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| Packages that use Sequence | |
|---|---|
| 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. |
| 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 Sequence in alonefichiers |
|---|
| Fields in alonefichiers declared as Sequence | |
|---|---|
private Sequence |
FichierConvert.cible
Current seqquence of file. |
private Sequence |
FichierBracket.cible
Current sequence of file. |
| Methods in alonefichiers that return Sequence | |
|---|---|
Sequence |
FichierConvert.getSequence()
To get the sequence of current instance. |
Sequence |
FichierBracket.getSequence()
To get the sequence of current instance. |
| Methods in alonefichiers with parameters of type Sequence | |
|---|---|
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 Sequence | |
|---|---|
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 Sequence in aloneinterfaces |
|---|
| Fields in aloneinterfaces declared as Sequence | |
|---|---|
private Sequence |
Interface1.cible
Identification of elements, which algorithm will work on. |
private Sequence |
AloneProcessus_old.cible
|
private Sequence |
AloneProcessus.cible
|
| Methods in aloneinterfaces that return Sequence | |
|---|---|
Sequence |
Interface1.getSequence()
One part of the compexty of this class comes from that data is on different objects. |
| Methods in aloneinterfaces with parameters of type Sequence | |
|---|---|
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.setListModelTest(Sequence cible,
SequenceListe selection,
int longueur)
Visualization of homologuous sequences selection. |
void |
Interface1.setSequence(Sequence sequence)
|
| Uses of Sequence in controller |
|---|
| Fields in controller declared as Sequence | |
|---|---|
private Sequence |
ListeBean.cible
Better record here than in session. |
| Methods in controller that return Sequence | |
|---|---|
Sequence |
ListeBean.getCible()
To get the target sequence. |
| Methods in controller with parameters of type Sequence | |
|---|---|
static ADN1cible |
ProcessusOrigin.convertFrom(Sequence cible)
To get a "cible sequence" from an instance of Sequence. |
static ADN1test |
ProcessusOrigin.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
void |
ListeBean.setCible(Sequence cible)
To record the target sequence. |
void |
ListeBean.setResults(Sequence cible,
PalindromeListeListe results)
This procedure to compute the RnaViz and Bracket file result. |
| Uses of Sequence in modele |
|---|
| Subclasses of Sequence in modele | |
|---|---|
class |
SequenceCible
Deprecated. Transfered to Sequence |
class |
SequenceTest
Deprecated. Transfered to Sequence |
| Fields in modele declared as Sequence | |
|---|---|
private Sequence |
Algorithms.cible
Deprecated. Current selected sequence where to find Palindrome's, helix... |
private Sequence[] |
SequenceListe.liste
The list of Sequence's. |
private Sequence |
Palindrome.mainSequence
Use when checking Conservation and relevance of palindrome. |
private Sequence |
Alignement.sequence1
Sequence of the alignment. |
private Sequence |
Alignement.sequence2
Sequence of the alignment. |
private Sequence[] |
OtherAlgorithmsStefan.tableauInitial
"Global attribute with signification. |
private Sequence[] |
AlgorithmsStefan.tableauInitial
"Global attribute with signification. |
private Sequence[] |
ConvertedProfil.tableauSequences
Homologuous / test sequences ? |
private Sequence |
ConvertedProfil.target
Target sequence ? |
| Methods in modele that return Sequence | |
|---|---|
private static Sequence[] |
OtherAlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest)
Deprecated. "old version" see also OtherAlgoStefanConverter.distance(Sequence, Sequence, Sequence[], int, int) |
private static Sequence[] |
AlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest)
Deprecated. "old version" see also AlgoStefanConverter.distance(Sequence, Sequence, Sequence[], int, int) |
