A B C D E F G H I J K L M N O P Q R S T U V W X Y

A

aacti - Static variable in class testsorigin.Alignedalphad

aacti - Static variable in class testssuite02.Alignedalphad

acact - Static variable in class testsorigin.Alignedtmrna

acact - Static variable in class testssuite02.Alignedtmrna

accept(File) - Method in class alonefichiers.Filtre

accept(File) - Method in class alonefichiers.FiltreAlignement

Accepted file extensions : aln ; fasta

accept(File) - Method in class alonefichiers.FiltreConvert

Accepted file extensions : aln ; fasta

accept(File) - Method in class alonefichiers.FiltreImages

interfaces.FiltreImages.java : tiff ; gif ; jpg

accept(File) - Method in class alonefichiers.FiltreResultat

Accepted file extensions : res ; ct ; b

accept(File) - Method in class alonefichiers.FiltreRnaviz

Accepted file extensions : ali

acfer - Static variable in class testsorigin.Alignedtmrna

acfer - Static variable in class testssuite02.Alignedtmrna

acgt - Variable in class modele.Base

acgt - Variable in class origincomment.Base

Base.

actact - Variable in class testssuite01.TestAlgorithmsPartIII

Act. act. tmRNA

actact - Variable in class testssuite01.TestAlgorithmsPartIV

Act. act. tmRNA

actif - Variable in class aloneinterfaces.AloneProcessus

actif - Variable in class aloneinterfaces.AloneProcessus_old

actionHelper() - Method in class aloneinterfaces.Interface1

This function to rationalize and to factor some items.

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface

Action which depends of item selected in selection menu.

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface0

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface1

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface10

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface11

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface12

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface2

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface3

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface4

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface5

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface6

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface7

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface8

actionPerformed(ActionEvent) - Method in class aloneinterfaces.Interface9

actionPerformed(ActionEvent) - Method in class aloneinterfaces.MaFrame

actionPerformed(ActionEvent) - Method in class aloneinterfaces.MonBureau

actionPerformed(ActionEvent) - Method in class aloneinterfaces.MonMenu

actualiser() - Method in class modele.ArbreExec

To set the structureS to be "in good mood".

actualiser() - Method in class origincomment.ArbrePalindrome

To set the structureS to be "in good mood".

addBoolean(Boolean) - Method in class alonefichiers.BooleanListe

To add a Boolean at the end of the list.

addConvertedAlignement(Alignement) - Method in class modele.ConvertedAlignementListe

Deprecated. To add a ConvertedAlignement at the end of the list.

addExecutionNodes(PalindromeListeListe) - Method in class modele.NoeudArbreExec

This method to add new son's to current Node.

addFils(NoeudArbreExec) - Method in class modele.NoeudArbreExec

addFils(NoeudArbreExecListe) - Method in class modele.NoeudArbreExec

addInteger(Integer) - Method in class alonefichiers.IntegerListe

To add a Integer at the end of the list.

addNoeudArbreExec(NoeudArbreExec, NoeudArbreExec) - Method in class modele.NoeudArbreExecListe

To add a NoeudArbreExec at the end of the list.

addObjet(Object) - Method in class modele.ObjectListe

Deprecated. Please do NOT use this function !

addPalindrome(Palindrome) - Method in class modele.PalindromeListe

To add a Palindrome at the end of the list.

addPalindromeListe(PalindromeListe) - Method in class modele.PalindromeListeListe

To add a PalindromeListe at the end of the list.

addPalindromeListe(Palindrome[]) - Method in class modele.PalindromeListeListe

To add a PalindromeListe at the end of the list.

addSequence(Sequence) - Method in class modele.SequenceListe

To add a Sequence at the end of the list.

addTexteResultat(String) - Method in class aloneinterfaces.Interface10

addToChamps(String) - Method in class alonefichiers.Fichier

addToResults(String) - Method in class controller.ListeBean

To add some more information to results (i.e. parameters...)

adn - Variable in class origincomment.Profil

Target sequence ?

ADN1 - Class in origincomment

The main class for sequences.

ADN1() - Constructor for class origincomment.ADN1

Default constructor : nothing happend.

ADN1(String, String) - Constructor for class origincomment.ADN1

Constructor with name and aligned sequence...

ADN1cible - Class in origincomment

"Tous les pseudonoeuds d'une sous sequence sont recherches"
"All pseudoknots of a sequence are searched.

ADN1cible() - Constructor for class origincomment.ADN1cible

Default constructor : nothing happend.

ADN1cible(String, String) - Constructor for class origincomment.ADN1cible

Constructor with name and aligned sequence...

