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T

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
Represents a particular instance (calculator and parameters) to be tested to find the best performing.
TestInstance(Calculator<Likelihood>, Parameters) - Constructor for class ModelTest.TestInstance
Creates an instance
TestInstance(Calculator<Likelihood>, Parameters, String) - Constructor for class ModelTest.TestInstance
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
A class to check whether a set amount of time has passed.
TimePassed(int, TimeUnit) - Constructor for class Utils.TimePassed
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
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
Provides classes to define a tree.
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