statalign.postprocess.plugins
Class Structure

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

public class Structure
extends Postprocess

Field Summary

static java.lang.String	currentDotBracketStructure
static java.lang.String	currentSequence
PPFold	ppfold
static float[][]	probMatrix
static float[]	singleMatrix
java.lang.String	title Postprocess which handles the consensus structure generated by PPFold.

Fields inherited from class statalign.postprocess.Postprocess

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

Constructor Summary

Structure()

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.
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)
java.util.ArrayList<javax.swing.JComponent>	getToolBarItems() Returns the toolbar that this plugin uses.
void	init(ModelExtManager manager) Called by PostprocessManager after setting the Postprocess.show field to allow initialisation, possibly involving GUI (toolbar etc.)
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	reloadPanel() Reinitializes panel to accommodate a new GUI
void	setSampling(boolean enabled) This function switches on or off the sampling mode.
static void	updateBasePairMatrix(float[][] newMatrix)
void	updateSequence()
static void	updateSingleMatrix(float[] newMatrix)
static void	updateStructure()

Methods inherited from class statalign.postprocess.Postprocess

addTrack, getFileExtension, getModExtPlugins, getTracks, 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

Postprocess which handles the consensus structure generated by PPFold.

probMatrix

public static float[][] probMatrix

singleMatrix

public static float[] singleMatrix

currentSequence

public static java.lang.String currentSequence

currentDotBracketStructure

public static java.lang.String currentDotBracketStructure

ppfold

public PPFold ppfold

Constructor Detail

Structure

public Structure()

Method Detail

init

public void init(ModelExtManager manager)

Description copied from class: Postprocess

Called by PostprocessManager after setting the Postprocess.show field to allow initialisation, possibly involving GUI (toolbar etc.)

Overrides:

init in class Postprocess

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.

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.

getJPanel

public javax.swing.JPanel getJPanel()

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()

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.

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.

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

updateBasePairMatrix

public static void updateBasePairMatrix(float[][] newMatrix)

updateSingleMatrix

public static void updateSingleMatrix(float[] newMatrix)

updateStructure

public static void updateStructure()

updateSequence

public void updateSequence()

getToolBarItems

public java.util.ArrayList<javax.swing.JComponent> getToolBarItems()

Description copied from class: Postprocess

Returns the toolbar that this plugin uses.

Overrides:

getToolBarItems in class Postprocess

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