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Packages that use Tree | |
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Alignments | Provides class for dealing with "alignments" and the sites in an alignment. |
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. |
Trees | Provides classes to define a tree and any constraints on that tree. |
Uses of Tree in Alignments |
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Methods in Alignments with parameters of type Tree | |
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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 Tree in Ancestors |
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Methods in Ancestors with parameters of type Tree | |
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static AncestralJoint |
AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
static AncestralJoint |
AncestralJoint.newInstance(Model m,
Alignment a,
Tree t)
Returns an object of this class that can be used for joint reconstruction. |
Constructors in Ancestors with parameters of type Tree | |
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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 |
Uses of Tree in Constraints |
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Methods in Constraints with parameters of type Tree | |
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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 Tree in Likelihood |
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Constructors in Likelihood with parameters of type Tree | |
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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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Calculator.SiteCalculator(Tree t,
Probabilities tp,
ArrayMap<java.lang.String,Likelihood.NodeLikelihood> nl)
Standard constructor |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t)
Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree. |
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Calculator(java.util.Map<java.lang.String,Model> m,
Alignment a,
Tree t,
Alignment unobserved)
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, and unobserved data. |
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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. |
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Calculator(Model m,
Alignment a,
Tree t)
Creates an object to calculate the likelihood for a given model, alignment, tree. |
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Calculator(Model m,
Alignment a,
Tree t,
Alignment unobserved)
Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints |
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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 |
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Probabilities(Model m,
Tree t,
Parameters p)
Constructor |
Uses of Tree in Simulations |
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Methods in Simulations with parameters of type Tree | |
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double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams)
Does a hpyothesis test on the given data and gives a p-value |
double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams,
java.util.Map<java.lang.String,java.lang.String> recode)
Does a hpyothesis test on the given data and gives a p-value |
Constructors in Simulations with parameters of type Tree | |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p)
Creates an object to simulate data for a given set of models, a tree and parameters. |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given set of models, a tree, parameters and unobserved sattes. |
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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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Simulate(Model m,
Tree t,
Parameters p)
Creates an object to simulate data for a given model, tree and parameters. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters and unobserved states. |
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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. |
Uses of Tree in Trees |
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Methods in Trees that return Tree | |
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static Tree |
Tree.fromFile(java.io.File f)
Creates a tree from a file containing a Newick string |
static Tree |
Tree.fromNewickString(java.lang.String newick)
Creates a tree from a newick string |
Tree |
Tree.midPointRoot(java.lang.String newRootName)
Mid point roots the tree and returns a new tree |
Tree |
Tree.scaledTo(double length)
Returns a new tree where the lengths are scales so the total length is different |
Constructors in Trees with parameters of type Tree | |
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Tree(Tree old,
Parameters p)
Duplicates a tree topology while replacing branch lengths using the appropiate parameter |
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TreeFigure(Tree t)
Constructor |
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