origincomment
Class ADN1cible

java.lang.Object
  origincomment.ADN1
      origincomment.ADN1cible

public class ADN1cible
extends ADN1

"Tous les pseudonoeuds d'une sous sequence sont recherches"
"All pseudoknots of a sequence are searched. "
This class for desaligned / unaligned sequences : methods works like that...
Most part of algorithms for P-DCFold in this class. Some french comments in procedures they have been written by Stefan Engelen and letted in in quote and translated...

Author:

Stéfan Engelen (2006) for coding..., Gabriel Chandesris (2008) for comments and makeing the code readable.

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean), diviser_regner(Palindrome1cible[], ADN1cible, ADN1test[], int, int, int, int, boolean, int), recherche_Palindrome(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int), recherche_Pseudonoeud(Base[], ADN1test[], boolean, int, int), recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), resultat_commun(Vector), traitement_Zone_Variable(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int), verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]), verifier_Conservation_Commune(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]), verifier_Conservation_Commune(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]), ADN1test, Palindrome1cible, Matrice_ALN, Base

Field Summary

static int	ALIGNEMENTHELICE "Global attributes of work" Helix alignment is 3.
static int	ARN_MESSAGER "Global attributes of work" Messenger RNA is 2.
static int	ARN_STRUCTURAL "Global attributes of work" Structural RNA is 1.
private boolean	chercher_pk "Global attribute with signification.
private int	decalage "Global attribute with signification.
private double	incertitude "Global attribute with signification.
static int	LONG_MUT "Global attributes of work" Mutation length is 2.
private int	longueur "Global attribute with signification.
private int	nb_prediction_max "Global attribute with signification.
static int	PROFILHELICE "Global attributes of work" Helix profile is 2.
private int	pseudonoeud "Global attributes of work" Current complexity of searching pseudoknots.
private Base[]	sequence "Global attribute with signification.
static int	STRUCTURECOMMUNE "Global attributes of work" Common structure is 1.
private ADN1test[]	tableauInitial "Global attribute with signification.
private ArbrePalindrome	tableauPalindrome "Global attribute with signification.
private int	taille_boucle_min "Global attribute with signification.
private int	taille_pal_min "Global attribute with signification.
static int	TAUX_MUT "Global attributes of work" Mutation rate is 1.
private boolean	trouvePseudonoeud "Global attributes of work" Have pseudoknots been found in current step...
private int	typeARN "Global attribute with signification.
private int	typeCritere "Global attribute with signification.
private int	typeRecherche "Global attribute with signification.

Fields inherited from class origincomment.ADN1

nom

Constructor Summary

ADN1cible()
Default constructor : nothing happend.

ADN1cible(java.lang.String nomFichier, java.lang.String sequence)
Constructor with name and aligned sequence...

