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

G

GC - Static variable in class modele.Alignement

Score for match between two nucleotides / bases.

GC - Static variable in class origincomment.Alignement

GC is 3.

GCeffect - Variable in class aloneinterfaces.Interface1

gesul - Static variable in class testsorigin.Alignedtmrna

gesul - Static variable in class testssuite02.Alignedtmrna

getAlignedSequences() - Static method in class testsorigin.Alignedalphad

getAlignedSequences() - Static method in class testsorigin.AlignedSequences

To get the original set of aligned sequences.

getAlignedSequences() - Static method in class testsorigin.Alignedtmrna

getAlignedSequences() - Static method in class testsorigin.Alignedtrna

getAlignedSequences() - Static method in class testssuite02.Alignedalphad

getAlignedSequences() - Static method in class testssuite02.AlignedSequences

To get the original set of aligned sequences.

getAlignedSequences() - Static method in class testssuite02.Alignedtmrna

getAlignedSequences() - Static method in class testssuite02.Alignedtrna

getAlignement() - Method in class aloneinterfaces.Interface0

getAlignement() - Method in class modele.Algorithms

Deprecated. To get the group of aligned Sequence's.

getAlignment() - Static method in class testsorigin.AlignedSequences

getAlignment() - Static method in class testssuite02.AlignedSequences

getAlignmentFile() - Method in class controller.ListeBean

To get the alignment in fasta format and as a String.

getAllPalindromes() - Method in class modele.NoeudArbreExec

A simple recursive ethod to get whole Palindrome's in the execution tree.

getAllStructures() - Method in class modele.NoeudArbreExec

A simple recursive mehtod to get all structures computed by algorithms.

getArnType() - Method in class aloneinterfaces.Interface1

getAutreSequence() - Method in class aloneinterfaces.Interface1

getBase() - Method in class modele.Base

getBase(int) - Method in class modele.Sequence

To get the Base at position [position] in the table of Base's.

getBaseAt(int) - Method in class modele.Sequence

To get the character at position [position] in the alignment.

getBaseChar(int) - Method in class modele.Sequence

To get the char of the Base at position [position] in the Base table.

getBaseIn(int) - Method in class modele.Sequence

To get the character at position [position] in the table of character's.

getBasePos(int) - Method in class modele.Sequence

To get the original position of the Base at position [position] in the Base table.

getBestpredictions() - Method in class controller.ListeBean

To get the output in HTML format for best predictions of SSCA.

getBestSequences() - Static method in class testsorigin.Alignedtmrna

getBestSequences() - Static method in class testssuite02.Alignedtmrna

getBoolean(int) - Method in class alonefichiers.BooleanListe

getBracketFile() - Method in class controller.ListeBean

The content of results in bracket file format in String.

getBracketFile() - Method in class modele.AlgorithmsStefan

getBracketFile() - Method in class modele.OriginAlgorithmsStefan

getBracketFile() - Method in class modele.OtherAlgorithmsStefan

getCarbonCopy() - Method in class modele.Sequence

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getChamp(int) - Method in class alonefichiers.Fichier

getChamps() - Method in class alonefichiers.Fichier

getChampsToString() - Method in class alonefichiers.Fichier

getCible(String) - Method in class alonefichiers.FichierFasta

To get a sequence with given name.

getCible() - Method in class controller.ListeBean

To get the target sequence.

getCible() - Method in class modele.Algorithms

Deprecated. To get the cible Sequence.

getCombiGUGC() - Method in class modele.Sequence

getContenuListe() - Method in class controller.ListeBean

To get the output in HTML format of what the list contain for selection.

getContenuListeJavaScript() - Method in class controller.ListeBean

To get the output in HTML/JavaScript format of what the list contain for selection.

getContenuListeMore() - Method in class controller.ListeBean

To get the output in HTML format of what the list contain for selection.

getConvertedAlignement(int) - Method in class modele.ConvertedAlignementListe

Deprecated.

getCount() - Method in class modele.Palindrome

getCritereType() - Method in class aloneinterfaces.Interface1

getCurrentNode() - Method in class modele.ArbreExec

getDacodac() - Method in class aloneinterfaces.Interface

getDebut() - Method in class aloneinterfaces.Interface4

getDebut() - Method in class aloneinterfaces.Interface6

getDecalage() - Static method in class modele.Algorithms

Deprecated.

