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

I

idecrit - Static variable in class modele.Algorithms

Deprecated. Identity percentage, originally I = 75.0 (percentage).

image - Variable in class aloneinterfaces.MonImage

incert - Variable in class aloneinterfaces.Interface1

incertitude - Variable in class modele.AlgorithmsStefan

"Global attribute with signification.

incertitude - Variable in class modele.OriginAlgorithmsStefan

"Global attribute with signification.

incertitude - Variable in class modele.OtherAlgorithmsStefan

"Global attribute with signification.

incertitude - Variable in class origincomment.ADN1cible

"Global attribute with signification.

inclu_dans(Palindrome) - Method in class modele.Palindrome

Cible : "Following methods sorted by use order in ADN1 Class". (16)
"this method to know if current instance is included in argument with common pairwise "

inclu_dans(Palindrome) - Method in class modele.PalindromeCible

Deprecated. "Following methods sorted by use order in ADN1 Class". (16)
"this method to know if current instance is included in argument with common pairwise "

inclu_dans(Palindrome1cible) - Method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (16)
"this method to know if current instance is included in argument with common pairwise "

incompatibilite_plusieurs_choix(PalindromeListeListe, int, int, int, double, boolean, int) - Static method in class modele.AlgorithmsStefan

"Following methods sorted by use order in ADN1 Class". (2)
Much choices to treat incompatibility.

incompatibilite_plusieurs_choix(Vector, int, int, int, double, boolean, int) - Static method in class modele.OriginAlgorithmsStefan

"Following methods sorted by use order in ADN1 Class". (2)
Much choices to treat incompatibility.

incompatibilite_plusieurs_choix(PalindromeListeListe, int, int, int, double, boolean, int) - Static method in class modele.OtherAlgorithmsStefan

"Following methods sorted by use order in ADN1 Class". (2)
Much choices to treat incompatibility.

incompatibilite_plusieurs_choix(Vector, int, int, int, double, boolean, int) - Static method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (2)
Much choices to treat incompatibility.

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

"Following methods sorted by use order in ADN1 Class". (3)
One choice in incompatibility to structure.

incompatibilite_un_choix(Palindrome1cible[], int, int) - Static method in class modele.OriginAlgorithmsStefan

"Following methods sorted by use order in ADN1 Class". (3)
One choice in incompatibility to structure.

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

"Following methods sorted by use order in ADN1 Class". (3)
One choice in incompatibility to structure.

incompatibilite_un_choix(Palindrome1cible[], int, int) - Static method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (3)
One choice in incompatibility to structure.

incompatibilitePlusieursChoix(PalindromeListeListe, int, int, int, double, boolean, int) - Static method in class modele.AlgorithmsCT01

Deprecated. When more than one choice of palindromes are present.

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

Deprecated. When one choice is present for prediction.

indeci - Variable in class modele.Palindrome

"Cible : Undecided" (default is false).

indeci - Variable in class modele.PalindromeCible

Deprecated. "Undecided" (default is false).

indeci - Variable in class origincomment.Palindrome1cible

"Internal attributes"
"Undecided" (default is false).

indels - Variable in class aloneinterfaces.Interface1

indels - Variable in class modele.Sequence

Percentage of insertions / deletions with cible sequence.

indeterminate - Variable in class modele.Sequence

Percentage of indetermination comparing with cible sequence.

init() - Method in class alonecontroller.AloneApplet

Deprecated. Initialisation when applet is downloaded.

init() - Static method in class modele.Alignement

Deprecated. Not to use in other cases...

initialisation() - Method in class modele.ConvertedProfil

Initialise the current score matrix with all to 0.

initialisation() - Method in class origincomment.Profil

Initialise the current score matrix with all to 0.

initialise() - Method in class modele.Alignement

Initialization of the scoring matrix.

initialiser() - Method in class aloneinterfaces.Interface

To initialize interface's items.

initialiser() - Method in class aloneinterfaces.Interface0

initialiser() - Method in class aloneinterfaces.Interface1

initialiser() - Method in class aloneinterfaces.Interface10

initialiser() - Method in class aloneinterfaces.Interface11

initialiser() - Method in class aloneinterfaces.Interface12

initialiser() - Method in class aloneinterfaces.Interface2

initialiser() - Method in class aloneinterfaces.Interface3

initialiser() - Method in class aloneinterfaces.Interface4

initialiser() - Method in class aloneinterfaces.Interface5

initialiser() - Method in class aloneinterfaces.Interface6

initialiser() - Method in class aloneinterfaces.Interface7

initialiser() - Method in class aloneinterfaces.Interface8

initialiser() - Method in class aloneinterfaces.Interface9

initialiser() - Method in class modele.AlgorithmsStefan

Initialization of algorithm.

initialiser() - Method in class modele.OriginAlgorithmsStefan

Initialization of algorithm.

initialiser() - Method in class modele.OtherAlgorithmsStefan

Initialization of algorithm.

initialiser() - Method in class origincomment.ADN1cible

Initialization of algorithm.