ADN1test - Class in origincomment

Class for tests sequence (homologuous), but already used for target (cible) sequence.

ADN1test(String, String) - Constructor for class origincomment.ADN1test

Constructor with given name and aligned sequence...

adncible - Variable in class origincomment.Matrice_ALN

Target sequence in format of test sequence.

adntest - Variable in class origincomment.Profil

Homologuous / test sequences ?

aersal - Variable in class testssuite01.TestAlgorithmsPartIII

Aer. sal. tmRNA

aersalliste - Variable in class testssuite01.TestAlgorithmsPartIII

lists of sequences

aesal - Static variable in class testsorigin.Alignedtmrna

aesal - Static variable in class testssuite02.Alignedtmrna

aff(int[][], String, String) - Static method in class origincomment.ADN1test

Methode pour afficher la matrice d'alignement

aff(int[][], String, String) - Method in class origincomment.StefanErrors

Not a static procedure, but could be useful to be...

affichageResultat - Variable in class aloneinterfaces.Interface10

Result text area visualization.

afficher(Palindrome1cible[]) - Static method in class origincomment.ADN1cible

SOME SHOW FOR VIEW
"This method to show the palindromes' tab"

afficher_Caracteristique(Sequence, AlgorithmsStefan, boolean) - Static method in class modele.AlgoStefanConverter

SOME SHOW FOR VIEW
"This method for show on a target sequence of DNA"

afficher_Caracteristique(ADN1cible, OriginAlgorithmsStefan, boolean) - Static method in class modele.OriginAlgoStefanConverter

SOME SHOW FOR VIEW
"This method for show on a target sequence of DNA"

afficher_Caracteristique(Sequence, OtherAlgorithmsStefan, boolean) - Static method in class modele.OtherAlgoStefanConverter

SOME SHOW FOR VIEW
"This method for show on a target sequence of DNA"

afficher_Caracteristique() - Method in class origincomment.ADN1

"Methode pour l'affichage des resultat sur une sequence d'ADN cible."

afficher_Caracteristique() - Method in class origincomment.ADN1cible

SOME SHOW FOR VIEW
"This method for show on a target sequence of DNA"

afficher_Caracteristique_Web(Sequence, AlgorithmsStefan, boolean) - Static method in class modele.AlgoStefanConverter

Some changes to this procedure to make results appears for web / HTML.

afficher_Caracteristique_Web(ADN1cible, OriginAlgorithmsStefan, boolean) - Static method in class modele.OriginAlgoStefanConverter

Some changes to this procedure to make results appears for web / HTML.

afficher_Caracteristique_Web(Sequence, OtherAlgorithmsStefan, boolean) - Static method in class modele.OtherAlgoStefanConverter

Some changes to this procedure to make results appears for web / HTML.

afficher_Caracteristique_Web() - Method in class origincomment.ADN1

Some changes to this procedure to make results appears for web / HTML.

afficher_Caracteristique_Web() - Method in class origincomment.ADN1cible

Some changes to this procedure to make results appears for web / HTML.

afficher_Sequences(Palindrome1cible, ADN1test[]) - Method in class origincomment.ADN1cible

RESULT TREAMENT
"This method show palindromes of tests sequences correponding to a target sequence palindrome et give informations about relevance of this palindrome"

afficherNom(Sequence[]) - Static method in class modele.AlgoStefanConverter

To bet the name of a tab of instances of Sequence.

afficherNom(ADN1test[]) - Static method in class modele.OriginAlgoStefanConverter

To bet the name of a tab of instances of ADN1test.

afficherNom(Sequence[]) - Static method in class modele.OtherAlgoStefanConverter

To bet the name of a tab of instances of Sequence.

afficherNom(ADN1test[]) - Static method in class origincomment.ADN1test

To bet the name of a tab of instances of ADN1test.

afficherNom_web(Sequence[]) - Static method in class modele.AlgoStefanConverter

Some changes to this procedure to make results appears for web / HTML.

afficherNom_web(ADN1test[]) - Static method in class modele.OriginAlgoStefanConverter

Some changes to this procedure to make results appears for web / HTML.

afficherNom_web(Sequence[]) - Static method in class modele.OtherAlgoStefanConverter

Some changes to this procedure to make results appears for web / HTML.

afficherNom_web(ADN1test[]) - Static method in class origincomment.ADN1test

Some changes to this procedure to make results appears for web / HTML.

afficherProgressBar(int, int, Interface1) - Method in class aloneinterfaces.AloneProcessus

Progression Bar is inserted in interface.