private static Sequence[] |
OtherAlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest,
int identity,
int deletion)
"procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores ! |
private static Sequence[] |
AlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest,
int identity,
int deletion)
"procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores ! |
Sequence |
Sequence.externalSequence(Palindrome P)
To get the external Sequence of a Palindrome on a Sequence. |
Sequence |
Sequence.getCarbonCopy()
==================================================================== |
Sequence |
Algorithms.getCible()
Deprecated. To get the cible Sequence. |
Sequence[] |
SequenceListe.getListe()
|
Sequence |
Palindrome.getSequence()
|
Sequence |
SequenceListe.getSequence(int i)
|
Sequence |
SequenceListe.getSequence(java.lang.String nom)
|
Sequence |
Alignement.getSequence1()
|
Sequence |
Alignement.getSequence2()
|
Sequence[] |
OtherAlgorithmsStefan.getTableauInitial()
|
Sequence[] |
AlgorithmsStefan.getTableauInitial()
|
Sequence |
Sequence.internalSequence(Palindrome P)
To get the internal sequence of a palindrome on a Sequence. |
static Sequence |
Algorithms.newSequenceDeduction(Sequence cible,
PalindromeListe Lg)
Deprecated. To get a new sequence without found palindromes in sequence. |
Sequence |
ConvertedProfil.quel_adn()
|
Sequence[] |
ConvertedProfil.quels_adns_tests()
|
private static Sequence[] |
OtherAlgoStefanConverter.trier(Sequence target_test,
Sequence[] adntest,
int quelscore)
To sort the tab... |
private static Sequence[] |
AlgoStefanConverter.trier(Sequence target_test,
Sequence[] adntest,
int quelscore)
To sort the tab... |
| Methods in modele with parameters of type Sequence | |
|---|---|
void |
SequenceListe.addSequence(Sequence elt)
To add a Sequence at the end of the list. |
private static java.lang.String |
AlgoStefanConverter.afficher_Caracteristique_Web(Sequence target,
AlgorithmsStefan algo,
boolean tfold)
Some changes to this procedure to make results appears for web / HTML. |
private static java.lang.String |
OtherAlgoStefanConverter.afficher_Caracteristique_Web(Sequence target,
OtherAlgorithmsStefan algo,
boolean tfold)
Some changes to this procedure to make results appears for web / HTML. |
private static java.lang.String |
AlgoStefanConverter.afficher_Caracteristique(Sequence target,
AlgorithmsStefan algo,
boolean tfold)
SOME SHOW FOR VIEW "This method for show on a target sequence of DNA" |
private static java.lang.String |
OtherAlgoStefanConverter.afficher_Caracteristique(Sequence target,
OtherAlgorithmsStefan algo,
boolean tfold)
SOME SHOW FOR VIEW "This method for show on a target sequence of DNA" |
private static java.lang.String |
OtherAlgoStefanConverter.afficherNom_web(Sequence[] tabAdn)
Some changes to this procedure to make results appears for web / HTML. |
private static java.lang.String |
AlgoStefanConverter.afficherNom_web(Sequence[] tabAdn)
Some changes to this procedure to make results appears for web / HTML. |
private static java.lang.String |
OtherAlgoStefanConverter.afficherNom(Sequence[] tabAdn)
To bet the name of a tab of instances of Sequence. |
private static java.lang.String |
AlgoStefanConverter.afficherNom(Sequence[] tabAdn)
To bet the name of a tab of instances of Sequence. |
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. |
private void |
OtherAlgorithmsStefan.calcul_Resultat(Sequence target,
Sequence[] tableauSequences,
int typeRecherche,
boolean plusieurs_resultats,
boolean chercher_pk)
MAIN COMPUTING RESULTS "This method to launch search and compute all wanted results" |
private void |
OtherAlgorithmsStefan.calcul_Resultat(Sequence target,
Sequence[] tableauSequences,
int typeRecherche,
boolean plusieurs_resultats,
boolean chercher_pk)
MAIN COMPUTING RESULTS "This method to launch search and compute all wanted results" |
private void |
AlgorithmsStefan.calcul_Resultat(Sequence target,
