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

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IDLE_STATUS_MESSAGE - Static variable in class statalign.ui.MainFrame

ignoreNode - Variable in class statalign.postprocess.plugins.TreeNode

IllegalFormatException - Exception in statalign.io.input

IllegalFormatException() - Constructor for exception statalign.io.input.IllegalFormatException

IllegalFormatException(String) - Constructor for exception statalign.io.input.IllegalFormatException

incrementCountMatrix(double[][], List<Integer>) - Static method in class statalign.postprocess.plugins.PPFold

incrementWeights() - Method in class statalign.mcmc.McmcModule

incrementWeights() - Method in class statalign.model.ext.ModelExtManager

indelLogLike - Variable in class statalign.base.Vertex

The log-sum of the cumulative insertion-deletion loglikelihoods up to this vertex (ie. summed over the subtree below this vertex.).

IndelMove - Class in statalign.base.mcmc

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

indelParams - Variable in class statalign.base.State

Indel model parameters (in the order: R, lambda, mu)

index - Variable in class statalign.base.Vertex

Index of this vertex in the Tree.vertex array

init(ArrayList<String>) - Method in class statalign.base.MainManager

Initialises submanagers after the command line has been processed.

init() - Method in class statalign.io.DataManager

init() - Method in class statalign.model.ext.ModelExtension

Called during StatAlign startup, after all ModelExtension plugins have been loaded and command line arguments have been processed (if present).

init(ArrayList<String>) - Method in class statalign.model.ext.ModelExtManager

Discovers model extension plugins and initialises them.

init() - Method in class statalign.model.ext.plugins.RNAAliFold

init() - Method in class statalign.model.ext.plugins.StructAlign

init(ModelExtManager) - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

init(ModelExtManager) - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

init(ModelExtManager) - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

init(ModelExtManager) - Method in class statalign.postprocess.plugins.structalign.StructTrace

init(ModelExtManager) - Method in class statalign.postprocess.plugins.Structure

init(ModelExtManager) - Method in class statalign.postprocess.Postprocess

Called by PostprocessManager after setting the Postprocess.show field to allow initialisation, possibly involving GUI (toolbar etc.)

init(ModelExtManager) - Method in class statalign.postprocess.PostprocessManager

init(TreeView[]) - Method in class statalign.postprocess.TreeVisualizer

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

FOR TESTING ONLY Function called to initialise the Network Tester hash table & rest of CTMain

initialize(TreeNode, int) - Method in class statalign.postprocess.plugins.contree.CTMain

Initialise a CTMain before usage with a first tree, going through and setting up the hash table etc.

initialize(int, int, int, long) - Method in class statalign.postprocess.plugins.contree.hash.HashUtils

Initializes the hash utilities.

initLSRotations(Tree, double[][][], double[][], double[][], double[]) - Static method in class statalign.model.ext.plugins.structalign.Funcs

initRun(InputData) - Method in class statalign.model.ext.ModelExtension

Called during the initialisation of a run if plugin is active.

initRun(InputData) - Method in class statalign.model.ext.ModelExtManager

Determines the list of active ModelExtension plugins.

initRun(InputData) - Method in class statalign.model.ext.plugins.StructAlign

Input - Class in statalign.base

This class is an extension of the Postprocess class and is for showing the actual input sequences.

Input(MainManager) - Constructor for class statalign.base.Input

A trivial constructor.

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

InputData - Class in statalign.base

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

inputData - Variable in class statalign.base.MainManager

Reference to all input data required to run StatAlign

inputgui - Variable in class statalign.base.Input

this is the graphical interface

inputgui - Variable in class statalign.base.MainManager

The graphical interface of the Input panel

InputGUI - Class in statalign.postprocess.gui

This is the graphical interface for showing the input data

InputGUI(MainManager) - Constructor for class statalign.postprocess.gui.InputGUI

This constructor makes an initial GUI for showing the input sequences and their names.

InputReader - Class in statalign.io.input

Deprecated class for testing purposes.

