Uses of Class
modele.SequenceListe

Packages that use SequenceListe

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.
testsorigin	These tests according to original code of Stefan Engelen (2006) Tests are using JUnit 3.8.1
testssuite01	Second part of tests : tests about algorithms of P-DCFold.
testssuite02	"Third" part of tests : tests about algorithms of P-DCFold.

Uses of SequenceListe in alonefichiers

Fields in alonefichiers declared as SequenceListe

private SequenceListe

FichierFasta.liste

Methods in alonefichiers that return SequenceListe

SequenceListe[]	FichierFasta.getCible(java.lang.String nom) To get a sequence with given name.
SequenceListe	FichierFasta.getListe() To get the liste of current instance of FichierFasta.

Constructors in alonefichiers with parameters of type SequenceListe

FichierFasta(SequenceListe liste)
Constructor with a given SequenceListe.

Uses of SequenceListe in aloneinterfaces

Fields in aloneinterfaces declared as SequenceListe

private SequenceListe	AloneProcessus_old.allSequences
private SequenceListe	AloneProcessus.allSequences
private SequenceListe	Interface1.autresSequences List of tother sequences.
private SequenceListe[]	AloneProcessus_old.optim
private SequenceListe[]	AloneProcessus.optim
private SequenceListe[]	AloneProcessus_old.other
private SequenceListe[]	AloneProcessus.other

Methods in aloneinterfaces that return SequenceListe

SequenceListe

Interface1.getAutreSequence()

Methods in aloneinterfaces with parameters of type SequenceListe

void	Interface1.setAutreSequence(SequenceListe autresSequences)
void	Interface12.setInterface(SequenceListe profil, Sequence cible, Palindrome palindrome) To fix how works the interface.
void	Interface7.setInterface(Sequence cible, SequenceListe[] optim, int debut, int fin, int lmin) Méthode pour fixer le fonctionnement de l'interface.
void	Interface5.setInterface(Sequence cible, SequenceListe[] optim, int debut, int fin, int longueur, int lmin, int typeRecherche) To fix how works the interface.
void	Interface3.setInterface(Sequence cible, SequenceListe[] other, PalindromeListe results) To fix how works the interface.
void	Interface3.setInterface(Sequence cible, SequenceListe[] other, PalindromeListeListe results) To fix how works the interface.
void	Interface1.setListModelCible(SequenceListe tabAdnTest) To compute a JList containing only the names of Sequence's.
void	Interface1.setListModelTest(Sequence cible, SequenceListe selection, int longueur) Visualization of homologuous sequences selection.

Uses of SequenceListe in controller

Subclasses of SequenceListe in controller

class

ListeBean This class to transmit informations to the Java Servlet Page.

Fields in controller declared as SequenceListe

private SequenceListe[]

ListeBean.more To get the many combinations selected after SSCA.

Methods in controller that return SequenceListe

SequenceListe[]	ListeBean.computePredictions() To compute and gain all possible predictions (combinations).
SequenceListe[]	ListeBean.computePredictionsBB() Deprecated. putted when conversion ProcessusOrigin.conversionFrom(origincomment.ADN1test, SequenceListe[])
SequenceListe[]	ListeBean.getMore(boolean tfold) To get the many combinations selected after SSCA.

Methods in controller with parameters of type SequenceListe

static java.util.Vector	ProcessusOrigin.conversionFrom(ADN1test adntcible, SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
static ADN1test[]	ProcessusOrigin.conversionFrom(SequenceListe liste) Conversion of a set of sequences listes to a tab of ADN1test's
static java.util.Vector	ProcessusOrigin.conversionFrom(SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's Do not forget that target sequence must be on position 0 of each table !

Uses of SequenceListe in modele

Fields in modele declared as SequenceListe

private SequenceListe

Algorithms.alignement Deprecated. The alignment submitted with all sequences.

Methods in modele that return SequenceListe

static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also OriginAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also AlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	Algorithms.algoSSCA(Sequence cible, SequenceListe homologues) Deprecated. SSCA algorithm.
static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also OriginAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also AlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
static SequenceListe[]	SequenceListe.combinationWithoutRepetition(int k, int n, SequenceListe C) Maybe not the best way to make combination / arrangement without repetition, but works well.
static SequenceListe[]	OtherAlgoStefanConverter.conversionFrom(Sequence adntcible, SequenceListe[] listes, boolean diff) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
static SequenceListe[]	AlgoStefanConverter.conversionFrom(Sequence adntcible, SequenceListe[] listes, boolean diff) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
SequenceListe	Algorithms.getAlignement() Deprecated. To get the group of aligned Sequence's.

