statalign.postprocess.plugins
Class Entropy

java.lang.Object
  statalign.postprocess.Postprocess
      statalign.postprocess.plugins.Entropy

public class Entropy
extends Postprocess

This is the implementation of the postprocess that handles entropy.

Author:

Preeti Arunapuram

Field Summary

static boolean	allowed
java.util.ArrayList<EntropyContainer>	entropyList
java.lang.String	title

Fields inherited from class statalign.postprocess.Postprocess

active, alignmentType, file, hasToolBar, mcmc, outputable, outputFile, postprocessable, postprocessWrite, rnaAssociated, sampling, screenable, selected, show

Constructor Summary

Entropy()
It constructs a postprocess handler that is screenable (=can be shown on the GUI), outputable (= can be written into the log file) and postprocessable (= can generate its own output file).

Method Summary

void	afterLastSample() It writes the sampled loglikelihood values into a separate file.
void	beforeFirstSample(InputData input) Initialises the graphical interface.
java.lang.String[]	getDependences() Override this and return an array of full-qualified class names of the plugins this plugin depends on.
java.lang.String	getFileExtension() Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.
javax.swing.Icon	getIcon() Returns the icon generated from the picture in file icons/loglikelihood1.gif.
javax.swing.JPanel	getJPanel() It generates a panel and returns it.
java.lang.String	getTabName() Returns the name of the postprocess, 'Loglikelihood'.
double	getTabOrder() Specifies the order of the tab for this plugin in the GUI.
java.lang.String	getTip() Returns the tip of the tabulated panel 'Log-likelihood trace' (shown when mouse is moved over the panel)
void	newSample(State state, int no, int total) Writes the loglikelihoods into a logfile, if sampling mode is switched on.
void	refToDependences(Postprocess[] plugins) Override this to get access to instances of the plugins your plugin depends on.
void	reloadPanel() Reinitializes panel to accommodate a new GUI
void	setSampling(boolean enabled) It switches on and off the sampling mode.

Methods inherited from class statalign.postprocess.Postprocess

addTrack, getModExtPlugins, getToolBarItems, getTracks, init, newPeek, newSample, newStep, setSelected

Methods inherited from class java.lang.Object

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

Field Detail

title

public java.lang.String title

entropyList

public java.util.ArrayList<EntropyContainer> entropyList

allowed

public static boolean allowed

Constructor Detail

Entropy

public Entropy()

It constructs a postprocess handler that is screenable (=can be shown on the GUI), outputable (= can be written into the log file) and postprocessable (= can generate its own output file). The default setting is that it writes loglikelihoods both into the logfile and its own output file.

Method Detail

getTabName

public java.lang.String getTabName()

Returns the name of the postprocess, 'Loglikelihood'.

Specified by:

getTabName in class Postprocess

Returns:

Returns with the name that will appear on the label of the tabulated panel.

getIcon

public javax.swing.Icon getIcon()

Returns the icon generated from the picture in file icons/loglikelihood1.gif.

Specified by:

getIcon in class Postprocess

Returns:

Returns with the icon that will appear on the label of the tabulated panel.

getJPanel

public javax.swing.JPanel getJPanel()

It generates a panel and returns it.

Specified by:

getJPanel in class Postprocess

Returns:

Returns with the panel of the GUI

reloadPanel

public void reloadPanel()

Description copied from class: Postprocess

Reinitializes panel to accommodate a new GUI

Overrides:

reloadPanel in class Postprocess

getTip

public java.lang.String getTip()

Returns the tip of the tabulated panel 'Log-likelihood trace' (shown when mouse is moved over the panel)

Specified by:

getTip in class Postprocess

getTabOrder

public double getTabOrder()

Description copied from class: Postprocess

Specifies the order of the tab for this plugin in the GUI.

E.g. we probably always want the "sequence input"-tab to appear first and therefore it returns a 1.0d here. The "current alignment"-tab returns 2.0d here and so if we want to make a tab get ordered between the "sequence input" and the "current alignment"-tabs we just make that plugin return 1.5d or something similar here. By default tabs get ordered last.

Overrides:

getTabOrder in class Postprocess

Returns:

the tab order of the tab associated with this plugin, if running in a GUI.

getFileExtension

public java.lang.String getFileExtension()

Description copied from class: Postprocess

Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.

Overrides:

getFileExtension in class Postprocess

getDependences

public java.lang.String[] getDependences()

Description copied from class: Postprocess

Override this and return an array of full-qualified class names of the plugins this plugin depends on.

Overrides:

getDependences in class Postprocess

refToDependences

public void refToDependences(Postprocess[] plugins)

Description copied from class: Postprocess

Override this to get access to instances of the plugins your plugin depends on. This function will be called by the PostprocessManager during its initialisation.

Overrides:

refToDependences in class Postprocess

Parameters:

plugins - reference to Postprocess objects in the order they are specified in getDependences() or null if it returns null

newSample

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

Writes the loglikelihoods into a logfile, if sampling mode is switched on.

Overrides:

newSample in class Postprocess

Parameters:

state - A State object representing the current state of the chain

no - The number of the current sample

total - The number of the total samples

beforeFirstSample

public void beforeFirstSample(InputData input)

Initialises the graphical interface.

Overrides:

beforeFirstSample in class Postprocess

afterLastSample

public void afterLastSample()

It writes the sampled loglikelihood values into a separate file.

Overrides:

afterLastSample in class Postprocess

setSampling

public void setSampling(boolean enabled)

It switches on and off the sampling mode.

Specified by:

setSampling in class Postprocess

Parameters:

enabled - Set it true if you need samples.