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

C

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

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

Calculates Felsenstein and indel likelihoods up to root, starting from `parent'

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

calcDistanceMatrix(Vertex, double[][], boolean) - Method in class statalign.model.ext.plugins.StructAlign

recursive algorithm to traverse tree and calculate distance matrix between leaves

calcEmProb(double[], double[]) - Static method in class statalign.base.Utils

Calculates emission probability from Felsenstein likelihoods

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

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

This function calculates the Felsenstein likelihood for the subtree below this.

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

return the full covariance matrix for the tree topology and branch lengths

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

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

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

calcLogEm(int[]) - Method in class statalign.model.ext.ModelExtension

calcLogEm(int[]) - Method in class statalign.model.ext.ModelExtManager

calcLogEm(int[]) - Method in class statalign.model.ext.plugins.StructAlign

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

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

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

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

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

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

Calculate the sum of branch lengths below on this vertex.

calcTransMatrix(double[][], double) - Method in class statalign.base.hmm.HmmTkf92

calculateAllOptimal(int, int, int) - Method in class statalign.model.ext.plugins.structalign.RotationProposal

calculateFScore(int[], int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Given an array of paired sites corresponding to the real structure and an array corresponding to the predicted structure returns the F-score.

calculateMPD(ArrayList<String>, ArrayList<String>) - Method in class statalign.postprocess.plugins.PPFold

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

calculatePairsOnlyReliabilityScore(int[], double[][], ArrayList<Double>) - Static method in class statalign.postprocess.utils.RNAFoldingTools

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

calculatePPV(int[], int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Given an array of paired sites corresponding to the real structure and an array corresponding to the predicted structure returns the PPV.

calculateSensitivity(int[], int[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Given an array of paired sites corresponding to the real structure and an array corrsponding to the predicted structure returns the sensitivity.

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

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

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

This function calculates the upper probability vectors, which contain the partial likelihoods for everything except this subtree.

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

changeDimension(int) - Method in class statalign.postprocess.gui.PPFoldGUI

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

Returns true if this path already contains an edge from the argument split, otherwise false.

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

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

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

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

this function checks if the pointers are all right...

checkRNAalifold() - Static method in class statalign.postprocess.utils.RNAalifold

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

The children of this node.

chooseOne(double, MuDouble) - Static method in class statalign.base.Utils

Behaves exactly like weightedChoose(new double[]{1-prob,prob}, selectLogLike), but faster

CircularArray<E> - Class in statalign.base

Dynamically growing circular array with extremely efficient deque and hash operations.

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

Constructs an empty CircularArray with an initial capacity of MIN_CAPACITY.

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

Constructs an empty CircularArray with a given minimal initial capacity but at least MIN_CAPACITY.

classesInPackage(String) - Static method in class statalign.base.Utils

Finds all classes in a given package and all of its subpackages by walking through class path.

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

Removes all sequences (and their names).

clone() - Method in class statalign.base.AlignColumn

Creates a new column as a clone of the this, copying (or cloning) all fields except prev and next.

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

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

Closes the underlying file.

close() - Method in class statalign.postprocess.utils.NewickParser

Cluster - Class in statalign.postprocess.plugins.contree

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

clusters - Variable in class statalign.postprocess.plugins.contree.CTree

CNetwork - Class in statalign.postprocess.plugins.contree

The Consensus network

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

Constructs a new Consensus Network.

CNetworkEdge - Class in statalign.postprocess.plugins.contree

Edges in the consensus network

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

Set up a new edge

CNetworkNode - Class in statalign.postprocess.plugins.contree

Nodes in the consensus network Also includes a substantial amount of code that draws the edges from the node.

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

Initialise the node

CNetworkPath - Class in statalign.postprocess.plugins.contree

Paths of incompatible splits in the consensus network

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

CNetworkSplit - Class in statalign.postprocess.plugins.contree

Splits in the consensus network Includes several functions to check degrees of compatibility with another split

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

Constructs a new split.

CNetworkView - Class in statalign.postprocess.gui

The graphical interface for showing the current network.

CNetworkView(JScrollPane) - Constructor for class statalign.postprocess.gui.CNetworkView

Initialise network viewer

collectLeaves(Vertex) - Static method in class statalign.model.ext.plugins.structalign.Funcs

color - Variable in class statalign.postprocess.Track

ColorGradient - Class in statalign.postprocess.gui

ColorGradient(Color, Color) - Constructor for class statalign.postprocess.gui.ColorGradient

ColorGradient(Color, Color, Color) - Constructor for class statalign.postprocess.gui.ColorGradient

ColorGradient(Color[]) - Constructor for class statalign.postprocess.gui.ColorGradient

ColorGradient(Color[], float[]) - Constructor for class statalign.postprocess.gui.ColorGradient

colours - Variable in class statalign.postprocess.gui.ColorGradient

columnContrib(int[]) - Method in class statalign.model.ext.plugins.StructAlign

Calculates the structural likelihood contribution of a single alignment column

combineWith(CNetworkPath, CNetworkNode) - Method in class statalign.postprocess.plugins.contree.CNetworkPath

Combines this path with the argument path across the argument node

CommandLine - Class in statalign

CommandLine(boolean) - Constructor for class statalign.CommandLine

Creates a CommandLine object with verbose set to false.

