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

E

eccart_mutation_double() - Method in class origincomment.Alignement

To get number of double mutations between 5' and 3'.

eccart_mutation_simple() - Method in class origincomment.Alignement

To get number of single mutations between 5' and 3'.

ecoli - Static variable in class testsorigin.Alignedalphad

ecoli - Static variable in class testsorigin.Alignedtmrna

ecoli - Static variable in class testsorigin.Alignedtrna

ecoli - Variable in class testssuite01.TestAlgorithmsPartII

E. coli tmRNA

ecoli - Variable in class testssuite01.TestAlgorithmsPartIII

E. coli tmRNA

ecoli - Variable in class testssuite01.TestAlgorithmsPartIV

E. coli tmRNA

ecoli - Static variable in class testssuite02.Alignedalphad

ecoli - Static variable in class testssuite02.Alignedtmrna

ecoli - Static variable in class testssuite02.Alignedtrna

ecoliliste - Variable in class testssuite01.TestAlgorithmsPartIII

lists of sequences

ecolist - Variable in class testssuite01.TestAlgorithmsPartII

List of ecoli

ecolist - Variable in class testssuite01.TestAlgorithmsPartIV

List of ecoli

effacer() - Method in class aloneinterfaces.Interface

To remove what interface's items contain.

effacer() - Method in class aloneinterfaces.Interface0

effacer() - Method in class aloneinterfaces.Interface1

effacer() - Method in class aloneinterfaces.Interface10

effacer() - Method in class aloneinterfaces.Interface11

effacer() - Method in class aloneinterfaces.Interface12

effacer() - Method in class aloneinterfaces.Interface2

effacer() - Method in class aloneinterfaces.Interface3

effacer() - Method in class aloneinterfaces.Interface4

effacer() - Method in class aloneinterfaces.Interface5

effacer() - Method in class aloneinterfaces.Interface6

effacer() - Method in class aloneinterfaces.Interface7

effacer() - Method in class aloneinterfaces.Interface8

effacer() - Method in class aloneinterfaces.Interface9

effetGC - Variable in class modele.Sequence

S_A : GC effect [(2/4) helix alignment selection].

effetGU - Variable in class modele.Sequence

S_A : GU effect [(1/4) helix alignment selection].

effetGUGC - Variable in class modele.Sequence

S_A : GU and GC effect [(3/4) helix alignment selection].

egaux(Appariement) - Method in class origincomment.Appariement

Equals method.

egaux(Palindrome1cible) - Method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (14')
"equals method"

egaux_inverse(Appariement) - Method in class origincomment.Appariement

Equals method with reverse positions.

en_appariements(Vector) - Method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (10)
"This method return a Vector of pairwise from a palindrome"
Current instance is computed to add pairwises in Vector.

en_paire_de_bases(BufferedReader) - Static method in class origincomment.Appariement

"Get the pairwises contain in a ct format file"

en_paire_de_bases(Palindrome1cible[]) - Method in class origincomment.Palindrome1cible

Deprecated. because calling procedure is deprecated...

enfaa - Static variable in class testsorigin.Alignedtmrna

enfaa - Static variable in class testssuite02.Alignedtmrna

enfab - Static variable in class testsorigin.Alignedtmrna

enfab - Static variable in class testssuite02.Alignedtmrna

enmargebas - Variable in class aloneinterfaces.MonImage

enmargedroite - Variable in class aloneinterfaces.MonImage

enmargegauche - Variable in class aloneinterfaces.MonImage

enmargehaut - Variable in class aloneinterfaces.MonImage

ensureFastaAlignment(String) - Static method in class alonefichiers.FichierFasta

Take care for treatment : aligned sequences are putted on the same line in the way to ensure format is [names on odd lines and alignes sequences in one line (even lines)]
Check if it is a fasta alignment before treatment.

equals(Alignement) - Method in class modele.Alignement

To know if instance of the class and an other are the same.

equals(Base) - Method in class modele.Base

To know if instance of the class and an other are the same.

equals(ConvertedAlignementListe) - Method in class modele.ConvertedAlignementListe

Deprecated. To know if two ConvertedAlignementListe are equals (local instance and an other).

equals(NoeudArbreExec) - Method in class modele.NoeudArbreExec

equals(NoeudArbreExecListe) - Method in class modele.NoeudArbreExecListe

To know if two NoeudArbreExecListe are equals (local instance and an other).

equals(ObjectListe) - Method in class modele.ObjectListe

Deprecated. Please do NOT use this function !

equals(Palindrome) - Method in class modele.Palindrome

To know if instance of the class and an other are the same.

equals(Palindrome) - Method in class modele.PalindromeCible

Deprecated. Sucharged method : real length added.

equals(PalindromeListe) - Method in class modele.PalindromeListe

To know if two PalindromeListe are equals (local instance and an other).

equals(Sequence) - Method in class modele.Sequence

To know if instance of the class and an other are the same.

equals(SequenceListe) - Method in class modele.SequenceListe

To know if two SequenceListe are equals (local instance and an other).

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

To know if two helix are equivalent : (helix1 in helix2) or (helix2 in helix1).

ERREUR - Static variable in class origincomment.Alignement

ERREUR is -1.

est_Compatible(Palindrome1cible, Palindrome1cible) - Static method in class modele.OriginAlgorithmsStefan

Deprecated. converted and put into PalindromeCible : PalindromeCible.est_Compatible(PalindromeCible, PalindromeCible)

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

Cible : "Following methods sorted by use order in ADN1 Class". (5)
"To know if two palindromes are compatibles"
After reading the code, not sure that fully correct...

est_Compatible(PalindromeCible, PalindromeCible) - Static method in class modele.PalindromeCible

Deprecated. "Following methods sorted by use order in ADN1 Class". (5)
"To know if two palindromes are compatibles"
After reading the code, not sure that fully correct...

est_Compatible(Palindrome1cible, Palindrome1cible) - Static method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (5)
"To know if two palindromes are compatibles"
After reading the code, not sure that fully correct...

est_Compatible(Palindrome1cible, Palindrome1cible) - Method in class origincomment.StefanErrors

Is result we are waiting for is correct ?

est_indeci() - Method in class modele.Palindrome

est_indeci() - Method in class modele.PalindromeCible

Deprecated.

est_indeci() - Method in class origincomment.Palindrome1cible

est_Une_Base(char) - Method in class modele.Sequence

Deprecated. Replace by use of Base.isBaseOrGap(char)...

est_Une_Base(char) - Method in class modele.SequenceTest

Deprecated. Replace by use of Base.isBaseOrGap(char)...

est_Une_Base(char) - Method in class origincomment.ADN1

"Methode qui teste si un caractere est une base"
"This method test if a character is a base

est_Une_Base(char) - Method in class origincomment.ADN1test

"Method which test if read character is a base in aligned sequences"

est_Une_Base(char) - Method in class origincomment.StefanErrors

Procedures which are not in the good class, in ADN / sequence and why not in Base ?

est_Une_Base_Test(char) - Method in class origincomment.ADN1cible

COMPATIBLE PALINDROME SEARCH
"This method test if a char is a base"

est_Une_Base_Test(char) - Method in class origincomment.StefanErrors

Procedures which are not in the good class, in ADN / sequence and why not in Base, or in the same as the other one ?

evoluer(int, Profil) - Method in class origincomment.ADN1test

Deprecated. (unused...)

exampleliste - Variable in class testssuite01.TestAlgorithmsPartIII

lists of sequences

externalSequence(Palindrome) - Method in class modele.Sequence

To get the external Sequence of a Palindrome on a Sequence.