Likelihood
Class Probabilities.RateProbabilities

java.lang.Object
  extended by 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
 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 fo 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 fo a single transition on a single branch

Parameters:
b - The branch
startState - The start state
endState - The end state
Returns:
The probabiluty of a transition from start state to end state along the given branch