Uses of Class
origincomment.Palindrome1cible

Packages that use Palindrome1cible

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.
origincomment	Model for objet representation and computing P-DCFold Algorithms ; original code made by Stefan Engelen in 2006 and use "as if" without any garanty...

Uses of Palindrome1cible in aloneinterfaces

Methods in aloneinterfaces with parameters of type Palindrome1cible

void	Interface12.setInterface(Profil profil, java.lang.String fichierpalindrome, Palindrome1cible palindrome, int numerosequence) Deprecated. [not used]

Uses of Palindrome1cible in modele

Methods in modele that return Palindrome1cible

static Palindrome1cible	OriginAlgoStefanConverter.convertFrom(Palindrome pal) To get a "target palindrome" from Palindrome.
static Palindrome1cible[]	OriginAlgoStefanConverter.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] 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"
Palindrome1cible	OriginAlgorithmsStefan.getPalindrome(int pos_struct, int pos_pal) To get a specific palindrome in a specific structure.
Palindrome1cible[]	OriginAlgorithmsStefan.getStructure(int pos) To get a specific structure.
private static Palindrome1cible[]	OriginAlgorithmsStefan.incompatibilite_un_choix(Palindrome1cible[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
private static Palindrome1cible[][]	OriginAlgorithmsStefan.palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private Palindrome1cible[]	OriginAlgorithmsStefan.recherche_Point_Ancrage(ADN1cible target, int debut, int fin, int taille, double lmin, ADN1test[] 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 Palindrome1cible[]	OriginAlgorithmsStefan.trier_Palindrome_Comp(Palindrome1cible[] 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 Palindrome1cible

private void	OriginAlgorithmsStefan.diviser_regner(Palindrome1cible[] tabPal, ADN1cible target, ADN1test[] tableauSequences, int debut, int fin, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH Divide and Conquer procedure...
private static boolean	OriginAlgorithmsStefan.est_Compatible(Palindrome1cible pal1, Palindrome1cible pal2) Deprecated. converted and put into PalindromeCible : PalindromeCible.est_Compatible(PalindromeCible, PalindromeCible)
static Palindrome1cible[]	OriginAlgoStefanConverter.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] 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 Palindrome1cible[]	OriginAlgoStefanConverter.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] 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"
private static Palindrome1cible[]	OriginAlgorithmsStefan.incompatibilite_un_choix(Palindrome1cible[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
private static Palindrome1cible[][]	OriginAlgorithmsStefan.palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static Palindrome1cible[][]	OriginAlgorithmsStefan.palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static java.util.Vector	OriginAlgorithmsStefan.traitement_Incompatibilite(Palindrome1cible[] 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 Palindrome1cible[]	OriginAlgorithmsStefan.trier_Palindrome_Comp(Palindrome1cible[] 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	OriginAlgorithmsStefan.verifier_Conservation_Alignement(ADN1cible target, Palindrome1cible palCourantReel, Palindrome1test palCourantFaux, double lmin, ADN1test[] 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	OriginAlgorithmsStefan.verifier_Conservation_Commune(ADN1cible target, Palindrome1cible palCourantReel, Palindrome1test palCourantFaux, double decalage, double lmin, int erreur, ADN1test[] 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.

Uses of Palindrome1cible in origincomment

Fields in origincomment declared as Palindrome1cible

private Palindrome1cible[]

NoeudPalindrome.tableauPalindrome Table of palindromes (default is size one and [0] not defined).

Methods in origincomment that return Palindrome1cible

static Palindrome1cible[][]	ADN1cible.comparaison_palindrome(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2) RESULT TREAMENT "Methods to compare recorded results in files.
Palindrome1cible	Palindrome1cible.copie() To get a clone of the current instance of Palindrome1cible.
static Palindrome1cible[]	StefanErrors.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] tabPalPrincipal) Curious it return two tables in one, but never suym of their length, but always 400...
static Palindrome1cible[]	Palindrome1cible.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] 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 Palindrome1cible[]	Palindrome1cible.incompatibilite_un_choix(Palindrome1cible[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
Palindrome1cible[]	ADN1cible.la_structure(int pos) To get a specific structure.
Palindrome1cible	ADN1cible.le_palindrome(int pos_struct, int pos_pal) To get a specific palindrome in a specific structure.
static Palindrome1cible[][]	ADN1cible.palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
Palindrome1cible	NoeudPalindrome.quel_palindrome(int i)
Palindrome1cible[]	NoeudPalindrome.quel_tableau()
Palindrome1cible[]	ArbrePalindrome.quelleStructure(int i) To get a specific structure in structureS.
Palindrome1cible	ArbrePalindrome.quelPalindrome(int pos_struct, int pos_pal) To get a specific palindrome in a psecific structure.
Palindrome1cible[]	ADN1cible.recherche_Point_Ancrage(ADN1cible adn, int debut, int fin, int taille, double lmin, ADN1test[] tableauSequence, 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 Palindrome1cible[]	Palindrome1cible.trier_Palindrome_Comp(Palindrome1cible[] 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
Palindrome1cible[]	Palindrome1cible.trier_Palindrome_Debut(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (8) "This method sort a table of palindromes by the begin position"
Palindrome1cible[]	Palindrome1cible.trier_Palindrome_Fin(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (7) "This method sort a table of palindromes by the end position"
static Palindrome1cible[]	Palindrome1cible.vec_to_tab(java.util.Vector vec) "Following methods sorted by use order in ADN1 Class". (18) "transform a vector of palindromes to a vector of palindroms"

