Uses of Class
statalign.mcmc.McmcMove

Packages that use McmcMove

statalign.base
statalign.base.mcmc
statalign.mcmc
statalign.model.ext
statalign.model.ext.plugins
statalign.model.ext.plugins.structalign

Uses of McmcMove in statalign.base

Methods in statalign.base with parameters of type McmcMove

boolean

Mcmc.isParamChangeAccepted(double logProposalRatio, McmcMove m) This function is called by the McmcMove objects in order to determine whether the proposed moves are to be accepted.

Uses of McmcMove in statalign.base.mcmc

Subclasses of McmcMove in statalign.base.mcmc

class	AlignmentMove
class	AllEdgeMove
class	EdgeMove
class	IndelMove
class	LambdaMove
class	LOCALTopologyMove
class	MuMove
class	PhiMove
class	RhoMove
class	RMove
class	SilentIndelMove
class	SubstMove
class	ThetaMove
class	TopologyMove

Uses of McmcMove in statalign.mcmc

Subclasses of McmcMove in statalign.mcmc

class	ContinuousPositiveParameterMove
class	McmcCombinationMove

Methods in statalign.mcmc that return McmcMove

McmcMove

McmcModule.getMcmcMove(java.lang.String name)

Methods in statalign.mcmc that return types with arguments of type McmcMove

java.util.List<McmcMove>

McmcModule.getMcmcMoves()

Methods in statalign.mcmc with parameters of type McmcMove

void	McmcModule.addMcmcMove(McmcMove m, int weight)
void	McmcModule.addMcmcMove(McmcMove m, int weight, int increment)
boolean	McmcModule.isParamChangeAccepted(double logProposalRatio, McmcMove m)

Constructor parameters in statalign.mcmc with type arguments of type McmcMove

McmcCombinationMove(java.util.ArrayList<McmcMove> moves)

Uses of McmcMove in statalign.model.ext

Methods in statalign.model.ext with parameters of type McmcMove

void	ModelExtManager.afterIndelParamChange(Tree tree, Hmm hmm, McmcMove m, boolean accepted)
void	ModelExtension.afterIndelParamChange(Tree tree, Hmm hmm, McmcMove m, boolean accepted) Called after a proposed indel parameter change (accepted or rejected).
void	ModelExtManager.beforeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)
void	ModelExtension.beforeIndelParamChange(Tree tree, Hmm hmm, McmcMove m) Called before an indel parameter change is proposed, but after the affected parameter is selected.
boolean	ModelExtManager.isParamChangeAccepted(double logProposalRatio, McmcMove m)
boolean	ModelExtension.isParamChangeAccepted(double logProposalRatio, McmcMove m) Should be called from McmcModule.proposeParamChange(Tree) to find out whether a proposed parameter change was accepted.
double	ModelExtManager.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m) Calculates the total log-likelihood of the state by adding the log-likelihood factor contributions from all model extension plugins to the log-likelihood of the tree.
double	ModelExtension.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)

Uses of McmcMove in statalign.model.ext.plugins

Methods in statalign.model.ext.plugins with parameters of type McmcMove

double

StructAlign.logLikeIndelParamChange(Tree tree, Hmm hmm, McmcMove m)

Uses of McmcMove in statalign.model.ext.plugins.structalign

Subclasses of McmcMove in statalign.model.ext.plugins.structalign

class	ContinuousPositiveStructAlignMove
class	HierarchicalContinuousPositiveStructAlignMove
class	LibraryMove
class	RotationMove
class	RotationOrTranslationMove
class	TranslationMove