origincomment
Class Palindrome1cible

java.lang.Object
  origincomment.Palindrome1
      origincomment.Palindrome1cible

public class Palindrome1cible
extends Palindrome1

This define palindromes of the target sequence (sometimes from test ?). some parts of the algorithms here... Incompatibility much choices and one choice are similar but do not return the same thing...

Author:

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

See Also:

ADN1cible, traitement_Incompatibilite(Palindrome1cible[], boolean, double, int, int), incompatibilite_plusieurs_choix(Vector, int, int, int, double, boolean, int), incompatibilite_un_choix(Palindrome1cible[], int, int)

Field Summary

private int[]	carac_max "Public attribute" Maximum character ?
private int[]	carac_min "Public attribute" Minimum character ?
private int	conservation "Public attribute" "Number of tests sequences where palindrome is maintained"
private boolean	indeci "Internal attributes" "Undecided" (default is false).
static int	LONG_MUT "Internal attributes" Mutation length is 2.
private double	longMut "Public attribute" Mutation length (default is 0).
private int	longueur "Public attribute" "length of the palindrome in target sequence, which is maintained in test sequences"
private int	longueurReelle "Public attribute" "Length of palindrome in target sequence"
private int	nombre_palindromes "Public attribute" Number of represented palindromes.
private int	nombreErreur "Public attribute" Number of errors.
private int	nombreMutationDouble "Public attribute" Number of double mutations.
private int	nombreMutationSimple "Public attribute" Number of single mutations.
private double	pertinence "Public attribute" Relevance (default is 1.0).
private double	poidsequence "Public attribute" Sequence weight.
private double	pourcentage_conservation "Internal attributes" Conservation rate / percentage (default is 1).
static int	TAUX_MUT "Internal attributes" Mutation rate is 1.
private double	tauxMut "Public attribute" Mutation rate (default is 0).
private int	typeCritere "Public attribute" Criterion type (default is TAUX_MUT).

Fields inherited from class origincomment.Palindrome1

positionDebut, positionFin

Constructor Summary

Palindrome1cible()
Default constructor : nothing happend.

Palindrome1cible(int debut, int fin, int longueur)
Constrcutor with given begin, end and length.

Palindrome1cible(int debut, int fin, int longueur, int type_critere)
Constructor with given begin, end, length and criterion.

Palindrome1cible(int debut, int fin, int longueur, int nbMutDoub, int nbMutSimp)
Constructor with given begin, end, length and number of mutations.