Method Summary

java.lang.String	afficher_Caracteristique_Web() Some changes to this procedure to make results appears for web / HTML.
java.lang.String	afficher_Caracteristique() SOME SHOW FOR VIEW "This method for show on a target sequence of DNA"
java.lang.String	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	afficher(Palindrome1cible[] tabPal) SOME SHOW FOR VIEW "This method to show the palindromes' tab"
void	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"
double[]	calcul_score_structure(ADN1cible adn_ref) RESULT TREAMENT "Compute the score of structure face to a reference (two DNA in input)"
static double[]	calcul_score_structure(java.lang.String entree_reference, java.lang.String entree_structure) RESULT TREAMENT "Compute the score of a structure face a reference (two structures files in input)"
static double[]	calcul_score_structure(java.util.Vector reference, java.util.Vector structure) RESULT TREAMENT "Compute the score of a strcuture face to a reference (two pairwise vector in input)"
int	calcul_Taille(Palindrome1cible pal) COMPATIBLE PALINDROME SEARCH "This method to compute internal sequence length at step i
void	change_chercher_pk(boolean nv)
void	change_decalage(int nvdec)
void	change_incertitude(double nvincertitude)
void	change_nb_prediction_max(int nbnv)
void	change_palindromes(Palindrome1cible[] tabPal) To set the table of palindrome and change the tree of algorithms.
void	change_taille_boucle_min(int nvmin)
void	change_taille_pal_min(int nvmin)
void	change_type_arn(int nvtype)
void	change_type_critere(int nvcritere)
static Palindrome1cible[][]	comparaison_palindrome(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2) RESULT TREAMENT "Methods to compare recorded results in files.
java.lang.String	comparaison_Resultat(java.io.BufferedReader entree1, java.io.BufferedReader entree2) RESULT TREAMENT "Methods to compare recorded results in files.
int	comparaison_structure(ADN1cible adn1, ADN1cible adn2) Deprecated. [never used]
static java.lang.String	comparaison(ADN1cible adn1, ADN1cible adn2) RESULT TREAMENT "Methods to compare recorded results in files.
ADN1cible	copier() To clone the current instance of ADN1cible.
private static java.lang.String	decoupeString_Web(java.lang.String chaineDecoupe) This method to cut a String by 80 characters length substring.
private static java.lang.String	decoupeString(java.lang.String chaineDecoupe) This method to cut a String by 80 characters length substring.
void	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...
boolean	est_Une_Base_Test(char base) COMPATIBLE PALINDROME SEARCH "This method test if a char is a base"
void	initialiser() Initialization of algorithm.
Palindrome1cible[]	la_structure(int pos) To get a specific structure.
Palindrome1cible	le_palindrome(int pos_struct, int pos_pal) To get a specific palindrome in a specific structure.
ADN1test[]	les_sequences_tests() To get test sequences.
java.util.Vector	les_structures() To get structures from algorithm tree.
void	load_File(java.io.BufferedReader entree) RESULT TREAMENT "This method create an object from recorded data in a file"
void	mettre_etoile(int pos_struct) PSEUDOKNOTS SEARCH "This method to put stars (*) in found palindromes in aim to find pseudoknots)"
static Palindrome1cible[][]	palindromes_communs(Palindrome1cible[] tabPal1, Palindrome1cible[] tabPal2, boolean struc_com) RESULT TREAMENT "Previous method variation [comparaison_palindrome] to find common palindromes between two predictions.
java.lang.String	pourcentage_base() Deprecated. [never used]
void	pourcentage_Mutation(ADN1test[] adntest, int pos_struct, boolean bool) Deprecated. [never used]
ArbrePalindrome	quel_tableau_palindrome() To get the algorithm tree.
int	quelle_longueur() To get the length of the sequence.
Base[]	quelle_sequence() To get the sequence tab.
int	recherche_commune() Common search.
private void	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[]	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	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"
void	resultat_commun_paire_de_base(java.util.Vector vec) Deprecated. [never used]
void	resultat_commun(java.util.Vector vec) RESULT TREAMENT "This method compute a common result from vector of tab of palindromes"
private static int	score(char x, char y) COMPATIBLE PALINDROME SEARCH Getting a score from two (2) bases.
static ADN1	sequenceCible(java.lang.String sequenceCible, boolean cible) SOME SHOW FOR VIEW "To get target sequence"
java.lang.String	to_File(java.lang.String fichier) RESULT TREAMENT "This method write results in a file"
java.lang.String	toString(int debut, int fin) SOME SHOW FOR VIEW "To visualize considered sequence [current instance]"
private void	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"
Base	une_base(int position) To get a Base at a specific position.
Base[]	une_sous_sequence(int debut, int fin) To get a subsequence of sequence.
boolean	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	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	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.

Methods inherited from class origincomment.ADN1

change_nom, est_Une_Base, match, quel_nom, to_File

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

longueur

private int longueur

"Global attribute with signification. "
Length of the sequence.

sequence

private Base[] sequence

"Global attribute with signification. "
The sequeence in a Base tab.

See Also:

Base, quelle_sequence()

tableauPalindrome

private ArbrePalindrome tableauPalindrome

"Global attribute with signification. "
A Palindrome Tree use in algorithm.

See Also:

ArbrePalindrome, quel_tableau_palindrome()

typeRecherche

private int typeRecherche

"Global attribute with signification. "
Search type (default is ALIGNEMENTHELICE / 3).

See Also:

ALIGNEMENTHELICE, PROFILHELICE, STRUCTURECOMMUNE, calcul_Resultat(ADN1test[], int, boolean, boolean)

chercher_pk

private boolean chercher_pk

"Global attribute with signification. "
Searching pseudoknots or not (default is true).

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

typeCritere

private int typeCritere

"Global attribute with signification. "
Criteria type (defaul is TAUX_MUT / 2).