initialiser() - Method in class origincomment.Matrice_ALN

Initialization of scoring matrix with new Cases, height and width +1 more than sequences.

initialiserToolTipText() - Method in class aloneinterfaces.Interface

To initialize contextual help.

initialiserToolTipText() - Method in class aloneinterfaces.Interface0

To initalize contextual help.

initialiserToolTipText() - Method in class aloneinterfaces.Interface1

To initalize contextual help messages.

initialiserToolTipText() - Method in class aloneinterfaces.Interface10

To initalize contextual help messages.

initialiserToolTipText() - Method in class aloneinterfaces.Interface3

To initialize contextual help messages.

initialiserToolTipText() - Method in class aloneinterfaces.Interface4

To initialize contextual help messages.

initialiserToolTipText() - Method in class aloneinterfaces.Interface5

To initialize contextual help messages.

initialiserToolTipText() - Method in class aloneinterfaces.Interface6

To initialize contextual help messages.

initialiserToolTipText() - Method in class aloneinterfaces.Interface7

To initalize contextual help messages.

INSERTION - Static variable in class origincomment.Case

Operation INSERTION is 1.

int0 - Variable in class aloneinterfaces.AloneProcessus

To choose / input alignment (and aligned) Sequence).

int0 - Variable in class aloneinterfaces.AloneProcessus_old

To choose / input alignment (and aligned) Sequence).

int1 - Variable in class aloneinterfaces.AloneProcessus

To choose cible and homologuous sequences then launch searching palindromes...

int1 - Variable in class aloneinterfaces.AloneProcessus_old

To choose cible and homologuous sequences then launch searching palindromes...

int10 - Variable in class aloneinterfaces.AloneProcessus

To records results as text and graphic for RNAviz.

int10 - Variable in class aloneinterfaces.AloneProcessus_old

To records results as text and graphic for RNAviz.

int11 - Variable in class aloneinterfaces.AloneProcessus

To see profiles of sequences and of a palindrome...

int11 - Variable in class aloneinterfaces.AloneProcessus_old

To see profiles of sequences and of a palindrome...

int12 - Variable in class aloneinterfaces.AloneProcessus

Results of profiles (from Interface11).

int12 - Variable in class aloneinterfaces.AloneProcessus_old

Results of profiles (from Interface11).

int2 - Variable in class aloneinterfaces.AloneProcessus

To choose an Optimal result.

int2 - Variable in class aloneinterfaces.AloneProcessus_old

To choose an Optimal result.

int3 - Variable in class aloneinterfaces.AloneProcessus

To visualize results of searching palindromes and different sets of selected sequences from Interface1.

int3 - Variable in class aloneinterfaces.AloneProcessus_old

To visualize results of searching palindromes and different sets of selected sequences from Interface1.

int4 - Variable in class aloneinterfaces.AloneProcessus

To check palindromes (results in Interface5).

int4 - Variable in class aloneinterfaces.AloneProcessus_old

To check palindromes (results in Interface5).

int5 - Variable in class aloneinterfaces.AloneProcessus

Result of checking palindromes (from Interface4).

int5 - Variable in class aloneinterfaces.AloneProcessus_old

Result of checking palindromes (from Interface4).

int6 - Variable in class aloneinterfaces.AloneProcessus

To select and launch a zone prediction (results in Interface7).

int6 - Variable in class aloneinterfaces.AloneProcessus_old

To select and launch a zone prediction (results in Interface7).

int7 - Variable in class aloneinterfaces.AloneProcessus

Results of zone prediction (from Interface6).

int7 - Variable in class aloneinterfaces.AloneProcessus_old

Results of zone prediction (from Interface6).

int8 - Variable in class aloneinterfaces.AloneProcessus

To compare two results files in FichierConvert (ct) format.

int8 - Variable in class aloneinterfaces.AloneProcessus_old

To compare two results files in FichierConvert (ct) format.

int9 - Variable in class aloneinterfaces.AloneProcessus

Results of results comparison (from Interface8).

int9 - Variable in class aloneinterfaces.AloneProcessus_old

Results of results comparison (from Interface8).

IntegerListe - Class in alonefichiers

To provide a set of Integer's.

IntegerListe() - Constructor for class alonefichiers.IntegerListe

Default constructor with a list of 0 elements.

IntegerListe(Integer[]) - Constructor for class alonefichiers.IntegerListe

Constructor with a pre-made table of Integer's.

Interface - Class in aloneinterfaces

Abstract class which extends JPanel and implements ActionListener.

Interface(AloneProcessus) - Constructor for class aloneinterfaces.Interface

Constructor.

Interface0 - Class in aloneinterfaces

Initial graphical interface of selection of a alignment sequence and lauching prediction algorithm.

Interface0(AloneProcessus) - Constructor for class aloneinterfaces.Interface0

Constructor.

Interface1 - Class in aloneinterfaces

The most complex interface in graphic implementation.

