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S

sapar - Static variable in class testsorigin.Alignedtmrna
 
sapar - Static variable in class testssuite02.Alignedtmrna
 
satyh - Static variable in class testsorigin.Alignedalphad
 
satyh - Static variable in class testssuite02.Alignedalphad
 
satyp - Static variable in class testsorigin.Alignedtmrna
 
satyp - Static variable in class testssuite02.Alignedtmrna
 
sauver - Variable in class aloneinterfaces.Interface0
Save / recording button.
sauver() - Method in class aloneinterfaces.MonBureau
Deprecated. (unused)
sauver - Variable in class aloneinterfaces.MonMenu
 
sauverFasta - Variable in class aloneinterfaces.Interface0
To remember to record.
score(char, char) - Static method in class modele.Alignement
Scoring alignment between two char of two sequences.
score - Variable in class modele.Palindrome
Palindrome score (S or M[i,j]).
score - Variable in class modele.Sequence
Tab of scores of current sequence of length 7.
score - Variable in class modele.SequenceTest
Deprecated. Tab of scores of current sequence of length 7.
score(char, char) - Static method in class origincomment.ADN1cible
COMPATIBLE PALINDROME SEARCH
Getting a score from two (2) bases.
score - Variable in class origincomment.ADN1test
Tab of scores of current sequence.
score(char, char) - Method in class origincomment.ADN1test
"Methodes pour calculer le cout d'alignement de deux bases"
score() - Method in class origincomment.Alignement
"Helix best mutate to stable pairwises
score - Variable in class origincomment.Case
Score.
score(char, char) - Method in class origincomment.Matrice_ALN
Scoring a pairwise...
score(Palindrome1cible) - Method in class origincomment.Palindrome1cible
Deprecated. [not used]
score - Variable in class origincomment.Palindrome1test
Weight of test palindrome (function of compensatory mutations).
score(char, char) - Method in class origincomment.StefanErrors
Not a static procedure, but could be useful to be...
score_normal - Variable in class origincomment.Case
Normal Score.
score_seq - Variable in class origincomment.Resultat
Scores of sequences.
scoreArea - Variable in class aloneinterfaces.Interface1
 
scoreBases(char, char) - Static method in class modele.Base
Score for two nuleotids (char): Watson-Cricks and Wooble accepted.
scoreBasic(char, char) - Static method in class modele.Alignement
Getting a score from two (2) bases.
scoreMax - Static variable in class origincomment.ADN1test
Maximal score (default is -300).
scoreScroll - Variable in class aloneinterfaces.Interface1
 
scrollListeCible - Variable in class aloneinterfaces.Interface1
Zone où s'affiche la liste des séquances cibles potentielles.
scrollListeTest - Variable in class aloneinterfaces.Interface1
Ensemble des listes où s'effectue la sélection des séquences tests.
searchAllStructuralPalindromes(NoeudArbreExec, Sequence, SequenceListe, int, int) - Static method in class modele.Algorithms
Deprecated. To search structural palindromes (helix) including pseudoknots.
searchAnchorPoints(Sequence, Alignement, double, SequenceListe, int, int) - Static method in class modele.Algorithms
Deprecated. Not the good prototype as algorithm is defined.
searchAnchorPoints(int, int, Alignement, double, SequenceListe, int, int, int) - Static method in class modele.Algorithms
Deprecated. M[i,j] too long...
searchAnchorPoints(Alignement, double, SequenceListe, int, int, int) - Static method in class modele.Algorithms
Deprecated. Search procedure of structural palindromes with pairing matrix and new selection criteria.
searchPseudoknots - Variable in class controller.ProcessusNew
 
searchPseudoknots - Variable in class controller.ProcessusOrigin
 
searchStructuralPalindrome(NoeudArbreExec, Sequence, int, SequenceListe, int, int) - Static method in class modele.Algorithms
Deprecated. Searching structural palindromes in a selected sequence (cible), with comparison in a whole alignment of tests sequences.
selectionBool - Variable in class aloneinterfaces.Interface1
Test bool's selection (was a Vector of booleans (selected predictions)).
selectionInt - Variable in class aloneinterfaces.Interface1
Test int's selection (was a Vector of table of ints (selected items in prediction)).
seq - Static variable in class alonefichiers.FiltreUtils
fasta sequence / alignment
seq3prime - Variable in class origincomment.Matrice_ALN
3' sequence (default is empty ("")).
seq5prime - Variable in class origincomment.Matrice_ALN
5' sequence (default is empty ("")).
SEQ_LENGTH - Static variable in class tests.TestSequence
 
