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

C

cacre - Static variable in class testsorigin.Alignedtmrna

cacre - Static variable in class testssuite02.Alignedtmrna

cajej - Static variable in class testsorigin.Alignedtmrna

cajej - Static variable in class testssuite02.Alignedtmrna

calcul_constantes(int) - Method in class origincomment.Resultat

To compute constant values...

calcul_pertinence() - Method in class origincomment.Alignement

To get relevance without computing...

calcul_Resultat(Sequence, Sequence[], int, boolean, boolean) - Method in class modele.AlgorithmsStefan

MAIN COMPUTING RESULTS
"This method to launch search and compute all wanted results"

calcul_Resultat(ADN1cible, ADN1test[], int, boolean, boolean) - Method in class modele.OriginAlgorithmsStefan

MAIN COMPUTING RESULTS
"This method to launch search and compute all wanted results"

calcul_Resultat(Sequence, Sequence[], int, boolean, boolean) - Method in class modele.OtherAlgorithmsStefan

MAIN COMPUTING RESULTS
"This method to launch search and compute all wanted results"

calcul_Resultat(ADN1test[], int, boolean, boolean) - Method in class origincomment.ADN1cible

MAIN COMPUTING RESULTS
"This method to launch search and compute all wanted results"

calcul_score(int[], Matrice_ALN[]) - Static method in class origincomment.Matrice_ALN

Score computing ?

calcul_score_structure(String, String) - Static method in class origincomment.ADN1cible

RESULT TREAMENT
"Compute the score of a structure face a reference (two structures files in input)"

calcul_score_structure(ADN1cible) - Method in class origincomment.ADN1cible

RESULT TREAMENT
"Compute the score of structure face to a reference (two DNA in input)"

calcul_score_structure(Vector, Vector) - Static method in class origincomment.ADN1cible

RESULT TREAMENT
"Compute the score of a strcuture face to a reference (two pairwise vector in input)"

calcul_Taille(Palindrome) - Method in class modele.Sequence

COMPATIBLE PALINDROME SEARCH
"This method to compute internal sequence length at step i.

calcul_Taille(PalindromeCible) - Method in class modele.SequenceCible

Deprecated. COMPATIBLE PALINDROME SEARCH
"This method to compute internal sequence length at step i

calcul_Taille(Palindrome1cible) - Method in class origincomment.ADN1cible

COMPATIBLE PALINDROME SEARCH
"This method to compute internal sequence length at step i

carac_max - Variable in class modele.Palindrome

Cible : Maximum characteristics ?

carac_max - Variable in class modele.PalindromeCible

Deprecated. Maximum characteristics ?

carac_max - Variable in class origincomment.Palindrome1cible

"Public attribute"
Maximum character ?

carac_min - Variable in class modele.Palindrome

Cible : Minimum characteristics ?

carac_min - Variable in class modele.PalindromeCible

Deprecated. Minimum characteristics ?

carac_min - Variable in class origincomment.Palindrome1cible

"Public attribute"
Minimum character ?

card - Variable in class aloneinterfaces.AloneProcessus

card - Variable in class aloneinterfaces.AloneProcessus_old

Case - Class in origincomment

An element of the matrix of score ?

Case() - Constructor for class origincomment.Case

Default constructor.

Case(int, int) - Constructor for class origincomment.Case

Deprecated. [never used]

Case(int, int, int) - Constructor for class origincomment.Case

Deprecated. [never used]

CG - Static variable in class origincomment.Alignement

CG is 4.

champs - Variable in class alonefichiers.Fichier

File String fields.

champs - Variable in class origincomment.StefanErrors

change_adn(Sequence) - Method in class modele.ConvertedProfil

change_adn(ADN1cible) - Method in class origincomment.Profil

change_alignement_3_prime(String) - Method in class origincomment.Alignement

change_alignement_5_prime(String) - Method in class origincomment.Alignement

change_app3prime(int) - Method in class origincomment.Appariement

change_app5prime(int) - Method in class origincomment.Appariement

change_base(int, char) - Method in class origincomment.ADN1test

change_base(char) - Method in class origincomment.Base

To set current base.

change_case(double, int, int) - Method in class modele.ConvertedProfil

change_case(double, int, int) - Method in class origincomment.Profil

change_chercher_pk(boolean) - Method in class origincomment.ADN1cible

change_choisi(boolean) - Method in class origincomment.Case

change_decalage(int) - Method in class origincomment.ADN1cible

change_fils(Vector) - Method in class origincomment.NoeudPalindrome

change_fils(NoeudPalindrome, int) - Method in class origincomment.NoeudPalindrome

change_incertitude(double) - Method in class origincomment.ADN1cible

change_meilleur_score(double[], boolean) - Static method in class origincomment.Matrice_ALN

To set the best scores.

