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

R

randomisationPeriod - Variable in class statalign.base.MCMCPars

Length of the period in which the MCMC chain should be allowed to drift randomly, with all moves accepted, before starting the burnin.

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

RawSequences - Class in statalign.io

Dynamic array of raw sequence data.

RawSequences() - Constructor for class statalign.io.RawSequences

RawSequences(String, String) - Constructor for class statalign.io.RawSequences

read(File) - Method in class statalign.io.DataManager

Tries to read file using all available input plugins.

read(File) - Method in class statalign.io.input.DataReader

read(String) - Method in class statalign.io.input.DataReader

read(Reader) - Method in class statalign.io.input.DataReader

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

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

Reads the contents (aligned/non-aligned sequences) of the given data source in Fasta format.

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

Parses tree.

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

readAllSamples(String) - Static method in class statalign.postprocess.plugins.PPFold

readDbl() - Method in class statalign.io.input.FileTokenReader

Reads the next token and tries to interpret it as a double value.

readInt() - Method in class statalign.io.input.FileTokenReader

Reads the next token and tries to interpret it as an integer value.

readStr() - Method in class statalign.io.input.FileTokenReader

Reads the next token and returns it as a String.

readTreesFromFile(String, int) - Static method in class statalign.postprocess.plugins.contree.CTMain

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

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

realignToParent(boolean) - Method in class statalign.base.Vertex

realignToParent(boolean, double) - Method in class statalign.base.Vertex

Samples a new alignment between the subtree rooted at this vertex and the rest of the sequences.

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

RecognitionError - Error in statalign.model.subst

An error message that is thrown if a model cannot accept a set of sequences.

RecognitionError(String) - Constructor for error statalign.model.subst.RecognitionError

Trivial constructor, it sets the message

recomputeCheckLogLike() - Method in class statalign.base.Tree

Recomputes the likelihood from scratch and checks whether everything was correct before.

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

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

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

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

recursivelyUpdateHmm2Matrices() - Method in class statalign.base.Vertex

recursivelyUpdateHmm3Matrices() - Method in class statalign.base.Vertex

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

redraw() - Method in class statalign.postprocess.gui.CNetworkView

It draws the network from our arrays to the correct size

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

It draws the network from our arrays to the correct size

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

refreshGUI() - Method in class statalign.postprocess.TreeVisualizer

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

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

refToDependences(Postprocess[]) - Method in class statalign.postprocess.plugins.Entropy

refToDependences(Postprocess[]) - Method in class statalign.postprocess.plugins.MpdAlignment

refToDependences(Postprocess[]) - Method in class statalign.postprocess.plugins.PPFold

refToDependences(Postprocess[]) - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

refToDependences(Postprocess[]) - Method in class statalign.postprocess.plugins.Structure

refToDependences(Postprocess[]) - Method in class statalign.postprocess.plugins.VisualDistance

refToDependences(Postprocess[]) - Method in class statalign.postprocess.Postprocess

Override this to get access to instances of the plugins your plugin depends on.

reliablityScore - Variable in class statalign.postprocess.plugins.RNAalifoldResult

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

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

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

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

Reinitializes panel to accommodate a new GUI

remove(int) - Method in class statalign.io.RawSequences

Removes a sequence and its name.

removeByName(String) - Method in class statalign.io.RawSequences

Removes a sequence and its name (given by name).

removeDataAssociatedWith(String) - Method in class statalign.base.Tree

removeDataAssociatedWith(String) - Method in interface statalign.io.DataType

removeDataAssociatedWith(String) - Method in class statalign.io.ProteinSkeletons

removeDataAssociatedWith(String) - Method in class statalign.io.RawSequences

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

Removes all gaps from each sequence.

removeParameter(String) - Method in class statalign.postprocess.PluginParameters

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

Reorders this path

repeatedString(String, int) - Static method in class statalign.base.Utils

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

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

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

restoreFiveWay(boolean) - Method in class statalign.base.Vertex

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

Empty method provided for models with no parameters (the evolutionary time is represented in the edge lengths).

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

Empty function (no model parameters)

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

restore the parameters to the old values when a parameter-changing proposal is not accepted.

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

Restores state just before the call of sampleParameter

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

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

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

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

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

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

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

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

restoreState(Object) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

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

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

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

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

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

restoreState(Object) - Method in class statalign.model.ext.plugins.structalign.RotationOrTranslationMove

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

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

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

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

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

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

Resumes execution of this thread if it has been previously paused by pauseSoft().

returnAngle(double) - Method in class statalign.postprocess.plugins.contree.CNetworkNode

Return an angle that is in the range 0 to 2*pi....

Reversed<T> - Class in statalign.utils

Reversed(List<T>) - Constructor for class statalign.utils.Reversed

reversed(List<T>) - Static method in class statalign.utils.Reversed

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

ReversibleNucleotide - Class in statalign.model.subst.plugins

This class implements the general time reversible parameter model.

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

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

RhoMove - Class in statalign.base.mcmc

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

right - Variable in class statalign.base.AlignColumn

This reference points to the right child of this Aligncolumn

right - Variable in class statalign.base.State

Tree representation: right descendant of each node (first nl are leaves), -1 for none

right - Variable in class statalign.base.Vertex

This reference points to the right child of the vertex.

RMove - Class in statalign.base.mcmc

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

RmsdTrace - Class in statalign.postprocess.plugins.structalign

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

RNAAliFold - Class in statalign.model.ext.plugins

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

RNAalifold - Class in statalign.postprocess.utils

Given an alignment of sequence this class shells to the RNAalifold appropriately and returns a RNAalifold secondary structure prediction.

RNAalifold() - Constructor for class statalign.postprocess.utils.RNAalifold

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

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

RNAalifoldResult - Class in statalign.postprocess.plugins

A class for storing an RNAalifoldResult.

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

rnaAssociated - Variable in class statalign.postprocess.Postprocess

True if it should show only when running an RNA/DNA file

rnaButton - Variable in class statalign.ui.MainFrame

RNAFoldingTools - Class in statalign.postprocess.utils

RNAFoldingTools() - Constructor for class statalign.postprocess.utils.RNAFoldingTools

RNAFoldingTools.MultiThreadedPosteriorDecoding - Class in statalign.postprocess.utils

A class, which given a base-pairing probability matrix and an array representing the probabilities of a single nucleotides being unpaired, performs a multi-threaded posterior-decoding and returns the MPD consensus structure.

RNAFoldingTools.MultiThreadedPosteriorDecoding(double[][], double[]) - Constructor for class statalign.postprocess.utils.RNAFoldingTools.MultiThreadedPosteriorDecoding

rnaMode - Static variable in class statalign.postprocess.PostprocessManager

RNASettingsDlg - Class in statalign.ui

This is the dialog window where users can set MCMC parameters.

root - Variable in class statalign.base.State

Root node of the tree

root - Variable in class statalign.base.Tree

The root of the tree

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

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

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

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

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

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

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

Alpha-C atomic coordinates under the current set of rotations/translations

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

independence rotation proposal distribution

rowSequences() - Method in class statalign.base.Tree

It generates the array of row sequences.

RtREV - Class in statalign.model.subst.plugins

Implements the retrovirus substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/12165843

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

Constructor used when instantiation is necessary.

run() - Method in class statalign.base.thread.MainThread

Start background MCMC calculation.