getDecalage() - Method in class modele.AlgorithmsStefan

getDecalage() - Method in class modele.OriginAlgorithmsStefan

getDecalage() - Method in class modele.OtherAlgorithmsStefan

getDelcrit() - Static method in class modele.Algorithms

Deprecated.

getDerniereSeq() - Method in class aloneinterfaces.Interface2

getDescription() - Method in class alonefichiers.Filtre

getDescription() - Method in class alonefichiers.FiltreAlignement

Return description of this filter ("alignment").

getDescription() - Method in class alonefichiers.FiltreConvert

Return description of this filter ("convert").

getDescription() - Method in class alonefichiers.FiltreImages

Return description of this filter ("images").

getDescription() - Method in class alonefichiers.FiltreResultat

Return description of this filter ("results").

getDescription() - Method in class alonefichiers.FiltreRnaviz

Return description of this filter ("rnaviz").

getEffetGC() - Method in class modele.Sequence

getEffetGU() - Method in class modele.Sequence

getEffetGUGC() - Method in class modele.Sequence

getExtension(File) - Static method in class alonefichiers.FiltreUtils

Get the extension of a file.

getFenetre() - Method in class aloneinterfaces.Interface

getFichier1() - Method in class aloneinterfaces.Interface8

getFichier2() - Method in class aloneinterfaces.Interface8

getFichierResOpt() - Method in class aloneinterfaces.Interface2

getFichierSauve() - Method in class aloneinterfaces.Interface10

getFils(int) - Method in class modele.NoeudArbreExec

getFils() - Method in class modele.NoeudArbreExec

getFin() - Method in class aloneinterfaces.Interface4

getFin() - Method in class aloneinterfaces.Interface6

getGeneration() - Method in class modele.NoeudArbreExec

To get the generation level of current node in the execution tree.

getGenerationIter() - Method in class modele.NoeudArbreExec

To get the generation level of current node in the execution tree.

getGraphiqueChemin() - Method in class aloneinterfaces.Interface10

getGraphiqueSauve() - Method in class aloneinterfaces.Interface10

getHomologie() - Method in class modele.Sequence

getHomoResults() - Method in class controller.ListeBean

To get the output in HTML format for homologuous results to appear in formselectionhomol.jsp.

getIdecrit() - Static method in class modele.Algorithms

Deprecated.

getIncertitude() - Method in class modele.AlgorithmsStefan

getIncertitude() - Method in class modele.OriginAlgorithmsStefan

getIncertitude() - Method in class modele.OtherAlgorithmsStefan

getIndels() - Method in class modele.Sequence

getIndeterminate() - Method in class modele.Sequence

getInteger(int) - Method in class alonefichiers.IntegerListe

getIteration() - Static method in class modele.Algorithms

Deprecated.

getLbmin() - Static method in class modele.Alignement

getListe() - Method in class alonefichiers.FichierBracket

To get the list of palindromes of current instance.

getListe() - Method in class alonefichiers.FichierConvert

To get the list of palindromes of current instance.

getListe() - Method in class alonefichiers.FichierFasta

To get the liste of current instance of FichierFasta.

getListe() - Method in class modele.ConvertedAlignementListe

Deprecated.

getListe() - Method in class modele.NoeudArbreExecListe

getListe() - Method in class modele.PalindromeListe

getListe() - Method in class modele.PalindromeListeListe

getListe() - Method in class modele.SequenceListe

getListeBoolean() - Method in class alonefichiers.BooleanListe

getListeCount(int) - Method in class modele.PalindromeListe

To get a PalindromeListe, sublist of current instance of PalindromeListe, whith a minimum count.

getListeInteger() - Method in class alonefichiers.IntegerListe

getListeObjects() - Method in class modele.ObjectListe

Deprecated. Please do NOT use this function !

getLmin() - Method in class aloneinterfaces.Interface4

getLmin() - Method in class aloneinterfaces.Interface6

getLongBoucleMin() - Static method in class modele.Algorithms

Deprecated.

