Uses of Class
modele.PalindromeListe

Packages that use PalindromeListe

alonefichiers	Classes to convert and save informations about aloneinterfaces package use ; some changes have been performed to optimize use of this package.
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.
tests	First part of tests : the simpliest classes of the model.
testsalone	Other part of tests : Some parts and classes of interface / use.
testssuite01	Second part of tests : tests about algorithms of P-DCFold.

Uses of PalindromeListe in alonefichiers

Fields in alonefichiers declared as PalindromeListe

private PalindromeListe	FichierConvert.liste Current list of palindromes of file.
private PalindromeListe	FichierBracket.liste Current list of palindromes of file.

Methods in alonefichiers that return PalindromeListe

PalindromeListe	FichierConvert.getListe() To get the list of palindromes of current instance.
PalindromeListe	FichierBracket.getListe() To get the list of palindromes of current instance.

Methods in alonefichiers with parameters of type PalindromeListe

private void

FichierRnaViz.annotation(Sequence adn, PalindromeListe liste) This procedure to annotate sequence with informations of secondary structure (palindromes tab) in input format of RNAviz.

Constructors in alonefichiers with parameters of type PalindromeListe

FichierBracket(Sequence cible, PalindromeListe liste)
Constructor with given sequence and a list of palindromes.

FichierConvert(Sequence cible, PalindromeListe liste)
Constructor with given sequence and a list of palindromes.

FichierRnaViz(java.lang.String nom, Sequence adn, PalindromeListe liste)
Constructor.

Uses of PalindromeListe in aloneinterfaces

Methods in aloneinterfaces with parameters of type PalindromeListe

void	Interface3.setInterface(Sequence cible, SequenceListe[] other, PalindromeListe results) To fix how works the interface.
private static java.lang.String	Interface3.visualize(PalindromeListe palList) To show results on what founded.

Uses of PalindromeListe in controller

Fields in controller declared as PalindromeListe

private PalindromeListe

ProcessusNew.userPalindromesTable

Uses of PalindromeListe in modele

Fields in modele declared as PalindromeListe

private PalindromeListe[]	PalindromeListeListe.liste The list of PalindromeListe's
private PalindromeListe	NoeudArbreExec.palindromes The node contain a list of Palindrome's.
private PalindromeListe	Alignement.palindromes List of the Palindrome's.
private PalindromeListe	OriginAlgorithmsStefan.userPalindromesTable To get the palindromes given by user and known.

Methods in modele that return PalindromeListe

static PalindromeListe	Algorithms.commonPrediction(Sequence cible, SequenceListe[] listes) Deprecated. To search common structure prediction using P-DCFold with a cible Sequence and several list of homologuous Sequence's.
static PalindromeListe	Algorithms.defaultPredictionOfStructure(Sequence cible, SequenceListe alignement, int numSelect) Deprecated. The default prediction of P-DCFold Software (Optimal Prediction).
PalindromeListe	NoeudArbreExec.getAllPalindromes() A simple recursive ethod to get whole Palindrome's in the execution tree.
PalindromeListe[]	PalindromeListeListe.getListe()
PalindromeListe	PalindromeListe.getListeCount(int countmin) To get a PalindromeListe, sublist of current instance of PalindromeListe, whith a minimum count.
PalindromeListe	PalindromeListeListe.getPalindromeListe(int i)
PalindromeListe	NoeudArbreExec.getPalindromes()
PalindromeListe	Alignement.getPalindromes() To get the PalindromeListe of Palindrome's calculating by current instance of Alignment.
PalindromeListe	ArbreExec.getStructure(int i)
static PalindromeListe	AlgorithmsCT01.incompatibiliteUnChoix(PalindromeListe tabPalCibleTrier, int i, int j) Deprecated. When one choice is present for prediction.
static PalindromeListe	Algorithms.searchAnchorPoints(Alignement calcul, double Smin, SequenceListe alignement, int nbErreursMax, int longPalindMin, int longBoucleMin) Deprecated. Search procedure of structural palindromes with pairing matrix and new selection criteria.
static PalindromeListe	Algorithms.searchAnchorPoints(int debut, int fin, Alignement calcul, double Smin, SequenceListe alignement, int nbErreursMax, int longPalindMin, int longBoucleMin) Deprecated. M[i,j] too long...
static PalindromeListe	Algorithms.searchAnchorPoints(Sequence cible, Alignement calcul, double Lmin, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. Not the good prototype as algorithm is defined.
static PalindromeListe	Algorithms.variableZonesTreatment(Sequence cible, int tailleCible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. When no palindrome is found with searchAnchorPoints...