Methods in modele with parameters of type SequenceListe

static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also OriginAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous) Deprecated. "old version" see also AlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int)
static SequenceListe	Algorithms.algoSSCA(Sequence cible, SequenceListe homologues) Deprecated. SSCA algorithm.
static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int identity, int deletion) A default call to SSCA algorithm to get all list of homologuous with scores computed.
static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also OtherAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also OriginAlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection) Deprecated. "old version" see also AlgoStefanConverter.algoSSCA(Sequence, SequenceListe, int, int, double, double, boolean, int, int)
static SequenceListe	OtherAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
static SequenceListe	OriginAlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
static SequenceListe	AlgoStefanConverter.algoSSCA(Sequence target, SequenceListe homologuous, int nbMinSequences, int nbMaxSequences, double minHomology, double maxHomology, boolean selection, int identity, int deletion) The whole computing of SSCA.
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
static SequenceListe[]	SequenceListe.combinationWithoutRepetition(int k, int n, SequenceListe C) Maybe not the best way to make combination / arrangement without repetition, but works well.
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.
void	OtherAlgorithmsStefan.computing(SequenceListe[] tabsadn, Sequence target, boolean morePrediction, boolean searchPseudoknots) Computing the main algorithm made by Stefan Engelen.
void	AlgorithmsStefan.computing(SequenceListe[] tabsadn, Sequence target, boolean morePrediction, boolean searchPseudoknots) Computing the main algorithm made by Stefan Engelen.
static java.util.Vector	OriginAlgoStefanConverter.conversionFrom(ADN1test adntcible, SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
static ADN1test[]	OriginAlgoStefanConverter.conversionFrom(SequenceListe liste) Conversion of a set of sequences listes to a tab of ADN1test's.
static java.util.Vector	OriginAlgoStefanConverter.conversionFrom(SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's Do not forget that target sequence must be on position 0 of each table !
static java.util.Vector	OtherAlgoStefanConverter.conversionFrom(Sequence adntcible, SequenceListe[] listes) Deprecated. [only for information, please use OtherAlgoStefanConverter.conversionFrom(Sequence, SequenceListe[], boolean)]
static java.util.Vector	AlgoStefanConverter.conversionFrom(Sequence adntcible, SequenceListe[] listes) Deprecated. [only for information, please use AlgoStefanConverter.conversionFrom(Sequence, SequenceListe[], boolean)]
static SequenceListe[]	OtherAlgoStefanConverter.conversionFrom(Sequence adntcible, SequenceListe[] listes, boolean diff) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
static SequenceListe[]	AlgoStefanConverter.conversionFrom(Sequence adntcible, SequenceListe[] listes, boolean diff) Conversion of a set of sequences listes to a vector of tabs of ADN1test's and put the target sequence at position 0 on each table.
static PalindromeListe	Algorithms.defaultPredictionOfStructure(Sequence cible, SequenceListe alignement, int numSelect) Deprecated. The default prediction of P-DCFold Software (Optimal Prediction).
boolean	SequenceListe.equals(SequenceListe toCompare) To know if two SequenceListe are equals (local instance and an other).
static java.lang.String	AlgoStefanConverter.getScreenToSee(SequenceListe[] tabsadn, Sequence target, AlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
static java.lang.String	OtherAlgoStefanConverter.getScreenToSee(SequenceListe[] tabsadn, Sequence target, OtherAlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
static java.lang.String	AlgoStefanConverter.getScreenToSeeHTML(SequenceListe[] tabsadn, Sequence target, AlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
static java.lang.String	OtherAlgoStefanConverter.getScreenToSeeHTML(SequenceListe[] tabsadn, Sequence target, OtherAlgorithmsStefan algo, boolean tfold) Working about what will be on screen.
boolean	SequenceListe.isIn(SequenceListe[] listes) To know if current instance of SequenceListe is in a table of SequenceListe's.
void	OriginAlgorithmsStefan.launch(Sequence target, SequenceListe[] listes, boolean optimal) To launch the computing (target is automatically treated in the set).
void	OtherAlgorithmsStefan.launch(Sequence target, SequenceListe[] listes, boolean optimal) To launch the computing (target is automatically treated in the set).
void	AlgorithmsStefan.launch(Sequence target, SequenceListe[] listes, boolean optimal) To launch the computing (target is automatically treated in the set).
static void	Algorithms.searchAllStructuralPalindromes(NoeudArbreExec Nd, Sequence cible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. To search structural palindromes (helix) including pseudoknots.
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 void	Algorithms.searchStructuralPalindrome(NoeudArbreExec Nd, Sequence cible, int tailleCible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. Searching structural palindromes in a selected sequence (cible), with comparison in a whole alignment of tests sequences.
static PalindromeListe	Algorithms.variableZonesTreatment(Sequence cible, int tailleCible, SequenceListe alignement, int decalage, int nbErreursMax) Deprecated. When no palindrome is found with searchAnchorPoints...

