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

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HashEntry - Class in statalign.postprocess.plugins.contree.hash

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

HashEntry(int, BitSet, double) - Constructor for class statalign.postprocess.plugins.contree.hash.HashEntry

hashKey2 - Variable in class statalign.postprocess.plugins.contree.hash.HashEntry

The bucket hash key relevant to this entry.

HashTable - Class in statalign.postprocess.plugins.contree.hash

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

HashUtils - Class in statalign.postprocess.plugins.contree.hash

Details about this class can be found in papers on consensus tree construction algorithms: - An Experimental Analysis of Consensus Tree Algorithm [..].

HashUtils() - Constructor for class statalign.postprocess.plugins.contree.hash.HashUtils

hasProperty(String) - Method in class statalign.postprocess.plugins.TreeNode

Determines whether a certain key exists in the properties associated with this node.

hasToolBar - Variable in class statalign.postprocess.Postprocess

True, if the plugin implements the Postprocess.getToolBarItems() function.

heat - Variable in class statalign.base.McmcStep

heat of the chain

heat - Variable in class statalign.base.Tree

The heat parameter for this MCMC chain.

height - Variable in class statalign.postprocess.gui.CNetworkView

height - Variable in class statalign.postprocess.gui.treeviews.NetworkTreeView

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

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

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

HelpWindow - Class in statalign.ui

This is a help window for displaying html pages.

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

This constructs a dialog window displaying html messages.

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

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

hierarchicalPrior - Variable in class statalign.model.ext.plugins.structalign.HierarchicalContinuousPositiveStructAlignMove

HKY85 - Class in statalign.model.subst.plugins

This class implements the HKY85 parameter model.

HKY85() - Constructor for class statalign.model.subst.plugins.HKY85

This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.

Hmm - Class in statalign.base.hmm

The abstract class of Hidden Markov Models.

Hmm() - Constructor for class statalign.base.hmm.Hmm

Hmm2 - Class in statalign.base.hmm

This is an abstract class for HMMs that are pair-HMMs and do not emit characters into unobservable sequences.

Hmm2() - Constructor for class statalign.base.hmm.Hmm2

hmm2 - Variable in class statalign.base.Tree

When two fragments of two sequences on two neighbor vertices of the tree are realigned, the proposed new alignment is drawn from a forward-backward sampling of this HMM.

hmm2AlignWithSave() - Method in class statalign.base.Vertex

Samples a new alignment between `this' & `this.parent', taking window sizes into account.

hmm2AlignWithSave(double) - Method in class statalign.base.Vertex

hmm3 - Variable in class statalign.base.Tree

When two fragments of two sequences on two sibling vertices are realigned drawing a novel ancestral substring for their parent vertex, the proposed new alignment is drawn from a forward-backward sampling of this HMM.

HmmNonParam - Class in statalign.base.hmm

An implementation of the abstract pair-HMM that emits characters into non-observable sequences Used when a new alignment is proposed that aligns together two substrings via an ancestral sequence.

HmmNonParam() - Constructor for class statalign.base.hmm.HmmNonParam

Constructs a HMMSilent for Tree.

HmmSilent - Class in statalign.base.hmm

This is the abstract class of pair-HMMs that emit characters into one unobservable sequence, namely that aligns two observable sequences via an unobservable ancestral sequence.

HmmSilent() - Constructor for class statalign.base.hmm.HmmSilent

HmmTkf92 - Class in statalign.base.hmm

This class implements a simplified version of the TKF92 pair-HMM.

HmmTkf92(double[]) - Constructor for class statalign.base.hmm.HmmTkf92

This constructor creates a TKF92 pair-HMM for the tree

HorizontalCladogramTreeView - Class in statalign.postprocess.gui.treeviews

The graphical interface for showing the current tree.

HorizontalCladogramTreeView() - Constructor for class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

HorizontalPhylogramTreeView - Class in statalign.postprocess.gui.treeviews

The graphical interface for showing the current tree.

HorizontalPhylogramTreeView() - Constructor for class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

HyperbolicPrior - Class in statalign.mcmc

HyperbolicPrior() - Constructor for class statalign.mcmc.HyperbolicPrior