Uses of Class
modele.Palindrome

Packages that use Palindrome

aloneinterfaces	Classes to control, transmit and visualize informations for the Java Swing interface ; useful for quick start of use application.
modele	Model for objet representation and computing P-DCFold Algorithms.
tests	First part of tests : the simpliest classes of the model.

Uses of Palindrome in aloneinterfaces

Fields in aloneinterfaces declared as Palindrome

private Palindrome

Interface11.palindrome

Methods in aloneinterfaces that return Palindrome

Palindrome

Interface11.getPalindrome()

Methods in aloneinterfaces with parameters of type Palindrome

void	Interface12.setInterface(SequenceListe profil, Sequence cible, Palindrome palindrome) To fix how works the interface.

Uses of Palindrome in modele

Subclasses of Palindrome in modele

class	PalindromeCible Deprecated. Transfered to Palindrome
class	PalindromeTest Deprecated. Transfered to Palindrome

Fields in modele declared as Palindrome

private Palindrome[]

PalindromeListe.liste The list of Palindrome's

Methods in modele that return Palindrome

static Palindrome[]	Palindrome.choisir_meilleur(int nb, Palindrome[] tabpal) Deprecated. [unused] Calling method ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]) is not maintained in OtherAlgorithmsStefan...
Palindrome	Palindrome.copie() Cible : To get a clone of the current instance of PalindromeCible.
static Palindrome[]	OtherAlgoStefanConverter.fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
static Palindrome[]	AlgoStefanConverter.fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
Palindrome[]	PalindromeListe.getListe()
Palindrome	NoeudArbreExec.getPalindrome(int i)
Palindrome	Alignement.getPalindrome(int score) To get a Palindrome with a given score.
Palindrome	PalindromeListe.getPalindrome(int i)
Palindrome	ArbreExec.getPalindrome(int i, int j)
Palindrome	OtherAlgorithmsStefan.getPalindrome(int pos_struct, int pos_pal) To get a specific palindrome in a specific structure.
Palindrome	AlgorithmsStefan.getPalindrome(int pos_struct, int pos_pal) To get a specific palindrome in a specific structure.
Palindrome	Alignement.getPalindrome(int i, int j) To get Palindrome from a score at a specific position in the matrix.
Palindrome[]	OtherAlgorithmsStefan.getStructure(int pos) To get a specific structure.
Palindrome[]	AlgorithmsStefan.getStructure(int pos) To get a specific structure.
private static Palindrome[]	OtherAlgorithmsStefan.incompatibilite_un_choix(Palindrome[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
private static Palindrome[]	AlgorithmsStefan.incompatibilite_un_choix(Palindrome[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
private static Palindrome[][]	OtherAlgorithmsStefan.palindromes_communs(Palindrome[] tabPal1, Palindrome[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static Palindrome[][]	AlgorithmsStefan.palindromes_communs(Palindrome[] tabPal1, Palindrome[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private Palindrome[]	OtherAlgorithmsStefan.recherche_Point_Ancrage(Sequence target, int debut, int fin, int taille, double lmin, Sequence[] tableauSequences, int erreur) COMPATIBLE PALINDROME SEARCH "R=This method search anchor points at step i from palindrome search (on the subsequence i on starting sequence).
private Palindrome[]	AlgorithmsStefan.recherche_Point_Ancrage(Sequence target, int debut, int fin, int taille, double lmin, Sequence[] tableauSequences, int erreur) COMPATIBLE PALINDROME SEARCH "R=This method search anchor points at step i from palindrome search (on the subsequence i on starting sequence).
private static Palindrome[]	OtherAlgorithmsStefan.trier_Palindrome_Comp(Palindrome[] tabPal) "Following methods sorted by use order in ADN1 Class". (4) "This method sort palindromes found at step i of target sequence from their relevance This method is used by the method that search compatible palindromes
private static Palindrome[]	AlgorithmsStefan.trier_Palindrome_Comp(Palindrome[] tabPal) "Following methods sorted by use order in ADN1 Class". (4) "This method sort palindromes found at step i of target sequence from their relevance This method is used by the method that search compatible palindromes

