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

D

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

The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix.

dataAdded(File, DataType) - Method in class statalign.model.ext.ModelExtension

dataAdded(File, DataType) - Method in class statalign.model.ext.ModelExtManager

Called in GUI mode only when new data is added to the analysis.

dataAdded(File, DataType) - Method in class statalign.model.ext.plugins.StructAlign

dataMan - Variable in class statalign.base.MainManager

Data manager that handles all input files.

DataManager - Class in statalign.io

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

DataReader - Class in statalign.io.input

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

Dataset - Class in statalign.postprocess.plugins.benchmarks

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

DataType - Interface in statalign.io

Ancestor for all input/output data types in StatAlign.

Dayhoff - Class in statalign.model.subst.plugins

Implements the classic Dayhoff substitution model.

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

Constructor used when instantiation is necessary.

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

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

DEBUG - Static variable in class statalign.base.Utils

Debugging mode (various consistency checks done if on)

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

These are the posterior decoding values

DEFAULT_INVERSE_ABSOLUTE_ACCURACY - Static variable in class statalign.utils.BetaDistribution

Default inverse cumulative probability accuracy.

DEFAULT_INVERSE_ABSOLUTE_ACCURACY - Static variable in class statalign.utils.GammaDistribution

Default inverse cumulative probability accuracy.

DEFAULT_INVERSE_ABSOLUTE_ACCURACY - Static variable in class statalign.utils.NormalDistribution

Default inverse cumulative probability accuracy.

density(Transformation, double, double, double) - Method in class statalign.model.ext.plugins.structalign.Transformation

Calculates the rotation matrix from an axis and angle with axis x and angle r, the rotation matrix is cos(r)I + sin(r)cross(x) + (1-cos(r))outer(x) where cross(x) is the crossproduct matrix of x and outer(x) is the outer (tensor) product

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

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

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

DEV_MANUAL - Static variable in class statalign.ui.MainFrame

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

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

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

DisplayString - Class in statalign.postprocess.utils

A class that stores the strings to be displayed and thus enable zooming on the consensus trees / networks

DisplayString(String, int, int) - Constructor for class statalign.postprocess.utils.DisplayString

dist - Variable in class statalign.model.score.SubstitutionScore

The distance matrix for subtitutions.

Distance - Class in statalign.distance

A class that calculates the distance and similarity score between two alignments

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

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

So we can use Strings instead of list

distance(ArrayList<String>, ArrayList<String>) - Static method in class statalign.distance.Distance

Calculates the distance between two alignments, if the function returns 0, the alignments are the same.

DistanceGUI - Class in statalign.postprocess.gui

DistanceGUI(String, VisualDistance) - Constructor for class statalign.postprocess.gui.DistanceGUI

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

Pairwise distances implied by current tree topology

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

distances - Variable in class statalign.postprocess.plugins.VisualDistance

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

DNAScore - Class in statalign.model.score.plugins

This is an implementation of a DNA scoring.

DNAScore() - Constructor for class statalign.model.score.plugins.DNAScore

This constructor reads the distance matrix from data/dnadist.dat, and sets the which[][] array.

doMCMC() - Method in class statalign.base.Mcmc

Starts an MCMC run.

doReportDuringBurnin - Variable in class statalign.base.InputData

If true then logging information is also printed during the burnin.

doReportDuringBurnin - Variable in class statalign.base.MCMCPars

If true then logging information is also printed during the burnin.

DOWNWEIGHT_INDEL_LIKELIHOOD - Static variable in class statalign.base.Utils

If true then we downweight the indel contribution to the overall likelihood.

drawBasePair(VueVARNAGraphics, Point2D.Double, Point2D.Double, ModeleBP, double) - Method in class statalign.postprocess.gui.StructureGUI

DrawEdges(int) - Method in class statalign.postprocess.plugins.contree.CNetworkNode

Function to draw the network i.e. find x and y co-ordinates for nodes.

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

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

drawSymbol(VueVARNAGraphics, double, double, double, double, double, boolean, ModeleBP.Edge) - Method in class statalign.postprocess.gui.StructureGUI