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

S

sample() - Method in class statalign.mcmc.GammaProposal

sample() - Method in class statalign.mcmc.GaussianProposal

sample() - Method in class statalign.mcmc.LogisticProposal

sample() - Method in class statalign.mcmc.MultiplicativeProposal

sample() - Method in class statalign.mcmc.ProposalDistribution

sample() - Method in class statalign.mcmc.UniformProposal

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

This implementation uses the following algorithms: For 0 < shape < 1:
Ahrens, J.

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

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

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

sampleEntropy - Variable in class statalign.postprocess.utils.EntropyContainer

sampleFrequencies(double[], double) - Static method in class statalign.model.subst.plugins.NucleotideModelUtils

Class method for sampling new equilibrium frequency parameter for one of the frequencies in f, where the maximum allowed change is dmax.

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

It does nothing and returns 0, i.e log-probability 1.

sampleParameter() - Method in class statalign.model.subst.plugins.Felsenstein81

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.plugins.Felsenstein84

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.plugins.HKY85

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.plugins.JukesCantor

It does nothing, and always return with 0, namely, log-probability 1.

sampleParameter() - Method in class statalign.model.subst.plugins.Kimura3

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.plugins.ReversibleNucleotide

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.plugins.Tamura92

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.plugins.TamuraNei

This function implements a proposal for new parameter values.

sampleParameter() - Method in class statalign.model.subst.SubstitutionModel

Abstract method to sample a new model parameter and update v,w,d,e accordingly.

sampleRates(double[], double) - Static method in class statalign.model.subst.plugins.NucleotideModelUtils

Class method for sampling new rate parameter for one of the rates in r, where the maximum allowed change is dmax.

samples - Variable in class statalign.postprocess.plugins.benchmarks.AlignmentSample

sampleVertex(Tree) - Static method in class statalign.model.ext.plugins.structalign.Funcs

sampling - Variable in class statalign.postprocess.Postprocess

True if it writes into the log file

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

sampRate - Variable in class statalign.base.MCMCPars

One sampling after each sampRate cycles

saveAsFasta(ExperimentalData, File) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

saveAsFasta(ArrayList<String>, ArrayList<String>, File) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Save a list of sequences and sequence names as a FASTA file.

saveClustalW(List<String>, List<String>, File) - Static method in class statalign.postprocess.utils.RNAalifold

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

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

saveDatasetResult(File) - Method in class statalign.postprocess.plugins.benchmarks.Dataset

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

saveOptions() - Method in class statalign.ui.RNASettingsDlg

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

saveScores(File, double, double) - Method in class statalign.postprocess.plugins.PPFold

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

scores - Variable in class statalign.postprocess.Track

screenable - Variable in class statalign.postprocess.Postprocess

True if it can generate a GUI.

scroll - Variable in class statalign.postprocess.gui.CNetworkView

scroll - Variable in class statalign.postprocess.gui.treeviews.NetworkTreeView

ScrollAdapter - Class in statalign.ui

sd - Variable in class statalign.model.ext.plugins.structalign.RotationProposal

seed - Variable in class statalign.base.MCMCPars

The seed for the random number generator

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

This function cuts out a window and realigns in the selected subtree.

selectBest(Transformation[], double) - Method in class statalign.model.ext.plugins.structalign.RotationProposal

selected - Variable in class statalign.base.Vertex

selected - Variable in class statalign.postprocess.Postprocess

True if plugin is selected in the menu (and thus a tab is created for the plugin in the main window that can be used to allow the user to change settings before MCMC start and to show runtime information afterwards)

selectReferenceSequence(InputData) - Method in class statalign.postprocess.plugins.PPFold

selectSubtree(double[], int) - Method in class statalign.base.Vertex

Selects a subtree

seq - Variable in class statalign.base.AlignColumn

This double array contains the Felsenstein Likelihoods

seq - Variable in class statalign.base.State

All sequences as strings, including most likely ancestral characters

seqs - Variable in class statalign.base.InputData

The input sequences, optionally aligned

seqs - Variable in class statalign.io.ProteinSkeletons

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

sequencesAreRemovable - Variable in class statalign.postprocess.gui.InputGUI

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

Overloading the sequenceSimilarityScore method so one can use arrays instead of lists

sequenceSimilarityScore(List<String>) - Static method in class statalign.distance.Distance

Calculates the similarity of the sequences.