See Also:

TAUX_MUT, LONG_MUT, calcul_Resultat(ADN1test[], int, boolean, boolean)

typeARN

private int typeARN

"Global attribute with signification. "
RNA type (default is ARN_STRUCTURAL / 1).

See Also:

ARN_STRUCTURAL, ARN_MESSAGER, calcul_Resultat(ADN1test[], int, boolean, boolean)

incertitude

private double incertitude

"Global attribute with signification. "
(default is 0.0).

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

decalage

private int decalage

"Global attribute with signification. "
(default is 0).

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

taille_boucle_min

private int taille_boucle_min

"Global attribute with signification. "
Minimal length of loop (default is 4).

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

taille_pal_min

private int taille_pal_min

"Global attribute with signification. "
Minimal length of palindromes (default is 3).

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

nb_prediction_max

private int nb_prediction_max

"Global attribute with signification. "
Maximal number of predictions (default is 1).

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

tableauInitial

private ADN1test[] tableauInitial

"Global attribute with signification. "
Recording sequence tests used (default is null).

See Also:

les_sequences_tests()

pseudonoeud

private int pseudonoeud

"Global attributes of work"
Current complexity of searching pseudoknots. Start at 0.

trouvePseudonoeud

private boolean trouvePseudonoeud

"Global attributes of work"
Have pseudoknots been found in current step... Start at false.

ARN_STRUCTURAL

public static final int ARN_STRUCTURAL

"Global attributes of work"
Structural RNA is 1.

See Also:

Constant Field Values

ARN_MESSAGER

public static final int ARN_MESSAGER

"Global attributes of work"
Messenger RNA is 2.

See Also:

Constant Field Values

TAUX_MUT

public static final int TAUX_MUT

"Global attributes of work"
Mutation rate is 1.

See Also:

Constant Field Values

LONG_MUT

public static final int LONG_MUT

"Global attributes of work"
Mutation length is 2.

See Also:

Constant Field Values

STRUCTURECOMMUNE

public static final int STRUCTURECOMMUNE

"Global attributes of work"
Common structure is 1.

See Also:

Constant Field Values

PROFILHELICE

public static final int PROFILHELICE

"Global attributes of work"
Helix profile is 2.

See Also:

Constant Field Values

ALIGNEMENTHELICE

public static final int ALIGNEMENTHELICE

"Global attributes of work"
Helix alignment is 3.

See Also:

Constant Field Values

Constructor Detail

ADN1cible

public ADN1cible()

Default constructor : nothing happend.

See Also:

AloneProcessus.cible, calcul_score_structure(String, String), comparaison_Resultat(BufferedReader, BufferedReader), copier(), TestAln.main(String[]), ADN1test.resultat_Optimal(ADN1cible, ADN1test, ADN1test[], BufferedReader, int, int, int, boolean), Interface12.setInterface(Profil, String, Palindrome1cible, int)

ADN1cible

public ADN1cible(java.lang.String nomFichier,
                 java.lang.String sequence)

Constructor with name and aligned sequence...

Parameters:

nomFichier - (String) name of the file

sequence - (String) aligned sequence

See Also:

ADN1.est_Une_Base(char), est_Une_Base_Test(char)

Method Detail

quelle_longueur

public int quelle_longueur()

To get the length of the sequence.

Returns:

(int) length

See Also:

longueur

quelle_sequence

public Base[] quelle_sequence()

To get the sequence tab.

Returns:

(Base[])

See Also:

Base

une_base

public Base une_base(int position)

To get a Base at a specific position.

Parameters:

position - (int)

Returns:

(Base)

une_sous_sequence

public Base[] une_sous_sequence(int debut,
                                int fin)

To get a subsequence of sequence.

Parameters:

debut - (int) begin

fin - (int) end

Returns:

(Base[]

quel_tableau_palindrome

public ArbrePalindrome quel_tableau_palindrome()

To get the algorithm tree.

Returns:

(ArbrePalindrome)

See Also:

tableauPalindrome

les_structures

public java.util.Vector les_structures()

To get structures from algorithm tree.