Sequence - Class in modele
This class to define a nucleic sequence / alignment in different outpout format.
Sequence() - Constructor for class modele.Sequence
Default constructor (empty name and sequence).
Sequence(String, String) - Constructor for class modele.Sequence
Name and whole sequence constructor.
sequence - Variable in class origincomment.ADN1cible
"Global attribute with signification.
sequence - Variable in class origincomment.ADN1test
Current sequence in char tab.
sequence - Variable in class tests.TestSequence
 
sequence - Variable in class tests.TestSequenceListe
 
sequence1 - Variable in class modele.Alignement
Sequence of the alignment.
sequence1 - Variable in class tests.TestAlignement
 
sequence2 - Variable in class modele.Alignement
Sequence of the alignment.
sequence2 - Variable in class tests.TestAlignement
 
sequenceBase - Variable in class modele.Sequence
Base tabled/ formatted sequence without gap's/ indel's.
sequenceChar - Variable in class modele.Sequence
Char tabled / formatted sequence without gap's / indel's.
SequenceCible - Class in modele
Deprecated. Transfered to Sequence
SequenceCible(String, String) - Constructor for class modele.SequenceCible
Deprecated.  
sequenceCible(String, boolean) - Static method in class origincomment.ADN1cible
SOME SHOW FOR VIEW
"To get target sequence"
SequenceListe - Class in modele
This class to provide easy-to-use Sequence tables / Lists.
SequenceListe() - Constructor for class modele.SequenceListe
Default constructor with a list of 0 elements.
SequenceListe(Sequence[]) - Constructor for class modele.SequenceListe
Constructor with a pre-made table of Sequence.
sequenceString - Variable in class modele.Sequence
Original String alignment / sequence.
SequenceTest - Class in modele
Deprecated. Transfered to Sequence
SequenceTest(String, String) - Constructor for class modele.SequenceTest
Deprecated.  
sequenceTests(String) - Static method in class origincomment.ADN1test
Deprecated. [not used]
serialVersionUID - Static variable in class alonecontroller.AloneApplet
Deprecated.  
serialVersionUID - Static variable in class aloneinterfaces.Interface0
Interface serial number (0).
serialVersionUID - Static variable in class aloneinterfaces.Interface1
Interface Serial Number (1).
serialVersionUID - Static variable in class aloneinterfaces.Interface10
Interface Serial Number (10).
serialVersionUID - Static variable in class aloneinterfaces.Interface11
Interface Serial Number (11).
serialVersionUID - Static variable in class aloneinterfaces.Interface12
Interface Serial Number (12).
serialVersionUID - Static variable in class aloneinterfaces.Interface2
Interface Serial Number (2).
serialVersionUID - Static variable in class aloneinterfaces.Interface3
Interface Serial Number (3).
serialVersionUID - Static variable in class aloneinterfaces.Interface4
Interface Serial Number(4).
serialVersionUID - Static variable in class aloneinterfaces.Interface5
Interface Serial Number (5).
serialVersionUID - Static variable in class aloneinterfaces.Interface6
Interface Serial Number (6).
serialVersionUID - Static variable in class aloneinterfaces.Interface7
Interface Serial Number (7).
serialVersionUID - Static variable in class aloneinterfaces.Interface8
Interface Serial Number (8).
serialVersionUID - Static variable in class aloneinterfaces.Interface9
Interface Serial Number (9).
serialVersionUID - Static variable in class aloneinterfaces.MaFrame
Serial number (42).
serialVersionUID - Static variable in class aloneinterfaces.MonBouton
Serial number (43).
serialVersionUID - Static variable in class aloneinterfaces.MonBureau
Serial number (44).
serialVersionUID - Static variable in class aloneinterfaces.MonImage
Serial number (45).
serialVersionUID - Static variable in class aloneinterfaces.MonLayout
Serial number (46).
serialVersionUID - Static variable in class aloneinterfaces.MonMenu
Serial number (47).
serialVersionUID - Static variable in class controller.Processus
Deprecated. Servlet serial Number (42).
serialVersionUID - Static variable in class controller.Processus_old
Deprecated. Servlet serial Number (42).
serialVersionUID - Static variable in class controller.ProcessusNew
Servlet serial Number (42).
serialVersionUID - Static variable in class controller.ProcessusOrigin
Servlet serial Number (42).
setAlignement(String) - Method in class aloneinterfaces.Interface0
 