Sequence[] tableauSequences,
int typeRecherche,
boolean plusieurs_resultats,
boolean chercher_pk)
MAIN COMPUTING RESULTS "This method to launch search and compute all wanted results" |
private void |
AlgorithmsStefan.calcul_Resultat(Sequence target,
Sequence[] tableauSequences,
int typeRecherche,
boolean plusieurs_resultats,
boolean chercher_pk)
MAIN COMPUTING RESULTS "This method to launch search and compute all wanted results" |
void |
ConvertedProfil.change_adn(Sequence nv)
|
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 |
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 ADN1cible |
OriginAlgoStefanConverter.convertFrom(Sequence cible)
To get a "cible sequence" from an instance of Sequence. |
static ADN1test |
OriginAlgoStefanConverter.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
static PalindromeListe |
Algorithms.defaultPredictionOfStructure(Sequence cible,
SequenceListe alignement,
int numSelect)
Deprecated. The default prediction of P-DCFold Software (Optimal Prediction). |
private static Sequence[] |
OtherAlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest)
Deprecated. "old version" see also OtherAlgoStefanConverter.distance(Sequence, Sequence, Sequence[], int, int) |
private static Sequence[] |
OtherAlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest)
Deprecated. "old version" see also OtherAlgoStefanConverter.distance(Sequence, Sequence, Sequence[], int, int) |
private static Sequence[] |
AlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest)
Deprecated. "old version" see also AlgoStefanConverter.distance(Sequence, Sequence, Sequence[], int, int) |
private static Sequence[] |
AlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest)
Deprecated. "old version" see also AlgoStefanConverter.distance(Sequence, Sequence, Sequence[], int, int) |
private static Sequence[] |
OtherAlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest,
int identity,
int deletion)
"procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores ! |
private static Sequence[] |
OtherAlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest,
int identity,
int deletion)
"procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores ! |
private static Sequence[] |
AlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] adntest,
int identity,
int deletion)
"procedure which give a score to the test sequence and sort them. " First part of SSCA algorithm : scores ! |
private static Sequence[] |
AlgoStefanConverter.distance(Sequence target_cible,
Sequence target_test,
Sequence[] 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 |
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 |
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... |
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 |
Sequence.equals(Sequence toCompare)
To know if instance of the class and an other are the same. |
PalindromeListeListe |
OriginAlgorithmsStefan.getRecordingStructures(Sequence target)
To get the recording structure in a good conversion format. |
PalindromeListeListe |
OtherAlgorithmsStefan.getRecordingStructures(Sequence target)
To get the recording structure in a good conversion format. |
PalindromeListeListe |
AlgorithmsStefan.getRecordingStructures(Sequence target)
To get the recording structure in a good conversion format. |
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.has(Sequence elt)
To know if a Sequence is in this list. |
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 Sequence |
Algorithms.newSequenceDeduction(Sequence cible,
PalindromeListe Lg)
Deprecated. To get a new sequence without found palindromes in sequence. |
private void |
OtherAlgorithmsStefan.recherche_Palindrome(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 DNA sequence. |
private void |
OtherAlgorithmsStefan.recherche_Palindrome(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 DNA sequence. |
private void |