Methods in origincomment with parameters of type Palindrome1cible

java.lang.String	ADN1cible.afficher_Sequences(Palindrome1cible pal, ADN1test[] tabSeq) RESULT TREAMENT "This method show palindromes of tests sequences correponding to a target sequence palindrome et give informations about relevance of this palindrome"
static java.lang.String	ADN1cible.afficher(Palindrome1cible[] tabPal) SOME SHOW FOR VIEW "This method to show the palindromes' tab"
void	ArbrePalindrome.ajouteStructures(Palindrome1cible[] tab) To add new StructureS.
int	ADN1cible.calcul_Taille(Palindrome1cible pal) COMPATIBLE PALINDROME SEARCH "This method to compute internal sequence length at step i
void	NoeudPalindrome.change_palindrome(Palindrome1cible p, int i)
void	ADN1cible.change_palindromes(Palindrome1cible[] tabPal) To set the table of palindrome and change the tree of algorithms.
void	NoeudPalindrome.change_tableau(Palindrome1cible[] tab)
boolean	Palindrome1cible.chevauchant(Palindrome1cible p) "Following methods sorted by use order in ADN1 Class". (17) "to know if two palindrome are crossed together"
static Palindrome1cible[][]	ADN1cible.comparaison_palindrome(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2) RESULT TREAMENT "Methods to compare recorded results in files.
static Palindrome1cible[][]	ADN1cible.comparaison_palindrome(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2) RESULT TREAMENT "Methods to compare recorded results in files.
void	StefanErrors.diviser_regner(Palindrome1cible[] tabPal, ADN1cible adn, ADN1test[] tableauSequence, int debut, int fin, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) Instance of object is given in procedure of the same instance.
void	ADN1cible.diviser_regner(Palindrome1cible[] tabPal, ADN1cible adn, ADN1test[] tableauSequence, int debut, int fin, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH Divide and Conquer procedure...
private boolean	Palindrome1cible.egaux(Palindrome1cible p) "Following methods sorted by use order in ADN1 Class". (14') "equals method"
int[][]	Palindrome1cible.en_paire_de_bases(Palindrome1cible[] tabPal) Deprecated. because calling procedure is deprecated...
boolean	StefanErrors.est_Compatible(Palindrome1cible pal1, Palindrome1cible pal2) Is result we are waiting for is correct ?
private static boolean	Palindrome1cible.est_Compatible(Palindrome1cible pal1, Palindrome1cible pal2) "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...
static Palindrome1cible[]	StefanErrors.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] tabPalPrincipal) Curious it return two tables in one, but never suym of their length, but always 400...
static Palindrome1cible[]	StefanErrors.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] tabPalPrincipal) Curious it return two tables in one, but never suym of their length, but always 400...
static Palindrome1cible[]	Palindrome1cible.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] 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 Palindrome1cible[]	Palindrome1cible.fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] 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	Palindrome1cible.inclu_dans(Palindrome1cible p) "Following methods sorted by use order in ADN1 Class". (16) "this method to know if current instance is included in argument with common pairwise "
static Palindrome1cible[]	Palindrome1cible.incompatibilite_un_choix(Palindrome1cible[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
static Palindrome1cible[][]	ADN1cible.palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
static Palindrome1cible[][]	ADN1cible.palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
private static void	ArbrePalindrome.recuperation(java.util.Vector resultat, Palindrome1cible[] tabPal, NoeudPalindrome n) "Recuperation"
void	Profil.remplir(Palindrome1cible[] tabpal, int numerosequence) This procedure to make the profile will be not empty...
int	Palindrome1cible.score(Palindrome1cible pal2) Deprecated. [not used]
static java.util.Vector	Palindrome1cible.traitement_Incompatibilite(Palindrome1cible[] 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 Palindrome1cible[]	Palindrome1cible.trier_Palindrome_Comp(Palindrome1cible[] 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
Palindrome1cible[]	Palindrome1cible.trier_Palindrome_Debut(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (8) "This method sort a table of palindromes by the begin position"
Palindrome1cible[]	Palindrome1cible.trier_Palindrome_Fin(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (7) "This method sort a table of palindromes by the end position"
boolean	ADN1cible.verifier_Conservation_Alignement(Palindrome1cible palCourantReel, Palindrome1test palCourantFaux, double lmin, ADN1test[] tabSeq) 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.
boolean	ADN1cible.verifier_Conservation_Commune(Palindrome1cible palCourantReel, Palindrome1test palCourantFaux, double decalage, double lmin, int erreur, ADN1test[] tabSeq) 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.
boolean	ADN1cible.verifier_Conservation(Palindrome1cible palCourantReel, Palindrome1test palCourantFaux, double decalage, double lmin, int erreur, ADN1test[] tabSeq) 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.

Constructors in origincomment with parameters of type Palindrome1cible

NoeudPalindrome(Palindrome1cible[] tab)
Constructor with a given table of palindromes.

NoeudPalindrome(Palindrome1cible[] tab, NoeudPalindrome pere)
Constructor with given table of palindromes and a father node.