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java.lang.ObjectAncestors.AncestralJoint
public abstract class AncestralJoint
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.
Constructor Summary | |
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AncestralJoint()
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Method Summary | |
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abstract Alignment |
calculate(Parameters params)
Calculates the reconstruction |
static AncestralJoint |
newInstance(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
static AncestralJoint |
newInstance(Model m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AncestralJoint()
Method Detail |
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public abstract Alignment calculate(Parameters params) throws RateCategory.RateException, Model.ModelException, AncestralException, TreeException, Parameters.ParameterException, AlignmentException
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 alignmentpublic static AncestralJoint newInstance(Model m, Alignment a, Tree t)
a
- The alignmentm
- The modelt
- The tree
public static AncestralJoint newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) throws AlignmentException
a
- The alignmentm
- Map from site class to modelt
- The tree
AlignmentException
- Thrown if a model and constrainer isn't given
for each site class in the alignment
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