A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

T

Tamura92 - Class in statalign.model.subst.plugins

This class implements the Tamura 1992 model.

Tamura92() - Constructor for class statalign.model.subst.plugins.Tamura92

This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.

TamuraNei - Class in statalign.model.subst.plugins

This class implements the Tamura-Nei parameter model.

TamuraNei() - Constructor for class statalign.model.subst.plugins.TamuraNei

This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.

tau - Variable in class statalign.model.ext.plugins.StructAlign

tauPrior - Variable in class statalign.model.ext.plugins.StructAlign

TaxaMap - Class in statalign.postprocess.plugins.contree

TaxaMap(int) - Constructor for class statalign.postprocess.plugins.contree.TaxaMap

TaxaMap() - Constructor for class statalign.postprocess.plugins.contree.TaxaMap

Taxaname - Variable in class statalign.postprocess.plugins.contree.CNetworkNode

TaxonRefToNode(int, CNetwork) - Method in class statalign.postprocess.plugins.contree.CTMain

Find the taxon node in the network.

test(String, String, int) - Method in class statalign.postprocess.plugins.contree.test.CorrectnessTester

test() - Method in class statalign.postprocess.utils.RNAFoldingTools

testData() - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

TestNetwork - Class in statalign.postprocess.plugins.contree.test

Creates trees that create a network that exhibits many incompatible splits in order to test the network drawing feature.

TestNetwork() - Constructor for class statalign.postprocess.plugins.contree.test.TestNetwork

TestNetwork() - Method in class statalign.postprocess.plugins.contree.test.TestNetwork

Creates the test network by creating trees and storing them in the hash table using test functions in CTMain, running the consensus tree and network creating algorithms and then outputting the network in a window.

testTrees(String, String) - Method in class statalign.postprocess.plugins.contree.test.CorrectnessTester

testVariation() - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

testVariation2() - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

TextDlg - Class in statalign.ui

TextDlg(String, String) - Constructor for class statalign.ui.TextDlg

ThetaMove - Class in statalign.base.mcmc

ThetaMove(McmcModule, PriorDistribution<Double>, ProposalDistribution<Double>, String) - Constructor for class statalign.base.mcmc.ThetaMove

thread - Variable in class statalign.base.MainManager

Main (background) calculation thread of the application

title - Variable in class statalign.base.InputData

The file name (without path) that is chosen to be the base name for all output files, plugins will define their own output file names by adding extensions to this base name.

title - Variable in class statalign.base.Tree

The name of the tree

title - Variable in class statalign.postprocess.gui.AlignmentGUI

The title of the current analysis

title - Variable in class statalign.postprocess.gui.DistanceGUI

title - Variable in class statalign.postprocess.gui.EntropyGUI

title - Variable in class statalign.postprocess.gui.PPFoldGUI

title - Variable in class statalign.postprocess.gui.StructureGUI

title - Variable in class statalign.postprocess.plugins.benchmarks.Dataset

title - Variable in class statalign.postprocess.plugins.CurrentAlignment

title - Variable in class statalign.postprocess.plugins.Entropy

title - Variable in class statalign.postprocess.plugins.MpdAlignment

title - Variable in class statalign.postprocess.plugins.PPFold

title - Variable in class statalign.postprocess.plugins.Structure

Postprocess which handles the consensus structure generated by PPFold.

title - Variable in class statalign.postprocess.plugins.VisualDistance

TITLE_X - Static variable in class statalign.postprocess.gui.DistanceGUI

TITLE_X - Static variable in class statalign.postprocess.gui.EntropyGUI

TITLE_Y - Static variable in class statalign.postprocess.gui.DistanceGUI

TITLE_Y - Static variable in class statalign.postprocess.gui.EntropyGUI

toArray(E[]) - Method in class statalign.base.CircularArray

Copies contents of this CircularArray to a regular array.

toolBar - Variable in class statalign.ui.MainFrame

topologyChangeAcceptanceCount - Variable in class statalign.base.mcmc.TopologyMove

TopologyMove - Class in statalign.base.mcmc

TopologyMove(McmcModule, PriorDistribution<Double>, double, double, String) - Constructor for class statalign.base.mcmc.TopologyMove

toString() - Method in class statalign.distance.AlignmentSample

toString() - Method in class statalign.distance.Pair

toString() - Method in class statalign.io.input.DataReader

toString() - Method in class statalign.io.RawSequences

toString() - Method in class statalign.postprocess.gui.ColorGradient

toString() - Method in class statalign.postprocess.plugins.benchmarks.AlignmentSample

toString() - Method in class statalign.postprocess.plugins.benchmarks.ExperimentalData

toString() - Method in class statalign.postprocess.plugins.contree.CTree

toString() - Method in class statalign.postprocess.plugins.TreeNode

Constructs a Newick string from this subtree.

toString() - Method in class statalign.utils.SimpleStats

totalLogLike(Tree) - Method in class statalign.model.ext.ModelExtManager

Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.

totalLogPrior(Tree) - Method in class statalign.base.mcmc.CoreMcmcModule

totalLogPrior(Tree) - Method in class statalign.model.ext.ModelExtManager

Calculates the log of total prior probability by including contributions from model extension plugins.

traceBack(int[][], int, int, int[]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

Track - Class in statalign.postprocess

Track(Color, double[]) - Constructor for class statalign.postprocess.Track

Track(Color, double[], double, double, double) - Constructor for class statalign.postprocess.Track

Transformation - Class in statalign.model.ext.plugins.structalign

TranslationMove - Class in statalign.model.ext.plugins.structalign

TranslationMove(StructAlign, String) - Constructor for class statalign.model.ext.plugins.structalign.TranslationMove

tree - Variable in class statalign.base.InputData

The initial tree, if given, which is optionally fixed for the whole analysis

tree - Variable in class statalign.base.Mcmc

Current tree in the MCMC chain.

Tree - Class in statalign.base

This is the current tree in the MCMC run.

Tree() - Constructor for class statalign.base.Tree

TreeAlgo - Class in statalign.base

TreeAlgo() - Constructor for class statalign.base.TreeAlgo

TreeAlgo(int, int) - Constructor for class statalign.base.TreeAlgo

TreeNode - Class in statalign.postprocess.plugins

TreeNode() - Constructor for class statalign.postprocess.plugins.TreeNode

A constructor which does not specify a name nor a edge length.

TreeNode(String) - Constructor for class statalign.postprocess.plugins.TreeNode

A constructor specifying the name of the node.

TreeNode(String, double) - Constructor for class statalign.postprocess.plugins.TreeNode

A constructor specifying the name and the edge length of the node.

TreeView - Class in statalign.postprocess.gui.treeviews

TreeView() - Constructor for class statalign.postprocess.gui.treeviews.TreeView

TreeVisualizer - Class in statalign.postprocess

type - Static variable in class statalign.model.subst.plugins.AminoAcidModel

type - Static variable in class statalign.model.subst.plugins.NucleotideModel

type - Static variable in class statalign.model.subst.SubstitutionModel

Tells whether your plugin is a nucleotide or protein model (or something else) when declared with the same name and type.