setAutreSequence(SequenceListe) - Method in class aloneinterfaces.Interface1
 
setBase(char) - Method in class modele.Base
 
setBoolean(Boolean, int) - Method in class alonefichiers.BooleanListe
 
setChamps(String[]) - Method in class alonefichiers.Fichier
 
setChamps(int, String) - Method in class alonefichiers.Fichier
 
setChercher_pk(boolean) - Method in class modele.AlgorithmsStefan
 
setChercher_pk(boolean) - Method in class modele.OriginAlgorithmsStefan
 
setChercher_pk(boolean) - Method in class modele.OtherAlgorithmsStefan
 
setCible(int) - Method in class controller.ListeBean
To record the target sequence.
setCible(Sequence) - Method in class controller.ListeBean
To record the target sequence.
setCombiGUGC(double) - Method in class modele.Sequence
 
setConvertedAlignement(Alignement, int) - Method in class modele.ConvertedAlignementListe
Deprecated.  
setCouleur(int, int, int) - Method in class aloneinterfaces.MonImage
Panel background color.
setCountZero() - Method in class modele.Palindrome
 
setCurrentNode(NoeudArbreExec) - Method in class modele.ArbreExec
 
setDacodac(JButton) - Method in class aloneinterfaces.Interface
 
setDecalage(int) - Static method in class modele.Algorithms
Deprecated.  
setDecalage(int) - Method in class modele.AlgorithmsStefan
 
setDecalage(int) - Method in class modele.OriginAlgorithmsStefan
 
setDecalage(int) - Method in class modele.OtherAlgorithmsStefan
 
setDelcrit(double) - Static method in class modele.Algorithms
Deprecated. To set deletion criteria in SSCA to compute effects, if set under 0.000 : set to 0.00 ; if more than 100.0 : set to 1.00 (default value).
setEffetGC(double) - Method in class modele.Sequence
 
setEffetGU(double) - Method in class modele.Sequence
 
setEffetGUGC(double) - Method in class modele.Sequence
 
setFenetre(JPanel) - Method in class aloneinterfaces.Interface
 
setFichier(String) - Method in class aloneinterfaces.Interface0
 
setFils(NoeudArbreExecListe) - Method in class modele.NoeudArbreExec
 
setHomologie(double) - Method in class modele.Sequence
 
setIdecrit(double) - Static method in class modele.Algorithms
Deprecated. To set identity criteria in SSCA to compute effects, if set under 00.000 : set to 0.00 ; if more than 100.00 : set to 75.0 (default value).
setIncertitude(double) - Method in class modele.AlgorithmsStefan
 
