jebl.evolution.substmodel
public interface RateMatrix extends java.lang.Cloneable, java.io.Serializable
Modifier and Type | Method and Description |
---|---|
int |
getDimension() |
double[] |
getEquilibriumFrequencies() |
double |
getEquilibriumFrequency(int i) |
double[][] |
getRelativeRates() |
SequenceType |
getSequenceType()
Get the data type of this rate matrix
|
void |
getTransitionProbabilities(double[][] probabilityStore)
A utility method for speed, transfers trans prob information quickly
into store.
|
double |
getTransitionProbability(int fromState,
int toState) |
java.lang.String |
getUniqueName() |
void |
setDistance(double distance)
Sets the distance (such as time/branch length) used when calculating
the probabilities.
|
java.lang.String getUniqueName()
int getDimension()
double[] getEquilibriumFrequencies()
double getEquilibriumFrequency(int i)
SequenceType getSequenceType()
double[][] getRelativeRates()
double getTransitionProbability(int fromState, int toState)
fromState
- The state from which we are startingtoState
- The resulting statevoid getTransitionProbabilities(double[][] probabilityStore)
void setDistance(double distance)
http://code.google.com/p/jebl2/