AlgorithmsStefan.recherche_Palindrome(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 DNA sequence. |
private void |
AlgorithmsStefan.recherche_Palindrome(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 DNA sequence. |
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[] |
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 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 void |
OtherAlgorithmsStefan.recherche_Pseudonoeud(Sequence target,
Base[] sequencepseudonoeud,
Sequence[] 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 |
OtherAlgorithmsStefan.recherche_Pseudonoeud(Sequence target,
Base[] sequencepseudonoeud,
Sequence[] 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 |
AlgorithmsStefan.recherche_Pseudonoeud(Sequence target,
Base[] sequencepseudonoeud,
Sequence[] 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 |
AlgorithmsStefan.recherche_Pseudonoeud(Sequence target,
Base[] sequencepseudonoeud,
Sequence[] 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" |
void |
SequenceListe.removeSequence(Sequence elt)
To remove a specific Sequence. |
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(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. |
void |
SequenceListe.setListe(Sequence[] liste)
|
void |
Palindrome.setSequence(Sequence mainSequence)
|
void |
SequenceListe.setSequence(Sequence elt,
int i)
|
void |
OtherAlgorithmsStefan.setTableauInitial(Sequence[] tableauInitial)
|
void |
AlgorithmsStefan.setTableauInitial(Sequence[] tableauInitial)
|
private void |
OtherAlgorithmsStefan.traitement_Zone_Variable(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 void |
OtherAlgorithmsStefan.traitement_Zone_Variable(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 void |
AlgorithmsStefan.traitement_Zone_Variable(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 void |
AlgorithmsStefan.traitement_Zone_Variable(Sequence target,
int debut,
int fin,
int taille,
Sequence[] 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 static Sequence[] |
OtherAlgoStefanConverter.trier(Sequence target_test,
Sequence[] adntest,
int quelscore)
To sort the tab... |
private static Sequence[] |
OtherAlgoStefanConverter.trier(Sequence target_test,
Sequence[] adntest,
int quelscore)
To sort the tab... |
private static Sequence[] |
AlgoStefanConverter.trier(Sequence target_test,
Sequence[] adntest,
int quelscore)
To sort the tab... |
private static Sequence[] |
AlgoStefanConverter.trier(Sequence target_test,
Sequence[] adntest,
int quelscore)
To sort the tab... |
static PalindromeListe |
Algorithms.variableZonesTreatment(Sequence cible,
int tailleCible,
SequenceListe alignement,
int decalage,
int nbErreursMax)
Deprecated. When no palindrome is found with searchAnchorPoints... |
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 |
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 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 |
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. |
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. |
| Constructors in modele with parameters of type Sequence | |
|---|---|
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. |
|
Alignement(Sequence sequence)
Deprecated. Not easy to well understand it without source code. |
|
Alignement(Sequence sequence,
double lpmin,
double lbmin)
Deprecated. Not easy to well understand it without source code. |
|
Alignement(Sequence sequence1,
Sequence sequence2)
Constructor of the alignment. lpmin is set to 3.0 and lbmin to 4.0. |
|
Alignement(Sequence sequence1,
Sequence sequence2,
double lpmin,
double lbmin)
Constructor of the alignment with given lpmin. |
|
ConvertedProfil(Sequence target,
Sequence[] tableauSequences)
Constrcutor with given target sequence and table of test sequences. |
|
ConvertedProfil(Sequence target,
Sequence[] tableauSequences)
Constrcutor with given target sequence and table of test sequences. |
