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Packages that use Constrainer | |
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Ancestors | Provides classed to calculate ancestral reconstruction. |
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. |
Simulations | Provides a class to create simulate data. |
Uses of Constrainer in Ancestors |
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Constructors in Ancestors with parameters of type Constrainer | |
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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 |
Constructor parameters in Ancestors with type arguments of type Constrainer | |
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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. |
Uses of Constrainer in Constraints |
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Classes in Constraints that implement Constrainer | |
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class |
NoConstraints
Simple implementation of Constrainer that imposes no constraints |
Uses of Constrainer in Likelihood |
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Constructors in Likelihood with parameters of type Constrainer | |
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Calculator(Model m,
Alignment a,
Tree t,
Alignment unobserved,
Constrainer con)
Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints |
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Calculator(Model m,
Alignment a,
Tree t,
Constrainer con)
Creates a class to calculate the likelihood for a given model, alignment, tree and constraints |
Constructor parameters in Likelihood with type arguments of type Constrainer | |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
Alignment unobserved,
java.util.Map<java.lang.String,Constrainer> con)
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints. |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
java.util.Map<java.lang.String,Constrainer> con)
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints. |
Uses of Constrainer in Simulations |
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Constructors in Simulations with parameters of type Constrainer | |
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HypothesisTest(Model nullModel,
Model altModel,
Constrainer nullConstrainer,
Constrainer altConstrainer,
Optimizer o,
int reps)
Constructor for use when one or both of the null hypothesis and alternative hypothesis have constraints. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved,
Constrainer con)
Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints. |
Constructor parameters in Simulations with type arguments of type Constrainer | |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p,
Alignment unobserved,
java.util.Map<java.lang.String,Constrainer> con)
Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers. |
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