jebl.evolution.substmodel
public abstract class AbstractRateMatrix extends java.lang.Object implements RateMatrix
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) |
void |
rebuild() |
void |
scale(double scale) |
void |
setDistance(double distance)
Sets the distance (such as time/branch length) used when calculating
the probabilities.
|
void |
setDistanceTranspose(double distance)
Sets the distance (such as time/branch length) used when calculating
the probabilities.
|
double |
setParametersNoScale(double[] parameters) |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getUniqueName
public int getDimension()
getDimension
in interface RateMatrix
public double[] getEquilibriumFrequencies()
getEquilibriumFrequencies
in interface RateMatrix
public double getEquilibriumFrequency(int i)
getEquilibriumFrequency
in interface RateMatrix
public SequenceType getSequenceType()
RateMatrix
getSequenceType
in interface RateMatrix
public double[][] getRelativeRates()
getRelativeRates
in interface RateMatrix
public double getTransitionProbability(int fromState, int toState)
getTransitionProbability
in interface RateMatrix
fromState
- The state from which we are startingtoState
- The resulting statepublic final void rebuild()
public final void setDistance(double distance)
setDistance
in interface RateMatrix
public final void setDistanceTranspose(double distance)
public final void getTransitionProbabilities(double[][] probabilityStore)
getTransitionProbabilities
in interface RateMatrix
public void scale(double scale)
public double setParametersNoScale(double[] parameters)
http://code.google.com/p/jebl2/