Uses of Class
origincomment.ADN1cible

Packages that use ADN1cible

aloneinterfaces	Classes to control, transmit and visualize informations for the Java Swing interface ; useful for quick start of use application.
controller	Classes to control and transmit informations for the Java Servlet Pages mechanism.
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...
testsorigin	These tests according to original code of Stefan Engelen (2006) Tests are using JUnit 3.8.1
testssuite02	"Third" part of tests : tests about algorithms of P-DCFold.

Uses of ADN1cible in aloneinterfaces

Methods in aloneinterfaces with parameters of type ADN1cible

void	Interface7.setInterface(ADN1cible adn, ADN1test[] tabAdn, int debut, int fin, int lmin) Deprecated. [not used]
void	Interface5.setInterface(ADN1cible adn, ADN1test[] tabAdn, int debut, int fin, int longueur, int lmin, int typeRecherche) Deprecated. [not used]
void	Interface9.setInterface(ADN1cible adn, java.lang.String fichier_ref, java.lang.String fichier_struct, double longueur) Deprecated. [not used]
void	Interface3.setInterface(ADN1cible adn, java.util.Vector vectabAdn) Deprecated. [not used]

Uses of ADN1cible in controller

Methods in controller that return ADN1cible

static ADN1cible

ProcessusOrigin.convertFrom(Sequence cible) To get a "cible sequence" from an instance of Sequence.

Methods in controller with parameters of type ADN1cible

static void	ProcessusOrigin.computing(java.util.Vector tabsadn, ADN1cible adncible, boolean morePrediction, boolean searchPseudoknots) Computing the main algorithm made by Stefan Engelen.
private static PalindromeListeListe	ProcessusOrigin.getRecordingStructures(ADN1cible adncible) To get the recording structure in a good conversion format.
static java.lang.String	ProcessusOrigin.getScreenToSee(java.util.Vector tabsadn, ADN1cible adncible) Working about what will be on screen
static java.lang.String	ProcessusOrigin.getScreenToSeeHTML(java.util.Vector tabsadn, ADN1cible adncible) Working about what will be on screen
private static void	ProcessusOrigin.setValues(ADN1cible adncible, boolean optimal, int maximumPredictions, boolean searchingPseudoknots) To be sure that good values are set as parameters...

Uses of ADN1cible in modele

Methods in modele that return ADN1cible

static ADN1cible

OriginAlgoStefanConverter.convertFrom(Sequence cible) To get a "cible sequence" from an instance of Sequence.

Methods in modele with parameters of type ADN1cible

private static java.lang.String	OriginAlgoStefanConverter.afficher_Caracteristique_Web(ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) Some changes to this procedure to make results appears for web / HTML.
private static java.lang.String	OriginAlgoStefanConverter.afficher_Caracteristique(ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) SOME SHOW FOR VIEW "This method for show on a target sequence of DNA"
private void	OriginAlgorithmsStefan.calcul_Resultat(ADN1cible target, ADN1test[] tableauSequences, int typeRecherche, boolean plusieurs_resultats, boolean chercher_pk) MAIN COMPUTING RESULTS "This method to launch search and compute all wanted results"
void	OriginAlgorithmsStefan.computing(java.util.Vector tabsadn, ADN1cible target, boolean morePrediction, boolean searchPseudoknots) Computing the main algorithm made by Stefan Engelen.
static void	OriginAlgoStefanConverter.computingStatic(java.util.Vector tabsadn, ADN1cible adncible, boolean morePrediction, boolean searchPseudoknots) Deprecated. [old test version]
private static ADN1test[]	OriginAlgoStefanConverter.distance(ADN1cible adn, ADN1test adncible, ADN1test[] adntest) Deprecated. "old version" see also OriginAlgoStefanConverter.distance(ADN1cible, ADN1test, ADN1test[], int, int)
private static ADN1test[]	OriginAlgoStefanConverter.distance(ADN1cible adn, ADN1test adncible, ADN1test[] adntest, int identity, int deletion) "procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores !
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 PalindromeListeListe	OriginAlgorithmsStefan.getRecordingStructures(ADN1cible target) To get the recording structure in a good conversion format.
static java.lang.String	OriginAlgoStefanConverter.getScreenToSee(java.util.Vector tabsadn, ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
static java.lang.String	OriginAlgoStefanConverter.getScreenToSeeHTML(java.util.Vector tabsadn, ADN1cible target, OriginAlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
void	OriginAlgorithmsStefan.mettre_etoile(ADN1cible target, int pos_struct) Deprecated. converted and put into SequenceCible : SequenceCible.mettre_etoile(PalindromeCible[])
private void	OriginAlgorithmsStefan.recherche_Palindrome(ADN1cible target, int debut, int fin, int taille, ADN1test[] tableauSequences, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH "Methode qui recherche des palindromes dans une sequence d'ADN" "This method search palindromes in a DNA sequence
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 void	OriginAlgorithmsStefan.recherche_Pseudonoeud(ADN1cible target, Base[] sequencepseudonoeud, ADN1test[] tableauSequences, boolean plusieurs_resultats, int pos_struct, int nb_prediction) 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"
private void	OriginAlgorithmsStefan.traitement_Zone_Variable(ADN1cible target, int debut, int fin, int taille, ADN1test[] tableauSequences, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH "This method to search anchors points in a highly varible part of sequence"
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 ADN1cible in origincomment