set(double) - Method in interface statalign.mcmc.ParameterInterface

set(double) - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.EpsilonInterface

set(double) - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.NuInterface

set(double) - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2HInterface

set(double) - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2Interface

set(double) - Method in class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.TauInterface

setActive(boolean) - Method in class statalign.model.ext.ModelExtension

Enables or disables this plugin.

setActive(boolean) - Method in class statalign.model.ext.plugins.PPFold

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

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

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

setAllowedDim(int) - Method in class statalign.io.input.plugins.CoorReader

setAutomateBurnIn(boolean) - Static method in class statalign.base.AutomateParameters

setAutomateNumberOfSamples(boolean) - Static method in class statalign.base.AutomateParameters

setAutomateProposalVariances(boolean) - Static method in class statalign.base.AutomateParameters

setAutomateStepRate(boolean) - Static method in class statalign.base.AutomateParameters

setBaseFile(File) - Method in class statalign.base.InputData

Fills both InputData.outputPath and InputData.title.

setBaseFileName(String) - Method in class statalign.postprocess.PostprocessManager

setContents(double, double) - Method in class statalign.postprocess.utils.EntropyContainer

setEdgeLength(double) - Method in class statalign.base.Vertex

setEdges(double, double, double) - Method in class statalign.base.mcmc.LOCALTopologyMove

Sets the three edges affected by the LOCAL move (nephew, parent and uncle) to the specified values.

setEnabled(Container, boolean) - Method in class statalign.ui.RNASettingsDlg

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

setIdentifier(String) - Method in class statalign.postprocess.gui.treeviews.TreeView

setLogLike(double) - Method in class statalign.mcmc.McmcModule

setManager(ModelExtManager) - Method in class statalign.model.ext.ModelExtension

setMatrix(float[][]) - Method in class statalign.postprocess.gui.PPFoldGUI

setMatrix(float[][]) - Method in class statalign.postprocess.gui.StructureGUI

setMaxValue(double) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

setMcmc(Mcmc) - Method in class statalign.mcmc.McmcModule

setMcmc(Mcmc) - Method in class statalign.model.ext.ModelExtManager

setMinValue(double) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

setName(String) - Method in class statalign.utils.SimpleStats

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

This function is called when command line arguments are specified for a plugin.

setParam(String, boolean) - Method in class statalign.model.ext.ModelExtension

setParam(String, Number) - Method in class statalign.model.ext.ModelExtension

setParam(String, boolean) - Method in class statalign.model.ext.plugins.PPFold

setParam(String, boolean) - Method in class statalign.model.ext.plugins.RNAAliFold

setParam(String, String) - Method in class statalign.model.ext.plugins.RNAAliFold

setParam(double) - Method in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

setParam(String, String) - Method in class statalign.model.ext.plugins.StructAlign

setParam(String, Number) - Method in class statalign.model.ext.plugins.StructAlign

setParam(String, boolean) - Method in class statalign.model.ext.plugins.StructAlign

setParameter(String, String) - Method in class statalign.postprocess.PluginParameters

Given a parameter and a value, sets the corresponding parameter value.

setParent(JScrollPane) - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

setParent(JScrollPane) - Method in class statalign.postprocess.gui.treeviews.TreeView

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

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

setPrintRNA(boolean) - Method in class statalign.model.subst.plugins.NucleotideModel

Selects whether to print RNA nucleotides (U for T) or default DNA ones.

setProposalFlags(StructAlignTraceParameters) - Method in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters

setProposalParamMultiplier(double) - Method in class statalign.base.mcmc.AlignmentMove

setResPercentage(double) - Method in class statalign.postprocess.plugins.contree.CTMain

setSampling(boolean) - Method in class statalign.base.Input

This is an empty function.

setSampling(boolean) - Method in class statalign.postprocess.plugins.ConsensusNetwork

Toggles sampling mode.

setSampling(boolean) - Method in class statalign.postprocess.plugins.CurrentAlignment

Toggles sampling mode.

setSampling(boolean) - Method in class statalign.postprocess.plugins.Entropy

It switches on and off the sampling mode.

setSampling(boolean) - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

It switches on and off the sampling mode.

setSampling(boolean) - Method in class statalign.postprocess.plugins.MpdAlignment

setSampling(boolean) - Method in class statalign.postprocess.plugins.PPFold

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

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

setSampling(boolean) - Method in class statalign.postprocess.plugins.Structure

setSampling(boolean) - Method in class statalign.postprocess.plugins.VisualDistance

setSampling(boolean) - Method in class statalign.postprocess.Postprocess

This function switches on or off the sampling mode.