getLongMut() - Method in class modele.Palindrome

getLongPalindMin() - Static method in class modele.Algorithms

Deprecated.

getLongueur() - Method in class aloneinterfaces.Interface4

getLongueur() - Method in class aloneinterfaces.Interface8

getLpmin() - Static method in class modele.Alignement

getMatrice() - Method in class modele.Alignement

To get the score matrix.

getMatriceScore(int, int) - Method in class modele.Alignement

To get a score at a specific position in the score matrix of reverse alignment.

getMaxCount() - Method in class modele.PalindromeListe

To get the maximum number of count for a Palindrome in current instance of PalindromeListe.

getMaxHomology() - Static method in class modele.Algorithms

Deprecated.

getMenu() - Method in class aloneinterfaces.Interface

getMinHomology() - Static method in class modele.Algorithms

Deprecated.

getMinicadre(boolean) - Static method in class controller.ListeBean

Deprecated. [see the include]

getMonlayout() - Method in class aloneinterfaces.Interface

getMore(boolean) - Method in class controller.ListeBean

To get the many combinations selected after SSCA.

getMoyenneVariabilite() - Method in class modele.SequenceListe

getN() - Method in class controller.ListeBean

getNb_prediction_max() - Method in class modele.AlgorithmsStefan

getNb_prediction_max() - Method in class modele.OriginAlgorithmsStefan

getNb_prediction_max() - Method in class modele.OtherAlgorithmsStefan

getNbErreursMax() - Static method in class modele.Algorithms

Deprecated.

getNbMaxSequences() - Static method in class modele.Algorithms

Deprecated.

getNbMinSequences() - Static method in class modele.Algorithms

Deprecated.

getNoeudArbreExec(int) - Method in class modele.NoeudArbreExecListe

getNoeudCourant() - Method in class modele.Algorithms

Deprecated. Default node : result node (contain list of Palindrome's after exxecution).

getNom() - Method in class alonefichiers.Fichier

getNom() - Method in class modele.Sequence

getNombreDecimale() - Static method in class modele.Sequence

getNombreErreur() - Method in class modele.Palindrome

getNombreMutationDouble() - Method in class modele.Palindrome

getNombreMutationSimple() - Method in class modele.Palindrome

getNombreSequences() - Method in class controller.ListeBean

To get the number of sequences.

getNomFichier() - Method in class aloneinterfaces.Interface0

getNT() - Method in class controller.ListeBean

getNumberPredictionMax() - Method in class aloneinterfaces.Interface1

getObject(int) - Method in class modele.ObjectListe

Deprecated. Please do NOT use this function !

getPalindrome() - Method in class aloneinterfaces.Interface11

getPalindrome(int, int) - Method in class modele.AlgorithmsStefan

To get a specific palindrome in a specific structure.

getPalindrome(int, int) - Method in class modele.Alignement

To get Palindrome from a score at a specific position in the matrix.

getPalindrome(int) - Method in class modele.Alignement

To get a Palindrome with a given score.

getPalindrome(int, int) - Method in class modele.ArbreExec

getPalindrome(int) - Method in class modele.NoeudArbreExec

getPalindrome(int, int) - Method in class modele.OriginAlgorithmsStefan

To get a specific palindrome in a specific structure.

getPalindrome(int, int) - Method in class modele.OtherAlgorithmsStefan

To get a specific palindrome in a specific structure.

getPalindrome(int) - Method in class modele.PalindromeListe

getPalindromeListe(int) - Method in class modele.PalindromeListeListe

getPalindromes() - Method in class modele.Alignement

To get the PalindromeListe of Palindrome's calculating by current instance of Alignment.

getPalindromes() - Method in class modele.NoeudArbreExec

getPere() - Method in class modele.NoeudArbreExec

getPertinence() - Method in class modele.Palindrome

getPoid() - Method in class modele.Palindrome

getPosition() - Method in class modele.Base

getPositionDebut() - Method in class modele.Palindrome

getPositionFin() - Method in class modele.Palindrome

getPremiereSeq() - Method in class aloneinterfaces.Interface2

getProcessusParent() - Method in class aloneinterfaces.Interface

getPseudonoeud() - Method in class modele.AlgorithmsStefan

getPseudonoeud() - Method in class modele.OriginAlgorithmsStefan

getPseudonoeud() - Method in class modele.OtherAlgorithmsStefan

getQueueTrans() - Method in class aloneinterfaces.AloneProcessus

Getting alignment sequences and queuing them.

