aloneinterfaces
Class AloneProcessus

java.lang.Object
  aloneinterfaces.AloneProcessus

All Implemented Interfaces:

java.lang.Runnable

public class AloneProcessus
extends java.lang.Object
implements java.lang.Runnable

Main item of graphical interface (it is NOT a graphical item), it is used for computing and drive the user from interface to interface

Author:

Stéfan Engelen (2006), Gabriel Chandesris (2008)

Field Summary

private java.lang.Thread	actif
private SequenceListe	allSequences
private java.awt.CardLayout	card
private Sequence	cible
private int	courant
private int	destination
private javax.swing.JInternalFrame	fenetre
private Interface0	int0 To choose / input alignment (and aligned) Sequence).
private Interface1	int1 To choose cible and homologuous sequences then launch searching palindromes...
private Interface10	int10 To records results as text and graphic for RNAviz.
private Interface11	int11 To see profiles of sequences and of a palindrome...
private Interface12	int12 Results of profiles (from Interface11).
private Interface2	int2 To choose an Optimal result.
private Interface3	int3 To visualize results of searching palindromes and different sets of selected sequences from Interface1.
private Interface4	int4 To check palindromes (results in Interface5).
private Interface5	int5 Result of checking palindromes (from Interface4).
private Interface6	int6 To select and launch a zone prediction (results in Interface7).
private Interface7	int7 Results of zone prediction (from Interface6).
private Interface8	int8 To compare two results files in FichierConvert (ct) format.
private Interface9	int9 Results of results comparison (from Interface8).
private SequenceListe[]	optim
private SequenceListe[]	other
private javax.swing.JProgressBar	progressBar
private PalindromeListeListe	results
private boolean	stop
private Interface[]	tabInterface
private int	temps

Constructor Summary

AloneProcessus(int temps)
Constructor.

AloneProcessus(javax.swing.JInternalFrame fenetre)
Constructor.

Method Summary

void	afficherProgressBar(int min, int max, Interface1 inter) Progression Bar is inserted in interface.
void	arreter() Stop AloneProcessus for a computing time or as user ask.
void	avance() AloneProcessus instance is driving and get the destination token to select and visualize the good interface with content.
void	avanceProgressBar(int val) When computing, to make progression bar to progress.
void	changerDestination(int destination) Destination / interface is changed for user.
void	deplacement() AloneProcessus moving control.
private void	getQueueTrans() Getting alignment sequences and queuing them.
void	recule() Go to previous step.
void	run()
void	start() When current instance is launched.
void	termineProgressBar(Interface1 inter) Stop Progression Bar.
private void	testSequencesChoice() To find the good Sequences to use for computing.

Methods inherited from class java.lang.Object

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

Field Detail

fenetre

private javax.swing.JInternalFrame fenetre

tabInterface

private Interface[] tabInterface

card

private java.awt.CardLayout card

progressBar

private javax.swing.JProgressBar progressBar

courant

private int courant

destination

private int destination

temps

private int temps

stop

private boolean stop

actif

private java.lang.Thread actif

cible

private Sequence cible

other

private SequenceListe[] other

optim

private SequenceListe[] optim

results

private PalindromeListeListe results

allSequences

private SequenceListe allSequences

int0

private Interface0 int0

To choose / input alignment (and aligned) Sequence).

See Also:

Interface0

int1

private Interface1 int1

To choose cible and homologuous sequences then launch searching palindromes...

See Also:

Interface1

int2

private Interface2 int2

To choose an Optimal result.

See Also:

Interface2

int3

private Interface3 int3

To visualize results of searching palindromes and different sets of selected sequences from Interface1.

See Also:

Interface3

int4

private Interface4 int4

To check palindromes (results in Interface5).

See Also:

Interface4

int5

private Interface5 int5

Result of checking palindromes (from Interface4).

See Also:

Interface5

int6

private Interface6 int6

To select and launch a zone prediction (results in Interface7).

int7

private Interface7 int7

Results of zone prediction (from Interface6).

int8

private Interface8 int8

To compare two results files in FichierConvert (ct) format.

