Ancestors
Class AncestralJoint
java.lang.Object
Ancestors.AncestralJoint
- Direct Known Subclasses:
- AncestralJointBB, AncestralJointDP
public abstract class AncestralJoint
- extends java.lang.Object
Abstract class that the two different ways of doing ancestral reconstruction
extend. By using the static method in tis class users can avoid worrying
about whether their model has a single rate category.
- Version:
- 1.0
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AncestralJoint
public AncestralJoint()
calculate
public abstract Alignment calculate(Parameters params)
throws RateCategory.RateException,
Model.ModelException,
AncestralException,
TreeException,
Parameters.ParameterException,
AlignmentException
- Calculates the reconstruction
- Parameters:
params
- 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
newInstance
public static AncestralJoint newInstance(Model m,
Alignment a,
Tree t)
- Returns an object of this class that can be used for joint reconstruction.
If the model has a single rate category it returns an object that will do
reconstruction using the dynamic pogramming method of Pupko 2000, else
an object that will use the branch and bound method of Pupoko 2002. *
- Parameters:
a
- The alignmentm
- The modelt
- The tree
- Returns:
- An object that can be used for reconstruction