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

F

f(Double) - Method in class statalign.model.ext.plugins.structalign.LinearLink

f(Double) - Method in class statalign.model.ext.plugins.structalign.QuadraticLink

f(T) - Method in interface statalign.utils.LinkFunction

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

FastaReader - Class in statalign.io.input.plugins

Class to read files in FASTA format.

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

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

Restores the exact state just before the call of Vertex.fastSwapWithUncle().

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

Swaps this with its uncle, but keeps alignment columns where this, its parent, the uncle node and its parent are all aligned unchanged with a given probability, and only proposes new alignments between these selected alignment anchors columns.

favouredDestination(int) - Method in class statalign.base.Vertex

felsen - Variable in class statalign.base.State

Felsenstein likelihoods for each sequence and each character therein

Felsenstein81 - Class in statalign.model.subst.plugins

This class implements the Felsenstein 1981 parameter model.

Felsenstein81() - Constructor for class statalign.model.subst.plugins.Felsenstein81

This constructor uses the analytical solution to diagonalising the rate matrix to set diagonalising matrices.

Felsenstein84 - Class in statalign.model.subst.plugins

This class implements the Felsenstein 1984 parameter model.

Felsenstein84() - Constructor for class statalign.model.subst.plugins.Felsenstein84

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

file - Variable in class statalign.postprocess.Postprocess

This is the logfile writer that is written during the running and gets information from all postprocesses.

FileTokenReader - Class in statalign.io.input

Class that allows reading the contents of a file token by token, without worrying about line ends and whitespace.

FileTokenReader(String) - Constructor for class statalign.io.input.FileTokenReader

Constructs a FileTokenReader reading a given file.

fillParams(String[], MainManager) - Method in class statalign.CommandLine

Fills run-time parameters using a list of command-line arguments.

findFirstNonSubset(CNetworkSplit, ArrayList<CNetworkNode>, boolean, int) - Method in class statalign.postprocess.plugins.contree.CNetworkNode

Recursive function used to find node at which we can add a split compatible with the network Goes up from first node and finds where edges joining are no longer subset of specified side of split we want to add

findPlugins(Class<T>) - Static method in class statalign.base.Utils

Locates all plugins that are descendants of the specified plugin superclass.

FindPositions(int) - Method in class statalign.postprocess.plugins.contree.CNetwork

Calculates positions for network nodes and edges linking them to output to the network visualiser.

findRefSubtrees(Tree, int) - Static method in class statalign.model.ext.plugins.structalign.Funcs

FindWeighting(CNetworkEdge, int) - Method in class statalign.postprocess.plugins.contree.CNetworkNode

Finds the weighting of this this node using the joins that join to it.

finished(int, Exception) - Method in class statalign.base.MainManager

Called when the MCMC thread terminates, signals end of the process back to MainFrame.

finished(int, Exception) - Method in class statalign.ui.MainFrame

Enables several menu items that were kept disabled during the run.

first - Variable in class statalign.base.Vertex

firstHalfBurnin - Variable in class statalign.base.Mcmc

True while the MCMC is in the first half of burn-in phase.

fixAlign - Variable in class statalign.base.MCMCPars

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

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

Value to fix epsilon at if we're not estimating it.

fixEdge - Variable in class statalign.base.MCMCPars

fixedSigma2 - Variable in class statalign.model.ext.plugins.StructAlign

fixedSigma2Value - Variable in class statalign.model.ext.plugins.StructAlign

Value to fix sigma at if we're not estimating it.

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

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

fixTopology - Variable in class statalign.base.MCMCPars

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

fold(List<String>, List<String>, String) - Static method in class statalign.postprocess.utils.RNAalifold

fold(List<String>, List<String>, String, boolean) - Static method in class statalign.postprocess.utils.RNAalifold

fold(List<String>, List<String>, String, boolean, boolean) - Static method in class statalign.postprocess.utils.RNAalifold

frame - Variable in class statalign.base.MainManager

The main window of the program.

frequency - Variable in class statalign.postprocess.plugins.MpdAlignment

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

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

Covariance matrix implied by current tree topology

fullPath - Variable in class statalign.base.MainManager

The full path of the input file from which we read the sequences.

fullPathWithExtensions - Variable in class statalign.base.MainManager

After adding on extensions from ModelExtension objects.

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

Funcs() - Constructor for class statalign.model.ext.plugins.structalign.Funcs

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

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

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