Package pal.substmodel
Class MatrixExponential
- java.lang.Object
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- pal.substmodel.MatrixExponential
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
public class MatrixExponential extends java.lang.Object implements java.lang.Cloneable, java.io.Serializable
compute matrix exponential and, subsequently, transition probabilities for a given rate matrix- Version:
- $Id: MatrixExponential.java,v 1.20 2004/08/05 03:00:22 matt Exp $
- Author:
- Korbinian Strimmer
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description MatrixExponential(int dimension)
create moduleMatrixExponential(RateMatrix r)
create module
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getDimension()
void
getTransitionProbabilities(double[][] probabilityStore)
A utility method for speed, transfers trans prob information quickly into storedouble
getTransitionProbability(int from, int to)
void
setDistance(double arc)
compute transition probabilities for a expected distance using the prespecified rate matrixvoid
setDistanceTranspose(double arc)
compute transition probabilities for a expected distance using the prespecified rate matrixvoid
setMatrix(RateMatrix r)
update rate matrix used in present modulevoid
updateByRelativeRates(double[][] relativeRates)
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Constructor Detail
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MatrixExponential
public MatrixExponential(int dimension)
create module- Parameters:
r
- rate matrix
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MatrixExponential
public MatrixExponential(RateMatrix r)
create module- Parameters:
r
- rate matrix
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Method Detail
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getTransitionProbability
public final double getTransitionProbability(int from, int to)
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getDimension
public int getDimension()
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updateByRelativeRates
public void updateByRelativeRates(double[][] relativeRates)
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setMatrix
public void setMatrix(RateMatrix r)
update rate matrix used in present module- Parameters:
r
- rate matrix
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getTransitionProbabilities
public final void getTransitionProbabilities(double[][] probabilityStore)
A utility method for speed, transfers trans prob information quickly into store
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setDistance
public final void setDistance(double arc)
compute transition probabilities for a expected distance using the prespecified rate matrix- Parameters:
arc
- expected distance
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setDistanceTranspose
public final void setDistanceTranspose(double arc)
compute transition probabilities for a expected distance using the prespecified rate matrix- Parameters:
arc
- expected distance
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