statalign.model.ext.plugins
Class PPFold

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

public class PPFold
extends ModelExtension

Field Summary

Fields inherited from class statalign.mcmc.McmcModule

curLogLike, printExtraInfo

Constructor Summary

PPFold()

Method Summary

java.lang.String	getPluginID()
java.lang.String	getUsageInfo() Prints the usage information for this plugin.
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)

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, init, initRun, isActive, isParamChangeAccepted, isSelectable, logLikeAlignChange, logLikeEdgeLenChange, logLikeIndelParamChange, logLikeModExtParamChange, logLikeSubstParamChange, logLikeTreeChange, setManager, setParam, 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

PPFold

public PPFold()

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

getUsageInfo

public java.lang.String getUsageInfo()

Description copied from class: ModelExtension

Prints the usage information for this plugin.

Overrides:

getUsageInfo in class ModelExtension