Returns:

(Vector)

See Also:

ArbrePalindrome.quellesStructures(), afficher_Caracteristique(), calcul_Resultat(ADN1test[], int, boolean, boolean), calcul_score_structure(ADN1cible), comparaison_structure(ADN1cible, ADN1cible), comparaison(ADN1cible, ADN1cible), ADN1.to_File(PrintWriter)

la_structure

public Palindrome1cible[] la_structure(int pos)

To get a specific structure.

Parameters:

pos - (int)

Returns:

(Palindrome1cible[])

le_palindrome

public Palindrome1cible le_palindrome(int pos_struct,
                                      int pos_pal)

To get a specific palindrome in a specific structure.

Parameters:

pos_struct - (int) position of the structure.

pos_pal - (int) position of palindrome in structure.

Returns:

(Palindrome1cible)

See Also:

ArbrePalindrome.quelPalindrome(int, int)

les_sequences_tests

public ADN1test[] les_sequences_tests()

To get test sequences.

Returns:

(ADN1test[])

See Also:

tableauInitial

recherche_commune

public int recherche_commune()

Common search.

Returns:

(int)

See Also:

typeRecherche

change_palindromes

public void change_palindromes(Palindrome1cible[] tabPal)

To set the table of palindrome and change the tree of algorithms.

Parameters:

tabPal - (Palindrome1cible[])

See Also:

Interface12.setInterface(Profil, String, Palindrome1cible, int), ArbrePalindrome.ArbrePalindrome(NoeudPalindrome), NoeudPalindrome.NoeudPalindrome(Palindrome1cible[])

change_decalage

public void change_decalage(int nvdec)

change_taille_boucle_min

public void change_taille_boucle_min(int nvmin)

change_taille_pal_min

public void change_taille_pal_min(int nvmin)

change_type_critere

public void change_type_critere(int nvcritere)

change_type_arn

public void change_type_arn(int nvtype)

change_incertitude

public void change_incertitude(double nvincertitude)

change_nb_prediction_max

public void change_nb_prediction_max(int nbnv)

change_chercher_pk

public void change_chercher_pk(boolean nv)

initialiser

public void initialiser()

Initialization of algorithm. Set the tree to new ; the complexity of pseudoknots to 0 and the initial tab of sequences to null.

See Also:

tableauPalindrome, pseudonoeud, tableauInitial

copier

public ADN1cible copier()

To clone the current instance of ADN1cible.

Returns:

(ADN1cible)

See Also:

Interface12.setInterface(Profil, String, Palindrome1cible, int)

recherche_Palindrome

private void 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.

Parameters:

adn - (ADN1cible) target sequence

debut - (int) begin analysis

fin - (int) end of analysis

taille - (int) lengt of target

tableauSequence - (ADN1test[]) homologuous sequences

erreur - (int)

etape - (int) step

plusieurs_resultats - (boolean) much results

nb_prediction - (int) number of predictions

See Also:

diviser_regner(Palindrome1cible[], ADN1cible, ADN1test[], int, int, int, int, boolean, int), recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), traitement_Zone_Variable(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int)

diviser_regner

public void 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...

Parameters:

tabPal - (Palindrome1cible[])

adn - (ADN1cible) target sequence

tableauSequence - (ADN1test[]) homologuous

debut - (int) begin

fin - (int) end

erreur - (int)

etape - (int) step

plusieurs_resultats - (boolean)

nb_prediction - (int)

See Also:

recherche_Palindrome(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int), Palindrome1cible.trier_Palindrome_Fin(Palindrome1cible[]), calcul_Taille(Palindrome1cible)

recherche_Point_Ancrage

public Palindrome1cible[] 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). "

Parameters:

adn - (ADN1cible) target

debut - (int) begin

fin - (int) end

taille - (int) length

lmin - (int)

tableauSequence - (ADN1test[])

erreur - (int)

Returns:

(Palindrome1cible[])

score

private static int score(char x,
                         char y)

COMPATIBLE PALINDROME SEARCH
Getting a score from two (2) bases.
AU / UA gives 2
CG / GC gives 3
GU / UG gives 1
other combinations give 0.

Parameters:

x - (char)

y - (char)

Returns:

(int) 0 ; 1 ; 2 ; 3 .