getQueueTrans() - Method in class aloneinterfaces.AloneProcessus_old

getRecordingStructures(ADN1cible) - Static method in class controller.ProcessusOrigin

To get the recording structure in a good conversion format.

getRecordingStructures(Sequence) - Method in class modele.AlgorithmsStefan

To get the recording structure in a good conversion format.

getRecordingStructures(Sequence) - Method in class modele.OriginAlgorithmsStefan

To get the recording structure in a good conversion format.

getRecordingStructures(ADN1cible) - Method in class modele.OriginAlgorithmsStefan

To get the recording structure in a good conversion format.

getRecordingStructures(Sequence) - Method in class modele.OtherAlgorithmsStefan

To get the recording structure in a good conversion format.

getResolution() - Static method in class modele.Algorithms

Deprecated.

getResults() - Method in class controller.ListeBean

Use on page exportresults.jsp.

getResults() - Method in class modele.AlgorithmsStefan

getResults() - Method in class modele.OriginAlgorithmsStefan

getResults() - Method in class modele.OtherAlgorithmsStefan

getResultsHTML() - Method in class modele.AlgorithmsStefan

getResultsHTML() - Method in class modele.OriginAlgorithmsStefan

getResultsHTML() - Method in class modele.OtherAlgorithmsStefan

getRnavizFile() - Method in class controller.ListeBean

The content of results in RnaViz file format in String.

getRnavizFile() - Method in class modele.AlgorithmsStefan

getRnavizFile() - Method in class modele.OriginAlgorithmsStefan

getRnavizFile() - Method in class modele.OtherAlgorithmsStefan

getScore() - Method in class modele.Palindrome

getScore(int) - Method in class modele.Sequence

Return a score in the following (default is homology).

getScreenToSee(Vector, ADN1cible) - Static method in class controller.ProcessusOrigin

Working about what will be on screen

getScreenToSee(SequenceListe[], Sequence, AlgorithmsStefan, boolean) - Static method in class modele.AlgoStefanConverter

Working about what will be on screen.

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

Working about what will be on screen.

getScreenToSee(SequenceListe[], Sequence, OtherAlgorithmsStefan, boolean) - Static method in class modele.OtherAlgoStefanConverter

Working about what will be on screen.

getScreenToSee(Vector, ADN1cible) - Static method in class testsorigin.TestPDCFold00

Working about what will be on screen

getScreenToSeeHTML(Vector, ADN1cible) - Static method in class controller.ProcessusOrigin

Working about what will be on screen

getScreenToSeeHTML(SequenceListe[], Sequence, AlgorithmsStefan, boolean) - Static method in class modele.AlgoStefanConverter

Working about what will be on screen.

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

Working about what will be on screen.

getScreenToSeeHTML(SequenceListe[], Sequence, OtherAlgorithmsStefan, boolean) - Static method in class modele.OtherAlgoStefanConverter

Working about what will be on screen.

getScriptDestination(int) - Static method in class controller.Processus

Deprecated. To get the page where to go...

getScriptDestination(int) - Static method in class controller.Processus_old

Deprecated. To get the page where to go...

getScriptDestination(int) - Static method in class controller.ProcessusNew

To get the page where to go...

getScriptDestination(int) - Static method in class controller.ProcessusOrigin

To get the page where to go...

getSelectionBool() - Method in class aloneinterfaces.Interface1

getSelectionInt() - Method in class aloneinterfaces.Interface1

getSequence() - Method in class alonefichiers.FichierBracket

To get the sequence of current instance.

getSequence() - Method in class alonefichiers.FichierConvert

To get the sequence of current instance.

getSequence() - Method in class aloneinterfaces.Interface1

One part of the compexty of this class comes from that data is on different objects.

