java.io.Serializable
, java.lang.Cloneable
public class MatrixExponential
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable
Constructor | Description |
---|---|
MatrixExponential(int dimension) |
|
MatrixExponential(RateMatrix r) |
create module
|
Modifier and Type | Method | Description |
---|---|---|
int |
getDimension() |
|
void |
getTransitionProbabilities(double[][] probabilityStore) |
A utility method for speed, transfers trans prob information quickly
into store
|
double |
getTransitionProbability(int from,
int to) |
|
void |
setDistance(double arc) |
compute transition probabilities for a expected distance
using the prespecified rate matrix
|
void |
setDistanceTranspose(double arc) |
compute transition probabilities for a expected distance
using the prespecified rate matrix.
|
void |
setMatrix(RateMatrix r) |
update rate matrix used in present module
|
void |
updateByRelativeRates(double[][] relativeRates) |
public MatrixExponential(int dimension)
public 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 distancehttp://code.google.com/p/jebl2/