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

M

m1 - Variable in class statalign.postprocess.plugins.contree.hash.HashUtils

m2 - Variable in class statalign.postprocess.plugins.contree.hash.HashUtils

main(String[]) - Static method in class statalign.base.hmm.HmmNonParam

For testing/debugging purposes.

main(String[]) - Static method in class statalign.base.hmm.HmmTkf92

For testing purposes.

main(String[]) - Static method in class statalign.base.State

main(String[]) - Static method in class statalign.io.input.InputReader

useage: java InputReader input_file_name burnin cycles sampling

main(String[]) - Static method in class statalign.io.input.plugins.NewickReader

main(String[]) - Static method in class statalign.io.RawSequences

main(String[]) - Static method in class statalign.model.subst.plugins.Dayhoff

Only for testing.

main(String[]) - Static method in class statalign.postprocess.gui.ColorGradient

main(String[]) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

main(String[]) - Static method in class statalign.postprocess.plugins.contree.CTMain

main(String[]) - Static method in class statalign.postprocess.plugins.contree.hash.HashUtils

For debugging purposes only.

main(String[]) - Static method in class statalign.postprocess.plugins.contree.test.ConsensusNetworkTester

Main class to run Consensus Network Testing script, TestNetwork.java

main(String[]) - Static method in class statalign.postprocess.plugins.contree.test.CorrectnessTester

main(String[]) - Static method in class statalign.postprocess.plugins.contree.test.EdgeLengthTester

main(String[]) - Static method in class statalign.postprocess.utils.RNAalifold

main(String[]) - Static method in class statalign.postprocess.utils.RNAFoldingTools

main(String[]) - Static method in class statalign.StatAlign

Only method of the class.

main(String[]) - Static method in class statalign.StatAlignParallel

main(String[]) - Static method in class statalign.ui.AboutDlg

main(String[]) - Static method in class statalign.ui.HelpWindow

For testing purposes

main(String[]) - Static method in class statalign.ui.MainFrame

Merely for testing purposes.

main(String[]) - Static method in class statalign.ui.RNASettingsDlg

main(String[]) - Static method in class statalign.utils.SimpleStats

main2(String[]) - Static method in class statalign.base.Mcmc

Code to test that various samplers are working correctly.

main3(String[]) - Static method in class statalign.base.Mcmc

Code to test that the moves are being sampled according to the correct weights (i.e. that there is not some bias arising from the choose function and/or random number generator).

main4(String[]) - Static method in class statalign.base.Mcmc

main5(String[]) - Static method in class statalign.base.Mcmc

MainFrame - Class in statalign.ui

The main frame of the program.

MainFrame() - Constructor for class statalign.ui.MainFrame

The only constructor of the class.

MainManager - Class in statalign.base

This is the central class in the information flow amongst classes.

MainManager(MainFrame) - Constructor for class statalign.base.MainManager

A trivial constructor that only sets MainFrame and substModels.

mainManager - Variable in class statalign.postprocess.PostprocessManager

This is the Main manager that manages the MCMC run.

MainThread - Class in statalign.base.thread

The main (suspendable) thread for background MCMC calculation.

MainThread(MainManager) - Constructor for class statalign.base.thread.MainThread

Constructs a new MainThread that can be used to fire a background MCMC calculation.

majorVersion - Static variable in class statalign.StatAlign

StatAlign version data.

makeRoot(String) - Method in class statalign.base.Tree

It roots the tree on a taxon

manager - Variable in class statalign.ui.MainFrame

The main manager that handles the MCMC run.

Mapping - Class in statalign.postprocess.utils

Mapping() - Constructor for class statalign.postprocess.utils.Mapping

markDepth(TreeNode, int) - Method in class statalign.postprocess.plugins.contree.test.CorrectnessTester

matrix - Variable in class statalign.postprocess.plugins.RNAalifoldResult

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

max - Variable in class statalign.postprocess.Track

MAX_ACCEPTANCE - Static variable in class statalign.base.Utils

During the burnin, the proposalWidthControlVariable for all continuous parameters is adjusted in order to ensure that the average acceptance rate is between MIN_ACCEPTANCE and MAX_ACCEPTANCE where possible.

