statalign.model.ext.plugins
Class PPFold

java.lang.Object
  extended by statalign.mcmc.McmcModule
      extended by statalign.model.ext.ModelExtension
          extended by 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