Uses of Class
statalign.base.State

Packages that use State

statalign.base
statalign.postprocess
statalign.postprocess.plugins
statalign.postprocess.plugins.structalign

Uses of State in statalign.base

Methods in statalign.base that return State

State	Tree.getState() Returns a State object representing the current state.
State	Mcmc.getState() Returns a State object that describes the current state of the MCMC.

Uses of State in statalign.postprocess

Methods in statalign.postprocess with parameters of type State

void	Postprocess.newPeek(State state) Allows peeking into the Markov chain before actual sampling begins.
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)
void	Postprocess.newSample(State state, int no, int total) This function is called when we sample from the Markov chain.

Uses of State in statalign.postprocess.plugins

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

void	CurrentTreeVisualizer.newPeek(State state)
void	CurrentAlignment.newPeek(State state) Updates the alignment.
void	LogLikelihoodTrace.newSample(McmcModule coreModel, State state, int no, int total) Writes the loglikelihoods into a logfile, if sampling mode is switched on.
void	VisualDistance.newSample(State state, int no, int total)
void	Structure.newSample(State state, int no, int total)
void	PPFold.newSample(State state, int no, int total)
void	MpdAlignment.newSample(State state, int no, int total)
void	Entropy.newSample(State state, int no, int total) Writes the loglikelihoods into a logfile, if sampling mode is switched on.
void	CurrentTreeVisualizer.newSample(State state, int no, int total)
void	CurrentAlignment.newSample(State state, int no, int total) At each mcmc sampling point, the current alignment is shown on the GUI.
void	ConsensusTreeVisualizer.newSample(State state, int no, int total)
void	ConsensusNetwork.newSample(State state, int no, int total) At each MCMC sampling point, the current alignment is shown on the GUI.

Uses of State in statalign.postprocess.plugins.structalign

Methods in statalign.postprocess.plugins.structalign with parameters of type State

void	StructTrace.newPeek(State state)
void	RmsdTrace.newPeek(State state)
void	StructTrace.newSample(State state, int no, int total)
void	RmsdTrace.newSample(State state, int no, int total)