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

E

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

This array tells the equilibrium distribution

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

edgeLen - Variable in class statalign.base.State

Edge length to parent, for each node (first nl are leaves)

edgeLength - Variable in class statalign.base.Vertex

The length of the edge that connects this vertex with its parent.

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

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

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

The branch length of this node.

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

The sum of the edge lengths

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

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

EdgeMove - Class in statalign.base.mcmc

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

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

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

emptyValue - Static variable in class statalign.postprocess.utils.RNAFoldingTools

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

Returns the node at the end of the path

Entropy - Class in statalign.postprocess.plugins

This is the implementation of the postprocess that handles entropy.

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

It constructs a postprocess handler that is screenable (=can be shown on the GUI), outputable (= can be written into the log file) and postprocessable (= can generate its own output file).

EntropyContainer - Class in statalign.postprocess.utils

EntropyContainer(double, double, double) - Constructor for class statalign.postprocess.utils.EntropyContainer

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

EntropyGUI - Class in statalign.postprocess.gui

This class implements the graphical interface for showing the observed, expected, and individual sample entropies of a given alignment space.

EntropyGUI(String, Entropy) - Constructor for class statalign.postprocess.gui.EntropyGUI

Constructor to initialise the GUI for entropy

entropyList - Variable in class statalign.postprocess.plugins.Entropy

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

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

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

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

equals(Object) - Method in class statalign.distance.Pair

ErrorMessage - Class in statalign.ui

A dialog window for showing error messages.

ErrorMessage(JFrame, Exception, boolean) - Constructor for class statalign.ui.ErrorMessage

ErrorMessage(JFrame, String, boolean) - Constructor for class statalign.ui.ErrorMessage

It constructs a dialog window.

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

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

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

exciseSilentIndel(AlignColumn, boolean) - Method in class statalign.base.Vertex

exciseSilentIndelBlock(AlignColumn, boolean) - Method in class statalign.base.Vertex

executable - Static variable in class statalign.postprocess.utils.RNAalifold

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

ExperimentalData - Class in statalign.postprocess.plugins.benchmarks

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