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

N

name - Variable in class statalign.base.State

Names of the leaf sequences

name - Variable in class statalign.base.Vertex

The name of the sequence associated to the vertex.

name - Variable in class statalign.mcmc.McmcMove

name - Variable in class statalign.postprocess.plugins.structalign.StructAlignTraceParameters.PlottableParameter

name - Variable in class statalign.postprocess.plugins.TreeNode

The name/identifier of this node.

nameLengthSum - Variable in class statalign.postprocess.plugins.TreeNode

The sum of the length of the names below this vertex.

names - Variable in class statalign.base.Tree

The name of the sequences

names - Variable in class statalign.io.ProteinSkeletons

names of sequences

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

nephewUncleSwapFixedColumns2() - Method in class statalign.base.Vertex

nephewUncleSwapFixedColumns3() - Method in class statalign.base.Vertex

network - Variable in class statalign.base.Mcmc

network - Variable in class statalign.base.Tree

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

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

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

NetworkTreeView - Class in statalign.postprocess.gui.treeviews

The graphical interface for showing the current network.

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

NewickParser - Class in statalign.postprocess.utils

NewickParser(String) - Constructor for class statalign.postprocess.utils.NewickParser

NewickParser(Reader) - Constructor for class statalign.postprocess.utils.NewickParser

NewickParserException - Exception in statalign.postprocess.utils

NewickParserException(String) - Constructor for exception statalign.postprocess.utils.NewickParserException

NewickParserException(Throwable) - Constructor for exception statalign.postprocess.utils.NewickParserException

NewickReader - Class in statalign.io.input.plugins

Class to parse Newick format tree files or strings.

NewickReader() - Constructor for class statalign.io.input.plugins.NewickReader

Constructs a NewickReader with the default minimum edge length of 0.

NewickReader(double) - Constructor for class statalign.io.input.plugins.NewickReader

Constructs a NewickReader with a specified minimum edge length.

NewickReader.FormatException - Exception in statalign.io.input.plugins

NewickReader.FormatException(NewickReader.FormatExceptType) - Constructor for exception statalign.io.input.plugins.NewickReader.FormatException

NewickReader.FormatException(NewickReader.FormatExceptType, String) - Constructor for exception statalign.io.input.plugins.NewickReader.FormatException

NewickReader.FormatExceptType - Enum in statalign.io.input.plugins

newLogLike - Variable in class statalign.base.McmcStep

loglikelihood after this step (McmcStep.accepted ?

newPeek(State) - Method in class statalign.postprocess.plugins.CurrentAlignment

Updates the alignment.

newPeek(State) - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

newPeek(State) - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

newPeek(State) - Method in class statalign.postprocess.plugins.structalign.StructTrace

newPeek(State) - Method in class statalign.postprocess.Postprocess

Allows peeking into the Markov chain before actual sampling begins.

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

Calls the plug-ins after an MCMC step.

newSample(TreeNode) - Method in class statalign.postprocess.gui.treeviews.HorizontalCladogramTreeView

newSample(TreeNode) - Method in class statalign.postprocess.gui.treeviews.HorizontalPhylogramTreeView

newSample(TreeNode) - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

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

newSample(State, int, int) - Method in class statalign.postprocess.plugins.ConsensusNetwork

At each MCMC sampling point, the current alignment is shown on the GUI.

newSample(State, int, int) - Method in class statalign.postprocess.plugins.ConsensusTreeVisualizer

newSample(State, int, int) - Method in class statalign.postprocess.plugins.CurrentAlignment

At each mcmc sampling point, the current alignment is shown on the GUI.

newSample(State, int, int) - Method in class statalign.postprocess.plugins.CurrentTreeVisualizer

newSample(State, int, int) - Method in class statalign.postprocess.plugins.Entropy

Writes the loglikelihoods into a logfile, if sampling mode is switched on.

newSample(McmcModule, State, int, int) - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

Writes the loglikelihoods into a logfile, if sampling mode is switched on.

newSample(State, int, int) - Method in class statalign.postprocess.plugins.MpdAlignment

newSample(State, int, int) - Method in class statalign.postprocess.plugins.PPFold

newSample(State, int, int) - Method in class statalign.postprocess.plugins.structalign.RmsdTrace

newSample(State, int, int) - Method in class statalign.postprocess.plugins.structalign.StructTrace

newSample(State, int, int) - Method in class statalign.postprocess.plugins.Structure

newSample(State, int, int) - Method in class statalign.postprocess.plugins.VisualDistance

newSample(State, int, int) - Method in class statalign.postprocess.Postprocess

This function is called when we sample from the Markov chain.

newSample(McmcModule, State, int, int) - Method in class statalign.postprocess.Postprocess

newSample(McmcModule, State, int, int) - Method in class statalign.postprocess.PostprocessManager

Calls the plug-ins at a new sample.

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

This is an empty function.

newStep(McmcStep) - Method in class statalign.postprocess.plugins.LogLikelihoodTrace

It makes a dynamically updated list containing <300 samples evenly distributed from the steps already made.

newStep(McmcStep) - Method in class statalign.postprocess.plugins.structalign.StructTrace

newStep(McmcStep) - Method in class statalign.postprocess.Postprocess

Called after a new step is made.

newStep(McmcStep) - Method in class statalign.postprocess.PostprocessManager

Calls the plug-ins after an MCMC step.

next - Variable in class statalign.base.AlignColumn

This reference points to the next AlignColumn in the alignment

nl - Variable in class statalign.base.State

Number of leaves (input sequences)

nn - Variable in class statalign.base.State

Number of nodes

nodeList - Variable in class statalign.postprocess.plugins.contree.CTree

nodeRefA - Variable in class statalign.postprocess.plugins.contree.Cluster

nodeRefB - Variable in class statalign.postprocess.plugins.contree.Cluster

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

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

noOfOccurrences - Variable in class statalign.postprocess.plugins.contree.Cluster

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

NormalDistribution - Class in statalign.utils

Implementation of the normal (gaussian) distribution.

NormalDistribution() - Constructor for class statalign.utils.NormalDistribution

Create a normal distribution with mean equal to zero and standard deviation equal to one.

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

Create a normal distribution using the given mean and standard deviation.

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

Create a normal distribution using the given mean, standard deviation and inverse cumulative distribution accuracy.

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

Creates a normal distribution.

nSilentIndels - Variable in class statalign.base.Vertex

nTopologyChanges - Variable in class statalign.base.mcmc.LOCALTopologyMove

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

NucleotideModel - Class in statalign.model.subst.plugins

This is the abstract class for nucleotide models.

NucleotideModelUtils - Class in statalign.model.subst.plugins

This class implements various utility methods for nucleotide models.

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

numericalDiagonalisation(NucleotideModel, double[][]) - Static method in class statalign.model.subst.plugins.NucleotideModelUtils

Class method for numerical diagonalisation of rate matrix Q for nucleotide model M.

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