getSequence() - Method in class modele.Palindrome

getSequence() - Method in class modele.Sequence

getSequence(String) - Method in class modele.SequenceListe

getSequence(int) - Method in class modele.SequenceListe

getSequence1() - Method in class modele.Alignement

getSequence2() - Method in class modele.Alignement

getSequenceBase() - Method in class modele.Sequence

getSequenceBaseToString() - Method in class modele.Sequence

getSequenceChar() - Method in class modele.Sequence

getSequenceCharToString() - Method in class modele.Sequence

getSequencesToString() - Method in class alonefichiers.FichierFasta

To get the whole alignment of Sequence's.

getSequenceToString() - Method in class modele.Sequence

getSeuil() - Method in class aloneinterfaces.Interface2

getSSCAResult() - Method in class controller.ListeBean

The content of SSCA sresult ins a XML String format.

getStest() - Method in class modele.PalindromeListe

getStructure(int) - Method in class modele.AlgorithmsStefan

To get a specific structure.

getStructure(int) - Method in class modele.ArbreExec

getStructure(int) - Method in class modele.OriginAlgorithmsStefan

To get a specific structure.

getStructure(int) - Method in class modele.OtherAlgorithmsStefan

To get a specific structure.

getStructures() - Method in class modele.AlgorithmsStefan

To get structures from algorithm tree.

getStructures() - Method in class modele.ArbreExec

getStructures() - Method in class modele.OriginAlgorithmsStefan

To get structures from algorithm tree.

getStructures() - Method in class modele.OtherAlgorithmsStefan

To get structures from algorithm tree.

getSubSequence(int, int) - Method in class modele.Sequence

To get a subsequence of the sequence (not of the alignment), start from 0 (positions debut AND fin are included).

getTableauInitial() - Method in class modele.AlgorithmsStefan

getTableauInitial() - Method in class modele.OriginAlgorithmsStefan

getTableauInitial() - Method in class modele.OtherAlgorithmsStefan

getTableauPalindrome() - Method in class modele.AlgorithmsStefan

getTableauPalindrome() - Method in class modele.OriginAlgorithmsStefan

getTableauPalindrome() - Method in class modele.OtherAlgorithmsStefan

getTaille_boucle_min() - Method in class modele.AlgorithmsStefan

getTaille_boucle_min() - Method in class modele.OriginAlgorithmsStefan

getTaille_boucle_min() - Method in class modele.OtherAlgorithmsStefan

getTaille_pal_min() - Method in class modele.AlgorithmsStefan

getTaille_pal_min() - Method in class modele.OriginAlgorithmsStefan

getTaille_pal_min() - Method in class modele.OtherAlgorithmsStefan

getTaux() - Method in class modele.Palindrome

getType() - Method in class alonefichiers.Fichier

getTypeARN() - Method in class modele.AlgorithmsStefan

getTypeARN() - Method in class modele.OriginAlgorithmsStefan

getTypeARN() - Method in class modele.OtherAlgorithmsStefan

getTypeCritere() - Method in class modele.AlgorithmsStefan

getTypeCritere() - Method in class modele.OriginAlgorithmsStefan

getTypeCritere() - Method in class modele.OtherAlgorithmsStefan

getTypeRecherche() - Method in class aloneinterfaces.Interface1

getTypeRecherche() - Method in class modele.AlgorithmsStefan

getTypeRecherche() - Method in class modele.OriginAlgorithmsStefan

getTypeRecherche() - Method in class modele.OtherAlgorithmsStefan

getValeur1() - Method in class testssuite01.HyperTest

Deprecated.

getValeur2() - Method in class testssuite01.HyperTest

Deprecated.

getVariabilite() - Method in class modele.Sequence

gif - Static variable in class alonefichiers.FiltreUtils

jpeg image

graphiquechemin - Variable in class aloneinterfaces.Interface10

String of name used for recording.

graphiquesauve - Variable in class aloneinterfaces.Interface10

String of name used for recording.

GU - Static variable in class modele.Alignement

Score for match between two nucleotides / bases.

GU - Static variable in class origincomment.Alignement

GU is 5.

GUeffect - Variable in class aloneinterfaces.Interface1

GUGCeffect - Variable in class aloneinterfaces.Interface1

guthe - Static variable in class testsorigin.Alignedtmrna

guthe - Static variable in class testssuite02.Alignedtmrna