Method Summary

void	changer_carac_max(int quelle_carac, int nv_carac)
void	changer_carac_min(int quelle_carac, int nv_carac)
void	changer_conservation(int conservation)
void	changer_indeci(boolean b)
void	changer_longMut(double nv)
void	changer_longueur_Reelle(int longueur)
void	changer_longueur(int longueur)
void	changer_nb_pal(int nv)
void	changer_nombre_erreur(int nberrreur)
void	changer_nombre_mutation_double(int nbMutDouble)
void	changer_nombre_mutation_simple(int nbMutSimple)
void	changer_pertinence(double nv)
void	changer_poid_sequence(double score)
void	changer_pourcentage_conservation(double nv)
void	changer_tauxMut(double nv)
void	changer_type_critere(int nvcritere)
boolean	chevauchant(Palindrome1cible p) "Following methods sorted by use order in ADN1 Class". (17) "to know if two palindrome are crossed together"
Palindrome1cible	copie() To get a clone of the current instance of Palindrome1cible.
private boolean	egaux(Palindrome1cible p) "Following methods sorted by use order in ADN1 Class". (14') "equals method"
java.util.Vector	en_appariements(java.util.Vector appariements) "Following methods sorted by use order in ADN1 Class". (10) "This method return a Vector of pairwise from a palindrome" Current instance is computed to add pairwises in Vector.
int[][]	en_paire_de_bases(Palindrome1cible[] tabPal) Deprecated. because calling procedure is deprecated...
private static boolean	est_Compatible(Palindrome1cible pal1, Palindrome1cible pal2) "Following methods sorted by use order in ADN1 Class". (5) "To know if two palindromes are compatibles" After reading the code, not sure that fully correct...
boolean	est_indeci()
static Palindrome1cible[]	fusion_Palindrome(Palindrome1cible[] tabPalCourant, Palindrome1cible[] tabPalPrincipal) "Following methods sorted by use order in ADN1 Class". (6) "Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"
boolean	inclu_dans(Palindrome1cible p) "Following methods sorted by use order in ADN1 Class". (16) "this method to know if current instance is included in argument with common pairwise "
static void	incompatibilite_plusieurs_choix(java.util.Vector listeTabPal, int pos_tab, int i, int j, double incertitude, boolean plusieurs_resultats, int nb_prediction_max) "Following methods sorted by use order in ADN1 Class". (2) Much choices to treat incompatibility.
static Palindrome1cible[]	incompatibilite_un_choix(Palindrome1cible[] tabPalCibleTrier, int i, int j) "Following methods sorted by use order in ADN1 Class". (3) One choice in incompatibility to structure.
void	load_File(java.io.BufferedReader entree) "Following methods sorted by use order in ADN1 Class". (13) "This method create an _object_ (palindrome tab) from data in a file
int	nombre_erreur()
int	nombre_mutation_double()
int	nombre_mutation_simple()
int	nombre_sequence_conserve()
double	quel_critere() By default (TAUX_MUT) : replace by calling quel_tauxMut() or equivalent.
double	quel_longMut()
int	quel_nb_pal()
double	quel_poid_sequence()
double	quel_pourcentage_conservation()
double	quel_tauxMut()
int	quel_type_critere()
int	quelle_carac_max(int i)
int	quelle_carac_min(int i)
int	quelle_longueur_reelle()
int	quelle_longueur()
double	quelle_pertinence()
int	rechercher_approx(java.util.Vector tabPal) "Following methods sorted by use order in ADN1 Class". (15) "to find an approximate palindrome in a vector of palindromes."
int	rechercher(java.util.Vector tabPal) "Following methods sorted by use order in ADN1 Class". (14) "to find a palindrome in a Vector of palindromes"
int	score(Palindrome1cible pal2) Deprecated. [not used]
void	to_File(java.io.PrintWriter sortie) "Following methods sorted by use order in ADN1 Class". (12) Add the "real length" to the file.
java.lang.String	toString_web() Some changes to this procedure to make results appears for web / HTML.
java.lang.String	toString() "This method to permit show of characteristiks of each palindromeof sequence
static java.util.Vector	traitement_Incompatibilite(Palindrome1cible[] tabPalCible, boolean plusieurs_resultats, double incertitude, int nb_prediction, int nb_prediction_max) "Following methods sorted by use order in ADN1 Class". (1) "This method is about incompatibility between palindromes of same sequence, sorting palindromes by relevance (single and double mutations) then removing every palindrome incompatible with previous more relevant.
private static Palindrome1cible[]	trier_Palindrome_Comp(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (4) "This method sort palindromes found at step i of target sequence from their relevance This method is used by the method that search compatible palindromes
Palindrome1cible[]	trier_Palindrome_Debut(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (8) "This method sort a table of palindromes by the begin position"
Palindrome1cible[]	trier_Palindrome_Fin(Palindrome1cible[] tabPal) "Following methods sorted by use order in ADN1 Class". (7) "This method sort a table of palindromes by the end position"
static Palindrome1cible[]	vec_to_tab(java.util.Vector vec) "Following methods sorted by use order in ADN1 Class". (18) "transform a vector of palindromes to a vector of palindroms"

Methods inherited from class origincomment.Palindrome1

change_position_debut, change_position_fin, quelle_position_debut, quelle_position_fin

Methods inherited from class java.lang.Object

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

Field Detail

longueur

private int longueur

"Public attribute"
"length of the palindrome in target sequence, which is maintained in test sequences"

longueurReelle

private int longueurReelle

"Public attribute"
"Length of palindrome in target sequence"

nombreMutationDouble

private int nombreMutationDouble

"Public attribute"
Number of double mutations.

nombreMutationSimple

private int nombreMutationSimple

"Public attribute"
Number of single mutations.

nombreErreur

private int nombreErreur

"Public attribute"
Number of errors.

conservation

private int conservation

"Public attribute"
"Number of tests sequences where palindrome is maintained"

poidsequence

private double poidsequence

"Public attribute"
Sequence weight.

tauxMut

private double tauxMut

"Public attribute"
Mutation rate (default is 0).

longMut

private double longMut

"Public attribute"
Mutation length (default is 0).

typeCritere

private int typeCritere

"Public attribute"
Criterion type (default is TAUX_MUT).

