Likelihood

Class Probabilities.RateProbabilities

java.lang.Object

Likelihood.Probabilities.RateProbabilities

Enclosing class:

Probabilities

public class Probabilities.RateProbabilities
extends java.lang.Object

Stores the values of each transition, frequency etc for one set of parameters and for a single rate category.

Version:

1.0

Method Summary

Methods

Modifier and Type	Method and Description
SquareMatrix	getP(Branch b) Gets the probability matrix for a single branch
double	getP(Branch b, java.lang.String startState, java.lang.String endState) Gets the probability of a single transition on a single branch

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getP

public SquareMatrix getP(Branch b)

Gets the probability matrix for a single branch

Parameters:

b - The branch to get the matrix for

Returns:

The probability matrix associated with that branch

getP

public double getP(Branch b,
          java.lang.String startState,
          java.lang.String endState)

Gets the probability of a single transition on a single branch

Parameters:

b - The branch

startState - The start state

endState - The end state

Returns:

The probability of a transition from start state to end state along the given branch