Interface1(AloneProcessus) - Constructor for class aloneinterfaces.Interface1

Constructeur.

Interface10 - Class in aloneinterfaces

Recording results and RNAviz file interface.

Interface10(AloneProcessus) - Constructor for class aloneinterfaces.Interface10

Constructor.

Interface11 - Class in aloneinterfaces

??

Interface11(AloneProcessus) - Constructor for class aloneinterfaces.Interface11

Constructor.

Interface12 - Class in aloneinterfaces

??

Interface12(AloneProcessus) - Constructor for class aloneinterfaces.Interface12

Constructor.

Interface2 - Class in aloneinterfaces

Reading optimal resut file and treshold input.

Interface2(AloneProcessus) - Constructor for class aloneinterfaces.Interface2

Constructor.

Interface3 - Class in aloneinterfaces

To visualize results of searching palindromes and different sets of selected sequences.

Interface3(AloneProcessus) - Constructor for class aloneinterfaces.Interface3

Constructeur.

Interface4 - Class in aloneinterfaces

Palindrome selection

Interface4(AloneProcessus) - Constructor for class aloneinterfaces.Interface4

Constructor.

Interface5 - Class in aloneinterfaces

Interface for palindromes search and to know if conservation.

Interface5(AloneProcessus) - Constructor for class aloneinterfaces.Interface5

Constructor.

Interface6 - Class in aloneinterfaces

Area analysis : input of search anchor points parameters (start,end,length).

Interface6(AloneProcessus) - Constructor for class aloneinterfaces.Interface6

Constructor.

Interface7 - Class in aloneinterfaces

Zone analysis / palindrome visualization interface and searching anchor points.

Interface7(AloneProcessus) - Constructor for class aloneinterfaces.Interface7

Constructor.

Interface8 - Class in aloneinterfaces

Results comparison, reference File and structure File.

Interface8(AloneProcessus) - Constructor for class aloneinterfaces.Interface8

Constructor.

Interface9 - Class in aloneinterfaces

Results comparison interface.

Interface9(AloneProcessus) - Constructor for class aloneinterfaces.Interface9

Constructeur.

internalSequence(Palindrome) - Method in class modele.Sequence

To get the internal sequence of a palindrome on a Sequence.

isBase(char) - Static method in class modele.Base

To test if a char symbolize a nucleotids, all nucleotidic code is tested as UPPERCASE.

isBaseOrGap(char) - Static method in class modele.Base

To test if nucleotids or gap / indel symbolized with '-'.

isChercher_pk() - Method in class modele.AlgorithmsStefan

isChercher_pk() - Method in class modele.OriginAlgorithmsStefan

isChercher_pk() - Method in class modele.OtherAlgorithmsStefan

isCompatible(Palindrome) - Method in class modele.Palindrome

isCompatibleWith(Palindrome) - Method in class modele.Palindrome

Deprecated. not exact... (see tests)

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

To know if the alignment is a FASTA alignment.

isGoodPalindrome(int, int, int) - Static method in class modele.Alignement

To know if a palindrome has to be selected or not, with criteria of length and loop (minimal length of palindrome and loop).

isIn(SequenceListe[]) - Method in class modele.SequenceListe

To know if current instance of SequenceListe is in a table of SequenceListe's.

isMore_predictions() - Method in class modele.AlgorithmsStefan

isMore_predictions() - Method in class modele.OriginAlgorithmsStefan

isMore_predictions() - Method in class modele.OtherAlgorithmsStefan

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

To know if a sequence is a nucleic sequence.

isPlusieursPredictions() - Method in class aloneinterfaces.Interface1

isRecherchePseudonoeud() - Method in class aloneinterfaces.Interface1

isScore(int) - Method in class modele.Palindrome

To check if current Palindrome has a given score.

isSelected(int) - Method in class modele.Palindrome

Deprecated. DCFold => PDCFold

isSelectedCible(double, double, boolean) - Method in class modele.Palindrome

For selection of Palindrome cible, if conservation is true : equation 4.11, else 4.12.

isSelectedTest(double) - Method in class modele.Palindrome

For selection of Palindrome test.

isToSave() - Method in class aloneinterfaces.Interface0

isTreeNotFull(int) - Method in class modele.NoeudArbreExec

This method to know if palindrome's search can continue or not.

isTrouvePseudonoeud() - Method in class modele.AlgorithmsStefan

isTrouvePseudonoeud() - Method in class modele.OriginAlgorithmsStefan

isTrouvePseudonoeud() - Method in class modele.OtherAlgorithmsStefan

isValid() - Method in class alonefichiers.Fichier

itemStateChanged(ItemEvent) - Method in class aloneinterfaces.MonMenu

iteration - Static variable in class modele.Algorithms

Deprecated. Count number of iterations in compatibilityTreatment.

iteration - Static variable in class modele.AlgorithmsCT03

Deprecated.

iterationLessLess() - Static method in class modele.Algorithms

Deprecated.

iterationPlusPlus() - Static method in class modele.Algorithms

Deprecated.