Serialized Form

Package alonecontroller

Class alonecontroller.AloneApplet extends java.applet.Applet implements Serializable

serialVersionUID: 42L

Package aloneinterfaces

Class aloneinterfaces.Interface extends javax.swing.JPanel implements Serializable

Serialized Fields

fenetre

javax.swing.JPanel fenetre

Background interface image.

processusParent

AloneProcessus processusParent

Parent Processus.

See Also:

AloneProcessus

dacodac

javax.swing.JButton dacodac

Bouton OK.

menu

javax.swing.JComboBox menu

Selection Menu.

monlayout

MonLayout monlayout

Current layout.

font

java.awt.Font font

Visualization text.

background

java.awt.Color background

Background color.

foreground

java.awt.Color foreground

Foreground color.

Class aloneinterfaces.Interface0 extends Interface implements Serializable

serialVersionUID: 0L

Serialized Fields

texteFichier

javax.swing.JTextField texteFichier

File name area visualization.

texteSequence

javax.swing.JTextArea texteSequence

Area where user can paste alignment.

sauver

javax.swing.JRadioButton sauver

Save / recording button.

parcourir

MonBouton parcourir

To select FASTA format file alignment.

aide

javax.swing.JLabel aide

Help area.

nomfichier

java.lang.String nomfichier

Interface memory.

alignement

java.lang.String alignement

Interface memory.

sauverFasta

boolean sauverFasta

To remember to record.

Class aloneinterfaces.Interface1 extends Interface implements Serializable

serialVersionUID: 1L

Serialized Fields

cible

Sequence cible

Identification of elements, which algorithm will work on.
Paramter. Other elements have to be getted in graphical interface or when execution.

See Also:

Sequence

autresSequences

SequenceListe autresSequences

List of tother sequences.

See Also:

SequenceListe

selectionInt

IntegerListe[] selectionInt

Test int's selection (was a Vector of table of ints (selected items in prediction)).

selectionBool

BooleanListe selectionBool

Test bool's selection (was a Vector of booleans (selected predictions)).

listeCible

javax.swing.JList listeCible

Graphical list of possible choice of cible sequences.

listModelCible

javax.swing.DefaultListModel listModelCible

listeTest

javax.swing.JList[] listeTest

Tab of graphical lists of homologuous sequences.

unePrediction

javax.swing.JRadioButton[] unePrediction

Tab of selection buttons to mae prediction with selection.

listModelTest

javax.swing.DefaultListModel listModelTest

scoreArea

javax.swing.JTextArea[] scoreArea

scoreScroll

javax.swing.JScrollPane[] scoreScroll

dec

javax.swing.JTextField dec

incert

javax.swing.JTextField incert

nbPred

javax.swing.JTextField nbPred

tauxMutation

javax.swing.JRadioButton tauxMutation

longMutation

javax.swing.JRadioButton longMutation

typeCritere

javax.swing.ButtonGroup typeCritere

arnStructural

javax.swing.JRadioButton arnStructural

arnMessager

javax.swing.JRadioButton arnMessager

typeARN

javax.swing.ButtonGroup typeARN

plusieursStructures

javax.swing.JRadioButton plusieursStructures

pseudoNoeud

javax.swing.JRadioButton pseudoNoeud

tailleBoucle

javax.swing.JTextField tailleBoucle

taillePal

javax.swing.JTextField taillePal

scrollListeCible

javax.swing.JScrollPane scrollListeCible

Zone où s'affiche la liste des séquances cibles potentielles.

scrollListeTest

javax.swing.JScrollPane[] scrollListeTest

Ensemble des listes où s'effectue la sélection des séquences tests.