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

change_mutations_3_prime(int, int, int) - Method in class origincomment.Alignement

change_mutations_5_prime(int, int, int) - Method in class origincomment.Alignement

change_nb_prediction_max(int) - Method in class origincomment.ADN1cible

change_nom(String) - Method in class origincomment.ADN1

change_operation(int) - Method in class origincomment.Case

change_palindrome(Palindrome1cible, int) - Method in class origincomment.NoeudPalindrome

change_palindromes(Palindrome1cible[]) - Method in class origincomment.ADN1cible

To set the table of palindrome and change the tree of algorithms.

change_pere(NoeudPalindrome) - Method in class origincomment.NoeudPalindrome

change_position(int) - Method in class origincomment.Base

To set current position.

change_position_debut(int) - Method in class modele.Palindrome

change_position_debut(int) - Method in class modele.PalindromeCible

Deprecated.

change_position_debut(int) - Method in class origincomment.Palindrome1

change_position_fin(int) - Method in class modele.Palindrome

change_position_fin(int) - Method in class modele.PalindromeCible

Deprecated.

change_position_fin(int) - Method in class origincomment.Palindrome1

change_score(double[]) - Method in class modele.Sequence

To change current score of test sequence.

change_score(double[]) - Method in class modele.SequenceTest

Deprecated. To change current score of test sequence.

change_score(double[]) - Method in class origincomment.ADN1test

change_score(int) - Method in class origincomment.Case

change_score_normal(int) - Method in class origincomment.Case

change_tableau(Palindrome1cible[]) - Method in class origincomment.NoeudPalindrome

change_taille_boucle_min(int) - Method in class origincomment.ADN1cible

change_taille_pal_min(int) - Method in class origincomment.ADN1cible

change_taux_mut(double) - Method in class origincomment.Appariement

change_taux_mut(double) - Method in class origincomment.StefanErrors

A very single and simple procedure, but what is wrong ?

change_type_arn(int) - Method in class origincomment.ADN1cible

change_type_critere(int) - Method in class origincomment.ADN1cible

changeCourant(NoeudPalindrome) - Method in class origincomment.ArbrePalindrome

To set a new current node.

changer_carac_max(int, int) - Method in class modele.Palindrome

changer_carac_max(int, int) - Method in class modele.PalindromeCible

Deprecated.

changer_carac_max(int, int) - Method in class origincomment.Palindrome1cible

changer_carac_min(int, int) - Method in class modele.Palindrome

changer_carac_min(int, int) - Method in class modele.PalindromeCible

Deprecated.

changer_carac_min(int, int) - Method in class origincomment.Palindrome1cible

changer_conservation(int) - Method in class modele.Palindrome

changer_conservation(int) - Method in class modele.PalindromeCible

Deprecated.

changer_conservation(int) - Method in class origincomment.Palindrome1cible

changer_conservation(boolean) - Method in class origincomment.Palindrome1test

changer_indeci(boolean) - Method in class modele.Palindrome

changer_indeci(boolean) - Method in class modele.PalindromeCible

Deprecated.

changer_indeci(boolean) - Method in class origincomment.Palindrome1cible

changer_longMut(double) - Method in class origincomment.Palindrome1cible

changer_longueur(int) - Method in class modele.Palindrome

changer_longueur(int) - Method in class modele.PalindromeCible

Deprecated.

changer_longueur(int) - Method in class origincomment.Palindrome1cible

changer_longueur_Reelle(int) - Method in class modele.Palindrome

changer_longueur_Reelle(int) - Method in class modele.PalindromeCible

Deprecated.

changer_longueur_Reelle(int) - Method in class origincomment.Palindrome1cible

changer_nb_pal(int) - Method in class modele.Palindrome

changer_nb_pal(int) - Method in class modele.PalindromeCible

Deprecated.

