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

A

a1 - Variable in class statalign.postprocess.plugins.contree.hash.HashUtils

a2 - Variable in class statalign.postprocess.plugins.contree.hash.HashUtils

AboutDlg - Class in statalign.ui

AboutDlg(JFrame) - Constructor for class statalign.ui.AboutDlg

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

acceptable(RawSequences) - Method in class statalign.model.subst.plugins.AminoAcidModel

This function decides if the model can accept the input sequences.

acceptable(RawSequences) - Method in class statalign.model.subst.plugins.NucleotideModel

This function decides if this model can analyze input sequences.

acceptable(RawSequences) - Method in class statalign.model.subst.SubstitutionModel

If a model cannot accept the currently loaded sequences (for example, because the sequences contains a character that is not part of the model) then it returns a negative number.

acceptAllDuringFirstHalfBurnin - Variable in class statalign.mcmc.McmcMove

acceptanceCount - Variable in class statalign.mcmc.McmcMove

acceptanceDecision(double, double, double, boolean) - Method in class statalign.base.Mcmc

acceptanceRate() - Method in class statalign.mcmc.McmcMove

acceptanceRate - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters.PlottableParameter

accepted - Variable in class statalign.base.McmcStep

true if this step was accepted

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

actionPerformed(ActionEvent) - Method in class statalign.postprocess.gui.InputGUI

Handles removing sequences.

actionPerformed(ActionEvent) - Method in class statalign.ui.ErrorMessage

This function is for closing the window

actionPerformed(ActionEvent) - Method in class statalign.ui.HelpWindow

An Actionlistener is implemented, so must implement this method

actionPerformed(ActionEvent) - Method in class statalign.ui.MainFrame

An ActioListener is implemented, so we have to implement this function.

actionPerformed(ActionEvent) - Method in class statalign.ui.McmcSettingsDlg

This is inherited from the ActionListener interface.

actionPerformed(ActionEvent) - Method in class statalign.ui.OutputPreferences

actionPerformed(ActionEvent) - Method in class statalign.ui.RNASettingsDlg

This is inherited from the ActionListener interface.

active - Variable in class statalign.postprocess.Postprocess

True if plugin is active (must produce its output) either because other plugins depend on it or because it is selected

add(String, String) - Method in class statalign.io.RawSequences

Add a name and a sequence, that belong together.

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

addAlignSeqsToTree(Tree, String[], String[], SubstitutionModel, String) - Method in class statalign.base.TreeAlgo

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

Adds a child to this tree's list of children.

addChildMove(ContinuousPositiveStructAlignMove) - Method in class statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove

addData(double) - Method in class statalign.utils.SimpleStats

addData(double[]) - Method in class statalign.utils.SimpleStats

addData(int[]) - Method in class statalign.utils.SimpleStats

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

addEdgeLength(double[][], int[], double) - Method in class statalign.model.ext.plugins.StructAlign

addMcmcMove(McmcMove, int) - Method in class statalign.mcmc.McmcModule

addMcmcMove(McmcMove, int, int) - Method in class statalign.mcmc.McmcModule

addNewTree(TreeNode) - Method in class statalign.postprocess.plugins.contree.CTMain

Add a new tree to the hash table

addOrReplace(String, String) - Method in class statalign.io.RawSequences

addParent(HierarchicalContinuousPositiveStructAlignMove) - Method in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

addProperty(String, Object) - Method in class statalign.postprocess.plugins.TreeNode

Adds a key=value property to be associated with this node.

addSequences() - Method in class statalign.ui.MainFrame

addTestSplit(BitSet) - Method in class statalign.postprocess.plugins.contree.CTMain

FOR TESTING ONLY Add a single split to the hash table

addTestTree(ArrayList<BitSet>) - Method in class statalign.postprocess.plugins.contree.CTMain

FOR TESTING ONLY Add a tree to the hash table

addToFilenameExtension(String) - Method in class statalign.model.ext.ModelExtension

addToFilenameExtension(String) - Method in class statalign.model.ext.ModelExtManager

AddToPaths(CNetworkPath, ArrayList<CNetworkNode>) - Method in class statalign.postprocess.plugins.contree.CNetworkNode

Add a path to the node path list..

addTrack(Track) - Method in class statalign.postprocess.Postprocess

NB because the track is added as a Pair, it will be passed by reference, which allows it to be modified from the place where it was added, i.e.

afterAlignChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.ModelExtension

Called after an alignment change proposal (accepted or rejected).

afterAlignChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.ModelExtManager

afterAlignChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.plugins.StructAlign

afterContinuousParamChange(Tree, boolean) - Method in class statalign.model.ext.plugins.StructAlign

afterEdgeLenChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.ModelExtension

Called after a proposed edge length change (accepted or rejected).

afterEdgeLenChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.ModelExtManager

afterEdgeLenChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.plugins.StructAlign

afterFirstHalfBurnin() - Method in class statalign.base.mcmc.AlignmentMove

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

afterFirstHalfBurnin() - Method in class statalign.mcmc.McmcMove

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

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

afterFirstHalfBurnin() - Method in class statalign.model.ext.plugins.structalign.AlignmentMove

afterIndelParamChange(Tree, Hmm, McmcMove, boolean) - Method in class statalign.model.ext.ModelExtension

Called after a proposed indel parameter change (accepted or rejected).

afterIndelParamChange(Tree, Hmm, McmcMove, boolean) - Method in class statalign.model.ext.ModelExtManager

afterLastSample() - Method in class statalign.base.Input

This is an empty function.

afterLastSample() - Method in class statalign.postprocess.plugins.ConsensusNetwork

Empty function, since there is nothing to do after the last sample in this postprocess thread.

afterLastSample() - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

afterLastSample() - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

afterLastSample() - Method in class statalign.postprocess.plugins.Entropy

It writes the sampled loglikelihood values into a separate file.

afterLastSample() - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

It writes the sampled loglikelihood values into a separate file.

afterLastSample() - Method in class statalign.postprocess.plugins.MpdAlignment

afterLastSample() - Method in class statalign.postprocess.plugins.PPFold

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

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

afterLastSample() - Method in class statalign.postprocess.plugins.Structure

afterLastSample() - Method in class statalign.postprocess.plugins.VisualDistance

afterLastSample() - Method in class statalign.postprocess.Postprocess

This function is called after the MCMC runs.

afterLastSample() - Method in class statalign.postprocess.PostprocessManager

It is called after the last sample of MCMC.

afterModExtParamChange(Tree, ModelExtension, boolean) - Method in class statalign.model.ext.ModelExtension

Called after a proposed model extension parameter change (accepted or rejected).

afterModExtParamChange(Tree, boolean) - Method in class statalign.model.ext.ModelExtManager

afterMove(Object) - Method in class statalign.base.mcmc.AlignmentMove

afterMove(Object) - Method in class statalign.base.mcmc.AllEdgeMove

afterMove(Object) - Method in class statalign.base.mcmc.EdgeMove

afterMove(Object) - Method in class statalign.base.mcmc.IndelMove

afterMove(Object) - Method in class statalign.base.mcmc.LOCALTopologyMove

afterMove(Object) - Method in class statalign.base.mcmc.SilentIndelMove

afterMove(Object) - Method in class statalign.base.mcmc.SubstMove

afterMove(Object) - Method in class statalign.base.mcmc.TopologyMove

afterMove(Object) - Method in class statalign.mcmc.McmcCombinationMove

afterMove(Object) - Method in class statalign.mcmc.McmcMove

afterMove(Object) - Method in class statalign.model.ext.plugins.structalign.AlignmentMove

afterMove(Object) - Method in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

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

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

afterSubstParamChange(Tree, SubstitutionModel, int, boolean) - Method in class statalign.model.ext.ModelExtension

Called after a proposed indel parameter change (accepted or rejected).

afterSubstParamChange(Tree, SubstitutionModel, int, boolean) - Method in class statalign.model.ext.ModelExtManager

afterTreeChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.ModelExtension

Called after a proposed topology change (accepted or rejected).

afterTreeChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.ModelExtManager

afterTreeChange(Tree, Vertex, boolean) - Method in class statalign.model.ext.plugins.StructAlign

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

align - Variable in class statalign.base.State

Alignment: for each sequence and each character in the sequence the index of the ancestral character that it is aligned to, or -i-1 if it is not homologous to any character in the ancestor (gap) and the next character in the ancestor sequence (to the right) has index i

AlignColumn - Class in statalign.base

An AlignColumn is an object that represents an observed or a hidden character and stores a double array storing the Felsenstein likelihoods.