Methods in modele with parameters of type PalindromeListe

void	PalindromeListeListe.addPalindromeListe(PalindromeListe elt) To add a PalindromeListe at the end of the list.
static PalindromeListeListe	AlgorithmsCT01.compatibilityTreamentCT01(PalindromeListe L) Deprecated. Polymorphism of procedure.
static PalindromeListeListe	AlgorithmsCT02.compatibilityTreatment(PalindromeListe L) Deprecated. Polymorphism of procedure.
static PalindromeListeListe	AlgorithmsCT03.compatibilityTreatment(PalindromeListe L) Deprecated. Polymorphism of procedure.
static PalindromeListeListe	Algorithms.compatibilityTreatment(PalindromeListe L) Deprecated. Here is a procedure Launcher This procedure to treat compatibility of found palindromes on each recursivity step, see searchStructuralPalindrome for launch.
static PalindromeListeListe	AlgorithmsCT01.compatibilityTreatment01(PalindromeListe L) Deprecated. Other is used (changesDCFold to P-DCFold)
static PalindromeListeListe	AlgorithmsCT03.compatibilityTreatment01(PalindromeListe L) Deprecated.
static PalindromeListeListe	AlgorithmsCT01.compatibilityTreatment02(PalindromeListe L) Deprecated. results of tests are not very good...
static PalindromeListeListe	AlgorithmsCT03.compatibilityTreatment02(PalindromeListe L) Deprecated.
static PalindromeListeListe	AlgorithmsCT01.compatibilityTreatment03(PalindromeListe L) Deprecated. ...
static PalindromeListeListe	AlgorithmsCT01.compatibilityTreatment04(PalindromeListe L) Deprecated. July 2008
static PalindromeListeListe	AlgorithmsCT01.compatibilityTreatment05(PalindromeListe Lbis) Deprecated.
static PalindromeListeListe	AlgorithmsCT02.compatibilityTreatmentMore(PalindromeListe L) Deprecated.
static void	AlgorithmsCT01.compatibilityTreatmentOrigin(PalindromeListe L, int posi, int posj, PalindromeListeListe E) Deprecated. July 2008
boolean	PalindromeListe.equals(PalindromeListe toCompare) To know if two PalindromeListe are equals (local instance and an other).
boolean	PalindromeListeListe.has(PalindromeListe elt) To know if a PalindromeListe is in this list.
static PalindromeListe	AlgorithmsCT01.incompatibiliteUnChoix(PalindromeListe tabPalCibleTrier, int i, int j) Deprecated. When one choice is present for prediction.
static Sequence	Algorithms.newSequenceDeduction(Sequence cible, PalindromeListe Lg) Deprecated. To get a new sequence without found palindromes in sequence.
void	PalindromeListeListe.removePalindromeListe(PalindromeListe elt) To remove a specific Palindrome.
void	PalindromeListeListe.setListe(PalindromeListe[] liste)
void	PalindromeListeListe.setPalindromeListe(PalindromeListe elt, int i)
void	NoeudArbreExec.setPalindromes(PalindromeListe palindromes)
void	OriginAlgorithmsStefan.setUserPalindromesTable(PalindromeListe userPalindromesTable) To set the given known palindromes by user.
static PalindromeListeListe	AlgorithmsCT01.traitementIncompatibilite(PalindromeListe tabPalCible, boolean plusieursResultats, double incertitude, int nbPrediction, int nbPredictionMax) Deprecated. CompatibilityTreament...

Constructors in modele with parameters of type PalindromeListe

NoeudArbreExec(PalindromeListe palindromes)
Constrcutor with a given list of Palindrome's.

NoeudArbreExec(PalindromeListe palindromes, NoeudArbreExec father)
Constructor with a given list of Palindrome's and a father node.

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

Uses of PalindromeListe in tests

Fields in tests declared as PalindromeListe

private PalindromeListe	TestPalindromeListe.basetest1
private PalindromeListe	TestPalindromeListe.basetest2

Uses of PalindromeListe in testsalone

Fields in testsalone declared as PalindromeListe

private PalindromeListe	TestFichierRnaViz.liste
private PalindromeListe	TestFichierBracket.liste

Uses of PalindromeListe in testssuite01

Methods in testssuite01 with parameters of type PalindromeListe

static void

TestAlgorithmsPartII.visualize(PalindromeListe palList)