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Packages that use ArrayMap | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Models | Provides classes for defing a phylogenetic model. |
Uses of ArrayMap in Alignments |
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Methods in Alignments that return ArrayMap | |
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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. |
Methods in Alignments with parameters of type ArrayMap | |
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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 ArrayMap in Likelihood |
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Methods in Likelihood that return ArrayMap | |
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ArrayMap<java.lang.String,java.lang.Integer> |
Probabilities.getArrayMap()
Gets an ArrayMap linking states to position in an array |
Constructors in Likelihood with parameters of type ArrayMap | |
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Calculator.SiteCalculator(Tree t,
Probabilities tp,
ArrayMap<java.lang.String,Likelihood.NodeLikelihood> nl)
Standard constructor |
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Likelihood.NodeLikelihood(ArrayMap<java.lang.String,java.lang.Integer> states,
java.util.Set<java.lang.String> allowedStates)
Default constructor |
Uses of ArrayMap in Models |
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Methods in Models that return ArrayMap | |
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ArrayMap<java.lang.String,java.lang.Integer> |
Model.getArrayMap()
Gets a map from the rate name to its index in the rate matrix Called this as Model.getMap() is kept for comptability |
ArrayMap<java.lang.String,java.lang.Integer> |
RateCategory.getArrayMap()
Gets the map that maps state to position in matrix Called this as RateCategory.getMap() is kept for comptability |
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