See Also:

Interface8, FichierConvert

int9

private Interface9 int9

Results of results comparison (from Interface8).

int10

private Interface10 int10

To records results as text and graphic for RNAviz.

See Also:

Interface10

int11

private Interface11 int11

To see profiles of sequences and of a palindrome...

See Also:

Interface11

int12

private Interface12 int12

Results of profiles (from Interface11).

See Also:

Interface12

Constructor Detail

AloneProcessus

public AloneProcessus(int temps)

Constructor.

Parameters:

temps - int

AloneProcessus

public AloneProcessus(javax.swing.JInternalFrame fenetre)

Constructor.

Parameters:

fenetre - int

Method Detail

start

public void start()

When current instance is launched.

See Also:

run()

run

public void run()

Specified by:

run in interface java.lang.Runnable

arreter

public void arreter()

Stop AloneProcessus for a computing time or as user ask.

See Also:

run(), Interface.actionPerformed(java.awt.event.ActionEvent), Interface1.actionPerformed(java.awt.event.ActionEvent), Interface2.actionPerformed(java.awt.event.ActionEvent), Interface3.actionPerformed(java.awt.event.ActionEvent), Interface4.actionPerformed(java.awt.event.ActionEvent), Interface5.actionPerformed(java.awt.event.ActionEvent), Interface6.actionPerformed(java.awt.event.ActionEvent), Interface7.actionPerformed(java.awt.event.ActionEvent), Interface8.actionPerformed(java.awt.event.ActionEvent), Interface9.actionPerformed(java.awt.event.ActionEvent), Interface11.actionPerformed(java.awt.event.ActionEvent), Interface12.actionPerformed(java.awt.event.ActionEvent)

getQueueTrans

private void getQueueTrans()

Getting alignment sequences and queuing them.

testSequencesChoice

private void testSequencesChoice()

To find the good Sequences to use for computing.
Use this.cible ; this.allSequences ; this.int1.getSelectionInt() ; this.int1.getSelectionbool()
set a value to this.other...

avance

public void avance()

AloneProcessus instance is driving and get the destination token to select and visualize the good interface with content.

recule

public void recule()

Go to previous step.

See Also:

avance()

deplacement

public void deplacement()

AloneProcessus moving control.

See Also:

avance(), recule()

changerDestination

public void changerDestination(int destination)

Destination / interface is changed for user.

Parameters:

destination - int

See Also:

Interface0.actionPerformed(java.awt.event.ActionEvent), Interface1.actionPerformed(java.awt.event.ActionEvent), Interface1.valueChanged(javax.swing.event.ListSelectionEvent), Interface2.actionPerformed(java.awt.event.ActionEvent), Interface3.actionPerformed(java.awt.event.ActionEvent), Interface4.actionPerformed(java.awt.event.ActionEvent), Interface5.actionPerformed(java.awt.event.ActionEvent), Interface6.actionPerformed(java.awt.event.ActionEvent), Interface7.actionPerformed(java.awt.event.ActionEvent), Interface8.actionPerformed(java.awt.event.ActionEvent), Interface9.actionPerformed(java.awt.event.ActionEvent), Interface10.actionPerformed(java.awt.event.ActionEvent), Interface11.actionPerformed(java.awt.event.ActionEvent), Interface12.actionPerformed(java.awt.event.ActionEvent)

afficherProgressBar

public void afficherProgressBar(int min,
                                int max,
                                Interface1 inter)

Progression Bar is inserted in interface.

Parameters:

min - int

max - int

inter - Interface1

See Also:

avance(), Interface1

termineProgressBar

public void termineProgressBar(Interface1 inter)

Stop Progression Bar. Arrêt de la barre de progression et retrait de l'interface graphique.

Parameters:

inter - Interface1

See Also:

avance(), Interface1

avanceProgressBar

public void avanceProgressBar(int val)

When computing, to make progression bar to progress.

Parameters:

val - int

See Also:

avance(), Interface1