InputReader() - Constructor for class statalign.io.input.InputReader

insertSilentIndel() - Method in class statalign.base.Vertex

insertSilentIndel(AlignColumn) - Method in class statalign.base.Vertex

insertSilentIndelBlock(AlignColumn) - Method in class statalign.base.Vertex

InverseGammaPrior - Class in statalign.mcmc

InverseGammaPrior(double, double) - Constructor for class statalign.mcmc.InverseGammaPrior

IQR(ArrayList<Double>) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Calculates the Interquartile Range from a given list of values.

isActive() - Method in class statalign.model.ext.ModelExtension

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

isBurnin - Variable in class statalign.base.State

true if this state comes from the burnin.

isCompatible(CNetworkSplit, int) - Method in class statalign.postprocess.plugins.contree.CNetworkSplit

Compares an input split to see if it is compatible with this one.

isFirstHalfBurnin() - Method in class statalign.mcmc.McmcModule

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

Determines whether this node is a leaf or not.

isMajority - Variable in class statalign.postprocess.plugins.contree.Cluster

isMajority - Variable in class statalign.postprocess.plugins.contree.hash.HashEntry

If this is a majority partition this will be set to true, otherwise false.

isMaster(int) - Static method in class statalign.MPIUtils

Determines if a process with a certain rank is the master.

isParallel - Variable in class statalign.base.InputData

Are we using the parallel version?

isParamChangeAccepted(double, McmcMove) - Method in class statalign.base.Mcmc

This function is called by the McmcMove objects in order to determine whether the proposed moves are to be accepted.

isParamChangeAccepted(double, McmcMove) - Method in class statalign.mcmc.McmcModule

isParamChangeAccepted(double) - Method in class statalign.mcmc.McmcMove

isParamChangeAccepted(double, McmcMove) - Method in class statalign.model.ext.ModelExtension

Should be called from McmcModule.proposeParamChange(Tree) to find out whether a proposed parameter change was accepted.

isParamChangeAccepted(double, McmcMove) - Method in class statalign.model.ext.ModelExtManager

isPlottable() - Method in class statalign.model.ext.plugins.structalign.StructAlignMoveParams

isPrime(long) - Static method in class statalign.postprocess.plugins.contree.hash.HashUtils

Determines if a number is a prime or not.

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

isRNAalignment(ArrayList<String>) - Static method in class statalign.postprocess.utils.RNAFoldingTools

isSelectable() - Method in class statalign.model.ext.ModelExtension

isSplitSide(CNetworkSplit, int) - Method in class statalign.postprocess.plugins.contree.CNetworkPath

This function sees if adjoining splits at the nodes at the path ends create subsets on both sides of the input split...

isSubset(CNetworkSplit, boolean, int) - Method in class statalign.postprocess.plugins.contree.CNetworkSplit

Compares an input split to see if the argument split is a subset of the specified side of this split?

isSupportConnected() - Method in class statalign.utils.BetaDistribution

The support of this distribution is connected.

isSupportConnected() - Method in class statalign.utils.GammaDistribution

The support of this distribution is connected.

isSupportConnected() - Method in class statalign.utils.NormalDistribution

The support of this distribution is connected.

isSupportLowerBoundInclusive() - Method in class statalign.utils.BetaDistribution

isSupportLowerBoundInclusive() - Method in class statalign.utils.GammaDistribution

isSupportLowerBoundInclusive() - Method in class statalign.utils.NormalDistribution

isSupportUpperBoundInclusive() - Method in class statalign.utils.BetaDistribution

isSupportUpperBoundInclusive() - Method in class statalign.utils.GammaDistribution

isSupportUpperBoundInclusive() - Method in class statalign.utils.NormalDistribution

isValidHistory(boolean, boolean, boolean[]) - Static method in class statalign.base.Utils

For a tree of the form: gg / g / \ p u / \ t b this function determines valid possible indel states for p and g given fixed states for the neighbouring nodes.

isValidHistory(boolean, boolean, boolean[], boolean) - Static method in class statalign.base.Utils

For a tree of the form: gg / g / \ p u / \ t b or, if gIsRoot = true, then for a tree of the form g / \ p u / \ t b this function determines valid possible indel states for p and g given fixed states for the neighbouring nodes.

isVerbose() - Method in class statalign.CommandLine

iterate(Enumeration<T>) - Static method in class statalign.base.Utils

Makes Enumeration iterable.

iterator() - Method in class statalign.utils.Reversed