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java.lang.ObjectAncestors.AncestralMarginal
public class AncestralMarginal
Class to perform marginal reconstruction of internal nodes. Uses the principles of Yang, Kurma and Nei 1995.
Nested Class Summary | |
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class |
AncestralMarginal.Result
Class to store the results of a marginal ancestral reconstruction |
class |
AncestralMarginal.SiteResult
Class to store the results of a marginal ancestral reconstruction for a single site |
Constructor Summary | |
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AncestralMarginal(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree. |
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AncestralMarginal(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
java.util.Map<java.lang.String,Constrainer> con)
Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment, a tree and s et of constrainers. |
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AncestralMarginal(Model m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree |
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AncestralMarginal(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and a constrainter |
Method Summary | |
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AncestralMarginal.Result |
calculate(Parameters params)
Calculates the 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 AncestralMarginal(Model m, Alignment a, Tree t)
m
- The modela
- The alignmentt
- The treepublic AncestralMarginal(Model m, Alignment a, Tree t, Constrainer con)
m
- The modela
- The alignmentt
- The treecon
- The constraints on the internal nodespublic AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) throws AlignmentException
m
- Map from site class to modela
- The alignmentt
- The tree
AlignmentException
- Thrown if a model isn't given
for each site class in the alignmentpublic AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, java.util.Map<java.lang.String,Constrainer> con) throws AlignmentException
m
- Map from site class to modela
- The alignmentt
- The treecon
- Map from site class to constrainer
AlignmentException
- Thrown if a model and constrainer isn't given
for each site class in the alignmentMethod Detail |
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public AncestralMarginal.Result calculate(Parameters params) throws RateCategory.RateException, Model.ModelException, 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)
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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