See Also:

recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), Matrice_ALN.score(char, char)

traitement_Zone_Variable

private void 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"

Parameters:

adn - (ADN1cible)

debut - (int) begin

fin - (int) end

taille - (int) length

tableauSequence - (ADN1test)

erreur - (int)

etape - (int) step

plusieurs_resultats - (boolean)

nb_prediction - (int)

See Also:

recherche_Palindrome(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int)

verifier_Conservation_Commune

public boolean 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.
First is checking conservation in following common structure of test sequences.

Parameters:

palCourantReel - (Palindrome1cible)

palCourantFaux - (Palindrome1test)

decalage - (double)

lmin - (double)

erreur - (int)

tabSeq - (ADN1test) homologuous

Returns:

(boolean)

See Also:

recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int)

verifier_Conservation

public boolean 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.
Second is to check the conservaton in considerating helix independants.

Parameters:

palCourantReel - (Palindrome1cible)

palCourantFaux - (Palindrome1test)

decalage - (double)

lmin - (double)

erreur - (int)

tabSeq - (ADN1test[])

Returns:

(boolean)

See Also:

Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int)

verifier_Conservation_Alignement

public boolean 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.
Third...

Parameters:

palCourantReel - (Palindrome1cible)

palCourantFaux - (Palindrome1test)

lmin - (double)

tabSeq - (ADN1test[])

Returns:

(boolean)

See Also:

recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int), TestAln.main(String[]), Matrice_ALN

calcul_Taille

public int calcul_Taille(Palindrome1cible pal)

COMPATIBLE PALINDROME SEARCH
"This method to compute internal sequence length at step i. "

Parameters:

pal - (Palinrome1cible)

Returns:

(int)

See Also:

diviser_regner(Palindrome1cible[], ADN1cible, ADN1test[], int, int, int, int, boolean, int), recherche_Pseudonoeud(Base[], ADN1test[], boolean, int, int)

est_Une_Base_Test

public boolean est_Une_Base_Test(char base)

COMPATIBLE PALINDROME SEARCH
"This method test if a char is a base"

Parameters:

base - (char)

Returns:

(boolean)

See Also:

ADN1cible(String, String), Profil.remplir(Palindrome1cible[], int)

recherche_Pseudonoeud

private void 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"

Parameters:

sequencepseudonoeud - (Base[])

tabAdn - (ADN1test[])

plusieurs_resultats - (boolean)

pos_struct - (int)

nb_prediction - (int)

See Also:

calcul_Resultat(ADN1test[], int, boolean, boolean)

mettre_etoile

public void mettre_etoile(int pos_struct)

PSEUDOKNOTS SEARCH
"This method to put stars (*) in found palindromes in aim to find pseudoknots)"

Parameters:

pos_struct - (int)

See Also:

recherche_Pseudonoeud(Base[], ADN1test[], boolean, int, int), calcul_Resultat(ADN1test[], int, boolean, boolean), Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int)

calcul_Resultat

public void calcul_Resultat(ADN1test[] tabAdn,
                            int typeRecherche,
                            boolean plusieurs_resultats,
                            boolean chercher_pk)
                     throws java.lang.Exception

MAIN COMPUTING RESULTS
"This method to launch search and compute all wanted results"

Parameters:

tabAdn - (ADN1test[]) target sequence at 0 then tests sequences...

typeRecherche - (int) 3 (very good default option) ALIGNEMENTHELICE

plusieurs_resultats - (boolean) (true for maybe some structures)

chercher_pk - (boolean) true (default is better to search and find pseudoKnots)

Throws:

java.lang.Exception - e

See Also:

typeRecherche, typeCritere, chercher_pk, nb_prediction_max, incertitude, decalage, typeARN, taille_boucle_min, taille_pal_min, ProcessusOrigin.computing(Vector, ADN1cible, boolean, boolean), OriginAlgorithmsStefan.computing(Vector, ADN1cible, boolean, boolean), ADN1test.meilleur_combinaison_sequence(ADN1cible, ADN1cible, ADN1test, ADN1test[], int[], int, int, int, int, int, Resultat, boolean)

to_File

public java.lang.String to_File(java.lang.String fichier)

RESULT TREAMENT
"This method write results in a file"

Parameters:

fichier - (String)

Returns:

(String)

See Also:

ProcessusOrigin.computing(Vector, ADN1cible, boolean, boolean), OriginAlgorithmsStefan.computing(Vector, ADN1cible, boolean, boolean)

load_File

public void load_File(java.io.BufferedReader entree)
               throws java.lang.Exception

