- t - Variable in class Likelihood.Calculator
-
The tree to do the calculation on.
- test(Tree, Alignment, Alignment, Parameters, Parameters) - Method in class ModelTest.HypothesisTest
-
Does a hypothesis test on the given data and gives a p-value
- test(Tree, Alignment, Alignment, Parameters, Parameters, Map<String, String>) - Method in class ModelTest.HypothesisTest
-
Does a hypothesis test on the given data and gives a p-value
- test(Map<String, Tree>, Alignment, Alignment, Parameters, Parameters) - Method in class ModelTest.HypothesisTest
-
Does a hypothesis test on the given data and gives a p-value
- test(Map<String, Tree>, Alignment, Alignment, Parameters, Parameters, Map<String, String>) - Method in class ModelTest.HypothesisTest
-
Does a hypothesis test on the given data and gives a p-value
- TestInstance - Class in ModelTest
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Represents a particular instance (calculator and parameters) to be tested
to find the best performing.
- TestInstance(Calculator<Likelihood>, Parameters) - Constructor for class ModelTest.TestInstance
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Creates an instance
- TestInstance(Calculator<Likelihood>, Parameters, String) - Constructor for class ModelTest.TestInstance
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Creates a named instance.
- TestInstance(Calculator<Likelihood>, Parameters, Adapter, Alignment) - Constructor for class ModelTest.TestInstance
-
Creates a named instance.
- TestInstance(Calculator<Likelihood>, Parameters, String, Adapter, Alignment) - Constructor for class ModelTest.TestInstance
-
Creates a named instance.
- TimePassed - Class in Utils
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A class to check whether a set amount of time has passed.
- TimePassed(int, TimeUnit) - Constructor for class Utils.TimePassed
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Default constructor.
- toDouble() - Method in interface Maths.Real
-
Returns this real as a double.
- toDouble() - Method in class Maths.SmallDouble
-
- toDouble() - Method in class Maths.StandardDouble
-
- toFile(File) - Method in class Parameters.Parameters
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Writes the parameter values to a file.
- toFile(File, double) - Method in class Parameters.Parameters
-
Writes the parameter values to a file and writes a line labeled likelihood
and which gives the likelihood given as input.
- toFile(File) - Method in class Trees.Tree
-
Writes the tree to a file in Newick format.
- toFile(File, boolean) - Method in class Trees.Tree
-
Write the tree to a file in Newick format.
- toFilePAML(File) - Method in class Trees.Tree
-
Writes the tree to a file with taxa names limited to 25 characters
for use in PAML.
- toSmallDouble() - Method in interface Maths.Real
-
Returns this real as a SmallDouble
- toSmallDouble() - Method in class Maths.SmallDouble
-
- toSmallDouble() - Method in class Maths.StandardDouble
-
- toString() - Method in class Alignments.Site
-
- toString() - Method in class Alignments.UniqueSite
-
- toString() - Method in exception Exceptions.GeneralException
-
- toString() - Method in class Likelihood.Likelihood
-
- toString() - Method in class Likelihood.SiteLikelihood.NodeLikelihood
-
- toString() - Method in class Likelihood.SiteLikelihood.RateLikelihood
-
- toString() - Method in class Likelihood.SiteLikelihood
-
- toString() - Method in class Maths.SmallDouble
-
- toString() - Method in class Maths.SquareMatrix
-
- toString() - Method in class Maths.StandardDouble
-
- toString() - Method in class Models.RateCategory
-
- toString() - Method in class Parameters.Parameter
-
- toString() - Method in class Parameters.Parameters
-
- toString(boolean) - Method in class Parameters.Parameters
-
Returns a string representation of the parameters
- toString() - Method in class Trees.Branch
-
- toString() - Method in class Trees.Split
-
- toString() - Method in class Trees.Tree
-
- toString(boolean) - Method in class Trees.Tree
-
Returns a textual representation of the tree in Newick format
- toString() - Method in class Utils.SetSettings
-
- transpose() - Method in class Maths.SquareMatrix
-
Transposes the matrix and returns a new matrix as the result
- transpose(double[][]) - Static method in class Utils.Array2D
-
Transposes the array
- Tree - Class in Trees
-
Represents a phylogenetic tree.
- Tree(List<Branch>) - Constructor for class Trees.Tree
-
Creates a tree from a list of branches
- Tree(Tree, Parameters) - Constructor for class Trees.Tree
-
Duplicates a tree topology while replacing branch lengths using
the appropriate parameter
- TreeException - Exception in Trees
-
Exception thrown when there is a problem with a tree
- TreeException(String) - Constructor for exception Trees.TreeException
-
Default constructor
- TreeFigure - Class in Trees
-
Class for visualising trees.
- TreeFigure(Tree) - Constructor for class Trees.TreeFigure
-
Constructor
- Trees - package Trees
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Provides classes to define a tree.