statalign.model.ext.plugins
Class RNAAliFold

java.lang.Object
  statalign.mcmc.McmcModule
      statalign.model.ext.ModelExtension
          statalign.model.ext.plugins.RNAAliFold

public class RNAAliFold
extends ModelExtension

Field Summary

Fields inherited from class statalign.mcmc.McmcModule

curLogLike, printExtraInfo

Constructor Summary

RNAAliFold()

Method Summary

java.lang.String	getPluginID()
java.lang.String	getUsageInfo() Prints the usage information for this plugin.
void	init() Called during StatAlign startup, after all ModelExtension plugins have been loaded and command line arguments have been processed (if present).
double	logLikeFactor(Tree tree) This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space.
void	setActive(boolean active) Enables or disables this plugin.
void	setParam(java.lang.String paramName, boolean paramValue)
void	setParam(java.lang.String paramName, java.lang.String paramValue) This function is called when command line arguments are specified for a plugin.

Methods inherited from class statalign.model.ext.ModelExtension

addToFilenameExtension, afterAlignChange, afterEdgeLenChange, afterIndelParamChange, afterModExtParamChange, afterSubstParamChange, afterTreeChange, beforeAlignChange, beforeEdgeLenChange, beforeIndelParamChange, beforeModExtParamChange, beforeSubstParamChange, beforeTreeChange, calcLogEm, dataAdded, getFilenameExtension, getParamChangeWeight, getPluginList, getToolBarItems, initRun, isActive, isParamChangeAccepted, isSelectable, logLikeAlignChange, logLikeEdgeLenChange, logLikeIndelParamChange, logLikeModExtParamChange, logLikeSubstParamChange, logLikeTreeChange, setManager, setParam, useInAlignmentProposals

Methods inherited from class statalign.mcmc.McmcModule

addMcmcMove, addMcmcMove, afterFirstHalfBurnin, afterSampling, beforeSampling, getLogLike, getMcmcInfo, getMcmcMove, getMcmcMoves, incrementWeights, isFirstHalfBurnin, logPrior, modifyProposalWidths, proposeParamChange, setAllMovesNotProposed, setLogLike, setMcmc, setWeight, zeroAllMoveCounts

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RNAAliFold

public RNAAliFold()

Method Detail

getPluginID

public java.lang.String getPluginID()

Overrides:

getPluginID in class ModelExtension

Returns:

The command line identifier string for the plugin.

logLikeFactor

public double logLikeFactor(Tree tree)

Description copied from class: McmcModule

This should return the log of the model's contribution to the likelihood, it will be added on to the log-likelihood of the current point in the MCMC state space. Normally it will be called once at the initialisation of the MCMC process and from then on once in each MCMC step, when proposing any change. In debug mode, will be called more often (including after proposed changes) to ensure consistency.

Specified by:

logLikeFactor in class McmcModule

Parameters:

tree - current tree

Returns:

log of model extension likelihood, conditional on current tree, alignment and params

setActive

public void setActive(boolean active)

Description copied from class: ModelExtension

Enables or disables this plugin.

Overrides:

setActive in class ModelExtension

Parameters:

active - true if plugin should be enabled

setParam

public void setParam(java.lang.String paramName,
                     boolean paramValue)

Overrides:

setParam in class ModelExtension

setParam

public void setParam(java.lang.String paramName,
                     java.lang.String paramValue)

Description copied from class: ModelExtension

This function is called when command line arguments are specified for a plugin. If the specific ModelExtension does not override these methods then it cannot handle any command line arguments, and so the default error is returned. The overriding method should call super.setParam(paramName,paramValue) in the case that paramName is unrecognised. An overriding method can also include a call such as addToFilenameExtension(paramName+"_"+paramValue); which will result in an informative string being appended to the names of any output files generated by the Postprocess plugins.

Overrides:

setParam in class ModelExtension

Parameters:

paramName - The name of a parameter that is to be set.

paramValue - The value to which it will be set.

init

public void init()

Description copied from class: ModelExtension

Called during StatAlign startup, after all ModelExtension plugins have been loaded and command line arguments have been processed (if present).

Overrides:

init in class ModelExtension

getUsageInfo

public java.lang.String getUsageInfo()

Description copied from class: ModelExtension

Prints the usage information for this plugin.

Overrides:

getUsageInfo in class ModelExtension