RESULT TREAMENT
"This method create an object from recorded data in a file"

Overrides:

load_File in class ADN1

Parameters:

entree - (BufferedReader)

Throws:

java.lang.Exception - e

See Also:

calcul_score_structure(String, String), comparaison_Resultat(BufferedReader, BufferedReader), ADN1test.resultat_Optimal(ADN1cible, ADN1test, ADN1test[], BufferedReader, int, int, int, boolean)

comparaison_Resultat

public java.lang.String comparaison_Resultat(java.io.BufferedReader entree1,
                                             java.io.BufferedReader entree2)
                                      throws java.lang.Exception

RESULT TREAMENT
"Methods to compare recorded results in files. Methods return text containing new palindromes and lost palindromes"

Parameters:

entree1 - (BufferedReader)

entree2 - (BufferedReader)

Returns:

(String)

Throws:

java.lang.Exception - e

See Also:

comparaison(ADN1cible, ADN1cible), comparaison_palindrome(Palindrome1cible[], Palindrome1cible[]), comparaison_Resultat(BufferedReader, BufferedReader)

comparaison

public static java.lang.String comparaison(ADN1cible adn1,
                                           ADN1cible adn2)

RESULT TREAMENT
"Methods to compare recorded results in files. Methods return text containing new palindromes and lost palindromes"

Parameters:

adn1 - (ADN1cible)

adn2 - (ADN1cible)

Returns:

(String)

See Also:

comparaison(ADN1cible, ADN1cible), comparaison_palindrome(Palindrome1cible[], Palindrome1cible[]), comparaison_Resultat(BufferedReader, BufferedReader)

comparaison_palindrome

public static Palindrome1cible[][] comparaison_palindrome(Palindrome1cible[] tabPal1,
                                                          Palindrome1cible[] tabPal2)

RESULT TREAMENT
"Methods to compare recorded results in files. Methods return text containing new palindromes and lost palindromes"

Parameters:

tabPal1 - (Palindrome1cible[])

tabPal2 - (Palindrome1cible[])

Returns:

(Palindrome1cible[][])

See Also:

comparaison(ADN1cible, ADN1cible), comparaison_palindrome(Palindrome1cible[], Palindrome1cible[]), comparaison_Resultat(BufferedReader, BufferedReader), palindromes_communs(Palindrome1cible[], Palindrome1cible[], boolean)

palindromes_communs

public static Palindrome1cible[][] palindromes_communs(Palindrome1cible[] tabPal1,
                                                       Palindrome1cible[] tabPal2,
                                                       boolean struc_com)

RESULT TREAMENT
"Previous method variation [comparaison_palindrome] to find common palindromes between two predictions. Two palindromes are common as they are included one in the other"

Parameters:

tabPal1 - (Palindrome1cible[])

tabPal2 - (Palindrome1cible[])

struc_com - (boolean)

Returns:

(Palindrome1cible[][])

See Also:

comparaison_palindrome(Palindrome1cible[], Palindrome1cible[]), resultat_commun(Vector)

calcul_score_structure

public static double[] calcul_score_structure(java.lang.String entree_reference,
                                              java.lang.String entree_structure)
                                       throws java.lang.Exception

RESULT TREAMENT
"Compute the score of a structure face a reference (two structures files in input)"

Parameters:

entree_reference - (String)

entree_structure - (String)

Returns:

(double[])

Throws:

java.lang.Exception - e

See Also:

Appariement.en_paire_de_bases(BufferedReader), Interface9.setInterface(ADN1cible, String, String, double), calcul_score_structure(ADN1cible), calcul_score_structure(String, String), calcul_score_structure(Vector, Vector)

calcul_score_structure

public double[] calcul_score_structure(ADN1cible adn_ref)

RESULT TREAMENT
"Compute the score of structure face to a reference (two DNA in input)"

Parameters:

adn_ref - (ADN1cible)

Returns:

(double[])

See Also:

calcul_score_structure(ADN1cible), calcul_score_structure(String, String), calcul_score_structure(Vector, Vector)

calcul_score_structure

public static double[] calcul_score_structure(java.util.Vector reference,
                                              java.util.Vector structure)

RESULT TREAMENT
"Compute the score of a strcuture face to a reference (two pairwise vector in input)"