|
SequenceListe(Sequence[] liste)
Constructor with a pre-made table of Sequence. |
|
| Uses of Sequence in tests |
|---|
| Fields in tests declared as Sequence | |
|---|---|
private Sequence |
TestSequence.basetest1
|
private Sequence |
TestSequence.basetest2
|
private Sequence |
TestAlignement.sequence1
|
private Sequence |
TestAlignement.sequence2
|
| Uses of Sequence in testsalone |
|---|
| Fields in testsalone declared as Sequence | |
|---|---|
private Sequence |
TestFichierRnaViz.cible
|
private Sequence |
TestFichierBracket.cible
|
| Uses of Sequence in testsorigin |
|---|
| Fields in testsorigin declared as Sequence | |
|---|---|
static Sequence |
Alignedalphad.aacti
|
static Sequence |
Alignedtmrna.acact
|
static Sequence |
Alignedtmrna.acfer
|
static Sequence |
Alignedtmrna.aesal
|
static Sequence |
Alignedtmrna.aleut
|
static Sequence |
Alignedtmrna.alhal
|
static Sequence |
Alignedtmrna.anspe
|
static Sequence |
Alignedtrna.aqaeo
|
static Sequence |
Alignedtmrna.aqaeo
|
static Sequence |
Alignedtmrna.baant
|
static Sequence |
Alignedtmrna.bameg
|
static Sequence |
Alignedtrna.basub
|
static Sequence |
Alignedtmrna.basub
|
static Sequence |
Alignedtmrna.bobro
|
static Sequence |
Alignedtrna.bobur
|
static Sequence |
Alignedtmrna.bobur
|
static Sequence |
Alignedtmrna.boper
|
static Sequence |
Alignedalphad.bpaha
|
static Sequence |
Alignedtmrna.brjap
|
static Sequence |
Alignedalphad.bspap
|
static Sequence |
Alignedtmrna.cacre
|
static Sequence |
Alignedtmrna.cajej
|
static Sequence |
Alignedtmrna.chmur
|
static Sequence |
Alignedtmrna.chpne
|
static Sequence |
Alignedtmrna.chpsi
|
static Sequence |
Alignedtmrna.chtep
|
static Sequence |
Alignedtmrna.chtra
|
static Sequence |
Alignedtmrna.clace
|
static Sequence |
Alignedtmrna.cldif
|
static Sequence |
Alignedtmrna.codip
|
static Sequence |
Alignedtmrna.cypar
|
static Sequence |
Alignedtmrna.dedes
|
static Sequence |
Alignedtmrna.derad
|
static Sequence |
Alignedtmrna.devul
|
static Sequence |
Alignedtmrna.dinod
|
static Sequence |
Alignedalphad.ecoli
|
static Sequence |
Alignedtrna.ecoli
|
static Sequence |
Alignedtmrna.ecoli
|
static Sequence |
Alignedtmrna.enfaa
|
static Sequence |
Alignedtmrna.enfab
|
static Sequence |
Alignedtmrna.frtul
|
static Sequence |
Alignedtmrna.funuc
|
static Sequence |
Alignedtmrna.gesul
|
static Sequence |
Alignedtmrna.guthe
|
static Sequence |
Alignedtmrna.haduc
|
static Sequence |
Alignedalphad.hainf
|
static Sequence |
Alignedtrna.hainf
|
static Sequence |
Alignedtmrna.hainf
|
static Sequence |
Alignedtrna.hepyl
|
static Sequence |
Alignedtmrna.hepyl
|
static Sequence |
Alignedalphad.hinfl
|
static Sequence |
Alignedtmrna.klpne
|
static Sequence |
Alignedalphad.kpneu
|
static Sequence |
Alignedtmrna.lepne
|
static Sequence |
Alignedtmrna.mahyd
|
static Sequence |
Alignedtmrna.meext
|
static Sequence |
Alignedtmrna.myavi
|
static Sequence |
Alignedtmrna.mybov
|
static Sequence |
Alignedtmrna.mycap
|
static Sequence |
Alignedtrna.mygen
|
static Sequence |
Alignedtmrna.mygen
|
static Sequence |
Alignedtmrna.mylep
|
static Sequence |
Alignedtmrna.mypen
|
static Sequence |
Alignedtrna.mypne
|
static Sequence |
Alignedtmrna.mytub
|
static Sequence |
Alignedtmrna.negon
|
static Sequence |
Alignedtmrna.nemea
|
static Sequence |
Alignedtmrna.nemeb
|
static Sequence |
Alignedtmrna.nieur
|
static Sequence |
Alignedtmrna.nopum
|
static Sequence |
Alignedtmrna.odsin
|
static Sequence |
Alignedalphad.paeru
|
static Sequence |
Alignedalphad.pamal
|
static Sequence |
Alignedtmrna.pamul
|
static Sequence |
Alignedalphad.pmult
|
static Sequence |
Alignedtmrna.pogin
|
static Sequence |
Alignedtmrna.popur
|
static Sequence |
Alignedalphad.pputi
|
static Sequence |
Alignedtmrna.psaer
|
static Sequence |
Alignedtmrna.pshal
|
static Sequence |
Alignedtmrna.psput
|
static Sequence |
Alignedalphad.psyri
|
static Sequence |
Alignedtmrna.reame
|
static Sequence |