setIncertitude(double) - Method in class modele.OriginAlgorithmsStefan
 
setIncertitude(double) - Method in class modele.OtherAlgorithmsStefan
 
setIndels(double) - Method in class modele.Sequence
 
setIndeterminate(double) - Method in class modele.Sequence
 
setInteger(Integer, int) - Method in class alonefichiers.IntegerListe
 
setInterface() - Method in class aloneinterfaces.Interface
Some inheritants interfaces have a method called setInterface (with differents arguments and exceptions throws).
setInterface(String) - Method in class aloneinterfaces.Interface0
To fix how works the interface.
setInterface() - Method in class aloneinterfaces.Interface0
To fix how works the interface.
setInterface() - Method in class aloneinterfaces.Interface1
Not active here.
setInterface() - Method in class aloneinterfaces.Interface10
Not active here.
setInterface() - Method in class aloneinterfaces.Interface11
Not active here.
setInterface(SequenceListe, Sequence, Palindrome) - Method in class aloneinterfaces.Interface12
To fix how works the interface.
setInterface(Profil, String, Palindrome1cible, int) - Method in class aloneinterfaces.Interface12
Deprecated. [not used]
setInterface() - Method in class aloneinterfaces.Interface12
To fix how works the interface.
setInterface() - Method in class aloneinterfaces.Interface2
Not active here.
setInterface(String) - Method in class aloneinterfaces.Interface3
Putting direct results in the interface.
setInterface(Sequence, SequenceListe[], PalindromeListeListe) - Method in class aloneinterfaces.Interface3
To fix how works the interface.
setInterface(Sequence, SequenceListe[], PalindromeListe) - Method in class aloneinterfaces.Interface3
To fix how works the interface.
setInterface(ADN1cible, Vector) - Method in class aloneinterfaces.Interface3
Deprecated. [not used]
setInterface() - Method in class aloneinterfaces.Interface3
To fix how works the interface.
setInterface() - Method in class aloneinterfaces.Interface4
Not active here.
setInterface(Sequence, SequenceListe[], int, int, int, int, int) - Method in class aloneinterfaces.Interface5
To fix how works the interface.
setInterface(ADN1cible, ADN1test[], int, int, int, int, int) - Method in class aloneinterfaces.Interface5
Deprecated. [not used]
setInterface() - Method in class aloneinterfaces.Interface5
To fix how works the interface.
setInterface() - Method in class aloneinterfaces.Interface6
Not active here.
setInterface(Sequence, SequenceListe[], int, int, int) - Method in class aloneinterfaces.Interface7
Méthode pour fixer le fonctionnement de l'interface.
setInterface(ADN1cible, ADN1test[], int, int, int) - Method in class aloneinterfaces.Interface7
Deprecated. [not used]
setInterface() - Method in class aloneinterfaces.Interface7
To fix how works the interface.
setInterface() - Method in class aloneinterfaces.Interface8
Not active here.
setInterface(String, String, double) - Method in class aloneinterfaces.Interface9
To fix how works the interface.
setInterface(ADN1cible, String, String, double) - Method in class aloneinterfaces.Interface9
Deprecated. [not used]
setInterface() - Method in class aloneinterfaces.Interface9
To fix how works the interface.
SetIterationZero() - Static method in class modele.Algorithms
Deprecated.  
setLbmin(double) - Static method in class modele.Alignement
 
setLength(int) - Method in class modele.Palindrome
 
setListe(Boolean[]) - Method in class alonefichiers.BooleanListe
 
setListe(Integer[]) - Method in class alonefichiers.IntegerListe
 
setListe(Alignement[]) - Method in class modele.ConvertedAlignementListe
Deprecated.  
setListe(NoeudArbreExec[]) - Method in class modele.NoeudArbreExecListe
 
setListe(Object[]) - Method in class modele.ObjectListe
Deprecated. Please do NOT use this function !
setListe(Palindrome[]) - Method in class modele.PalindromeListe
 
setListe(PalindromeListe[]) - Method in class modele.PalindromeListeListe
 
setListe(Sequence[]) - Method in class modele.SequenceListe
 
setListModelCible(SequenceListe) - Method in class aloneinterfaces.Interface1
To compute a JList containing only the names of Sequence's.
setListModelTest(Sequence, SequenceListe, int) - Method in class aloneinterfaces.Interface1
Visualization of homologuous sequences selection.
setLongBoucleMin(int) - Static method in class modele.Algorithms
Deprecated.  
setLongMut(double) - Method in class modele.Palindrome
 