changer_nb_pal(int) - Method in class origincomment.Palindrome1cible

changer_nberreur(int) - Method in class origincomment.Palindrome1test

changer_nbmutdouble(int) - Method in class origincomment.Palindrome1test

changer_nbmutsimple(int) - Method in class origincomment.Palindrome1test

changer_nombre_erreur(int) - Method in class origincomment.Palindrome1cible

changer_nombre_mutation_double(int) - Method in class origincomment.Palindrome1cible

changer_nombre_mutation_simple(int) - Method in class origincomment.Palindrome1cible

changer_pertinence(double) - Method in class origincomment.Alignement

changer_pertinence(double) - Method in class origincomment.Palindrome1cible

changer_poid_sequence(double) - Method in class modele.PalindromeCible

Deprecated.

changer_poid_sequence(double) - Method in class origincomment.Palindrome1cible

changer_pourcentage_conservation(double) - Method in class modele.Palindrome

changer_pourcentage_conservation(double) - Method in class modele.PalindromeCible

Deprecated.

changer_pourcentage_conservation(double) - Method in class origincomment.Palindrome1cible

changer_score(int) - Method in class origincomment.Palindrome1test

changer_tauxMut(double) - Method in class origincomment.Palindrome1cible

changer_type_critere(int) - Method in class origincomment.Palindrome1cible

changerDestination(int) - Method in class aloneinterfaces.AloneProcessus

Destination / interface is changed for user.

changerDestination(int) - Method in class aloneinterfaces.AloneProcessus_old

Destination / interface is changed for user.

changeStructures(Vector) - Method in class origincomment.ArbrePalindrome

To set new structureS.

checkConservation(Palindrome, SequenceListe, int) - Static method in class modele.Algorithms

Deprecated. To check a Palindrome is present in a group of Sequence's.

checkConservationOldVersion(Palindrome, SequenceListe, int) - Static method in class modele.Algorithms

Deprecated. Old and inacurate method

chercher_meilleur() - Method in class origincomment.Matrice_ALN

Searching the best...

chercher_pk - Variable in class modele.AlgorithmsStefan

"Global attribute with signification.

chercher_pk - Variable in class modele.OriginAlgorithmsStefan

"Global attribute with signification.

chercher_pk - Variable in class modele.OtherAlgorithmsStefan

"Global attribute with signification.

chercher_pk - Variable in class origincomment.ADN1cible

"Global attribute with signification.

chevauchant(Palindrome) - Method in class modele.Palindrome

Deprecated. see also Palindrome.chevauchant(Palindrome, Palindrome) and Palindrome.equivalence(Palindrome, Palindrome)

chevauchant(Palindrome, Palindrome) - Static method in class modele.Palindrome

Cible : "Following methods sorted by use order in ADN1 Class". (17)
"to know if two palindrome are crossed together"

chevauchant(Palindrome) - Method in class modele.PalindromeCible

Deprecated. "Following methods sorted by use order in ADN1 Class". (17)
"to know if two palindrome are crossed together"

chevauchant(Palindrome1cible) - Method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (17)
"to know if two palindrome are crossed together"

chmur - Static variable in class testsorigin.Alignedtmrna

chmur - Static variable in class testssuite02.Alignedtmrna

choisi() - Method in class origincomment.Case

choisi_aln(int[], Matrice_ALN[], int) - Static method in class origincomment.Matrice_ALN

Alignment choice ?

choisi_seq(Matrice_ALN[], int[], int, int) - Static method in class origincomment.Matrice_ALN

Sequence choice ?

choisir_meilleur(int, Palindrome[]) - Static method in class modele.Palindrome

Deprecated. [unused] Calling method ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]) is not maintained in OtherAlgorithmsStefan...

choisir_meilleur(int, PalindromeTest[]) - Static method in class modele.PalindromeTest

Deprecated. [unused] Calling method ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]) is not maintained in OtherAlgorithmsStefan...

choisir_meilleur(int, Palindrome1test[]) - Static method in class origincomment.Palindrome1test

"This method choose the best _nb_ test palindromes"

choisir_meilleur(int, Palindrome1test[]) - Method in class origincomment.StefanErrors

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

choisirSequencesTests(ADN1cible, ADN1test[], Vector, Vector) - Static method in class origincomment.ADN1test

"Procedure to choose tests sequences by default or not"
Work on the selection made by user on original graphical interface.

chpne - Static variable in class testsorigin.Alignedtmrna

chpne - Static variable in class testssuite02.Alignedtmrna

chpsi - Static variable in class testsorigin.Alignedtmrna

chpsi - Static variable in class testssuite02.Alignedtmrna

chtep - Static variable in class testsorigin.Alignedtmrna

chtep - Static variable in class testssuite02.Alignedtmrna

chtra - Static variable in class testsorigin.Alignedtmrna

chtra - Static variable in class testssuite02.Alignedtmrna

cible - Variable in class alonefichiers.FichierBracket

Current sequence of file.