cibleChoice

javax.swing.JLabel cibleChoice

aide

javax.swing.JLabel aide

homologChoice

javax.swing.JLabel homologChoice

homologCharac

javax.swing.JLabel homologCharac

GCeffect

javax.swing.JLabel GCeffect

GUeffect

javax.swing.JLabel GUeffect

GUGCeffect

javax.swing.JLabel GUGCeffect

indels

javax.swing.JLabel indels

homology

javax.swing.JLabel homology

l10

javax.swing.JLabel l10

private JLabel l9 = new JLabel("Nombre de predictions");

l10_aide

javax.swing.JLabel l10_aide

l11

javax.swing.JLabel l11

l12

javax.swing.JLabel l12

l13

javax.swing.JLabel l13

l14

javax.swing.JLabel l14

l15

javax.swing.JLabel l15

label_lg

javax.swing.JLabel label_lg

label_lg_boucle

javax.swing.JLabel label_lg_boucle

label_lg_pal

javax.swing.JLabel label_lg_pal

label_decalage

javax.swing.JLabel label_decalage

label_incertitude

javax.swing.JLabel label_incertitude

label_critere

javax.swing.JLabel label_critere

label_type_arn

javax.swing.JLabel label_type_arn

Class aloneinterfaces.Interface10 extends Interface implements Serializable

serialVersionUID: 10L

Serialized Fields

affichageResultat

javax.swing.JTextArea affichageResultat

Result text area visualization.

textefichiersauve

javax.swing.JTextField textefichiersauve

Text area for name of file recording.

textegraphiquesauve

javax.swing.JTextField textegraphiquesauve

Text area for name of graphic recording.

parcourirFichier

MonBouton parcourirFichier

Selection button for file recording.

parcourirGraphique

MonBouton parcourirGraphique

Selection button for graphic recording.

fichiersauve

java.lang.String fichiersauve

String of name used for recording.

graphiquesauve

java.lang.String graphiquesauve

String of name used for recording.

graphiquechemin

java.lang.String graphiquechemin

String of name used for recording.

Class aloneinterfaces.Interface11 extends Interface implements Serializable

serialVersionUID: 11L

Serialized Fields

textedebut

javax.swing.JTextField textedebut

To indicate beginning of palindrome.

textefin

javax.swing.JTextField textefin

To indicate end of palindrome.

textelongueur

javax.swing.JTextField textelongueur

To indicate length of palindrome.

palindrome

Palindrome palindrome

Class aloneinterfaces.Interface12 extends Interface implements Serializable

serialVersionUID: 12L

Serialized Fields

resultat

javax.swing.JTextArea resultat

Result text area interface.

Class aloneinterfaces.Interface2 extends Interface implements Serializable

serialVersionUID: 2L

Serialized Fields

premiereSequence

javax.swing.JTextField premiereSequence

First sequence text area visualization

derniereSequence

javax.swing.JTextField derniereSequence

Last sequence text area visualization.

nomFichierResultatOptimal

javax.swing.JTextField nomFichierResultatOptimal

Optimal result file name area of visualization.

parcourirFichier

MonBouton parcourirFichier

To select optimal result file.

leSeuil

javax.swing.JTextField leSeuil

Threshold text area visualization.

premiereSeq

int premiereSeq

Interface memory.

derniereSeq

int derniereSeq

Interface memory.

seuil

int seuil

Interface memory.

fichierResOpt

java.lang.String fichierResOpt

Optimal results.

Class aloneinterfaces.Interface3 extends Interface implements Serializable

serialVersionUID: 3L

Serialized Fields

resultat

javax.swing.JTextArea resultat

Result text area visualization.

aide

javax.swing.JLabel aide

Help text area visualization.

Class aloneinterfaces.Interface4 extends Interface implements Serializable

serialVersionUID: 4L

Serialized Fields

textedebut

javax.swing.JTextField textedebut

Result text area visualization.

textefin

javax.swing.JTextField textefin

Result text area visualization.

textelongueur

javax.swing.JTextField textelongueur

Result text area visualization.

textelmin

javax.swing.JTextField textelmin

Result text area visualization.

debut

int debut

Palindrome values.

fin

int fin

Palindrome values.

longueur

int longueur

Palindrome values.

lmin

int lmin

Palindrome values.