See Also:

TAUX_MUT

pertinence

private double pertinence

"Public attribute"
Relevance (default is 1.0).

nombre_palindromes

private int nombre_palindromes

"Public attribute"
Number of represented palindromes.

carac_max

private int[] carac_max

"Public attribute"
Maximum character ?

carac_min

private int[] carac_min

"Public attribute"
Minimum character ?

pourcentage_conservation

private double pourcentage_conservation

"Internal attributes"
Conservation rate / percentage (default is 1).

indeci

private boolean indeci

"Internal attributes"
"Undecided" (default is false).

TAUX_MUT

public static final int TAUX_MUT

"Internal attributes"
Mutation rate is 1.

See Also:

Constant Field Values

LONG_MUT

public static final int LONG_MUT

"Internal attributes"
Mutation length is 2.

See Also:

Constant Field Values

Constructor Detail

Palindrome1cible

public Palindrome1cible()

Default constructor : nothing happend.

See Also:

ADN1cible.load_File(BufferedReader), TestAln.main(String[]), Interface12.setInterface(Profil, String, Palindrome1cible, int)

Palindrome1cible

public Palindrome1cible(int debut,
                        int fin,
                        int longueur)

Constrcutor with given begin, end and length.
Number of mutations, errors and conservation are initialized to 0.
Characters are initialized to "{debut,fin,longueur}".
Number of palindromes initialized to 1.

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

See Also:

Interface11.actionPerformed(java.awt.event.ActionEvent), Interface11.initialiser(), Interface11.palindrome, Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int), Interface12.setInterface(Profil, String, Palindrome1cible, int), ProcessusOrigin.computing(Vector, ADN1cible, boolean, boolean), OriginAlgorithmsStefan.computing(Vector, ADN1cible, boolean, boolean), ADN1cible.comparaison_palindrome(Palindrome1cible[], Palindrome1cible[]), ADN1cible.comparaison(ADN1cible, ADN1cible), ADN1cible.palindromes_communs(Palindrome1cible[], Palindrome1cible[], boolean), ADN1cible.recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), ADN1cible.resultat_commun(Vector), ADN1test.distance(ADN1cible, ADN1test, ADN1test[]), ArbrePalindrome.tous_les_palindromes(), fusion_Palindrome(Palindrome1cible[], Palindrome1cible[]), incompatibilite_un_choix(Palindrome1cible[], int, int), trier_Palindrome_Debut(Palindrome1cible[])

Palindrome1cible

public Palindrome1cible(int debut,
                        int fin,
                        int longueur,
                        int type_critere)

Constructor with given begin, end, length and criterion.
Number of mutations, errors and conservation are initialized to 0.
Characters are initialized to "{debut,fin,longueur}".
Number of palindromes initialized to 1.

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

type_critere - (int) criterion

See Also:

ADN1cible.diviser_regner(Palindrome1cible[], ADN1cible, ADN1test[], int, int, int, int, boolean, int), ADN1cible.pourcentage_Mutation(ADN1test[], int, boolean), ADN1cible.recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), ADN1cible.recherche_Pseudonoeud(Base[], ADN1test[], boolean, int, int)

Palindrome1cible

public Palindrome1cible(int debut,
                        int fin,
                        int longueur,
                        int nbMutDoub,
                        int nbMutSimp)

Constructor with given begin, end, length and number of mutations.
Number of errors and conservation are initialized to 0.
Characters are initialized to "{debut,fin,longueur}".
Number of palindromes initialized to 1.