cible - Variable in class alonefichiers.FichierConvert

Current seqquence of file.

cible - Variable in class aloneinterfaces.AloneProcessus

cible - Variable in class aloneinterfaces.AloneProcessus_old

cible - Variable in class aloneinterfaces.Interface1

Identification of elements, which algorithm will work on.

cible - Variable in class controller.ListeBean

Better record here than in session.

cible - Variable in class modele.Algorithms

Deprecated. Current selected sequence where to find Palindrome's, helix...

cible - Variable in class testsalone.TestFichierBracket

cible - Variable in class testsalone.TestFichierRnaViz

cible - Variable in class testssuite01.TestAlgorithmsPartI

cible - Variable in class testssuite01.TestAlgorithmsPartII

Randomly generated sequence.

cible - Variable in class testssuite01.TestAlgorithmsPartIV

Randomly generated sequence.

cibleChoice - Variable in class aloneinterfaces.Interface1

ciblist - Variable in class testssuite01.TestAlgorithmsPartIV

List of cible

clace - Static variable in class testsorigin.Alignedtmrna

clace - Static variable in class testssuite02.Alignedtmrna

cldif - Static variable in class testsorigin.Alignedtmrna

cldif - Static variable in class testssuite02.Alignedtmrna

clone() - Method in class modele.Sequence

To get a copy of the current Sequence (only name and sequence).

clone() - Method in class modele.SequenceListe

To get a copy of the current SequenceListe.

codip - Static variable in class testsorigin.Alignedtmrna

codip - Static variable in class testssuite02.Alignedtmrna

combiGUGC - Variable in class modele.Sequence

S_A : GU and GC combination effect [(4/4) helix alignment selection].

combinationWithoutRepetition(int, int, SequenceListe) - Static method in class modele.SequenceListe

Maybe not the best way to make combination / arrangement without repetition, but works well.

combinatoire(int, int) - Static method in class modele.SequenceListe

The classic k!

commonPrediction(Sequence, SequenceListe[]) - Static method in class modele.Algorithms

Deprecated. To search common structure prediction using P-DCFold with a cible Sequence and several list of homologuous Sequence's.

comparaison(ADN1cible, ADN1cible) - Static method in class origincomment.ADN1cible

RESULT TREAMENT
"Methods to compare recorded results in files.

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

RESULT TREAMENT
"Methods to compare recorded results in files.

comparaison_Resultat(BufferedReader, BufferedReader) - Method in class origincomment.ADN1cible

RESULT TREAMENT
"Methods to compare recorded results in files.

comparaison_structure(ADN1cible, ADN1cible) - Method in class origincomment.ADN1cible

Deprecated. [never used]

comparisonScore(FichierConvert) - Method in class alonefichiers.FichierConvert

Comparison between two (2) results of palindrome's search in convert file format.

compatibilityTreamentCT01(PalindromeListe) - Static method in class modele.AlgorithmsCT01

Deprecated. Polymorphism of procedure.

compatibilityTreatment(PalindromeListe) - Static method in class modele.Algorithms

Deprecated. Here is a procedure Launcher
This procedure to treat compatibility of found palindromes on each recursivity step, see searchStructuralPalindrome for launch.

compatibilityTreatment(PalindromeListe) - Static method in class modele.AlgorithmsCT02

Deprecated. Polymorphism of procedure.

compatibilityTreatment(PalindromeListe) - Static method in class modele.AlgorithmsCT03

Deprecated. Polymorphism of procedure.

compatibilityTreatment01(PalindromeListe) - Static method in class modele.AlgorithmsCT01

Deprecated. Other is used (changesDCFold to P-DCFold)

compatibilityTreatment01(PalindromeListe) - Static method in class modele.AlgorithmsCT03

Deprecated.

compatibilityTreatment02(PalindromeListe) - Static method in class modele.AlgorithmsCT01

Deprecated. results of tests are not very good...

compatibilityTreatment02(PalindromeListe) - Static method in class modele.AlgorithmsCT03

Deprecated.

compatibilityTreatment03(PalindromeListe) - Static method in class modele.AlgorithmsCT01

Deprecated. ...

compatibilityTreatment04(PalindromeListe) - Static method in class modele.AlgorithmsCT01

Deprecated. July 2008

compatibilityTreatment05(PalindromeListe) - Static method in class modele.AlgorithmsCT01