Methods in modele with parameters of type Palindrome

void	PalindromeListe.addPalindrome(Palindrome elt) To add a Palindrome at the end of the list.
void	PalindromeListeListe.addPalindromeListe(Palindrome[] elt) To add a PalindromeListe at the end of the list.
int	Sequence.calcul_Taille(Palindrome pal) COMPATIBLE PALINDROME SEARCH "This method to compute internal sequence length at step i.
static boolean	Algorithms.checkConservation(Palindrome current, SequenceListe alignement, int nbErreursMax) Deprecated. To check a Palindrome is present in a group of Sequence's.
static boolean	Algorithms.checkConservationOldVersion(Palindrome current, SequenceListe alignement, int nbErreursMax) Deprecated. Old and inacurate method
boolean	PalindromeCible.chevauchant(Palindrome p) Deprecated. "Following methods sorted by use order in ADN1 Class". (17) "to know if two palindrome are crossed together"
boolean	Palindrome.chevauchant(Palindrome p) Deprecated. see also chevauchant(Palindrome, Palindrome) and equivalence(Palindrome, Palindrome)
static boolean	Palindrome.chevauchant(Palindrome pal1, Palindrome pal2) Cible : "Following methods sorted by use order in ADN1 Class". (17) "to know if two palindrome are crossed together"
static Palindrome[]	Palindrome.choisir_meilleur(int nb, Palindrome[] tabpal) Deprecated. [unused] Calling method ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]) is not maintained in OtherAlgorithmsStefan...
void	Palindrome.computeNumbers(Palindrome current) This procedure to compute compensatory and single mutations number, and errors number between a test Palindrome (current instance) and a cible Palindrome.
static Palindrome1cible	OriginAlgoStefanConverter.convertFrom(Palindrome pal) To get a "target palindrome" from Palindrome.
private void	OtherAlgorithmsStefan.diviser_regner(Palindrome[] tabPal, Sequence target, Sequence[] tableauSequences, int debut, int fin, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH Divide and Conquer procedure...
private void	AlgorithmsStefan.diviser_regner(Palindrome[] tabPal, Sequence target, Sequence[] tableauSequences, int debut, int fin, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH Divide and Conquer procedure...
boolean	PalindromeCible.equals(Palindrome toCompare) Deprecated. Sucharged method : real length added.
boolean	Palindrome.equals(Palindrome toCompare) To know if instance of the class and an other are the same.
static boolean	Palindrome.equivalence(Palindrome helix1, Palindrome helix2) To know if two helix are equivalent : (helix1 in helix2) or (helix2 in helix1).
static boolean	Palindrome.est_Compatible(Palindrome pal1, Palindrome pal2) 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...
Sequence	Sequence.externalSequence(Palindrome P) To get the external Sequence of a Palindrome on a Sequence.
static Palindrome[]	OtherAlgoStefanConverter.fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
static Palindrome[]	OtherAlgoStefanConverter.fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
static Palindrome[]	AlgoStefanConverter.fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
static Palindrome[]	AlgoStefanConverter.fusion_Palindrome(Palindrome[] tabPalCourant, Palindrome[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
boolean	PalindromeListe.has(Palindrome elt) To know if a Palindrome is in this list.
boolean	NoeudArbreExecListe.hasNoeudArbreExecWith(Palindrome elt) To know if a NoeudArbreExec of this list contain a specific Palindrome.
boolean	NoeudArbreExec.hasPalindrome(Palindrome elt)
boolean	PalindromeCible.inclu_dans(Palindrome p) 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 "
boolean	Palindrome.inclu_dans(Palindrome p) 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 "
private static Palindrome[]	OtherAlgorithmsStefan.incompatibilite_un_choix(Palindrome[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
private static Palindrome[]	AlgorithmsStefan.incompatibilite_un_choix(Palindrome[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
Sequence	Sequence.internalSequence(Palindrome P) To get the internal sequence of a palindrome on a Sequence.
boolean	Palindrome.isCompatible(Palindrome with)
boolean	Palindrome.isCompatibleWith(Palindrome other) Deprecated. not exact... (see tests)
void	Sequence.mettre_etoile(Palindrome[] structure) PSEUDOKNOTS SEARCH "This method to put stars (*) in found palindromes in aim to find pseudoknots" CIBLE SEQUENCE
private static Palindrome[][]	OtherAlgorithmsStefan.palindromes_communs(Palindrome[] tabPal1, Palindrome[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static Palindrome[][]	OtherAlgorithmsStefan.palindromes_communs(Palindrome[] tabPal1, Palindrome[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static Palindrome[][]	AlgorithmsStefan.palindromes_communs(Palindrome[] tabPal1, Palindrome[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static Palindrome[][]	AlgorithmsStefan.palindromes_communs(Palindrome[] tabPal1, Palindrome[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
int	PalindromeListe.rechercher_approx(Palindrome toSearch) Deprecated. Tranformed to PalindromeListe.whichPositionApprox(Palindrome)
int	PalindromeListe.rechercher(Palindrome toSearch) Deprecated. Transformed to PalindromeListe.whichPosition(Palindrome)