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

MAX_SILENT_LENGTH - Static variable in class statalign.base.Utils

MAX_WINDOW_MULTIPLIER - Static variable in class statalign.base.mcmc.AlignmentMove

MAX_WINDOW_MULTIPLIER - Static variable in class statalign.model.ext.plugins.structalign.AlignmentMove

maxAcceptance - Variable in class statalign.mcmc.McmcMove

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

Calculate the maximum depth below on this vertex.

maxDepth() - Method in class statalign.postprocess.plugins.TreeNode

Calculate the maximum depth below on this vertex.

maxProposalWidthControlVariable - Variable in class statalign.mcmc.McmcMove

maxSteps() - Method in class statalign.postprocess.plugins.TreeNode

Calculate the nodes needed to cross to get to the most distant leaf Used in tree visualisation.

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

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

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

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

Mcmc - Class in statalign.base

This class handles an MCMC run.

Mcmc(Tree, MCMCPars, PostprocessManager, ModelExtManager) - Constructor for class statalign.base.Mcmc

Mcmc(Tree, MCMCPars, PostprocessManager, ModelExtManager, int, int, double) - Constructor for class statalign.base.Mcmc

mcmc - Variable in class statalign.postprocess.Postprocess

TODO: REMOVE!!!!!!!!!!

mcmc - Variable in class statalign.postprocess.PostprocessManager

This is the Mcmc that is analyzed

McmcCombinationMove - Class in statalign.mcmc

McmcCombinationMove(ArrayList<McmcMove>) - Constructor for class statalign.mcmc.McmcCombinationMove

McmcModule - Class in statalign.mcmc

Generic class for a group of McmcMove objects.

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

McmcMove - Class in statalign.mcmc

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

mcmcpars - Variable in class statalign.base.Mcmc

MCMC parameters including the number of burn-in steps, the total number of steps in the MCMC and the sampling rate.

MCMCPars - Class in statalign.base

This is a container class containing the MCMC parameters described below.

MCMCPars(int, int, int, long, long, int) - Constructor for class statalign.base.MCMCPars

This constructor sets the values in the class

MCMCPars(int, int, int, long, long, int, int) - Constructor for class statalign.base.MCMCPars

This constructor sets the values in the class

McmcSettingsDlg - Class in statalign.ui

This is the dialog window where users can set MCMC parameters.

mcmcStep - Variable in class statalign.base.Mcmc

McmcStep - Class in statalign.base

Provides information on an MCMC step and additional MCMC statistics.

McmcStep() - Constructor for class statalign.base.McmcStep

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

mean(ArrayList<Double>) - Static method in class statalign.postprocess.plugins.benchmarks.Benchmarks

Calculates the mean from a list values

mean - Variable in class statalign.postprocess.Track

meanVector(RealMatrix) - Static method in class statalign.model.ext.plugins.structalign.Funcs

For an n X 3 coordinate matrix, calculate the 1 X 3 mean vector

menuName - Static variable in class statalign.model.subst.plugins.Blosum

menuName - Static variable in class statalign.model.subst.plugins.Dayhoff

menuName - Static variable in class statalign.model.subst.plugins.Felsenstein81

menuName - Static variable in class statalign.model.subst.plugins.Felsenstein84

menuName - Static variable in class statalign.model.subst.plugins.HKY85

menuName - Static variable in class statalign.model.subst.plugins.Jones

menuName - Static variable in class statalign.model.subst.plugins.JukesCantor

menuName - Static variable in class statalign.model.subst.plugins.Kimura3

menuName - Static variable in class statalign.model.subst.plugins.MtMam

menuName - Static variable in class statalign.model.subst.plugins.MtREV

menuName - Static variable in class statalign.model.subst.plugins.ReversibleNucleotide

menuName - Static variable in class statalign.model.subst.plugins.RtREV

menuName - Static variable in class statalign.model.subst.plugins.Tamura92

menuName - Static variable in class statalign.model.subst.plugins.TamuraNei

menuName - Static variable in class statalign.model.subst.plugins.Vt

menuName - Static variable in class statalign.model.subst.plugins.Wag

menuName - Static variable in class statalign.model.subst.SubstitutionModel

Sets the name of the model plugin that will appear in the menu when declared with the same name and type.

message - Variable in error statalign.model.subst.RecognitionError

The message of the error

min - Variable in class statalign.postprocess.Track

MIN_ACCEPTANCE - Static variable in class statalign.base.Utils

During the burnin, the proposalWidthControlVariable for all McmcMove objects is adjusted (if McmcMove.autoTune=true) in order to ensure that the average acceptance rate is between MIN_ACCEPTANCE and MAX_ACCEPTANCE where possible.

MIN_EDGE_LENGTH - Static variable in class statalign.base.Utils

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

Minimum value for epsilon, to prevent numerical errors.

MIN_SAMPLES_FOR_ACC_ESTIMATE - Static variable in class statalign.base.Utils

Number of samples during burnin used to get a rough estimate of the current acceptance rate, for the purposes of tuning the proposal variance control parameters.