Alignedtmrna.rhpal
|
static Sequence |
Alignedtmrna.ripro
|
static Sequence |
Alignedtmrna.sapar
|
static Sequence |
Alignedalphad.satyh
|
static Sequence |
Alignedtmrna.satyp
|
static Sequence |
Alignedtmrna.shput
|
static Sequence |
Alignedalphad.shvio
|
static Sequence |
Alignedtmrna.simel
|
static Sequence |
Alignedalphad.spara
|
static Sequence |
Alignedalphad.sputr
|
static Sequence |
Alignedtmrna.staur
|
static Sequence |
Alignedtmrna.stcoe
|
static Sequence |
Alignedtmrna.stepi
|
static Sequence |
Alignedtmrna.stequ
|
static Sequence |
Alignedtmrna.stgor
|
static Sequence |
Alignedtmrna.stmut
|
static Sequence |
Alignedtmrna.stpne
|
static Sequence |
Alignedtmrna.stpyo
|
static Sequence |
Alignedalphad.stymu
|
static Sequence |
Alignedalphad.styph
|
static Sequence |
Alignedtrna.synsp
|
static Sequence |
Alignedtmrna.syspa
|
static Sequence |
Alignedtmrna.syspb
|
static Sequence |
Alignedtmrna.thmar
|
static Sequence |
Alignedtmrna.ththe
|
static Sequence |
Alignedtmrna.thwei
|
static Sequence |
Alignedtmrna.trpal
|
static Sequence |
Alignedtmrna.urure
|
static Sequence |
Alignedalphad.vchol
|
static Sequence |
Alignedtmrna.vicho
|
static Sequence |
Alignedtmrna.xyfas
|
static Sequence |
Alignedalphad.yepes
|
static Sequence |
Alignedtmrna.yepes
|
static Sequence |
Alignedalphad.ypesi
|
| Methods in testsorigin with parameters of type Sequence | |
|---|---|
static ADN1cible |
AlignedSequences.convertFrom(Sequence cible)
To get a "cible sequence" from an instance of Sequence. |
static ADN1test |
AlignedSequences.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
| Uses of Sequence in testssuite01 |
|---|
| Fields in testssuite01 declared as Sequence | |
|---|---|
private Sequence |
TestAlgorithmsPartIII.actact
Act. act. tmRNA |
private Sequence |
TestAlgorithmsPartIV.actact
Act. act. tmRNA |
private Sequence |
TestAlgorithmsPartIII.aersal
Aer. sal. tmRNA |
private Sequence |
TestAlgorithmsPartII.cible
Randomly generated sequence. |
private Sequence |
TestAlgorithmsPartI.cible
|
private Sequence |
TestAlgorithmsPartIV.cible
Randomly generated sequence. |
private Sequence |
TestAlgorithmsPartIII.ecoli
E. coli tmRNA |
private Sequence |
TestAlgorithmsPartII.ecoli
E. coli tmRNA |
private Sequence |
TestAlgorithmsPartIV.ecoli
E. coli tmRNA |
private Sequence |
TestAlgorithmsPartIII.haeinf
Hae. inf. tmRNA |
private Sequence |
TestAlgorithmsPartIV.haeinf
Hae. inf. tmRNA |
private Sequence |
TestAlgorithmsPartIII.pasmul
Pas. mul. tmRNA |
private Sequence |
TestAlgorithmsPartIV.pasmul
Pas. mul. tmRNA |
private Sequence |
TestAlgorithmsPartIII.sheput
She. put. tmRNA |
private Sequence |
TestAlgorithmsPartIII.vibchol
Vib. cho. tmRNA |
private Sequence |
TestAlgorithmsPartIV.vibchol
Vib. cho. tmRNA |
| Uses of Sequence in testssuite02 |
|---|
| Fields in testssuite02 declared as Sequence | |
|---|---|
static Sequence |
Alignedalphad.aacti
|
static Sequence |
Alignedtmrna.acact
|
static Sequence |
Alignedtmrna.acfer
|
static Sequence |
Alignedtmrna.aesal
|
static Sequence |
Alignedtmrna.aleut
|
static Sequence |
Alignedtmrna.alhal
|
static Sequence |
Alignedtmrna.anspe
|
static Sequence |
Alignedtrna.aqaeo
|
static Sequence |
Alignedtmrna.aqaeo
|
static Sequence |
Alignedtmrna.baant
|
static Sequence |
Alignedtmrna.bameg
|
static Sequence |
Alignedtrna.basub
|
static Sequence |
Alignedtmrna.basub
|
static Sequence |
Alignedtmrna.bobro
|
static Sequence |
Alignedtrna.bobur
|
static Sequence |
Alignedtmrna.bobur
|
static Sequence |
Alignedtmrna.boper
|
static Sequence |
Alignedalphad.bpaha
|
static Sequence |
Alignedtmrna.brjap
|
static Sequence |
Alignedalphad.bspap
|
static Sequence |
Alignedtmrna.cacre
|
static Sequence |
Alignedtmrna.cajej
|
static Sequence |
Alignedtmrna.chmur
|
static Sequence |
Alignedtmrna.chpne
|
static Sequence |
Alignedtmrna.chpsi
|
static Sequence |
Alignedtmrna.chtep
|
static Sequence |
Alignedtmrna.chtra
|
