pal.substmodel
Class MatrixExponential
java.lang.Object
|
+--pal.substmodel.MatrixExponential
- All Implemented Interfaces:
- java.lang.Cloneable, java.io.Serializable
- 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
- See Also:
- Serialized Form
Field Summary |
int |
dimension
dimension of rate matrix |
double[][] |
transProb
transition probability matrix |
Method Summary |
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 |
setMatrix(RateMatrix r)
update rate matrix used in present module |
void |
setSpan(double start,
double end)
compute transition probabilities for a expected distance
using the prespecified rate matrix |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
dimension
public int dimension
- dimension of rate matrix
transProb
public double[][] transProb
- transition probability matrix
MatrixExponential
public MatrixExponential(RateMatrix r)
- create module
- Parameters:
r
- rate matrix
getTransitionProbability
public final double getTransitionProbability(int from,
int to)
getDimension
public int getDimension()
setMatrix
public void setMatrix(RateMatrix r)
- update rate matrix used in present module
- Parameters:
r
- rate matrix
setSpan
public void setSpan(double start,
double end)
- compute transition probabilities for a expected distance
using the prespecified rate matrix
- Parameters:
arc
- expected distance
getTransitionProbabilities
public final void getTransitionProbabilities(double[][] probabilityStore)
- A utility method for speed, transfers trans prob information quickly
into store
setDistance
public final void setDistance(double arc)
- compute transition probabilities for a expected distance
using the prespecified rate matrix
- Parameters:
arc
- expected distance