private static void	ArbreExec.recuperation(PalindromeListeListe resultat, Palindrome[] tabPal, NoeudArbreExec n) "Recuperation" This method to keep compatibility with algorithms' implementation of Stefan Engelen and its conversion.
void	NoeudArbreExecListe.removeNoeudArbreExec(Palindrome elt) To remove a specific NoeudArbreExec with Palindrome (first one remove).
void	PalindromeListe.removePalindrome(Palindrome elt) To remove a specific Palindrome.
void	ConvertedProfil.remplir(Palindrome[] tabpal, int numerosequence) This procedure to make the profile will be not empty...
static boolean	Palindrome.rssh(Palindrome helix1, Palindrome helix2) To know if on two helix (Palindrome here), the second is included into the first.
void	PalindromeListe.setListe(Palindrome[] liste)
void	PalindromeListe.setPalindrome(Palindrome elt, int i)
void	PalindromeListeListe.setPalindromeListe(Palindrome[] elt, int i)
void	NoeudArbreExec.setPalindromes(Palindrome[] palindromes)
private static PalindromeListeListe	OtherAlgorithmsStefan.traitement_Incompatibilite(Palindrome[] tabPalCible, boolean plusieurs_resultats, double incertitude, int nb_prediction, int nb_prediction_max) "Following methods sorted by use order in ADN1 Class". (1) "This method is about incompatibility between palindromes of same sequence, sorting palindromes by relevance (single and double mutations) then removing every palindrome incompatible with previous more relevant.
private static PalindromeListeListe	AlgorithmsStefan.traitement_Incompatibilite(Palindrome[] tabPalCible, boolean plusieurs_resultats, double incertitude, int nb_prediction, int nb_prediction_max) "Following methods sorted by use order in ADN1 Class". (1) "This method is about incompatibility between palindromes of same sequence, sorting palindromes by relevance (single and double mutations) then removing every palindrome incompatible with previous more relevant.
private static Palindrome[]	OtherAlgorithmsStefan.trier_Palindrome_Comp(Palindrome[] tabPal) "Following methods sorted by use order in ADN1 Class". (4) "This method sort palindromes found at step i of target sequence from their relevance This method is used by the method that search compatible palindromes
private static Palindrome[]	AlgorithmsStefan.trier_Palindrome_Comp(Palindrome[] tabPal) "Following methods sorted by use order in ADN1 Class". (4) "This method sort palindromes found at step i of target sequence from their relevance This method is used by the method that search compatible palindromes
private boolean	OtherAlgorithmsStefan.verifier_Conservation_Alignement(Sequence target, Palindrome palCourantReel, Palindrome palCourantFaux, double lmin, Sequence[] tableauSequences) COMPATIBLE PALINDROME SEARCH "this method compare palindromes found on each step of palindrome search to know if there are palindromes at the same place but they can be different (it is in that case they are relevant)This method compute in the same time the number of singles and compensatory (double) mutations.
private boolean	AlgorithmsStefan.verifier_Conservation_Alignement(Sequence target, Palindrome palCourantReel, Palindrome palCourantFaux, double lmin, Sequence[] tableauSequences) COMPATIBLE PALINDROME SEARCH "this method compare palindromes found on each step of palindrome search to know if there are palindromes at the same place but they can be different (it is in that case they are relevant)This method compute in the same time the number of singles and compensatory (double) mutations.
private static boolean	OtherAlgorithmsStefan.verifier_Conservation_Commune(Sequence target, Palindrome palCourantReel, Palindrome palCourantFaux, double decalage, double lmin, int erreur, Sequence[] tableauSequences) COMPATIBLE PALINDROME SEARCH "this method compare palindromes found on each step of palindrome search to know if there are palindromes at the same place but they can be different (it is in that case they are relevant)This method compute in the same time the number of singles and compensatory (double) mutations.
private static boolean	AlgorithmsStefan.verifier_Conservation_Commune(Sequence target, Palindrome palCourantReel, Palindrome palCourantFaux, double decalage, double lmin, int erreur, Sequence[] tableauSequences) COMPATIBLE PALINDROME SEARCH "this method compare palindromes found on each step of palindrome search to know if there are palindromes at the same place but they can be different (it is in that case they are relevant)This method compute in the same time the number of singles and compensatory (double) mutations.
int	PalindromeListe.whichPosition(Palindrome elt) If a palindrome is present, give his position.
int	PalindromeListe.whichPositionApprox(Palindrome elt) If a palindrome is appromately present, give his position.

Constructors in modele with parameters of type Palindrome

NoeudArbreExec(Palindrome[] palindromes)
Constrcutor with a given table of Palindrome's.

NoeudArbreExec(Palindrome[] palindromes, NoeudArbreExec father)
Constructor with a given table of Palindrome's and a father node.

PalindromeListe(Palindrome[] liste)
Constructor with a pre-made table of Palindrome's.

Uses of Palindrome in tests

Fields in tests declared as Palindrome

private Palindrome	TestPalindrome.basetest1
private Palindrome	TestPalindrome.basetest2