static Sequence |
Alignedtmrna.clace
|
static Sequence |
Alignedtmrna.cldif
|
static Sequence |
Alignedtmrna.codip
|
static Sequence |
Alignedtmrna.cypar
|
static Sequence |
Alignedtmrna.dedes
|
static Sequence |
Alignedtmrna.derad
|
static Sequence |
Alignedtmrna.devul
|
static Sequence |
Alignedtmrna.dinod
|
static Sequence |
Alignedtrna.ecoli
|
static Sequence |
Alignedtmrna.ecoli
|
static Sequence |
Alignedalphad.ecoli
|
static Sequence |
Alignedtmrna.enfaa
|
static Sequence |
Alignedtmrna.enfab
|
static Sequence |
Alignedtmrna.frtul
|
static Sequence |
Alignedtmrna.funuc
|
static Sequence |
Alignedtmrna.gesul
|
static Sequence |
Alignedtmrna.guthe
|
static Sequence |
Alignedtmrna.haduc
|
static Sequence |
Alignedtrna.hainf
|
static Sequence |
Alignedtmrna.hainf
|
static Sequence |
Alignedalphad.hainf
|
static Sequence |
Alignedtrna.hepyl
|
static Sequence |
Alignedtmrna.hepyl
|
static Sequence |
Alignedalphad.hinfl
|
static Sequence |
Alignedtmrna.klpne
|
static Sequence |
Alignedalphad.kpneu
|
static Sequence |
Alignedtmrna.lepne
|
static Sequence |
Alignedtmrna.mahyd
|
static Sequence |
Alignedtmrna.meext
|
static Sequence |
Alignedtmrna.myavi
|
static Sequence |
Alignedtmrna.mybov
|
static Sequence |
Alignedtmrna.mycap
|
static Sequence |
Alignedtrna.mygen
|
static Sequence |
Alignedtmrna.mygen
|
static Sequence |
Alignedtmrna.mylep
|
static Sequence |
Alignedtmrna.mypen
|
static Sequence |
Alignedtrna.mypne
|
static Sequence |
Alignedtmrna.mytub
|
static Sequence |
Alignedtmrna.negon
|
static Sequence |
Alignedtmrna.nemea
|
static Sequence |
Alignedtmrna.nemeb
|
static Sequence |
Alignedtmrna.nieur
|
static Sequence |
Alignedtmrna.nopum
|
static Sequence |
Alignedtmrna.odsin
|
static Sequence |
Alignedalphad.paeru
|
static Sequence |
Alignedalphad.pamal
|
static Sequence |
Alignedtmrna.pamul
|
static Sequence |
Alignedalphad.pmult
|
static Sequence |
Alignedtmrna.pogin
|
static Sequence |
Alignedtmrna.popur
|
static Sequence |
Alignedalphad.pputi
|
static Sequence |
Alignedtmrna.psaer
|
static Sequence |
Alignedtmrna.pshal
|
static Sequence |
Alignedtmrna.psput
|
static Sequence |
Alignedalphad.psyri
|
static Sequence |
Alignedtmrna.reame
|
static Sequence |
Alignedtmrna.rhpal
|
static Sequence |
Alignedtmrna.ripro
|
static Sequence |
Alignedtmrna.sapar
|
static Sequence |
Alignedalphad.satyh
|
static Sequence |
Alignedtmrna.satyp
|
static Sequence |
Alignedtmrna.shput
|
static Sequence |
Alignedalphad.shvio
|
static Sequence |
Alignedtmrna.simel
|
static Sequence |
Alignedalphad.spara
|
static Sequence |
Alignedalphad.sputr
|
static Sequence |
Alignedtmrna.staur
|
static Sequence |
Alignedtmrna.stcoe
|
static Sequence |
Alignedtmrna.stepi
|
static Sequence |
Alignedtmrna.stequ
|
static Sequence |
Alignedtmrna.stgor
|
static Sequence |
Alignedtmrna.stmut
|
static Sequence |
Alignedtmrna.stpne
|
static Sequence |
Alignedtmrna.stpyo
|
static Sequence |
Alignedalphad.stymu
|
static Sequence |
Alignedalphad.styph
|
static Sequence |
Alignedtrna.synsp
|
static Sequence |
Alignedtmrna.syspa
|
static Sequence |
Alignedtmrna.syspb
|
private Sequence |
TestGlobalPDCFold00.target
|
static Sequence |
Alignedtmrna.thmar
|
static Sequence |
Alignedtmrna.ththe
|
static Sequence |
Alignedtmrna.thwei
|
static Sequence |
Alignedtmrna.trpal
|
static Sequence |
Alignedtmrna.urure
|
static Sequence |
Alignedalphad.vchol
|
static Sequence |
Alignedtmrna.vicho
|
static Sequence |
Alignedtmrna.xyfas
|
static Sequence |
Alignedtmrna.yepes
|
static Sequence |
Alignedalphad.yepes
|
static Sequence |
Alignedalphad.ypesi
|
| Methods in testssuite02 with parameters of type Sequence | |
|---|---|
static ADN1cible |
AlignedSequences.convertFrom(Sequence cible)
To get a "cible sequence" from an instance of Sequence. |
static ADN1test |
AlignedSequences.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
|
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