Parameters:

reference - (Vector)

structure - (Vector)

Returns:

(double[])

See Also:

calcul_score_structure(ADN1cible), calcul_score_structure(String, String), calcul_score_structure(Vector, Vector)

comparaison_structure

public int comparaison_structure(ADN1cible adn1,
                                 ADN1cible adn2)

Deprecated. [never used]

RESULT TREAMENT
"This method to compare palindromes of two DNAs. One difference score in function of base pairs is compute. Score is 1 000 000 if the two DNAs have no palindromes (only if one strcuture by DNA or by default the first structure)"

Parameters:

adn1 - (ADN1cible)

adn2 - (ADN1cible)

Returns:

(int)

resultat_commun

public void resultat_commun(java.util.Vector vec)

RESULT TREAMENT
"This method compute a common result from vector of tab of palindromes"

Parameters:

vec - (Vector)

See Also:

ProcessusOrigin.computing(Vector, ADN1cible, boolean, boolean), OriginAlgorithmsStefan.computing(Vector, ADN1cible, boolean, boolean)

resultat_commun_paire_de_base

public void resultat_commun_paire_de_base(java.util.Vector vec)

Deprecated. [never used]

RESULT TREAMENT
"This method to compute common result between some predictions. Result is return in base pairs and not in helix"

Parameters:

vec - (Vector)

pourcentage_Mutation

public void pourcentage_Mutation(ADN1test[] adntest,
                                 int pos_struct,
                                 boolean bool)

Deprecated. [never used]

RESULT TREAMENT
"This method show the percentage of mutation of test sequences face to target sequence"

Parameters:

adntest - (ADN1test[])

pos_struct - (int)

bool - (boolean)

afficher_Sequences

public java.lang.String 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"

Parameters:

pal - (Palindrome1cible)

tabSeq - (ADN1text[])

Returns:

(String)

See Also:

Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int)

afficher_Caracteristique

public java.lang.String afficher_Caracteristique()

SOME SHOW FOR VIEW
"This method for show on a target sequence of DNA"

Overrides:

afficher_Caracteristique in class ADN1

Returns:

(String)

See Also:

Interface3.setInterface(ADN1cible, Vector)

afficher_Caracteristique_Web

public java.lang.String afficher_Caracteristique_Web()

Some changes to this procedure to make results appears for web / HTML.

Overrides:

afficher_Caracteristique_Web in class ADN1

Returns:

(String) HTML view.

Since:

August 2008

See Also:

Palindrome1cible.toString_web()

decoupeString

private static java.lang.String decoupeString(java.lang.String chaineDecoupe)

This method to cut a String by 80 characters length substring.

Parameters:

chaineDecoupe - (String)

Returns:

(String)

Since:

August 2008

decoupeString_Web

private static java.lang.String decoupeString_Web(java.lang.String chaineDecoupe)

This method to cut a String by 80 characters length substring.

Parameters:

chaineDecoupe - (String)

Returns:

(String)

Since:

August 2008

afficher

public static java.lang.String afficher(Palindrome1cible[] tabPal)

SOME SHOW FOR VIEW
"This method to show the palindromes' tab"

Parameters:

tabPal - (Palindrome1cible[])

Returns:

(String)

See Also:

comparaison(ADN1cible, ADN1cible), Interface7.setInterface(ADN1cible, ADN1test[], int, int, int)

toString

public java.lang.String toString(int debut,
                                 int fin)

SOME SHOW FOR VIEW
"To visualize considered sequence [current instance]"

Parameters:

debut - (int) begin

fin - (int) end

Returns:

(String)

See Also:

afficher_Caracteristique(), Interface12.setInterface(Profil, String, Palindrome1cible, int)

sequenceCible

public static ADN1 sequenceCible(java.lang.String sequenceCible,
                                 boolean cible)

SOME SHOW FOR VIEW
"To get target sequence"

Parameters:

sequenceCible -

cible -

Returns:

(ADN1)

See Also:

ProcessusOrigin.computing(Vector, ADN1cible, boolean, boolean), OriginAlgorithmsStefan.computing(Vector, ADN1cible, boolean, boolean)

pourcentage_base

public java.lang.String pourcentage_base()

Deprecated. [never used]

SOME SHOW FOR VIEW
"This method to compute percentage of each base"

Returns:

(String)