finalize ()  throws Throwable \fC [inline]\fP"
Finalize this instance
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This function finalizes the instance by releasing allocated memory 
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Implements \fBbeagle\&.Beagle\fP\&.
.SS "\fBInstanceDetails\fP beagle\&.GeneralBeagleImpl\&.getDetails ()\fC [inline]\fP"
Get a details class for this instance 
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\fBReturns:\fP
.RS 4

.RE
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Implements \fBbeagle\&.Beagle\fP\&.
.SS "void beagle\&.GeneralBeagleImpl\&.resetScaleFactors (intcumulativeScaleIndex)\fC [inline]\fP"
Reset scalefactors
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This function resets a cumulative scale buffer\&.
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\fBParameters:\fP
.RS 4
\fIcumulativeScaleIndex\fP Index number of cumulative scaleBuffer (input) 
.RE
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Implements \fBbeagle\&.Beagle\fP\&.
.SS "void beagle\&.GeneralBeagleImpl\&.setPatternWeights (final double[]patternWeights)\fC [inline]\fP"
Set the weights for each pattern 
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\fBParameters:\fP
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\fIpatternWeights\fP Array containing patternCount weights 
.RE
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Implements \fBbeagle\&.Beagle\fP\&.
.SS "void beagle\&.GeneralBeagleImpl\&.setTipStates (inttipIndex, int[]states)\fC [inline]\fP"
Sets partials for a tip - these are numbered from 0 and remain constant throughout the run\&.
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\fBParameters:\fP
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\fItipIndex\fP the tip index 
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\fIstates\fP an array of patternCount state indices 
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.SS "void beagle\&.GeneralBeagleImpl\&.updatePartials (final int[]operations, final intoperationCount, final intcumulativeScaleIndex)\fC [inline]\fP"
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} 
.SS "int beagle\&.GeneralBeagleImpl\&.updateStatesPartials (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3)\fC [inline]\fP, \fC [protected]\fP"
Calculates partial likelihoods at a node when one child has states and one has partials\&. 
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Reimplemented in \fBbeagle\&.FourStateBeagleImpl\fP\&.
.SS "int beagle\&.GeneralBeagleImpl\&.updateStatesStates (intbufferIndex1, intmatrixIndex1, intbufferIndex2, intmatrixIndex2, intbufferIndex3)\fC [inline]\fP, \fC [protected]\fP"
Calculates partial likelihoods at a node when both children have states\&. 
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\fBReturns:\fP
.RS 4
the larges absolute exponent 
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Reimplemented in \fBbeagle\&.FourStateBeagleImpl\fP\&.

.SH "Author"
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Generated automatically by Doxygen for HMSBEAGLE from the source code\&.