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

R

R5GU - Static variable in class modele.Alignement

Special score for GU pair when configuration.

readFile(String) - Static method in class alonefichiers.Fichier

To obtain the content of a given file.

realLength - Variable in class modele.Palindrome

Cible : "Real length"

realLength - Variable in class modele.PalindromeCible

Deprecated. "Real length"

reame - Static variable in class testsorigin.Alignedtmrna

reame - Static variable in class testssuite02.Alignedtmrna

recherche_commune() - Method in class origincomment.ADN1cible

Common search.

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

COMPATIBLE PALINDROME SEARCH
"Methode qui recherche des palindromes dans une sequence d'ADN"
This method search palindromes in DNA sequence.

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

COMPATIBLE PALINDROME SEARCH
"Methode qui recherche des palindromes dans une sequence d'ADN"
"This method search palindromes in a DNA sequence

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

COMPATIBLE PALINDROME SEARCH
"Methode qui recherche des palindromes dans une sequence d'ADN"
This method search palindromes in DNA sequence.

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

COMPATIBLE PALINDROME SEARCH
"Methode qui recherche des palindromes dans une sequence d'ADN"
This method search palindromes in DNA sequence.

recherche_Point_Ancrage(Sequence, int, int, int, double, Sequence[], int) - Method in class modele.AlgorithmsStefan

COMPATIBLE PALINDROME SEARCH
"R=This method search anchor points at step i from palindrome search (on the subsequence i on starting sequence).

recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int) - Method in class modele.OriginAlgorithmsStefan

COMPATIBLE PALINDROME SEARCH
"R=This method search anchor points at step i from palindrome search (on the subsequence i on starting sequence).

recherche_Point_Ancrage(Sequence, int, int, int, double, Sequence[], int) - Method in class modele.OtherAlgorithmsStefan

COMPATIBLE PALINDROME SEARCH
"R=This method search anchor points at step i from palindrome search (on the subsequence i on starting sequence).

recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int) - Method in class origincomment.ADN1cible

COMPATIBLE PALINDROME SEARCH
"R=This method search anchor points at step i from palindrome search (on the subsequence i on starting sequence).

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

PSEUDOKNOTS SEARCH
"This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"

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

PSEUDOKNOTS SEARCH
"This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"

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

PSEUDOKNOTS SEARCH
"This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"

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

PSEUDOKNOTS SEARCH
"This method for pseudoknots search : we launch search on each internal sequence of palindromes (form more external to more internal) as selection criteria decrease"

rechercher(Vector) - Method in class modele.Palindrome

Deprecated. see also PalindromeListe.rechercher(Palindrome) and PalindromeListe.whichPosition(Palindrome)

rechercher(Vector) - Method in class modele.PalindromeCible

Deprecated. "Following methods sorted by use order in ADN1 Class". (14)
"to find a palindrome in a Vector of palindromes"

rechercher(Palindrome) - Method in class modele.PalindromeListe

Deprecated. Transformed to PalindromeListe.whichPosition(Palindrome)

rechercher(Vector) - Method in class origincomment.Appariement

rechercher(Vector) - Method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (14)
"to find a palindrome in a Vector of palindromes"

rechercher_approx(Vector) - Method in class modele.Palindrome

Deprecated. see also PalindromeListe.rechercher_approx(Palindrome) and PalindromeListe.whichPositionApprox(Palindrome)

rechercher_approx(Vector) - Method in class modele.PalindromeCible

Deprecated. "Following methods sorted by use order in ADN1 Class". (15)
"to find an approximate palindrome in a vector of palindromes."

rechercher_approx(Palindrome) - Method in class modele.PalindromeListe

Deprecated. Tranformed to PalindromeListe.whichPositionApprox(Palindrome)

rechercher_approx(Vector) - Method in class origincomment.Palindrome1cible

"Following methods sorted by use order in ADN1 Class". (15)
"to find an approximate palindrome in a vector of palindromes."

recoverPalindromes() - Method in class modele.Alignement

Searching for Palindrome's, only on the half of the matrix score.

recule() - Method in class aloneinterfaces.AloneProcessus

Go to previous step.

recule() - Method in class aloneinterfaces.AloneProcessus_old

Go to previous step.

recuperation(PalindromeListeListe, Palindrome[], NoeudArbreExec) - Static method in class modele.ArbreExec

"Recuperation"
This method to keep compatibility with algorithms' implementation of Stefan Engelen and its conversion.

recuperation(Vector, Palindrome1cible[], NoeudPalindrome) - Static method in class origincomment.ArbrePalindrome

"Recuperation"

recupere_alignement(Alignement, int[], int) - Method in class origincomment.Matrice_ALN

To gain the alignment ?

remonter() - Method in class modele.ArbreExec

To get up in the tree : change current node to the father of current node.

remonter() - Method in class origincomment.ArbrePalindrome

To get up in the tree : change current node to the father of current node.

removeBoolean(Boolean) - Method in class alonefichiers.BooleanListe

To remove a specific Boolean.

removeBoolean(int) - Method in class alonefichiers.BooleanListe

To remove a Boolean at a specific place in the list.

removeConvertedAlignement(Alignement) - Method in class modele.ConvertedAlignementListe

Deprecated. To remove a specific ConvertedAlignement.

removeConvertedAlignement(int) - Method in class modele.ConvertedAlignementListe

Deprecated. To remove a ConvertedAlignement at a specific place in the list.

removeInteger(Integer) - Method in class alonefichiers.IntegerListe

To remove a specific Integer.

removeInteger(int) - Method in class alonefichiers.IntegerListe

To remove a Integer at a specific place in the list.