Constructors in modele with parameters of type SequenceListe

Algorithms(Sequence cible, SequenceListe alignement)
Deprecated. A constructor to launch searchAllStructuralPalindromes on elements.

AlgorithmsCT01(Sequence cible, SequenceListe alignement)
Deprecated. Do not instanciate this class.

AlgorithmsCT02(Sequence cible, SequenceListe alignement)
Deprecated. Do not instanciate this class.

AlgorithmsCT03(Sequence cible, SequenceListe alignement)
Deprecated. Do not instanciate this class.

Uses of SequenceListe in tests

Fields in tests declared as SequenceListe

private SequenceListe	TestSequenceListe.basetest1
private SequenceListe	TestSequenceListe.basetest2

Uses of SequenceListe in testsorigin

Subclasses of SequenceListe in testsorigin

class	Alignedalphad Here is 21 sequences of alphad RNA, original selection made by Stefan Engelen in 2006 and before for tests.
class	AlignedSequences This class to provide some records of sets of tests aligned sequences.
class	Alignedtmrna Here is a set of 87 sequences of tmRNA, original selection made by Stefan Engelen in 2006 and before for tests.
class	Alignedtrna Here is 9 sequences of tRNA, original selection made by Stefan Engelen in 2006 and before for tests.

Methods in testsorigin with parameters of type SequenceListe

static ADN1test[]	AlignedSequences.conversionFrom(SequenceListe liste) Conversion of a set of sequences listes to a tab of ADN1test's
static java.util.Vector	AlignedSequences.conversionFrom(SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's

Uses of SequenceListe in testssuite01

Fields in testssuite01 declared as SequenceListe

private SequenceListe	TestAlgorithmsPartIII.aersalliste lists of sequences
private SequenceListe	TestAlgorithmsPartI.alignement
private SequenceListe	TestAlgorithmsPartIV.ciblist List of cible
private SequenceListe	TestAlgorithmsPartIII.ecoliliste lists of sequences
private SequenceListe	TestAlgorithmsPartII.ecolist List of ecoli
private SequenceListe	TestAlgorithmsPartIV.ecolist List of ecoli
private SequenceListe	TestAlgorithmsPartIII.exampleliste lists of sequences
private SequenceListe	TestAlgorithmsPartIII.haeinfliste lists of sequences
private SequenceListe	TestAlgorithmsPartII.liste1 List of randomly generated sequences.
private SequenceListe	TestAlgorithmsPartII.liste2 List of this.cible.
private SequenceListe	TestAlgorithmsPartIII.sheputliste lists of sequences
private SequenceListe	TestAlgorithmsPartIII.teslist lists of sequences
private SequenceListe	TestAlgorithmsPartIV.teslist Test liste
private SequenceListe	TestAlgorithmsPartIII.vibcholliste lists of sequences

Uses of SequenceListe in testssuite02

Fields in testssuite02 declared as SequenceListe

private SequenceListe[]	TestGlobalPDCFold00.tabsadn
private SequenceListe	TestGlobalPDCFold00.tests

Methods in testssuite02 with parameters of type SequenceListe

static ADN1test[]	AlignedSequences.conversionFrom(SequenceListe liste) Conversion of a set of sequences listes to a tab of ADN1test's
static java.util.Vector	AlignedSequences.conversionFrom(SequenceListe[] listes) Conversion of a set of sequences listes to a vector of tabs of ADN1test's