setLongPalindMin(int) - Static method in class modele.Algorithms
Deprecated.  
setLpmin(double) - Static method in class modele.Alignement
 
setMarge(int, int, int, int) - Method in class aloneinterfaces.MonImage
To determine distance between image and panel border.
setMaxHomology(double) - Static method in class modele.Algorithms
Deprecated. To set the T=threshold of selection of strict maximal homology in SSCA, if set under 0.0 or minHomology : no changes ; if more than 100.0 : 100.0.
setMenu(JComboBox) - Method in class aloneinterfaces.Interface
 
setMinHomology(double) - Static method in class modele.Algorithms
Deprecated. To set the threshold of selection of strict minimal homology in SSCA, if set under 0.0 : set to 0.0 ; if more than 100.0 or maxHomology : no changes.
setMonlayout(MonLayout) - Method in class aloneinterfaces.Interface
 
setMore_Predictions(boolean) - Method in class modele.AlgorithmsStefan
 
setMore_Predictions(boolean) - Method in class modele.OriginAlgorithmsStefan
 
setMore_Predictions(boolean) - Method in class modele.OtherAlgorithmsStefan
 
setN(int) - Method in class controller.ListeBean
 
setNb_prediction_max(int) - Method in class modele.AlgorithmsStefan
 
setNb_prediction_max(int) - Method in class modele.OriginAlgorithmsStefan
 
setNb_prediction_max(int) - Method in class modele.OtherAlgorithmsStefan
 
setNbErreursMax(int) - Static method in class modele.Algorithms
Deprecated.  
setNbMaxSequences(int) - Static method in class modele.Algorithms
Deprecated. To set the maximal number of selection of sequences in SSCA.
setNbMinSequences(int) - Static method in class modele.Algorithms
Deprecated. To set the minimal number of selection of sequences in SSCA.
setNoeudArbreExec(NoeudArbreExec, int) - Method in class modele.NoeudArbreExecListe
 
setNom(String) - Method in class modele.Sequence
 
setNombreDecimale(int) - Static method in class modele.Sequence
 
setNombreErreur(int) - Method in class modele.Palindrome
 
setNombreMutationDouble(int) - Method in class modele.Palindrome
 
setNombreMutationSimple(int) - Method in class modele.Palindrome
 
setObject(Object, int) - Method in class modele.ObjectListe
Deprecated. Please do NOT use this function !
setPalindrome(Palindrome, int) - Method in class modele.PalindromeListe
 
setPalindromeListe(PalindromeListe, int) - Method in class modele.PalindromeListeListe
 
setPalindromeListe(Palindrome[], int) - Method in class modele.PalindromeListeListe
 
setPalindromes(PalindromeListe) - Method in class modele.NoeudArbreExec
 
setPalindromes(Palindrome[]) - Method in class modele.NoeudArbreExec
 
setPere(NoeudArbreExec) - Method in class modele.NoeudArbreExec
 
setPertinence(double) - Method in class modele.Palindrome
 
setPoid(double) - Method in class modele.Palindrome
 
setPosition(int) - Method in class modele.Base
 
setPositionDebut(int) - Method in class modele.Palindrome
 
setPositionFin(int) - Method in class modele.Palindrome
 
setProcessusParent(AloneProcessus) - Method in class aloneinterfaces.Interface
 
setPseudonoeud(int) - Method in class modele.AlgorithmsStefan
 
setPseudonoeud(int) - Method in class modele.OriginAlgorithmsStefan
 
setPseudonoeud(int) - Method in class modele.OtherAlgorithmsStefan
 
setPseudonoeudPlusPlus() - Method in class modele.AlgorithmsStefan
 
setPseudonoeudPlusPlus() - Method in class modele.OriginAlgorithmsStefan
 
setPseudonoeudPlusPlus() - Method in class modele.OtherAlgorithmsStefan
 
setResolution(double) - Static method in class modele.Algorithms
Deprecated.  
setResults(Sequence, PalindromeListeListe) - Method in class controller.ListeBean
This procedure to compute the RnaViz and Bracket file result.
setResults(String) - Method in class controller.ListeBean
To set the text / plain results.
setScore(double) - Method in class modele.Palindrome
 