Parameters:

debut - (int) begin

fin - (int) end

longueur - (int) length

nbMutDoub - (int) number of double mutations

nbMutSimp - (int) number of single mutations

See Also:

copie(), trier_Palindrome_Comp(Palindrome1cible[])

Method Detail

quelle_longueur

public int quelle_longueur()

quelle_longueur_reelle

public int quelle_longueur_reelle()

quel_poid_sequence

public double quel_poid_sequence()

nombre_mutation_simple

public int nombre_mutation_simple()

nombre_mutation_double

public int nombre_mutation_double()

nombre_erreur

public int nombre_erreur()

nombre_sequence_conserve

public int nombre_sequence_conserve()

quel_tauxMut

public double quel_tauxMut()

quel_longMut

public double quel_longMut()

quel_critere

public double quel_critere()

By default (TAUX_MUT) : replace by calling quel_tauxMut() or equivalent.

quelle_pertinence

public double quelle_pertinence()

quel_type_critere

public int quel_type_critere()

est_indeci

public boolean est_indeci()

quel_pourcentage_conservation

public double quel_pourcentage_conservation()

quelle_carac_max

public int quelle_carac_max(int i)

quelle_carac_min

public int quelle_carac_min(int i)

quel_nb_pal

public int quel_nb_pal()

changer_nombre_mutation_simple

public void changer_nombre_mutation_simple(int nbMutSimple)

changer_nombre_mutation_double

public void changer_nombre_mutation_double(int nbMutDouble)

changer_poid_sequence

public void changer_poid_sequence(double score)

changer_nombre_erreur

public void changer_nombre_erreur(int nberrreur)

changer_longueur

public void changer_longueur(int longueur)

changer_longueur_Reelle

public void changer_longueur_Reelle(int longueur)

changer_conservation

public void changer_conservation(int conservation)

changer_tauxMut

public void changer_tauxMut(double nv)

changer_longMut

public void changer_longMut(double nv)

changer_pertinence

public void changer_pertinence(double nv)

changer_type_critere

public void changer_type_critere(int nvcritere)

changer_indeci

public void changer_indeci(boolean b)

changer_pourcentage_conservation

public void changer_pourcentage_conservation(double nv)

changer_carac_max

public void changer_carac_max(int quelle_carac,
                              int nv_carac)

changer_carac_min

public void changer_carac_min(int quelle_carac,
                              int nv_carac)

changer_nb_pal

public void changer_nb_pal(int nv)

copie

public Palindrome1cible copie()

To get a clone of the current instance of Palindrome1cible.

Returns:

(Palindrome1cible)

traitement_Incompatibilite

public static java.util.Vector traitement_Incompatibilite(Palindrome1cible[] tabPalCible,
                                                          boolean plusieurs_resultats,
                                                          double incertitude,
                                                          int nb_prediction,
                                                          int nb_prediction_max)

"Following methods sorted by use order in ADN1 Class". (1)
"This method is about incompatibility between palindromes of same sequence, sorting palindromes by relevance (single and double mutations) then removing every palindrome incompatible with previous more relevant.
This method return a table of palindromes compatibles together.
notice problem when AAAAAAAAAAAUUUUUUUUUUUU as incompatibvility remove palindromes 2 by 2. "
The number of choices is important for the number of structures to get...

Parameters:

tabPalCible - (Palindrome1cible[])

plusieurs_resultats - (boolean) much results

incertitude - (double) lack of precision

nb_prediction - (int) number of predictions

nb_prediction_max - (int) maximum number of predictions

Returns:

(Vector) vector of tables of palindromes (structure = table)

See Also:

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

incompatibilite_plusieurs_choix

public static void incompatibilite_plusieurs_choix(java.util.Vector listeTabPal,
                                                   int pos_tab,
                                                   int i,
                                                   int j,
                                                   double incertitude,
                                                   boolean plusieurs_resultats,
                                                   int nb_prediction_max)

"Following methods sorted by use order in ADN1 Class". (2)
Much choices to treat incompatibility.

Parameters:

listeTabPal - (Vector)

pos_tab - (int) position in table

i - (int)

j - (int)

incertitude - (double)

plusieurs_resultats - (boolean)

nb_prediction_max - (int) maximum number of predictions

See Also:

traitement_Incompatibilite(Palindrome1cible[], boolean, double, int, int)

incompatibilite_un_choix

public static Palindrome1cible[] incompatibilite_un_choix(Palindrome1cible[] tabPalCibleTrier,
                                                          int i,
                                                          int j)

"Following methods sorted by use order in ADN1 Class". (3)
One choice in incompatibility to structure.

