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| Packages that use ADN1test | |
|---|---|
| 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 ADN1test in aloneinterfaces |
|---|
| Methods in aloneinterfaces with parameters of type ADN1test | |
|---|---|
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] |
| Uses of ADN1test in controller |
|---|
| Methods in controller that return ADN1test | |
|---|---|
static ADN1test[] |
ProcessusOrigin.conversionFrom(SequenceListe liste)
Conversion of a set of sequences listes to a tab of ADN1test's |
static ADN1test |
ProcessusOrigin.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
| Methods in controller with parameters of type ADN1test | |
|---|---|
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. |
| Uses of ADN1test in modele |
|---|
| Fields in modele declared as ADN1test | |
|---|---|
private ADN1test[] |
OriginAlgorithmsStefan.tableauInitial
"Global attribute with signification. |
| Methods in modele that return ADN1test | |
|---|---|
static ADN1test[] |
OriginAlgoStefanConverter.conversionFrom(SequenceListe liste)
Conversion of a set of sequences listes to a tab of ADN1test's. |
static ADN1test |
OriginAlgoStefanConverter.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
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 ! |
ADN1test[] |
OriginAlgorithmsStefan.getTableauInitial()
|
private static ADN1test[] |
OriginAlgoStefanConverter.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
To sort the tab... |
| Methods in modele with parameters of type ADN1test | |
|---|---|
private static java.lang.String |
OriginAlgoStefanConverter.afficherNom_web(ADN1test[] tabAdn)
Some changes to this procedure to make results appears for web / HTML. |
private static java.lang.String |
OriginAlgoStefanConverter.afficherNom(ADN1test[] tabAdn)
To bet the name of a tab of instances of ADN1test. |
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" |
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. |
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)
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 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 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" |
void |
OriginAlgorithmsStefan.setTableauInitial(ADN1test[] tableauInitial)
|
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 static ADN1test[] |
OriginAlgoStefanConverter.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
To sort the tab... |
private static ADN1test[] |
OriginAlgoStefanConverter.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
To sort the tab... |
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 ADN1test in origincomment |
|---|
| Fields in origincomment declared as ADN1test | |
|---|---|
private ADN1test |
Matrice_ALN.adncible
Target sequence in format of test sequence. |
private ADN1test[] |
Profil.adntest
Homologuous / test sequences ? |
private static ADN1test[] |
ADN1test.meilleuresSeqTest
The best test sequences. |
private ADN1test[] |
ADN1cible.tableauInitial
"Global attribute with signification. |
| Methods in origincomment that return ADN1test | |
|---|---|
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 ! |
ADN1test[] |
ADN1test.evoluer(int nb_pas_tot,
Profil profil)
Deprecated. (unused...) |
ADN1test[] |
ADN1cible.les_sequences_tests()
To get test sequences. |
static ADN1test[] |
ADN1test.quelles_meilleures_sequences_test()
|
ADN1test[] |
Profil.quels_adns_tests()
|
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 |
static ADN1test[] |
ADN1test.sequenceTests(java.lang.String seqTests)
Deprecated. [not used] |
ADN1test[] |
StefanErrors.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
Instance of object is given in procedure of the same instance. |
static ADN1test[] |
ADN1test.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
To sort the tab... |
| Methods in origincomment with parameters of type ADN1test | |
|---|---|
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 |
ADN1test.afficherNom_web(ADN1test[] tabAdn)
Some changes to this procedure to make results appears for web / HTML. |
static java.lang.String |
ADN1test.afficherNom(ADN1test[] tabAdn)
To bet the name of a tab of instances of ADN1test. |
void |
ADN1cible.calcul_Resultat(ADN1test[] tabAdn,
int typeRecherche,
boolean plusieurs_resultats,
boolean chercher_pk)
MAIN COMPUTING RESULTS "This method to launch search and compute all wanted results" |
static void |
ADN1test.change_meilleures_sequences_test(ADN1test[] nvtabSeq)
|
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. |
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 ! |
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 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)
|
void |
ADN1cible.pourcentage_Mutation(ADN1test[] adntest,
int pos_struct,
boolean bool)
Deprecated. [never used] |
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). |
private void |
ADN1cible.recherche_Pseudonoeud(Base[] sequencepseudonoeud,
ADN1test[] tabAdn,
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" |
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 |
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 static void |
ADN1test.toutes_combinaisons(ADN1test[] tabSeq,
ADN1test[] quelleSeq,
java.util.Vector vecTabAdnFinal,
int etape,
int debut)
All combinations. |
private static void |
ADN1test.toutes_combinaisons(ADN1test[] tabSeq,
ADN1test[] quelleSeq,
java.util.Vector vecTabAdnFinal,
int etape,
int debut)
All combinations. |
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" |
ADN1test[] |
StefanErrors.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
Instance of object is given in procedure of the same instance. |
ADN1test[] |
StefanErrors.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
Instance of object is given in procedure of the same instance. |
static ADN1test[] |
ADN1test.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
To sort the tab... |
static ADN1test[] |
ADN1test.trier(ADN1test adncible,
ADN1test[] adntest,
int quelscore)
To sort the tab... |
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 ADN1test | |
|---|---|
Matrice_ALN(ADN1test seqcible,
ADN1test seqtest,
int debut5,
int fin5,
int debut3,
int fin3,
int nbaln,
double lgmin)
|
|
Profil(ADN1cible adn,
ADN1test[] tabAdnTest)
Constrcutor with given target sequence and table of test sequences. |
|
Resultat(ADN1test[] tabSeq)
Constructor with given table of test sequences. |
|
Resultat(int taille,
ADN1test[] tabSeq)
Deprecated. [not used] |
|
| Uses of ADN1test in testsorigin |
|---|
| Fields in testsorigin declared as ADN1test | |
|---|---|
private ADN1test[] |
TestPDCFold03.tests
|
private ADN1test[] |
TestPDCFold02.tests
|
private ADN1test[] |
TestPDCFold01.tests
|
private ADN1test[] |
TestPDCFold00.tests
|
| Methods in testsorigin that return ADN1test | |
|---|---|
static ADN1test[] |
AlignedSequences.conversionFrom(SequenceListe liste)
Conversion of a set of sequences listes to a tab of ADN1test's |
static ADN1test |
AlignedSequences.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
| Uses of ADN1test in testssuite02 |
|---|
| Methods in testssuite02 that return ADN1test | |
|---|---|
static ADN1test[] |
AlignedSequences.conversionFrom(SequenceListe liste)
Conversion of a set of sequences listes to a tab of ADN1test's |
static ADN1test |
AlignedSequences.convertFrom(Sequence cible,
int diff)
To get a "test sequence" from an instance of Sequence. |
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