Deprecated.

compatibilityTreatmentMore(PalindromeListe) - Static method in class modele.AlgorithmsCT02

Deprecated.

compatibilityTreatmentOrigin(PalindromeListe, int, int, PalindromeListeListe) - Static method in class modele.AlgorithmsCT01

Deprecated. July 2008

compteur - Static variable in class origincomment.ADN1test

"For the count of time of optimal result."

computeAverageTest() - Method in class modele.PalindromeListe

This procedure to compute the score average of the table each time it changes.

computeAverageVariabilite() - Method in class modele.SequenceListe

This procedure to compute the variabilite average of the table.

computeContenuListe() - Method in class controller.ListeBean

This procedure to compute the contenuListe to be correct.

computeEffectsInContenuListe() - Method in class controller.ListeBean

This procedure to compute results of SSCA algorithms (effects)
Black Box note : scores *(-1)

computeNumbers(Palindrome) - Method in class modele.Palindrome

This procedure to compute compensatory and single mutations number, and errors number between a test Palindrome (current instance) and a cible Palindrome.

computePredictions() - Method in class controller.ListeBean

To compute and gain all possible predictions (combinations).

computePredictionsBB() - Method in class controller.ListeBean

Deprecated. putted when conversion ProcessusOrigin.conversionFrom(origincomment.ADN1test, SequenceListe[])

computePredictionsListes(int) - Method in class controller.ListeBean

This procedure to compute the differents predictions, which can be selected.

computeSSCAresults() - Method in class controller.ListeBean

This to permit export of SSCA results in XML format.

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

Computing the main algorithm made by Stefan Engelen.

computing(SequenceListe[], Sequence, boolean, boolean) - Method in class modele.AlgorithmsStefan

Computing the main algorithm made by Stefan Engelen.

computing(Vector, ADN1cible, boolean, boolean) - Method in class modele.OriginAlgorithmsStefan

Computing the main algorithm made by Stefan Engelen.

computing(SequenceListe[], Sequence, boolean, boolean) - Method in class modele.OtherAlgorithmsStefan

Computing the main algorithm made by Stefan Engelen.

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

Computing the main algorithm made by Stefan Engelen.

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

Deprecated. [old test version]

CONSERVATION - Static variable in class origincomment.Alignement

CONSERVATION is -3.

conservation - Variable in class origincomment.Palindrome1cible

"Public attribute"
"Number of tests sequences where palindrome is maintained"

conservation - Variable in class origincomment.Palindrome1test

Is the palindrome conserved in this test sequence ?

conservation() - Method in class origincomment.Palindrome1test

conservationInSequences - Variable in class modele.Palindrome

Cible : Number of conservation in sequences"

conservationInSequences - Variable in class modele.PalindromeCible

Deprecated. "Number of conservation in sequences"

contenuListe - Variable in class controller.ListeBean

What will appear in the HTML form selection of following pages : .

contenuListeJavaScript - Variable in class controller.ListeBean

To provide selection and view in web interface (JavaScript power !).

contenuListeMore - Variable in class controller.ListeBean

What will appear in the HTML form selection of following page : .

controller - package controller

Classes to control and transmit informations for the Java Servlet Pages mechanism.

conversionFrom(SequenceListe[]) - Static method in class controller.ProcessusOrigin

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
Do not forget that target sequence must be on position 0 of each table !

conversionFrom(ADN1test, SequenceListe[]) - Static method in class controller.ProcessusOrigin

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
and put the target sequence at position 0 on each table.

conversionFrom(SequenceListe) - Static method in class controller.ProcessusOrigin

Conversion of a set of sequences listes to a tab of ADN1test's

conversionFrom(Sequence, SequenceListe[]) - Static method in class modele.AlgoStefanConverter

Deprecated. [only for information, please use AlgoStefanConverter.conversionFrom(Sequence, SequenceListe[], boolean)]

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

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
and put the target sequence at position 0 on each table.

conversionFrom(SequenceListe[]) - Static method in class modele.OriginAlgoStefanConverter

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
Do not forget that target sequence must be on position 0 of each table !

conversionFrom(ADN1test, SequenceListe[]) - Static method in class modele.OriginAlgoStefanConverter

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
and put the target sequence at position 0 on each table.

conversionFrom(SequenceListe) - Static method in class modele.OriginAlgoStefanConverter

Conversion of a set of sequences listes to a tab of ADN1test's.