removeNoeudArbreExec(NoeudArbreExec) - Method in class modele.NoeudArbreExecListe

To remove a specific NoeudArbreExec

removeNoeudArbreExec(Palindrome) - Method in class modele.NoeudArbreExecListe

To remove a specific NoeudArbreExec with Palindrome (first one remove).

removeNoeudArbreExec(int) - Method in class modele.NoeudArbreExecListe

To remove a NoeudArbreExec at a specific place in the list.

removeObject(Object) - Method in class modele.ObjectListe

Deprecated. Please do NOT use this function !

removeObject(int) - Method in class modele.ObjectListe

Deprecated. Please do NOT use this function !

removePalindrome(Palindrome) - Method in class modele.PalindromeListe

To remove a specific Palindrome.

removePalindrome(int) - Method in class modele.PalindromeListe

To remove a Palindrome at a specific place in the list.

removePalindromeListe(PalindromeListe) - Method in class modele.PalindromeListeListe

To remove a specific Palindrome.

removePalindromeListe(int) - Method in class modele.PalindromeListeListe

To remove a Palindrome at a specific place in the list.

removeSequence(Sequence) - Method in class modele.SequenceListe

To remove a specific Sequence.

removeSequence(int) - Method in class modele.SequenceListe

To remove a Sequence at a specific place in the list.

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

To remove a subSequence to the Base and Char Sequence, then including of alignment (removing bases replacing with gap's).

remplir(Palindrome[], int) - Method in class modele.ConvertedProfil

This procedure to make the profile will be not empty...

remplir(Palindrome1cible[], int) - Method in class origincomment.Profil

This procedure to make the profile will be not empty...

res - Static variable in class alonefichiers.FiltreUtils

resolution - Static variable in class modele.Algorithms

Deprecated. Resolution for search of Palindrome in Sequence.

resultat - Variable in class aloneinterfaces.Interface12

Result text area interface.

resultat - Variable in class aloneinterfaces.Interface3

Result text area visualization.

resultat - Variable in class aloneinterfaces.Interface5

Result text area visualization.

resultat - Variable in class aloneinterfaces.Interface7

Result text area interface visualization.

resultat - Variable in class aloneinterfaces.Interface9

Result text area visualization.

Resultat - Class in origincomment

A class for results ?

Resultat(ADN1test[]) - Constructor for class origincomment.Resultat

Constructor with given table of test sequences.

Resultat(int, ADN1test[]) - Constructor for class origincomment.Resultat

Deprecated. [not used]

resultat_commun(PalindromeListeListe) - Method in class modele.AlgorithmsStefan

RESULT TREAMENT
"This method compute a common result from vector of tab of palindromes"
Here some inside code indications about conversion from Vector to PalindromeListe : Post-comments with "<=>" inside : left about Vector, right about <Object>Liste

resultat_commun(Vector) - Method in class modele.OriginAlgorithmsStefan

RESULT TREAMENT
"This method compute a common result from vector of tab of palindromes"

resultat_commun(PalindromeListeListe) - Method in class modele.OtherAlgorithmsStefan

RESULT TREAMENT
"This method compute a common result from vector of tab of palindromes"
Here some inside code indications about conversion from Vector to PalindromeListe : Post-comments with "<=>" inside : left about Vector, right about <Object>Liste

resultat_commun(Vector) - Method in class origincomment.ADN1cible

RESULT TREAMENT
"This method compute a common result from vector of tab of palindromes"

resultat_commun_paire_de_base(Vector) - Method in class origincomment.ADN1cible

Deprecated. [never used]

resultat_Optimal(ADN1cible, ADN1test, ADN1test[], BufferedReader, int, int, int, boolean) - Static method in class origincomment.ADN1test

"Method which test all possibilities of permutations of test sequences

results - Variable in class aloneinterfaces.AloneProcessus

results - Variable in class aloneinterfaces.AloneProcessus_old

results - Variable in class controller.ListeBean

To get the results in text / plain format

results - Variable in class modele.AlgorithmsStefan

To get the results of current computing (plain text).

results - Variable in class modele.OriginAlgorithmsStefan

To get the results of current computing (plain text).

results - Variable in class modele.OtherAlgorithmsStefan

To get the results of current computing (plain text).

resultsHTML - Variable in class modele.AlgorithmsStefan

To get the results of current computing (HTML to include).

resultsHTML - Variable in class modele.OriginAlgorithmsStefan

To get the results of current computing (HTML to include).

resultsHTML - Variable in class modele.OtherAlgorithmsStefan

To get the results of current computing (HTML to include).

retireProgressBar(JProgressBar) - Method in class aloneinterfaces.Interface1

To remove the progression bar.

rhpal - Static variable in class testsorigin.Alignedtmrna

rhpal - Static variable in class testssuite02.Alignedtmrna

RIEN - Static variable in class origincomment.Alignement

RIEN (nothing) is 0.

ripro - Static variable in class testsorigin.Alignedtmrna

ripro - Static variable in class testssuite02.Alignedtmrna

rnavizFile - Variable in class controller.ListeBean

To get the result RnaViz File.

rnavizFile - Variable in class modele.AlgorithmsStefan

To get the result RnaViz File.

rnavizFile - Variable in class modele.OriginAlgorithmsStefan

To get the result RnaViz File.

rnavizFile - Variable in class modele.OtherAlgorithmsStefan

To get the result RnaViz File.

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

To know if on two helix (Palindrome here), the second is included into the first.

run() - Method in class aloneinterfaces.AloneProcessus

run() - Method in class aloneinterfaces.AloneProcessus_old