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

U

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

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

UniformPrior - Class in statalign.mcmc

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

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

UniformProposal - Class in statalign.mcmc

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

unsetPlottable() - Method in class statalign.model.ext.plugins.structalign.StructAlignMoveParams

unshift(E) - Method in class statalign.base.CircularArray

Adds new element at the beginning of the array (key startKey-1 is assigned), growing the array if full, then startKey is decreased.

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

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

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

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

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

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

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

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

updateAndDraw(String, String) - Method in class statalign.postprocess.gui.StructureGUI

updateBasePairMatrix(float[][]) - Static method in class statalign.postprocess.plugins.Structure

updateFoldingParameters() - Method in class statalign.ui.RNASettingsDlg

updateFoldingParametersAndTest() - Method in class statalign.ui.RNASettingsDlg

updateHmm2Matrices() - Method in class statalign.base.Vertex

updateHmm2Matrix(double[]) - Method in class statalign.base.Vertex

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

updateInterestThreshold() - Method in class statalign.postprocess.plugins.contree.CTMain

Simply update our interest threshold

updateLikelihood(Object) - Method in class statalign.base.mcmc.AlignmentMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.AllEdgeMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.EdgeMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.IndelMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.LOCALTopologyMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.SilentIndelMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.SubstMove

updateLikelihood(Object) - Method in class statalign.base.mcmc.TopologyMove

updateLikelihood(Object) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

updateLikelihood(Object) - Method in class statalign.mcmc.McmcCombinationMove

updateLikelihood(Object) - Method in class statalign.mcmc.McmcMove

updateLikelihood(Object) - Method in class statalign.model.ext.plugins.structalign.AlignmentMove

updateLikelihood(Object) - Method in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

updateLikelihood(Object) - Method in class statalign.model.ext.plugins.structalign.RotationOrTranslationMove

updateNewickStringWithLabels() - Method in class statalign.base.State

updateParam(double[]) - Method in class statalign.base.hmm.HmmNonParam

updateParam(double[]) - Method in class statalign.base.hmm.HmmSilent

updateProposal(double, Double) - Method in class statalign.mcmc.ContinuousPositiveParameterMove

updateProposal(double, Double) - Method in class statalign.mcmc.GammaProposal

updateProposal(double, Double) - Method in class statalign.mcmc.GaussianProposal

updateProposal(double, Double) - Method in class statalign.mcmc.LogisticProposal

updateProposal(double, Double) - Method in class statalign.mcmc.MultiplicativeProposal

updateProposal(double, T) - Method in class statalign.mcmc.ProposalDistribution

updateProposal(double, Double) - Method in class statalign.mcmc.UniformProposal

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

updateSequence() - Method in class statalign.postprocess.plugins.Structure

updateSequences() - Method in class statalign.postprocess.gui.InputGUI

It rereads sequences from MainManager

updateSingleMatrix(float[]) - Static method in class statalign.postprocess.plugins.Structure

updateSpan(double) - Method in class statalign.model.subst.SubstitutionModel

updateStructure() - Static method in class statalign.postprocess.plugins.Structure

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

updateTracks(String[]) - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

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

updateTransitionMatrix(double[][], double) - Method in class statalign.model.subst.SubstitutionModel

Updates externally stored transition matrix using current values of v, w, d, e and current edge length.

upp - Variable in class statalign.base.AlignColumn

This double array contains the upper Likelihoods

USE_FULL_WINDOWS - Static variable in class statalign.base.Utils

If this is set to true then the alignment moves operate on the whole alignment rather than selecting subwindows.

USE_INDEL_CORRECTION_FACTOR - Static variable in class statalign.base.Utils

If true then we divide out the stationary probability of the internal nodes from the indel likelihood, as per Redelings and Suchard (2005), using the TKF92 stationary distribution defined in Thorne et al. (1992).

USE_MODEXT_EM - Static variable in class statalign.base.Utils

If true, then ModelExtensions are allowed to offer a contribution to the emission probability used to compute the dynamic programming matrices for alignment proposals.

USE_MODEXT_UPP - Static variable in class statalign.base.Utils

If true, then ModelExtensions are allowed to offer an upper contribution to the emission probability used to compute the dynamic programming matrices for alignment proposals.

USE_UPPER - Static variable in class statalign.base.Utils

Whether to use information from the upper parts of the tree in order to fill out the hmm2 and hmm3 matrices.

useAlign - Variable in class statalign.base.InputData

Specifies how the alignment of the input sequences in InputData.seqs is used.

useDefaultOptions() - Method in class statalign.ui.RNASettingsDlg

useInAlignmentProposals() - Method in class statalign.model.ext.ModelExtension

If true, then this plugin is able to compute a column-wise contribution to the likelihood, and can be used to influence the alignment proposals that are carried out by functions inside statalign.base.Vertex By default this is false.

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

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

useModelExtInProposal() - Method in class statalign.base.mcmc.AlignmentMove

USER_MANUAL - Static variable in class statalign.ui.MainFrame

useTree - Variable in class statalign.base.InputData

Specifies how the given InputData.tree is used.

Utils - Class in statalign.base

This class contains multi-purpose static functions.

Utils - Class in statalign.postprocess.plugins.contree

Utils() - Constructor for class statalign.postprocess.plugins.contree.Utils