pal.substmodel
public class MatrixExponential extends java.lang.Object implements java.lang.Cloneable, java.io.Serializable
Constructor and Description |
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MatrixExponential(int dimension)
create module
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MatrixExponential(RateMatrix r)
create module
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Modifier and Type | Method and Description |
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int |
getDimension() |
void |
getTransitionProbabilities(double[][] probabilityStore)
A utility method for speed, transfers trans prob information quickly
into store
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double |
getTransitionProbability(int from,
int to) |
void |
setDistance(double arc)
compute transition probabilities for a expected distance
using the prespecified rate matrix
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void |
setDistanceTranspose(double arc)
compute transition probabilities for a expected distance
using the prespecified rate matrix
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void |
setMatrix(RateMatrix r)
update rate matrix used in present module
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void |
updateByRelativeRates(double[][] relativeRates) |
public MatrixExponential(int dimension)
r
- rate matrixpublic MatrixExponential(RateMatrix r)
r
- rate matrixpublic final double getTransitionProbability(int from, int to)
public int getDimension()
public void updateByRelativeRates(double[][] relativeRates)
public void setMatrix(RateMatrix r)
r
- rate matrixpublic final void getTransitionProbabilities(double[][] probabilityStore)
public final void setDistance(double arc)
arc
- expected distancepublic final void setDistanceTranspose(double arc)
arc
- expected distance