AlignColumn(Vertex) - Constructor for class statalign.base.AlignColumn

It constructs a new AlignColumn.

AlignColumn(AlignColumn, boolean) - Constructor for class statalign.base.AlignColumn

It creates a new AlignColumn, chains it to the next column (namely, it is used to generate a new ancestral sequence built in a traceback phase of a dynamic programming).

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

aligned - Variable in class statalign.base.AlignColumn

Vector indicating which characters are aligned to this column at the leaves below.

alignedUpp - Variable in class statalign.base.AlignColumn

Vector indicating which characters are aligned to the parent of this column.

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

The alignment that is written onto the screen is stored in this array

AlignmentGUI - Class in statalign.postprocess.gui

This is the graphical interface for showing alignments.

AlignmentGUI(String, SubstitutionModel) - Constructor for class statalign.postprocess.gui.AlignmentGUI

It initializes a new panel for alignments.

AlignmentGUI(String, SubstitutionModel, Postprocess) - Constructor for class statalign.postprocess.gui.AlignmentGUI

It initializes a new panel for alignments.

AlignmentMove - Class in statalign.base.mcmc

AlignmentMove(McmcModule, double, String) - Constructor for class statalign.base.mcmc.AlignmentMove

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

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

AlignmentSample - Class in statalign.distance

AlignmentSample() - Constructor for class statalign.distance.AlignmentSample

AlignmentSample - Class in statalign.postprocess.plugins.benchmarks

AlignmentSample() - Constructor for class statalign.postprocess.plugins.benchmarks.AlignmentSample

alignmentTransformation(String[], String[], String, InputData) - Static method in class statalign.base.Utils

Transforms an alignment into the prescribed format

alignmentType - Variable in class statalign.postprocess.Postprocess

This string tells the alignment type in which alignment must be presented

alignmentTypes - Static variable in class statalign.base.MainManager

Alignment formats in which StatAlign can generate output Implemented formats currently are StatAlign (our own format), Clustal, Fasta, Phylip, Nexus

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

Restores all the changes an alignment resampling on the currently selected subtree has produced.

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

AllEdgeMove - Class in statalign.base.mcmc

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

allowed - Static variable in class statalign.postprocess.plugins.Entropy

allowSpikeSelection() - Method in class statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove

allowVersionCheck - Static variable in class statalign.StatAlign

alphabet - Variable in class statalign.io.RawSequences

Sorted string of characters present in sequences.

alphabet - Variable in class statalign.model.subst.SubstitutionModel

This array contains the potential characters of the alphabet.

AMA(String[], String[]) - Static method in class statalign.distance.Distance

The same as Distance.AMA(ArrayList, ArrayList) but here you can use arrays instead of lists

AMA(ArrayList<String>, ArrayList<String>) - Static method in class statalign.distance.Distance

Does the same as the Distance.distance(ArrayList, ArrayList) but outputs a more meaningful number since it is between 0 and 1. 1 means we have the same alignments while 0 means they are as distance as possible.

amaScoreToDistance(ArrayList<String>, double) - Static method in class statalign.distance.Distance

Given a set of sequences and an AMA score, returns the corresponding distance.

AminoAcidModel - Class in statalign.model.subst.plugins

Common superclass for amino acid substitution models.

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

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

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

Starting value for rotation proposal tuning parameter.

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

Rotation angle for each protein along the rotation axis

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

appendAlignment(String, String[][], File, boolean) - Static method in class statalign.postprocess.plugins.PPFold

appendFolds(File, String, String, int[], int[], boolean) - Static method in class statalign.postprocess.plugins.PPFold

attachedScoringScheme - Variable in class statalign.model.subst.SubstitutionModel

This scoring scheme is used for constructing an initial tree.

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

automatedTest2() - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

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

AutomateParameters - Class in statalign.base

A class that contains the logic when to stop the burn-in, sampling, or how to determine the sampling rate.

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

autoTunable - Variable in class statalign.base.mcmc.AlignmentMove

autoTune - Variable in class statalign.mcmc.McmcMove

auxData - Variable in class statalign.base.InputData

Non-sequence type auxiliary data that has been loaded, can be used by model extension plugins

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

Axis of rotation for each sequence