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

O

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

OFFSET - Static variable in class statalign.postprocess.gui.PPFoldGUI

OFFSET_X - Static variable in class statalign.postprocess.gui.DistanceGUI

OFFSET_X - Static variable in class statalign.postprocess.gui.EntropyGUI

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

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

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

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

oldLogLike - Variable in class statalign.base.McmcStep

loglikelihood before this step

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

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

OnZeroSide(CNetworkSplit, int) - Method in class statalign.postprocess.plugins.contree.CNetworkSplit

Compares an input split to see if the input split occurs on the zero side of this split.

orphan - Variable in class statalign.base.AlignColumn

If true, then this AlignColumn is inserted, and its parent is the first ancestral character to the right in the alignment If it is false, then this AlignColumn is aligned to its parent

orphanLogLike - Variable in class statalign.base.Vertex

The log-sum of the Felsenstein's likelihoods of characters that are inserted into the sequence of this vertex.

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

outputable - Variable in class statalign.postprocess.Postprocess

True if this class can generate an output

outputFile - Variable in class statalign.postprocess.Postprocess

This is the output file writer, that is written by a specific postprocess.

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

outputPath - Variable in class statalign.base.InputData

The path where output files will be created.

OutputPreferences - Class in statalign.ui

The window for setting the input/output preferences.

OutputPreferences(MainFrame) - Constructor for class statalign.ui.OutputPreferences

Creates the window for setting the I/O preferences.

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

owner - Variable in class statalign.base.AlignColumn

The owner tells the tree vertex where this AlignColumn belongs to.

owner - Variable in class statalign.base.thread.MainThread

Reference to the (singleton) MainManager object encapsulating all settings and data that an MCMC run depends on.

owner - Variable in class statalign.postprocess.gui.PPFoldGUI