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

B

beforeAlignChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtension

Called before an alignment change is proposed, but after the affected subtree has been selected.

beforeAlignChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtManager

beforeAlignChange(Tree, Vertex) - Method in class statalign.model.ext.plugins.StructAlign

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

beforeEdgeLenChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtension

Called before an edge length change is proposed, but after the affected edge is selected.

beforeEdgeLenChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtManager

beforeEdgeLenChange(Tree, Vertex) - Method in class statalign.model.ext.plugins.StructAlign

beforeFirstSample() - Method in class statalign.base.Input

This is an empty function.

beforeFirstSample(int) - Method in class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

beforeFirstSample(int) - Method in class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

beforeFirstSample() - Method in class statalign.postprocess.gui.treeviews.TreeView

beforeFirstSample(int) - Method in class statalign.postprocess.gui.treeviews.TreeView

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.ConsensusNetwork

Initializes the graphical interface.

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.CurrentAlignment

Initializes the graphical interface.

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.Entropy

Initialises the graphical interface.

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

Initialises the graphical interface.

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.MpdAlignment

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.PPFold

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

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.structalign.StructTrace

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.Structure

beforeFirstSample(InputData) - Method in class statalign.postprocess.plugins.VisualDistance

beforeFirstSample(InputData) - Method in class statalign.postprocess.Postprocess

Called before MCMC start.

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

This function invoked before the first sample.

beforeFirstSample(InputData) - Method in class statalign.postprocess.TreeVisualizer

beforeIndelParamChange(Tree, Hmm, McmcMove) - Method in class statalign.model.ext.ModelExtension

Called before an indel parameter change is proposed, but after the affected parameter is selected.

beforeIndelParamChange(Tree, Hmm, McmcMove) - Method in class statalign.model.ext.ModelExtManager

beforeModExtParamChange(Tree, ModelExtension) - Method in class statalign.model.ext.ModelExtension

Called when a model extension plugin is to propose a parameter change.

beforeModExtParamChange(Tree) - Method in class statalign.model.ext.ModelExtManager

beforeSampling(Tree) - Method in class statalign.mcmc.McmcModule

Called before the start of MCMC sampling, but after the initial tree, alignment etc. have been generated.

beforeSampling(Tree) - Method in class statalign.model.ext.ModelExtManager

Calls McmcModule.beforeSampling(Tree) on each active plugin.

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

beforeSubstParamChange(Tree, SubstitutionModel, int) - Method in class statalign.model.ext.ModelExtension

Called before a substitution parameter change is proposed.

beforeSubstParamChange(Tree, SubstitutionModel, int) - Method in class statalign.model.ext.ModelExtManager

beforeTreeChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtension

Called before a topology change is proposed, but after the affected branches are selected.

beforeTreeChange(Tree, Vertex) - Method in class statalign.model.ext.ModelExtManager

beforeTreeChange(Tree, Vertex) - Method in class statalign.model.ext.plugins.StructAlign

Benchmarks - Class in statalign.postprocess.plugins.benchmarks

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

BetaDistribution - Class in statalign.utils

Implements the Beta distribution.

BetaDistribution(double, double) - Constructor for class statalign.utils.BetaDistribution

Build a new instance.

BetaDistribution(double, double, double) - Constructor for class statalign.utils.BetaDistribution

Build a new instance.

BetaDistribution(RandomGenerator, double, double, double) - Constructor for class statalign.utils.BetaDistribution

Creates a β distribution.

BetaPrior - Class in statalign.mcmc

BetaPrior(double, double) - Constructor for class statalign.mcmc.BetaPrior

bFactors - Variable in class statalign.io.ProteinSkeletons

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

Crystallographic temperature factors, for weighting epsilon.

BIGNUM - Variable in class statalign.base.TreeAlgo

bitsetToBinary(BitSet, int) - Static method in class statalign.postprocess.plugins.contree.Utils

Blosum - Class in statalign.model.subst.plugins

Implements the 'rate-matricized' Blosum substitution model.

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

Constructor used when instantiation is necessary.

Blosum62 - Class in statalign.model.score.plugins

An implementation of the BLOSUM62 distances This is the distance and not the similarity matrix!!!

Blosum62() - Constructor for class statalign.model.score.plugins.Blosum62

This constructor reads the distances from data/aadist.dat and sets the which[][] array.

bpp - Variable in class statalign.base.McmcStep

log of (backproposal probability / proposal probability)

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

browseManual(String, String) - Method in class statalign.ui.MainFrame

buildNJTree(String[], String[], SubstitutionModel, String) - Method in class statalign.base.TreeAlgo

burnin - Variable in class statalign.base.Mcmc

True while the MCMC is in the burn-in phase.

burnIn - Variable in class statalign.base.MCMCPars

Number of burn-in steps

burnIn - Variable in class statalign.base.McmcStep

true if this step was proposed in the burn-in period

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

burnin - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters

burnin - Variable in class statalign.postprocess.utils.LogLikelihoodTraceContainer

It tells if the sample comes from the burn-in phase or not.

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