Fields in origincomment declared as ADN1cible

private ADN1cible

Profil.adn Target sequence ?

Methods in origincomment that return ADN1cible

ADN1cible	ADN1cible.copier() To clone the current instance of ADN1cible.
ADN1cible	Profil.quel_adn()

Methods in origincomment with parameters of type ADN1cible

double[]	ADN1cible.calcul_score_structure(ADN1cible adn_ref) RESULT TREAMENT "Compute the score of structure face to a reference (two DNA in input)"
void	Profil.change_adn(ADN1cible nv)
static java.util.Vector	ADN1test.choisirSequencesTests(ADN1cible adn, ADN1test[] adntest, java.util.Vector seqTestVec, java.util.Vector boolTestVec) "Procedure to choose tests sequences by default or not" Work on the selection made by user on original graphical interface.
int	ADN1cible.comparaison_structure(ADN1cible adn1, ADN1cible adn2) Deprecated. [never used]
static java.lang.String	ADN1cible.comparaison(ADN1cible adn1, ADN1cible adn2) RESULT TREAMENT "Methods to compare recorded results in files.
static ADN1test[]	ADN1test.distance(ADN1cible adn, ADN1test adncible, ADN1test[] adntest) "procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores !
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 static void	ADN1test.meilleur_combinaison_sequence(ADN1cible adn, ADN1cible adnoptimal, ADN1test adntest, ADN1test[] tabSeq, int[] quelleSeq, int etape, int debut, int seuil, int typeRecherche, int scoreMax, Resultat resultat, boolean rechercher_pk)
private void	ADN1cible.recherche_Palindrome(ADN1cible adn, int debut, int fin, int taille, ADN1test[] tableauSequence, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH "Methode qui recherche des palindromes dans une sequence d'ADN" This method search palindromes in DNA sequence.
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).
static ADN1test[]	ADN1test.resultat_Optimal(ADN1cible adn, ADN1test adntest, ADN1test[] tabAdn, java.io.BufferedReader entree, int nbSeqTest, int seuil, int typeRecherche, boolean rechercher_pk) "Method which test all possibilities of permutations of test sequences
private void	ADN1cible.traitement_Zone_Variable(ADN1cible adn, int debut, int fin, int taille, ADN1test[] tableauSequence, int erreur, int etape, boolean plusieurs_resultats, int nb_prediction) COMPATIBLE PALINDROME SEARCH "This method to search anchors points in a highly varible part of sequence"

Constructors in origincomment with parameters of type ADN1cible

Profil(ADN1cible adn, ADN1test[] tabAdnTest)
Constrcutor with given target sequence and table of test sequences.

Uses of ADN1cible in testsorigin

Fields in testsorigin declared as ADN1cible

private ADN1cible	TestPDCFold03.target
private ADN1cible	TestPDCFold02.target
private ADN1cible	TestPDCFold01.target
private ADN1cible	TestPDCFold00.target

Methods in testsorigin that return ADN1cible

static ADN1cible

AlignedSequences.convertFrom(Sequence cible) To get a "cible sequence" from an instance of Sequence.

Methods in testsorigin with parameters of type ADN1cible

static void	TestPDCFold00.computing(java.util.Vector tabsadn, ADN1cible adncible, boolean morePrediction, boolean searchPseudoknots) Computing the main algorithm made by Stefan Engelen.
static java.lang.String	TestPDCFold00.getScreenToSee(java.util.Vector tabsadn, ADN1cible adncible) Working about what will be on screen

Uses of ADN1cible in testssuite02

Methods in testssuite02 that return ADN1cible

static ADN1cible

AlignedSequences.convertFrom(Sequence cible) To get a "cible sequence" from an instance of Sequence.