public class AncestralMarginal
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
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 and Description |
---|
AncestralMarginal(Model m,
Alignment a,
Tree t)
Creates an object to calculate an ancestral reconstruction for a given
model, alignment and tree
|
AncestralMarginal(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates an object to calculate an ancestral reconstruction for a given
model, alignment, tree and constraints
|
Modifier and Type | Method and Description |
---|---|
AncestralMarginal.Result |
calculate(Parameters params)
Calculates the reconstruction
|
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.Result calculate(Parameters params) throws RateCategory.RateException, Model.ModelException, TreeException, Parameters.ParameterException, AlignmentException
params
- The parameters to be used in the reconstructionRateCategory.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