afficherProgressBar(int, int, Interface1) - Method in class aloneinterfaces.AloneProcessus_old

Progression Bar is inserted in interface.

aide - Variable in class aloneinterfaces.Interface0

Help area.

aide - Variable in class aloneinterfaces.Interface1

aide - Variable in class aloneinterfaces.Interface3

Help text area visualization.

ajoute(int, int[]) - Method in class origincomment.Resultat

To add a score for a specified sequence...

ajoute_match(int) - Method in class origincomment.Alignement

Add 1 to nombre_match if more than 0.

ajouteProgressBar(JProgressBar) - Method in class aloneinterfaces.Interface1

To add and vizualise progression bar on this interface.

ajouteStructures(Palindrome1cible[]) - Method in class origincomment.ArbrePalindrome

To add new StructureS.

aleut - Static variable in class testsorigin.Alignedtmrna

aleut - Static variable in class testssuite02.Alignedtmrna

Algorithms - Class in modele

Deprecated. Implementation of STefan Engleen very specific with some tricks make results differents...

Algorithms(Sequence, SequenceListe) - Constructor for class modele.Algorithms

Deprecated. A constructor to launch searchAllStructuralPalindromes on elements.

AlgorithmsCT01 - Class in modele

Deprecated. see also Algorithms

AlgorithmsCT01(Sequence, SequenceListe) - Constructor for class modele.AlgorithmsCT01

Deprecated. Do not instanciate this class.

AlgorithmsCT02 - Class in modele

Deprecated. Tested as not very good... see also Algorithms

AlgorithmsCT02(Sequence, SequenceListe) - Constructor for class modele.AlgorithmsCT02

Deprecated. Do not instanciate this class.

AlgorithmsCT03 - Class in modele

Deprecated. see also Algorithms

AlgorithmsCT03(Sequence, SequenceListe) - Constructor for class modele.AlgorithmsCT03

Deprecated. Do not instanciate this class.

AlgorithmsStefan - Class in modele

This class to concentrate most part of algorithms and computing, as Stefan Eneglen implement them.

AlgorithmsStefan() - Constructor for class modele.AlgorithmsStefan

Default constructor.

AlgorithmsStefan(int, boolean, boolean) - Constructor for class modele.AlgorithmsStefan

Constructor with given maximal number of structures, if searching much structures and searching pseudoknots.

algoSSCA(Sequence, SequenceListe) - Static method in class modele.Algorithms

Deprecated. SSCA algorithm.

algoSSCA(Sequence, SequenceListe) - Static method in class modele.AlgoStefanConverter

Deprecated. "old version" see also AlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean) - Static method in class modele.AlgoStefanConverter

Deprecated. "old version" see also AlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)

algoSSCA(Sequence, SequenceListe, int, int) - Static method in class modele.AlgoStefanConverter

A default call to SSCA algorithm to get all list of homologuous with scores computed.

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int) - Static method in class modele.AlgoStefanConverter

The whole computing of SSCA.

algoSSCA(Sequence, SequenceListe) - Static method in class modele.OriginAlgoStefanConverter

Deprecated. "old version" see also OriginAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean) - Static method in class modele.OriginAlgoStefanConverter

Deprecated. "old version" see also OriginAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)

algoSSCA(Sequence, SequenceListe, int, int) - Static method in class modele.OriginAlgoStefanConverter

A default call to SSCA algorithm to get all list of homologuous with scores computed.

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int) - Static method in class modele.OriginAlgoStefanConverter

The whole computing of SSCA.

algoSSCA(Sequence, SequenceListe) - Static method in class modele.OtherAlgoStefanConverter

Deprecated. "old version" see also OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean) - Static method in class modele.OtherAlgoStefanConverter

Deprecated. "old version" see also OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)

algoSSCA(Sequence, SequenceListe, int, int) - Static method in class modele.OtherAlgoStefanConverter

A default call to SSCA algorithm to get all list of homologuous with scores computed.

algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int) - Static method in class modele.OtherAlgoStefanConverter

The whole computing of SSCA.

AlgoStefanConverter - Class in modele

Linked with class AlgorithmsStefan AlgorithmsStefan to avoid to be too long : some conversion procedures are here as sttatic statements.

AlgoStefanConverter() - Constructor for class modele.AlgoStefanConverter

alhal - Static variable in class testsorigin.Alignedtmrna

alhal - Static variable in class testssuite02.Alignedtmrna

ali - Static variable in class alonefichiers.FiltreUtils

ALIGN - Static variable in class origincomment.Case

Operation ALIGN is 4

Alignedalphad - Class in testsorigin

Here is 21 sequences of alphad RNA, original selection made by Stefan Engelen in 2006 and before for tests.

