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java.lang.ObjectAncestors.AncestralJoint
Ancestors.AncestralJointDP
public class AncestralJointDP
Class to perform joint ancestral reconstrion using the method of Pupko 2000
Method Summary | |
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Alignment |
calculate(Parameters params)
Calculates the reconstruction |
Methods inherited from class Ancestors.AncestralJoint |
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newInstance |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public Alignment calculate(Parameters params) throws RateCategory.RateException, Model.ModelException, AncestralException, TreeException, Parameters.ParameterException, AlignmentException
AncestralJoint
calculate
in class AncestralJoint
params
- The parameters to be used in the reconstruction
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
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