conversionFrom(Sequence, SequenceListe[]) - Static method in class modele.OtherAlgoStefanConverter

Deprecated. [only for information, please use OtherAlgoStefanConverter.conversionFrom(Sequence, SequenceListe[], boolean)]

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

Conversion of a set of sequences listes to a vector of tabs of ADN1test's
and put the target sequence at position 0 on each table.

conversionFrom(SequenceListe[]) - Static method in class testsorigin.AlignedSequences

Conversion of a set of sequences listes to a vector of tabs of ADN1test's

conversionFrom(SequenceListe) - Static method in class testsorigin.AlignedSequences

Conversion of a set of sequences listes to a tab of ADN1test's

conversionFrom(SequenceListe[]) - Static method in class testssuite02.AlignedSequences

Conversion of a set of sequences listes to a vector of tabs of ADN1test's

conversionFrom(SequenceListe) - Static method in class testssuite02.AlignedSequences

Conversion of a set of sequences listes to a tab of ADN1test's

convertBasesToString(Base[]) - Static method in class modele.Sequence

To get a String from a Base[] (maybe useful after getting a subsequence).

convertDecimale(double) - Static method in class modele.Sequence

To convert a double to a specific length after dot / comma (default is 3) : returning String to visualize.

ConvertedAlignementListe - Class in modele

Deprecated. [test with and without it : September 4, 2008]

ConvertedAlignementListe() - Constructor for class modele.ConvertedAlignementListe

Deprecated. Default constructor with a list of 0 elements.

ConvertedAlignementListe(Alignement[]) - Constructor for class modele.ConvertedAlignementListe

Deprecated. Constructor with a pre-made table of ConvertedAlignement.

ConvertedProfil - Class in modele

"A mutation profile is a 4*4 matrix" : in reality it is 4*7...

ConvertedProfil() - Constructor for class modele.ConvertedProfil

Deprecated. [not used]

ConvertedProfil(Sequence, Sequence[]) - Constructor for class modele.ConvertedProfil

Constrcutor with given target sequence and table of test sequences.

convertFrom(Sequence) - Static method in class controller.ProcessusOrigin

To get a "cible sequence" from an instance of Sequence.

convertFrom(Sequence, int) - Static method in class controller.ProcessusOrigin

To get a "test sequence" from an instance of Sequence.

convertFrom(Sequence) - Static method in class modele.OriginAlgoStefanConverter

To get a "cible sequence" from an instance of Sequence.

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

To get a "test sequence" from an instance of Sequence.

convertFrom(Palindrome) - Static method in class modele.OriginAlgoStefanConverter

To get a "target palindrome" from Palindrome.

convertFrom(Sequence) - Static method in class testsorigin.AlignedSequences

To get a "cible sequence" from an instance of Sequence.

convertFrom(Sequence, int) - Static method in class testsorigin.AlignedSequences

To get a "test sequence" from an instance of Sequence.

convertFrom(Sequence) - Static method in class testssuite02.AlignedSequences

To get a "cible sequence" from an instance of Sequence.

convertFrom(Sequence, int) - Static method in class testssuite02.AlignedSequences

To get a "test sequence" from an instance of Sequence.

convertNom(String) - Static method in class controller.ListeBean

This procedure to remove first ('>') and last ('\n') character in sequences' names.

copie() - Method in class modele.Palindrome

Cible : To get a clone of the current instance of PalindromeCible.

copie() - Method in class origincomment.Alignement

To make a clone of the current instance of Alignment.

copie() - Method in class origincomment.Palindrome1cible

To get a clone of the current instance of Palindrome1cible.

copie_clone() - Method in class modele.PalindromeCible

Deprecated. To get a clone of the current instance of PalindromeCible.

copier() - Method in class origincomment.ADN1cible

To clone the current instance of ADN1cible.

couleur - Variable in class aloneinterfaces.MonImage

count - Variable in class modele.Palindrome

For counting each time Palindrome / Helix is present.

countPlusPlus() - Method in class modele.Palindrome

courant - Variable in class aloneinterfaces.AloneProcessus

courant - Variable in class aloneinterfaces.AloneProcessus_old

courant - Variable in class origincomment.ArbrePalindrome

Current node (default is null).

courant - Variable in class origincomment.Matrice_ALN

A current tab of integers.

ct - Static variable in class alonefichiers.FiltreUtils

current - Variable in class modele.ArbreExec

cypar - Static variable in class testsorigin.Alignedtmrna

cypar - Static variable in class testssuite02.Alignedtmrna