setScore(int, double) - Method in class modele.Sequence
Return a score in the following (default is homology).
setSelectedIcon(URL) - Method in class aloneinterfaces.MonBouton
To change selected image.
setSequence(Sequence) - Method in class aloneinterfaces.Interface1
 
setSequence(String, String) - Method in class aloneinterfaces.Interface1
 
setSequence(Sequence) - Method in class modele.Palindrome
 
setSequence(Sequence, int) - Method in class modele.SequenceListe
 
setStructures(PalindromeListeListe) - Method in class modele.ArbreExec
 
setTableauInitial(Sequence[]) - Method in class modele.AlgorithmsStefan
 
setTableauInitial(ADN1test[]) - Method in class modele.OriginAlgorithmsStefan
 
setTableauInitial(Sequence[]) - Method in class modele.OtherAlgorithmsStefan
 
setTableauPalindrome(ArbreExec) - Method in class modele.AlgorithmsStefan
 
setTableauPalindrome(ArbrePalindrome) - Method in class modele.OriginAlgorithmsStefan
 
setTableauPalindrome(ArbreExec) - Method in class modele.OtherAlgorithmsStefan
 
setTaille(Container, int) - Method in class aloneinterfaces.MonLayout
To change the length of this layout.
setTaille_boucle_min(int) - Method in class modele.AlgorithmsStefan
 
setTaille_boucle_min(int) - Method in class modele.OriginAlgorithmsStefan
 
setTaille_boucle_min(int) - Method in class modele.OtherAlgorithmsStefan
 
setTaille_pal_min(int) - Method in class modele.AlgorithmsStefan
 
setTaille_pal_min(int) - Method in class modele.OriginAlgorithmsStefan
 
setTaille_pal_min(int) - Method in class modele.OtherAlgorithmsStefan
 
setTaux(double) - Method in class modele.Palindrome
 
setTexteFichier(String) - Method in class aloneinterfaces.Interface10
 
setTexteFichier1(String) - Method in class aloneinterfaces.Interface8
 
setTexteFichier2(String) - Method in class aloneinterfaces.Interface8
 
setTexteGraphique(String) - Method in class aloneinterfaces.Interface10
 
setTexteLongueur(String) - Method in class aloneinterfaces.Interface8
 
setTrouvePseudonoeud(boolean) - Method in class modele.AlgorithmsStefan
 
setTrouvePseudonoeud(boolean) - Method in class modele.OriginAlgorithmsStefan
 
setTrouvePseudonoeud(boolean) - Method in class modele.OtherAlgorithmsStefan
 
setTypeARN(int) - Method in class modele.AlgorithmsStefan
 
setTypeARN(int) - Method in class modele.OriginAlgorithmsStefan
 
setTypeARN(int) - Method in class modele.OtherAlgorithmsStefan
 
setTypeCritere(int) - Method in class modele.AlgorithmsStefan
 
setTypeCritere(int) - Method in class modele.OriginAlgorithmsStefan
 
setTypeCritere(int) - Method in class modele.OtherAlgorithmsStefan
 
setTypeRecherche(int) - Method in class modele.AlgorithmsStefan
 
setTypeRecherche(int) - Method in class modele.OriginAlgorithmsStefan
 
setTypeRecherche(int) - Method in class modele.OtherAlgorithmsStefan
 
setUp() - Method in class tests.TestAlignement
 
setUp() - Method in class tests.TestBase
At the beginning of the tests, to instanciate a Base Object (and test constructor).
setUp() - Method in class tests.TestNoeudArbreExec
 
