statalign.base
Class Input

java.lang.Object
  statalign.postprocess.Postprocess
      statalign.base.Input

public class Input
extends Postprocess

This class is an extension of the Postprocess class and is for showing the actual input sequences.

Author:

miklos, novak

Field Summary

InputGUI

inputgui this is the graphical interface

Fields inherited from class statalign.postprocess.Postprocess

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

Constructor Summary

Input(MainManager manager)
A trivial constructor.

Method Summary

void	afterLastSample() This is an empty function.
void	beforeFirstSample() This is an empty function.
javax.swing.Icon	getIcon()
javax.swing.JPanel	getJPanel()
java.lang.String	getTabName()
double	getTabOrder() Specifies the order of the tab for this plugin in the GUI.
java.lang.String	getTip() Returns with the tip information (shown when the mouse cursor is moved over the label of the tabulated panel)
void	newStep() This is an empty function.
void	setSampling(boolean enabled) This is an empty function.

Methods inherited from class statalign.postprocess.Postprocess

addTrack, beforeFirstSample, getDependences, getFileExtension, getModExtPlugins, getToolBarItems, getTracks, init, newPeek, newSample, newSample, newStep, refToDependences, reloadPanel, setSelected

Methods inherited from class java.lang.Object

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

Field Detail

inputgui

public InputGUI inputgui

this is the graphical interface

Constructor Detail

Input

public Input(MainManager manager)

A trivial constructor. Only sets the MainManager of this object.

Parameters:

manager - the MainManager via that the object could communicate and can get information.

Method Detail

getJPanel

public javax.swing.JPanel getJPanel()

Specified by:

getJPanel in class Postprocess

Returns:

Returns with the panel of the GUI

getIcon

public javax.swing.Icon getIcon()

Specified by:

getIcon in class Postprocess

Returns:

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

getTabName

public java.lang.String getTabName()

Specified by:

getTabName in class Postprocess

Returns:

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

getTip

public java.lang.String getTip()

Description copied from class: Postprocess

Returns with the tip information (shown when the mouse cursor is moved over the label of the tabulated 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.

newStep

public void newStep()

This is an empty function. Indeed we do not have to do anything with the input data when the MCMC makes a new step.

beforeFirstSample

public void beforeFirstSample()

This is an empty function. Indeed we do not have to do anything with the input data before the first step in the MCMC run.

afterLastSample

public void afterLastSample()

This is an empty function. Indeed we do not have to do anything with the input data after the last step in the MCMC run.

Overrides:

afterLastSample in class Postprocess

setSampling

public void setSampling(boolean enabled)

This is an empty function. Never used but has to be implemented as the class extends the Prostrocess class

Specified by:

setSampling in class Postprocess

Parameters:

enabled - Set it true if you need samples.