setSampling(boolean) - Method in class statalign.postprocess.TreeVisualizer

setScrollMultiplier(int) - Method in class statalign.ui.ScrollAdapter

setSeed(long) - Method in class statalign.postprocess.plugins.contree.CTMain

setSelected(boolean) - Method in class statalign.postprocess.Postprocess

setSeqs(RawSequences) - Method in class statalign.base.Tree

setSeqs(RawSequences) - Method in interface statalign.io.DataType

setSeqs(RawSequences) - Method in class statalign.io.ProteinSkeletons

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

setSpikeParams(double[]) - Method in class statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove

setVerbose(boolean) - Method in class statalign.CommandLine

setVisible(boolean) - Method in class statalign.ui.AboutDlg

setVisible(boolean) - Method in class statalign.ui.TextDlg

setWeight(String, int) - Method in class statalign.mcmc.McmcModule

setWindowDispose(Window) - Method in class statalign.ui.ScrollAdapter

SHAKE_IF_STUCK - Static variable in class statalign.base.Utils

If true then during the first half of the burnin if a particular McmcMove has been below its minimum acceptance rate for at least (LOW_COUNT_THRESHOLD * MIN_SAMPLES_FOR_ACC_ESTIMATE) iterations, then for the purposes of computing the acceptance ratio, we multiply the new log likelihood by LOW_COUNT_MULTIPLIER raised to a power that increases with the number of iterations beyond the threshold.

shift() - Method in class statalign.base.CircularArray

Retrieves the first element in the array (element with key startKey) and increases startKey.

shouldAutomateBurnIn() - Static method in class statalign.base.AutomateParameters

shouldAutomateNumberOfSamples() - Static method in class statalign.base.AutomateParameters

shouldAutomateProposalVariances() - Static method in class statalign.base.AutomateParameters

shouldAutomateStepRate() - Static method in class statalign.base.AutomateParameters

shouldStopBurnIn(ArrayList<Double>) - Static method in class statalign.base.AutomateParameters

If the logLikelihood has a major decline, we stop the burnin

shouldStopSampling(ArrayList<Double>) - Static method in class statalign.base.AutomateParameters

If the last element in the distances variable is larger than PERCENT_CONST we stop.

show - Variable in class statalign.postprocess.Postprocess

True if a GUI must be shown to the user.

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

Whether to plot the full alignment with internal nodes.

showPane(JFrame, String, String, boolean) - Static method in class statalign.ui.ErrorMessage

showPane(JFrame, Exception, boolean) - Static method in class statalign.ui.ErrorMessage

showPane(JFrame, String, boolean) - Static method in class statalign.ui.ErrorMessage

sigma2 - Variable in class statalign.model.ext.plugins.StructAlign

Parameters of structural drift

sigma2Hier - Variable in class statalign.model.ext.plugins.StructAlign

sigma2HPrior - Variable in class statalign.model.ext.plugins.StructAlign

sigma2Prior - Variable in class statalign.model.ext.plugins.StructAlign

SILENT_INSERT_PROB - Static variable in class statalign.base.Utils

SilentIndelMove - Class in statalign.base.mcmc

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

SimpleStats - Class in statalign.utils

Provides simple statistical information such as average and standard deviation for a set of values.

SimpleStats() - Constructor for class statalign.utils.SimpleStats

SimpleStats(String) - Constructor for class statalign.utils.SimpleStats

singleFilePrint(int, int) - Method in class statalign.postprocess.plugins.CurrentAlignment

Temporary fileprinting method to generate single files containing the current alignment.

singleMatrix - Static variable in class statalign.postprocess.plugins.Structure

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

Returns the number of sequences.

spaceAMA(ArrayList<String[]>) - Static method in class statalign.distance.Distance

Used when determining the step rate in the automation of the MCMC.

SPAN_MULTIPLIER - Static variable in class statalign.base.Utils

During the burnin, the proposalWidthControlVariable for all continuous parameters is adjusted in order to ensure that the average acceptance rate is between MIN_ACCEPTANCE and MAX_ACCEPTANCE where possible.

spanMultiplier - Variable in class statalign.mcmc.McmcMove

split - Variable in class statalign.postprocess.plugins.contree.CNetworkEdge

split - Variable in class statalign.postprocess.plugins.contree.CNetworkSplit

splits - Variable in class statalign.postprocess.plugins.contree.CNetwork

sqDistance(double[], double[]) - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

start() - Method in class statalign.base.MainManager

This function starts a new MCMC run.