Class aloneinterfaces.Interface5 extends Interface implements Serializable

serialVersionUID: 5L

Serialized Fields

resultat

javax.swing.JTextArea resultat

Result text area visualization.

Class aloneinterfaces.Interface6 extends Interface implements Serializable

serialVersionUID: 6L

Serialized Fields

textedebut

javax.swing.JTextField textedebut

Start of zone to analyse (test area).

textefin

javax.swing.JTextField textefin

End of zone to analyse (test area).

textelmin

javax.swing.JTextField textelmin

Lmin text area.

debut

int debut

Input values memory of instance.

fin

int fin

Input values memory of instance.

lmin

int lmin

Input values memory of instance.

Class aloneinterfaces.Interface7 extends Interface implements Serializable

serialVersionUID: 7L

Serialized Fields

resultat

javax.swing.JTextArea resultat

Result text area interface visualization.

l1

javax.swing.JLabel l1

Nucleotid numbers text area visualization.

Class aloneinterfaces.Interface8 extends Interface implements Serializable

serialVersionUID: 8L

Serialized Fields

textefichier1

javax.swing.JTextField textefichier1

textefichier2

javax.swing.JTextField textefichier2

textelongueur

javax.swing.JTextField textelongueur

parcourirFichier1

MonBouton parcourirFichier1

parcourirFichier2

MonBouton parcourirFichier2

fichier1

java.lang.String fichier1

fichier2

java.lang.String fichier2

longueur

double longueur

Class aloneinterfaces.Interface9 extends Interface implements Serializable

serialVersionUID: 9L

Serialized Fields

resultat

javax.swing.JTextArea resultat

Result text area visualization.

l1

javax.swing.JLabel l1

File title comparison text area comparison.

Class aloneinterfaces.MaFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 42L

Serialized Fields

barremenu

MonMenu barremenu

A menuBar.

See Also:

MonMenu

bureau

MonBureau bureau

A virtual Desktop.

See Also:

MonBureau

Class aloneinterfaces.MonBouton extends javax.swing.JButton implements Serializable

serialVersionUID: 43L

Serialized Fields

ButtonIcon

javax.swing.ImageIcon ButtonIcon

Icon with image.

ButtonIconSelected

javax.swing.ImageIcon ButtonIconSelected

Icon with image.

Class aloneinterfaces.MonBureau extends javax.swing.JDesktopPane implements Serializable

serialVersionUID: 44L

Class aloneinterfaces.MonImage extends javax.swing.JPanel implements Serializable

serialVersionUID: 45L

Serialized Fields

image

java.awt.Image image

longueur

boolean longueur

largeur

boolean largeur

enmargehaut

boolean enmargehaut

enmargebas

boolean enmargebas

enmargegauche

boolean enmargegauche

enmargedroite

boolean enmargedroite

margehaut

int margehaut

margebas

int margebas

margegauche

int margegauche

margedroite

int margedroite

dimMonImage

java.awt.Dimension dimMonImage

couleur

java.awt.Color couleur

Class aloneinterfaces.MonLayout extends java.awt.GridBagLayout implements Serializable

serialVersionUID: 46L

Serialized Fields

taille

int taille

Length.

dimUnitaire

java.awt.Dimension dimUnitaire

Unit Dimension.

Package controller

Class controller.Processus extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: 42L

Class controller.Processus_old extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: 42L

Class controller.ProcessusNew extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: 42L

Serialized Fields

muchpredictions

boolean muchpredictions

maxPredictions

int maxPredictions

searchPseudoknots

boolean searchPseudoknots

userPalindromesTable

PalindromeListe userPalindromesTable

Class controller.ProcessusOrigin extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: 42L

Serialized Fields

muchpredictions

boolean muchpredictions

maxPredictions

int maxPredictions

searchPseudoknots

boolean searchPseudoknots