Alignedalphad() - Constructor for class testsorigin.Alignedalphad

Alignedalphad - Class in testssuite02

Here is 21 sequences of alphad RNA, original selection made by Stefan Engelen in 2006 and before for tests.

Alignedalphad() - Constructor for class testssuite02.Alignedalphad

AlignedSequences - Class in testsorigin

This class to provide some records of sets of tests aligned sequences.

AlignedSequences() - Constructor for class testsorigin.AlignedSequences

AlignedSequences - Class in testssuite02

This class to provide some records of sets of tests aligned sequences.

AlignedSequences() - Constructor for class testssuite02.AlignedSequences

Alignedtmrna - Class in testsorigin

Here is a set of 87 sequences of tmRNA, original selection made by Stefan Engelen in 2006 and before for tests.

Alignedtmrna() - Constructor for class testsorigin.Alignedtmrna

Alignedtmrna - Class in testssuite02

Here is a set of 87 sequences of tmRNA, original selection made by Stefan Engelen in 2006 and before for tests.

Alignedtmrna() - Constructor for class testssuite02.Alignedtmrna

Alignedtrna - Class in testsorigin

Here is 9 sequences of tRNA, original selection made by Stefan Engelen in 2006 and before for tests.

Alignedtrna() - Constructor for class testsorigin.Alignedtrna

Alignedtrna - Class in testssuite02

Here is 9 sequences of tRNA, original selection made by Stefan Engelen in 2006 and before for tests.

Alignedtrna() - Constructor for class testssuite02.Alignedtrna

alignement - Variable in class aloneinterfaces.Interface0

Interface memory.

alignement - Variable in class modele.Algorithms

Deprecated. The alignment submitted with all sequences.

Alignement - Class in modele

This class to make alignments possible in searching Palindrome's and helix.

Alignement(Sequence) - Constructor for class modele.Alignement

Deprecated. Not easy to well understand it without source code.

Alignement(Sequence, double, double) - Constructor for class modele.Alignement

Deprecated. Not easy to well understand it without source code.

Alignement(Sequence, Sequence) - Constructor for class modele.Alignement

Constructor of the alignment. lpmin is set to 3.0 and lbmin to 4.0.

Alignement(Sequence, Sequence, double, double) - Constructor for class modele.Alignement

Constructor of the alignment with given lpmin.

alignement(int, int, int, int) - Method in class origincomment.ADN1test

Deprecated. (unused...)

Alignement - Class in origincomment

This class for alignment...

Alignement(int, int, String[]) - Constructor for class origincomment.Alignement

Main constructor

alignement - Variable in class origincomment.Alignement

Alignment.

alignement - Variable in class testssuite01.TestAlgorithmsPartI

ALIGNEMENTHELICE - Static variable in class modele.AlgorithmsStefan

"Global attributes of work"
Helix alignment is 3.

ALIGNEMENTHELICE - Static variable in class modele.OriginAlgorithmsStefan

"Global attributes of work"
Helix alignment is 3.

ALIGNEMENTHELICE - Static variable in class modele.OtherAlgorithmsStefan

"Global attributes of work"
Helix alignment is 3.

ALIGNEMENTHELICE - Static variable in class origincomment.ADN1cible

"Global attributes of work"
Helix alignment is 3.

alignements - Variable in class origincomment.Matrice_ALN

Vector of alignments.

aligner() - Method in class origincomment.Matrice_ALN

Local alignment (Smith and Waterman).

alignmentFile - Variable in class controller.ListeBean

To get the alignment FASTA File.

alignmentRecord(String) - Static method in class controller.Processus

Deprecated. Use of FichierFasta

alignmentRecord(String) - Static method in class controller.Processus_old

Deprecated. Making the recording of alignment in a file.

alignmentRecord(String) - Static method in class controller.ProcessusNew

Making the recording of alignment in a file.

alignmentRecord(String) - Static method in class controller.ProcessusOrigin

Making the recording of alignment in a file.

alignmentRecordTemp(String) - Static method in class controller.Processus

Deprecated. Use of FichierFasta

alignmentRecordTemp(String) - Static method in class controller.Processus_old

Deprecated. Making the recording of alignment in a file.

allSequences - Variable in class aloneinterfaces.AloneProcessus

allSequences - Variable in class aloneinterfaces.AloneProcessus_old

aln - Static variable in class alonefichiers.FiltreUtils

AloneApplet - Class in alonecontroller

Deprecated. August 2008

AloneApplet() - Constructor for class alonecontroller.AloneApplet

Deprecated.

alonecontroller - package alonecontroller

One class to launch the stand-alone application with Java Swing interface.

alonefichiers - package alonefichiers

Classes to convert and save informations about aloneinterfaces package use ; some changes have been performed to optimize use of this package.

aloneinterfaces - package aloneinterfaces

Classes to control, transmit and visualize informations for the Java Swing interface ; useful for quick start of use application.