setUp() - Method in class tests.TestNoeudArbreExecListe
 
setUp() - Method in class tests.TestPalindrome
 
setUp() - Method in class tests.TestPalindromeListe
 
setUp() - Method in class tests.TestPalindromeListeListe
 
setUp() - Method in class tests.TestSequence
 
setUp() - Method in class tests.TestSequenceListe
 
setUp() - Method in class testsalone.TestFichier
 
setUp() - Method in class testsalone.TestFichierBracket
 
setUp() - Method in class testsalone.TestFichierFasta
 
setUp() - Method in class testsalone.TestFichierRnaViz
 
setUp() - Method in class testsorigin.TestPDCFold00
 
setUp() - Method in class testsorigin.TestPDCFold01
 
setUp() - Method in class testsorigin.TestPDCFold02
 
setUp() - Method in class testsorigin.TestPDCFold03
 
setUp() - Method in class testssuite01.TestAlgorithmsPartI
 
setUp() - Method in class testssuite01.TestAlgorithmsPartII
 
setUp() - Method in class testssuite01.TestAlgorithmsPartIII
 
setUp() - Method in class testssuite01.TestAlgorithmsPartIV
 
setUp() - Method in class testssuite01.TestCompatibilityTreament01
 
setUp() - Method in class testssuite01.TestCompatibilityTreament01Bis
 
setUp() - Method in class testssuite01.TestCompatibilityTreament02
 
setUp() - Method in class testssuite01.TestCompatibilityTreament03
 
setUp() - Method in class testssuite02.TestGlobalPDCFold00
 
setUserPalindromesTable(PalindromeListe) - Method in class modele.OriginAlgorithmsStefan
To set the given known palindromes by user.
setValeur1(int) - Method in class testssuite01.HyperTest
Deprecated.  
setValeur2(int) - Method in class testssuite01.HyperTest
Deprecated.  
setValid(boolean) - Method in class alonefichiers.Fichier
 
setValues(ADN1cible, boolean, int, boolean) - Static method in class controller.ProcessusOrigin
To be sure that good values are set as parameters...
setValues(boolean, int, boolean, boolean) - Method in class modele.AlgorithmsStefan
To be sure that good values are set as parameters...
setValues(AlgorithmsStefan, boolean, int, boolean, boolean) - Static method in class modele.AlgorithmsStefan
To be sure that good values are set as parameters...
setValues(boolean, int, boolean, boolean) - Method in class modele.OriginAlgorithmsStefan
To be sure that good values are set as parameters...
setValues(OriginAlgorithmsStefan, boolean, int, boolean, boolean) - Static method in class modele.OriginAlgorithmsStefan
To be sure that good values are set as parameters...
setValues(boolean, int, boolean, boolean) - Method in class modele.OtherAlgorithmsStefan
To be sure that good values are set as parameters...
setValues(OtherAlgorithmsStefan, boolean, int, boolean, boolean) - Static method in class modele.OtherAlgorithmsStefan
To be sure that good values are set as parameters...
setVariabilite(double) - Method in class modele.Sequence
 
seuil - Variable in class aloneinterfaces.Interface2
Interface memory.
sheput - Variable in class testssuite01.TestAlgorithmsPartIII
She. put. tmRNA
sheputliste - Variable in class testssuite01.TestAlgorithmsPartIII
lists of sequences
shput - Static variable in class testsorigin.Alignedtmrna
 
shput - Static variable in class testssuite02.Alignedtmrna
 
shvio - Static variable in class testsorigin.Alignedalphad
 
shvio - Static variable in class testssuite02.Alignedalphad
 
simel - Static variable in class testsorigin.Alignedtmrna
 
simel - Static variable in class testssuite02.Alignedtmrna
 
sortByBeginPositionGrowing() - Method in class modele.PalindromeListe
To sort the table of Palindrome's by growing begin position.
sortByDecreasing(int) - Method in class modele.SequenceListe
Sort by decreasing (default = homology with cible sequence) : (0) variability sortByDecreasingRelevance() - Method in class modele.PalindromeListe
To sort the table of Palindrome's by decreasing relevance.
sortByEndPositionGrowing() - Method in class modele.PalindromeListe
To sort the table of Palindrome's by growing end position.
sortByIncreasing(int) - Method in class modele.SequenceListe
Sort by increasing (default = homology with cible sequence) : (0) variability spara - Static variable in class testsorigin.Alignedalphad
 