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

startNode() - Method in class statalign.postprocess.plugins.contree.CNetworkPath

Returns the node at the start of the path

startParallel(int, int) - Method in class statalign.base.MainManager

statalign - package statalign

StatAlign - Class in statalign

The entry point of the application.

StatAlign() - Constructor for class statalign.StatAlign

statalign.base - package statalign.base

statalign.base.hmm - package statalign.base.hmm

statalign.base.mcmc - package statalign.base.mcmc

statalign.base.thread - package statalign.base.thread

statalign.distance - package statalign.distance

statalign.io - package statalign.io

statalign.io.input - package statalign.io.input

statalign.io.input.plugins - package statalign.io.input.plugins

statalign.mcmc - package statalign.mcmc

statalign.model.ext - package statalign.model.ext

statalign.model.ext.plugins - package statalign.model.ext.plugins

statalign.model.ext.plugins.structalign - package statalign.model.ext.plugins.structalign

statalign.model.score - package statalign.model.score

statalign.model.score.plugins - package statalign.model.score.plugins

statalign.model.subst - package statalign.model.subst

statalign.model.subst.plugins - package statalign.model.subst.plugins

statalign.postprocess - package statalign.postprocess

statalign.postprocess.gui - package statalign.postprocess.gui

statalign.postprocess.gui.treeviews - package statalign.postprocess.gui.treeviews

statalign.postprocess.plugins - package statalign.postprocess.plugins

statalign.postprocess.plugins.benchmarks - package statalign.postprocess.plugins.benchmarks

statalign.postprocess.plugins.contree - package statalign.postprocess.plugins.contree

statalign.postprocess.plugins.contree.hash - package statalign.postprocess.plugins.contree.hash

statalign.postprocess.plugins.contree.test - package statalign.postprocess.plugins.contree.test

statalign.postprocess.plugins.structalign - package statalign.postprocess.plugins.structalign

statalign.postprocess.utils - package statalign.postprocess.utils

statalign.ui - package statalign.ui

statalign.utils - package statalign.utils

StatAlignParallel - Class in statalign

StatAlignParallel() - Constructor for class statalign.StatAlignParallel

StatAlignResult - Class in statalign.postprocess.plugins.benchmarks

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

State - Class in statalign.base

Objects of this class completely describe the state of the MCMC at a certain time.

State(int) - Constructor for class statalign.base.State

Constructs a new State object, filling the given parameter and pre-allocating arrays (first dimensions only).

stateChanged(ChangeEvent) - Method in class statalign.ui.RNASettingsDlg

statusText - Variable in class statalign.ui.MainFrame

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

Calculates the standard deviation of a list of values.

stopNoWait() - Method in class statalign.base.thread.StoppableThread

Similar to stopSoft() but non-blocking, and also will not wake up this thread if it is suspended.

Stoppable - Class in statalign.base.thread

Ancestor for classes that can define potential "stopping points" in (some of) their methods when called from within a StoppableThread.

Stoppable() - Constructor for class statalign.base.thread.Stoppable

Default constructor.

stoppable() - Method in class statalign.base.thread.Stoppable

Should be called from methods of the descendant classes at points where execution is allowed to be stopped by an external thread (by calling the StoppableThread's stopSoft() method) If this happens, a StoppedException is thrown that can be caught at any point within the StoppableThread to do things up before exiting.

StoppableThread - Class in statalign.base.thread

Objects of this class can be used in place of a Thread object if it is intended that they can be stopped or suspended "softly" by an external thread.

StoppableThread() - Constructor for class statalign.base.thread.StoppableThread

StoppedException - Exception in statalign.base.thread

Exception to be thrown by StoppableThread's stoppable() method when termination of the thread has been previously requested by an external thread (by calling stopSoft()).

StoppedException() - Constructor for exception statalign.base.thread.StoppedException

stopSoft() - Method in class statalign.base.thread.StoppableThread

Can be called by an external thread to request termination of this thread.

