statalign.postprocess.plugins
Class MpdAlignment

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

public class MpdAlignment
extends Postprocess

Field Summary

int	frequency
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

MpdAlignment()

Method Summary

void	afterLastSample() This function is called after the MCMC runs.
void	beforeFirstSample(InputData input) Called before MCMC start.
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()
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	newSample(State state, int no, int total) This function is called when we sample from the Markov chain.
void	refToDependences(Postprocess[] plugins) Override this to get access to instances of the plugins your plugin depends on.
void	setSampling(boolean enabled) This function switches on or off the sampling mode.

Methods inherited from class statalign.postprocess.Postprocess

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

frequency

public int frequency

Constructor Detail

MpdAlignment

public MpdAlignment()

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.

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

beforeFirstSample

public void beforeFirstSample(InputData input)

Description copied from class: Postprocess

Called before MCMC start. This is the first time you can use PostprocessManager.mcmc to access internal data structure

Overrides:

beforeFirstSample in class Postprocess

newSample

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

Description copied from class: Postprocess

This function is called when we sample from the Markov chain. Frequency is determined by the MCMC sampling parameter set by the user. Unlike Postprocess.newPeek(State state), this method is only called after the burn-in period.

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

afterLastSample

public void afterLastSample()

Description copied from class: Postprocess

This function is called after the MCMC runs.

Overrides:

afterLastSample in class Postprocess

setSampling

public void setSampling(boolean enabled)

Description copied from class: Postprocess

This function switches on or off the sampling mode.

Specified by:

setSampling in class Postprocess

Parameters:

enabled - Set it true if you need samples.