statalign.postprocess
Class PostprocessManager

java.lang.Object
  statalign.postprocess.PostprocessManager

public class PostprocessManager
extends java.lang.Object

This class manages the postprocesses.

Author:

miklos, novak

Field Summary

java.io.FileWriter	logFile This is the log-file writer
MainManager	mainManager This is the Main manager that manages the MCMC run.
Mcmc	mcmc This is the Mcmc that is analyzed
static PluginParameters	pluginParameters Static object holding parameters, which are visible to all plugins.
static boolean	rnaMode

Constructor Summary

PostprocessManager(MainManager mainManager)
This constructor recognizes the plugins

Method Summary

void	afterLastSample() It is called after the last sample of MCMC.
void	beforeFirstSample() This function invoked before the first sample.
void	createPluginFiles()
void	flushAll()
java.lang.String	getBaseFileName()
java.util.List<Postprocess>	getPlugins()
void	init(ModelExtManager modelExtMan)
void	newPeek() Calls the plug-ins after an MCMC step.
void	newSample(McmcModule coreModel, State state, int no, int total) Calls the plug-ins at a new sample.
void	newStep(McmcStep step) Calls the plug-ins after an MCMC step.
void	setBaseFileName(java.lang.String s)
void	updateSelectedList()

Methods inherited from class java.lang.Object

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

Field Detail

mcmc

public Mcmc mcmc

This is the Mcmc that is analyzed

logFile

public java.io.FileWriter logFile

This is the log-file writer

mainManager

public MainManager mainManager

This is the Main manager that manages the MCMC run.

rnaMode

public static boolean rnaMode

pluginParameters

public static PluginParameters pluginParameters

Static object holding parameters, which are visible to all plugins.

Constructor Detail

PostprocessManager

public PostprocessManager(MainManager mainManager)

This constructor recognizes the plugins

Parameters:

mainManager - The MainManager that manages the MCMC run.

Method Detail

getBaseFileName

public java.lang.String getBaseFileName()

setBaseFileName

public void setBaseFileName(java.lang.String s)

getPlugins

public java.util.List<Postprocess> getPlugins()

createPluginFiles

public void createPluginFiles()

init

public void init(ModelExtManager modelExtMan)

beforeFirstSample

public void beforeFirstSample()

This function invoked before the first sample. It opens information chanels towards postrocessing plug-ins.

newSample

public void newSample(McmcModule coreModel,
                      State state,
                      int no,
                      int total)

Calls the plug-ins at a new sample.

Parameters:

no - The number of the current sample

total - The total number of samples.

newStep

public void newStep(McmcStep step)

Calls the plug-ins after an MCMC step.

flushAll

public void flushAll()

newPeek

public void newPeek()

Calls the plug-ins after an MCMC step.

afterLastSample

public void afterLastSample()

It is called after the last sample of MCMC. It calls plug-ins to finalize their postprocessing activities.

updateSelectedList

public void updateSelectedList()