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Packages that use SiteConstraints | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Constraints | Provides classes to constrain the state of internal nodes. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Uses of SiteConstraints in Alignments |
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Methods in Alignments with parameters of type SiteConstraints | |
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ArrayMap<java.lang.String,Likelihood.NodeLikelihood> |
Site.getInitialNodeLikelihoods(Tree t,
ArrayMap<java.lang.String,java.lang.Integer> map,
SiteConstraints scon)
Gdets initial node likelihoods based on the site, tree and any constraints. |
Uses of SiteConstraints in Constraints |
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Methods in Constraints that return SiteConstraints | |
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SiteConstraints |
SiteConstraints.clone()
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SiteConstraints |
Constrainer.getConstraints(Tree t,
Site s)
Gets the consraints on an the external nodes of a site given the tree and the state of the leafs. |
SiteConstraints |
NoConstraints.getConstraints(Tree t,
Site s)
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Uses of SiteConstraints in Likelihood |
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Constructors in Likelihood with parameters of type SiteConstraints | |
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Calculator.SiteCalculator(Site s,
Tree t,
SiteConstraints con,
Probabilities tp)
Constructor mainly for backwards compitability although also still used by some of the ancestral calculations. |
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