MIN_SEQ_LENGTH - Static variable in class statalign.base.Utils

Minimum length for internal node sequence.

MIN_WINDOW_MULTIPLIER - Static variable in class statalign.base.mcmc.AlignmentMove

MIN_WINDOW_MULTIPLIER - Static variable in class statalign.model.ext.plugins.structalign.AlignmentMove

minAcceptance - Variable in class statalign.base.mcmc.AlignmentMove

minAcceptance - Variable in class statalign.mcmc.McmcMove

minAcceptance - Variable in class statalign.model.ext.plugins.structalign.AlignmentMove

MINEDGELEN - Static variable in class statalign.base.TreeAlgo

minMax(int, int, int) - Static method in class statalign.base.Utils

minorVersion - Static variable in class statalign.StatAlign

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

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

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

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

model - Variable in class statalign.base.InputData

The current substitution model that is used to analyse the sequences.

ModelExtension - Class in statalign.model.ext

Ancestral class for model extension plugins.

ModelExtension() - Constructor for class statalign.model.ext.ModelExtension

modelExtMan - Variable in class statalign.base.MainManager

Manager for model extension plugins

modelExtMan - Variable in class statalign.base.Mcmc

Manager that handles model extension plugins

ModelExtManager - Class in statalign.model.ext

Interface between StatAlign core and the ModelExtension plugins.

ModelExtManager(MainManager) - Constructor for class statalign.model.ext.ModelExtManager

modifyProposalWidths() - Method in class statalign.mcmc.McmcModule

modifyProposalWidths() - Method in class statalign.model.ext.ModelExtManager

modifySilentIndel(boolean) - Method in class statalign.base.Vertex

mostLikely(double[]) - Method in class statalign.model.subst.plugins.AminoAcidModel

Returns the most likely character given the Felsentein likelihood array.

mostLikely(double[]) - Method in class statalign.model.subst.plugins.NucleotideModel

Returns with the most likely character, given a Felsentein likelihood array.

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

mouseWheelMoved(MouseWheelEvent) - Method in class statalign.postprocess.gui.CNetworkView

It listens for mousewheel movement and sets the drawing appropriately.

mouseWheelMoved(MouseWheelEvent) - Method in class statalign.postprocess.gui.treeviews.NetworkTreeView

Event detector for mouse wheel movement.

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

moveDown(Vertex, List<Integer>) - Static method in class statalign.model.ext.plugins.structalign.Funcs

moveParams - Variable in class statalign.model.ext.plugins.structalign.AlignmentMove

moveParams - Variable in class statalign.model.ext.plugins.structalign.ContinuousPositiveStructAlignMove

moveParams - Variable in class statalign.model.ext.plugins.structalign.RotationOrTranslationMove

moveProposed - Variable in class statalign.mcmc.McmcMove

moveUp(Vertex, List<Integer>) - Static method in class statalign.model.ext.plugins.structalign.Funcs

mp13 - Static variable in class statalign.io.input.plugins.PDBReader

mp31 - Variable in class statalign.io.input.plugins.PDBReader

mpd - Variable in class statalign.postprocess.plugins.benchmarks.AlignmentSample

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

MpdAlignment - Class in statalign.postprocess.plugins

MpdAlignment() - Constructor for class statalign.postprocess.plugins.MpdAlignment

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

MPIUtils - Class in statalign

MPIUtils() - Constructor for class statalign.MPIUtils

MtMam - Class in statalign.model.subst.plugins

Implements the mammalian mitochondrial substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/9732458

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

Constructor used when instantiation is necessary.

MtREV - Class in statalign.model.subst.plugins

Implements the reversible mitochondrial substitution model, see also http://www.ncbi.nlm.nih.gov/pubmed/8642615

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

Constructor used when instantiation is necessary.

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

Adapted from org.apache.commons.math3.distribution.MultivariateNormalDistribution

MultiNormCholesky(double[], double[][]) - Constructor for class statalign.model.ext.plugins.structalign.MultiNormCholesky

Creates a multivariate normal distribution with the given mean vector and covariance matrix.

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

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

MultiplicativeProposal - Class in statalign.mcmc

Proposal that multiplies the current parameter by a log-normally distributed variable, which is equivalent to a Gaussian random walk on the logarithm of the parameter.

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

MuMove - Class in statalign.base.mcmc

MuMove(McmcModule, PriorDistribution<Double>, ProposalDistribution<Double>, String) - Constructor for class statalign.base.mcmc.MuMove