AloneProcessus - Class in aloneinterfaces

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

AloneProcessus(int) - Constructor for class aloneinterfaces.AloneProcessus

Constructor.

AloneProcessus(JInternalFrame) - Constructor for class aloneinterfaces.AloneProcessus

Constructor.

AloneProcessus_old - Class in aloneinterfaces

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

AloneProcessus_old(int) - Constructor for class aloneinterfaces.AloneProcessus_old

Constructor.

AloneProcessus_old(JInternalFrame) - Constructor for class aloneinterfaces.AloneProcessus_old

Constructor.

AloneServlet - Class in alonecontroller

This class is the MAIN for a stand-alone java application.

AloneServlet() - Constructor for class alonecontroller.AloneServlet

annotation(Sequence, PalindromeListe) - Method in class alonefichiers.FichierRnaViz

This procedure to annotate sequence with informations of secondary structure (palindromes tab) in input format of RNAviz.

anspe - Static variable in class testsorigin.Alignedtmrna

anspe - Static variable in class testssuite02.Alignedtmrna

Appariement - Class in origincomment

Class about pairwise and pair bases arrangement.

Appariement(int, int, double) - Constructor for class origincomment.Appariement

Constructor.

aqaeo - Static variable in class testsorigin.Alignedtmrna

aqaeo - Static variable in class testsorigin.Alignedtrna

aqaeo - Static variable in class testssuite02.Alignedtmrna

aqaeo - Static variable in class testssuite02.Alignedtrna

ArbreExec - Class in modele

To do like an ArbrePalindrome and NoeudPalindrome of Origin, tree of execution of algorithms.

ArbreExec() - Constructor for class modele.ArbreExec

ArbrePalindrome - Class in origincomment

Palindrome tree of execution in algorithm.

ArbrePalindrome() - Constructor for class origincomment.ArbrePalindrome

Default constructor with a new current node.

ArbrePalindrome(NoeudPalindrome) - Constructor for class origincomment.ArbrePalindrome

Constrcutor with a given node.

ARN_MESSAGER - Static variable in class modele.AlgorithmsStefan

"Global attributes of work"
Messenger RNA is 2.

ARN_MESSAGER - Static variable in class modele.OriginAlgorithmsStefan

"Global attributes of work"
Messenger RNA is 2.

ARN_MESSAGER - Static variable in class modele.OtherAlgorithmsStefan

"Global attributes of work"
Messenger RNA is 2.

ARN_MESSAGER - Static variable in class origincomment.ADN1cible

"Global attributes of work"
Messenger RNA is 2.

ARN_STRUCTURAL - Static variable in class modele.AlgorithmsStefan

"Global attributes of work"
Structural RNA is 1.

ARN_STRUCTURAL - Static variable in class modele.OriginAlgorithmsStefan

"Global attributes of work"
Structural RNA is 1.

ARN_STRUCTURAL - Static variable in class modele.OtherAlgorithmsStefan

"Global attributes of work"
Structural RNA is 1.

ARN_STRUCTURAL - Static variable in class origincomment.ADN1cible

"Global attributes of work"
Structural RNA is 1.

arnMessager - Variable in class aloneinterfaces.Interface1

arnStructural - Variable in class aloneinterfaces.Interface1

arreter() - Method in class aloneinterfaces.AloneProcessus

Stop AloneProcessus for a computing time or as user ask.

arreter() - Method in class aloneinterfaces.AloneProcessus_old

Stop AloneProcessus for a computing time or as user ask.

AU - Static variable in class modele.Alignement

Score for match between two nucleotides / bases.

AU - Static variable in class origincomment.Alignement

AU is 1.

AUCUNE - Static variable in class origincomment.Case

Operation AUCUNE (no one) is 0.

autresSequences - Variable in class aloneinterfaces.Interface1

List of tother sequences.

avance() - Method in class aloneinterfaces.AloneProcessus

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

avance() - Method in class aloneinterfaces.AloneProcessus_old

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

avanceProgressBar(int) - Method in class aloneinterfaces.AloneProcessus

When computing, to make progression bar to progress.

avanceProgressBar(int) - Method in class aloneinterfaces.AloneProcessus_old

When computing, to make progression bar to progress.