spara - Static variable in class testssuite02.Alignedalphad
 
sputr - Static variable in class testsorigin.Alignedalphad
 
sputr - Static variable in class testssuite02.Alignedalphad
 
SSCAResult - Variable in class controller.ListeBean
To get the results of SSCA
start() - Method in class alonecontroller.AloneApplet
Deprecated. Every time applet appears.
start() - Method in class aloneinterfaces.AloneProcessus
When current instance is launched.
start() - Method in class aloneinterfaces.AloneProcessus_old
When current instance is launched.
staur - Static variable in class testsorigin.Alignedtmrna
 
staur - Static variable in class testssuite02.Alignedtmrna
 
stcoe - Static variable in class testsorigin.Alignedtmrna
 
stcoe - Static variable in class testssuite02.Alignedtmrna
 
StefanAlgorithms - Class in origincomment
This class only for documentation and informations about the code and algorithms implemented by Stefan Engelen from 2002 to 2006.
StefanAlgorithms() - Constructor for class origincomment.StefanAlgorithms
 
StefanErrors - Class in origincomment
Some errors got in some places of Stefan Engelen original code / implementation.
StefanErrors(String, BufferedReader) - Constructor for class origincomment.StefanErrors
What a faboulus constructor !
stepi - Static variable in class testsorigin.Alignedtmrna
 
stepi - Static variable in class testssuite02.Alignedtmrna
 
stequ - Static variable in class testsorigin.Alignedtmrna
 
stequ - Static variable in class testssuite02.Alignedtmrna
 
Stest - Variable in class modele.PalindromeListe
Average of weight of Palindrome
stgor - Static variable in class testsorigin.Alignedtmrna
 
stgor - Static variable in class testssuite02.Alignedtmrna
 
stmut - Static variable in class testsorigin.Alignedtmrna
 
stmut - Static variable in class testssuite02.Alignedtmrna
 
stop() - Method in class alonecontroller.AloneApplet
Deprecated. Every time applet disappears.
stop - Variable in class aloneinterfaces.AloneProcessus
 
stop - Variable in class aloneinterfaces.AloneProcessus_old
 
stpne - Static variable in class testsorigin.Alignedtmrna
 
stpne - Static variable in class testssuite02.Alignedtmrna
 
stpyo - Static variable in class testsorigin.Alignedtmrna
 
stpyo - Static variable in class testssuite02.Alignedtmrna
 
STRUCTURECOMMUNE - Static variable in class modele.AlgorithmsStefan
"Global attributes of work"
Common structure is 1.
STRUCTURECOMMUNE - Static variable in class modele.OriginAlgorithmsStefan
"Global attributes of work"
Common structure is 1.
STRUCTURECOMMUNE - Static variable in class modele.OtherAlgorithmsStefan
"Global attributes of work"
Common structure is 1.
STRUCTURECOMMUNE - Static variable in class origincomment.ADN1cible
"Global attributes of work"
Common structure is 1.
structures - Variable in class modele.ArbreExec
Structures (default is instanciate as a new Vector).
structures - Variable in class origincomment.ArbrePalindrome
Structures (default is instanciate as a new Vector).
stymu - Static variable in class testsorigin.Alignedalphad
 
stymu - Static variable in class testssuite02.Alignedalphad
 
styph - Static variable in class testsorigin.Alignedalphad
 
styph - Static variable in class testssuite02.Alignedalphad
 
synsp - Static variable in class testsorigin.Alignedtrna
 
synsp - Static variable in class testssuite02.Alignedtrna
 
syspa - Static variable in class testsorigin.Alignedtmrna
 
syspa - Static variable in class testssuite02.Alignedtmrna
 
syspb - Static variable in class testsorigin.Alignedtmrna
 
syspb - Static variable in class testssuite02.Alignedtmrna
 
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