StructAlign - Class in statalign.model.ext.plugins

StructAlign() - Constructor for class statalign.model.ext.plugins.StructAlign

structAlign - Variable in class statalign.postprocess.plugins.structalign.RmsdTrace

structAlign - Variable in class statalign.postprocess.plugins.structalign.StructTrace

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

StructAlignMoveParams() - Constructor for class statalign.model.ext.plugins.structalign.StructAlignMoveParams

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

StructAlignParameterInterface(StructAlign) - Constructor for class statalign.model.ext.plugins.structalign.StructAlignParameterInterface

StructAlignParameterInterface.EpsilonInterface - Class in statalign.model.ext.plugins.structalign

StructAlignParameterInterface.EpsilonInterface() - Constructor for class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.EpsilonInterface

StructAlignParameterInterface.NuInterface - Class in statalign.model.ext.plugins.structalign

StructAlignParameterInterface.NuInterface() - Constructor for class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.NuInterface

StructAlignParameterInterface.Sigma2HInterface - Class in statalign.model.ext.plugins.structalign

StructAlignParameterInterface.Sigma2HInterface() - Constructor for class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2HInterface

StructAlignParameterInterface.Sigma2Interface - Class in statalign.model.ext.plugins.structalign

StructAlignParameterInterface.Sigma2Interface(int) - Constructor for class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.Sigma2Interface

StructAlignParameterInterface.TauInterface - Class in statalign.model.ext.plugins.structalign

StructAlignParameterInterface.TauInterface() - Constructor for class statalign.model.ext.plugins.structalign.StructAlignParameterInterface.TauInterface

StructAlignTraceGUI - Class in statalign.postprocess.gui

This class implements the graphical interface for showing the trace plots for the StructAlign parameters.

StructAlignTraceGUI(JPanel, StructTrace) - Constructor for class statalign.postprocess.gui.StructAlignTraceGUI

Constructor to initialise the GUI for StructAlign trace

StructAlignTraceParameters - Class in statalign.postprocess.plugins.structalign

A container class that stores a parameter values from the StructAlign plugin and a logical value indicating whether the sample comes from the burn-in period or not.

StructAlignTraceParameters(StructTrace, boolean) - Constructor for class statalign.postprocess.plugins.structalign.StructAlignTraceParameters

StructAlignTraceParameters.PlottableParameter - Class in statalign.postprocess.plugins.structalign

StructTrace - Class in statalign.postprocess.plugins.structalign

StructTrace() - Constructor for class statalign.postprocess.plugins.structalign.StructTrace

Structure - Class in statalign.postprocess.plugins

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

StructureDetails - Class in statalign.postprocess.gui

StructureDetails() - Constructor for class statalign.postprocess.gui.StructureDetails

StructureGUI - Class in statalign.postprocess.gui

StructureGUI(String) - Constructor for class statalign.postprocess.gui.StructureGUI

substitutionModel - Variable in class statalign.base.Tree

Characters on this tree undergo substitutions according to this model.

SubstitutionModel - Class in statalign.model.subst

Superclass of the substitution models.

SubstitutionModel() - Constructor for class statalign.model.subst.SubstitutionModel

SubstitutionScore - Class in statalign.model.score

The ancestral class of substitution scores

SubstitutionScore() - Constructor for class statalign.model.score.SubstitutionScore

substModels - Variable in class statalign.base.MainManager

Array of substitution model classes that can be selected for an analysis.

SubstMove - Class in statalign.base.mcmc

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

substParams - Variable in class statalign.base.State

Substitution model parameters, as given by the substitution plugin

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

Subtree() - Constructor for class statalign.model.ext.plugins.structalign.Subtree

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

DataReader plugins must override this to return a list of supported file extensions.

supportedExtensions() - Method in class statalign.io.input.plugins.CoorReader

supportedExtensions() - Method in class statalign.io.input.plugins.FastaReader

supportedExtensions() - Method in class statalign.io.input.plugins.NewickReader

supportedExtensions() - Method in class statalign.io.input.plugins.PDBReader

suspendSoft() - Method in class statalign.base.thread.StoppableThread

Can be called by an external thread to request suspension of this thread.

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

Restores the exact state just before the call to Vertex.swapWithUncleAlignToParent().

swapRate - Variable in class statalign.base.MCMCPars

How often to propose swaps between chains (per cycle).

swapSeed - Variable in class statalign.base.MCMCPars

The swap seed for the swap random number generator.

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

Swaps this with its uncle, but proposes new alignments only between this node and its parent, and the uncle node and its parent, every other alignment is kept fixed.