Uses of Class
statalign.mcmc.McmcModule

Packages that use McmcModule

statalign.base
statalign.base.mcmc
statalign.mcmc
statalign.model.ext
statalign.model.ext.plugins
statalign.postprocess
statalign.postprocess.plugins

Uses of McmcModule in statalign.base

Fields in statalign.base declared as McmcModule

McmcModule

Mcmc.coreModel McmcModule containing the moves for the core components of the model, i.e. the indel parameters, substitution model parameters, alignment, topology and edge lengths.

Uses of McmcModule in statalign.base.mcmc

Subclasses of McmcModule in statalign.base.mcmc

class

CoreMcmcModule curLogLike for this McmcModule includes the contributions from the ModelExtensions.

Constructors in statalign.base.mcmc with parameters of type McmcModule

AlignmentMove(McmcModule m, double _P, java.lang.String n)

AllEdgeMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

EdgeMove(McmcModule m, int edgeIndex, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, double propVar, java.lang.String n)

EdgeMove(McmcModule m, int edgeIndex, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

IndelMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

LambdaMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

LOCALTopologyMove(McmcModule m, PriorDistribution<java.lang.Double> pr, double propVar, double _fastSwapProb, java.lang.String n)

MuMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

PhiMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

RhoMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

RMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

SilentIndelMove(McmcModule m, java.lang.String n)

SubstMove(McmcModule m, java.lang.String n)

ThetaMove(McmcModule m, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

TopologyMove(McmcModule m, PriorDistribution<java.lang.Double> pr, double propVar, double _fastSwapProb, java.lang.String n)

Uses of McmcModule in statalign.mcmc

Methods in statalign.mcmc that return McmcModule

McmcModule	McmcMove.getOwner()
McmcModule	McmcCombinationMove.getOwner()

Constructors in statalign.mcmc with parameters of type McmcModule

ContinuousPositiveParameterMove(McmcModule m, ParameterInterface p, PriorDistribution<java.lang.Double> pr, ProposalDistribution<java.lang.Double> prop, java.lang.String n)

Uses of McmcModule in statalign.model.ext

Subclasses of McmcModule in statalign.model.ext

class

ModelExtension Ancestral class for model extension plugins.

Uses of McmcModule in statalign.model.ext.plugins

Subclasses of McmcModule in statalign.model.ext.plugins

class	PPFold
class	RNAAliFold
class	StructAlign

Uses of McmcModule in statalign.postprocess

Methods in statalign.postprocess with parameters of type McmcModule

void	PostprocessManager.newSample(McmcModule coreModel, State state, int no, int total) Calls the plug-ins at a new sample.
void	Postprocess.newSample(McmcModule coreModel, State state, int no, int total)

Uses of McmcModule in statalign.postprocess.plugins

Methods in statalign.postprocess.plugins with parameters of type McmcModule

void	LogLikelihoodTrace.newSample(McmcModule coreModel, State state, int no, int total) Writes the loglikelihoods into a logfile, if sampling mode is switched on.