compare(Pair<ArrayList<String>, String>, Pair<ArrayList<String>, String>) - Method in class statalign.distance.ComplexPair

compare(Pair<String, Integer>, Pair<String, Integer>) - Method in class statalign.distance.PairCompare

compareTo(Pair<String, Integer>, Pair<String, Integer>) - Method in class statalign.distance.Pair

compareTo(ArrayList<TreeNode>) - Method in class statalign.postprocess.plugins.contree.Cluster

ComplexPair - Class in statalign.distance

A class that makes it possible to compare two pairs where the first element of each pair is an ArrayList of Strings (alignment) and the second element is a String The String (the second element of the pair) determines which is bigger

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

compute() - Method in class statalign.postprocess.utils.RNAFoldingTools.MultiThreadedPosteriorDecoding

Initializes the posterior-decoding procedure by launching a specified number of threads.

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

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

computeNextSection() - Method in class statalign.postprocess.utils.RNAFoldingTools.MultiThreadedPosteriorDecoding

Launches new threads until no more sections are available.

computeWeights(Vertex.Neighbours, double[]) - Method in class statalign.base.Vertex

Computes the probability of all the possible imputations for parent and grandpa given the neighbouring AlignColumn objects.

ConfReader - Class in statalign.io.input

Currently unused, this class will be useful in the future console version for reading configuration files.

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

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

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

ConsensusNetwork - Class in statalign.postprocess.plugins

This is the postprocessmanager for showing the consensus network.

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

It construct a postprocess that is screenable (=can be shown on the GUI), outputable (= can be written into th elog file) but not postprocessable (= cannot generate its own output file).

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

Has a main class that runs the test network file

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

ConsensusTreeVisualizer - Class in statalign.postprocess.plugins

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

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

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

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

Constructs the majorityTree.

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

Constructs the network beginning with the consensus tree and then calls the network drawing function to calculate positions

ContinuousPositiveParameterMove - Class in statalign.mcmc

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

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

ContinuousPositiveStructAlignMove(StructAlign, ParameterInterface, PriorDistribution<Double>, ProposalDistribution<Double>, String) - Constructor for class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

convertTime(long) - Static method in class statalign.base.Utils

Takes a time in milliseconds and converts to a string to be printed.

coords - Variable in class statalign.io.ProteinSkeletons

coordinates

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

Alpha-C atomic coordinate for each sequence and each residue

CoorReader - Class in statalign.io.input.plugins

CoorReader() - Constructor for class statalign.io.input.plugins.CoorReader

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

CopyNode(ArrayList<CNetworkNode>, CNetworkSplit, CNetwork, ArrayList<CNetworkEdge>) - Method in class statalign.postprocess.plugins.contree.CTMain

Copy the list of nodes that need copying when adding a new split into a network.

copyOf(char[]) - Static method in class statalign.base.Utils

copyOf(int[]) - Static method in class statalign.base.Utils

copyOf(double[]) - Static method in class statalign.base.Utils

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

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

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

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

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

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

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

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

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

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

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

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

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

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

CoreMcmcModule - Class in statalign.base.mcmc

curLogLike for this McmcModule includes the contributions from the ModelExtensions.

CoreMcmcModule(Mcmc, ModelExtManager) - Constructor for class statalign.base.mcmc.CoreMcmcModule

coreModel - Variable in class statalign.base.Mcmc

McmcModule containing the moves for the core components of the model, i.e. the indel parameters, substitution model parameters, alignment, topology and edge lengths.

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

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

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

The number of times this bi-partition has been seen.

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

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

Calculated the number of leads that exists below this node

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

This function calculates the sum of the length of the strings representing the names of the leaves below this subtree.

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

CpRev - Class in statalign.model.subst.plugins

This class implements the Chloroplast reversible substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/10795826

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

Constructor used when instantiation is necessary.

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

CTMain - Class in statalign.postprocess.plugins.contree

The main thread for calculating consensus trees and networks.

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

Initialise the class

CTree - Class in statalign.postprocess.plugins.contree

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

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

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

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

cumulativeProbability(double) - Method in class statalign.utils.BetaDistribution

cumulativeProbability(double) - Method in class statalign.utils.GammaDistribution

The implementation of this method is based on: Chi-Squared Distribution, equation (9).

cumulativeProbability(double) - Method in class statalign.utils.NormalDistribution

If x is more than 40 standard deviations from the mean, 0 or 1 is returned, as in these cases the actual value is within Double.MIN_VALUE of 0 or 1.

cumulativeProbability(double, double) - Method in class statalign.utils.NormalDistribution

Deprecated. See RealDistribution.cumulativeProbability(double,double)

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

Current alignment between all leaf sequences

curLogLike - Variable in class statalign.mcmc.McmcModule

Current log-likelihood contribution

CurrentAlignment - Class in statalign.postprocess.plugins

This is the postprocessmanager for showing the current alignment.

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

It construct a postprocess that is screenable (=can be shown on the GUI), outputable (= can be written into th elog file) but not postprocessable (= cannot generate its own output file).

currentAlignmentType - Variable in class statalign.base.InputData

This integer stores the index of the current alignment type, as it is in alignmentTypes

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

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

CurrentTreeVisualizer - Class in statalign.postprocess.plugins

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

cycles - Variable in class statalign.base.MCMCPars

Number of cycles total after burn-in period