Ancestors
Class AncestralJointBB

java.lang.Object
  extended by Ancestors.AncestralJoint
      extended by Ancestors.AncestralJointBB

public class AncestralJointBB
extends AncestralJoint

Class to perform joint ancestral reconstrion using the method of Pupko 2002 slightly modified

Version:
1.0

Method Summary
 Alignment calculate(Parameters p)
          Calculates the reconstruction
 
Methods inherited from class Ancestors.AncestralJoint
newInstance
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

calculate

public Alignment calculate(Parameters p)
                    throws RateCategory.RateException,
                           Model.ModelException,
                           AncestralException,
                           TreeException,
                           Parameters.ParameterException,
                           AlignmentException
Description copied from class: AncestralJoint
Calculates the reconstruction

Specified by:
calculate in class AncestralJoint
Parameters:
p - The parameters to be used in the reconstruction
Returns:
An alignment based on the original alignment but augmented with the reconstruction
Throws:
RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).
Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)
AncestralException - Thrown if there is ambiguous data as these methods can't currently deasl with it
TreeException - Thrown if there is a problem with the tree.
Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a requied parameter is not present)
AlignmentException - Thrown if there is a problem with the alignment