Parameters:

tabPalCibleTrier - (Palindrome1cible[])

i - (int)

j - (int)

Returns:

(Vector) vector of tables of palindromes (structure = table)

See Also:

traitement_Incompatibilite(Palindrome1cible[], boolean, double, int, int), incompatibilite_plusieurs_choix(Vector, int, int, int, double, boolean, int)

trier_Palindrome_Comp

private static Palindrome1cible[] trier_Palindrome_Comp(Palindrome1cible[] tabPal)

"Following methods sorted by use order in ADN1 Class". (4)
"This method sort palindromes found at step i of target sequence from their relevance
This method is used by the method that search compatible palindromes. "

Parameters:

tabPal - (Palindrome1cible[])

Returns:

(Palindrome1cible[])

See Also:

traitement_Incompatibilite(Palindrome1cible[], boolean, double, int, int)

est_Compatible

private static boolean est_Compatible(Palindrome1cible pal1,
                                      Palindrome1cible pal2)

"Following methods sorted by use order in ADN1 Class". (5)
"To know if two palindromes are compatibles"
After reading the code, not sure that fully correct...

Parameters:

pal1 - (Palindrome1cible)

pal2 - (Palindrome1cible)

Returns:

(boolean) compatible or not

See Also:

incompatibilite_plusieurs_choix(Vector, int, int, int, double, boolean, int), incompatibilite_un_choix(Palindrome1cible[], int, int)

fusion_Palindrome

public static Palindrome1cible[] fusion_Palindrome(Palindrome1cible[] tabPalCourant,
                                                   Palindrome1cible[] tabPalPrincipal)

"Following methods sorted by use order in ADN1 Class". (6)
"Fusion method of two tables of palindromes to have the final table of result step by step ; used by palindromes' search"

Parameters:

tabPalCourant - (Palindrome1cible[])

tabPalPrincipal - (Palindrome1cible[])

Returns:

(Palindrome1cible[])

See Also:

ArbrePalindrome.recuperation(Vector, Palindrome1cible[], NoeudPalindrome), ADN1cible.recherche_Palindrome(ADN1cible, int, int, int, ADN1test[], int, int, boolean, int)

trier_Palindrome_Fin

public Palindrome1cible[] trier_Palindrome_Fin(Palindrome1cible[] tabPal)

"Following methods sorted by use order in ADN1 Class". (7)
"This method sort a table of palindromes by the end position"

Parameters:

tabPal - (Palindrome1cible[])

Returns:

(Palindrome1cible[])

See Also:

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

trier_Palindrome_Debut

public Palindrome1cible[] trier_Palindrome_Debut(Palindrome1cible[] tabPal)

"Following methods sorted by use order in ADN1 Class". (8)
"This method sort a table of palindromes by the begin position"

Parameters:

tabPal - (Palindrome1cible[])

Returns:

(Palindrome1cible[])

See Also:

ADN1cible.resultat_commun(Vector), ArbrePalindrome.trier_structures()

en_paire_de_bases

public int[][] en_paire_de_bases(Palindrome1cible[] tabPal)

Deprecated. because calling procedure is deprecated...

"Following methods sorted by use order in ADN1 Class". (9)
"This method to give equivalence in pbase pairs of a palindromes' table that must be sorted by begin position"

Parameters:

tabPal - (Palindrome1cible[])

Returns:

(int[][])

See Also:

ADN1cible.comparaison_structure(ADN1cible, ADN1cible)

en_appariements

public java.util.Vector en_appariements(java.util.Vector appariements)

"Following methods sorted by use order in ADN1 Class". (10)
"This method return a Vector of pairwise from a palindrome"
Current instance is computed to add pairwises in Vector.

Parameters:

appariements - (Vector) should be empty ? same is return with more inside...

Returns:

(Vector) Vector of Appariement

See Also:

Appariement.Appariement(int, int, double), ADN1cible.calcul_score_structure(ADN1cible), ADN1cible.calcul_score_structure(String, String), ADN1cible.resultat_commun_paire_de_base(Vector)

score

public int score(Palindrome1cible pal2)

Deprecated. [not used]

"Following methods sorted by use order in ADN1 Class". (11')
"This method to compute the score between two palindromes"
Between current instance and argument.

Parameters:

pal2 - (Palindrome1cible)

Returns:

(int)

to_File

public void to_File(java.io.PrintWriter sortie)

"Following methods sorted by use order in ADN1 Class". (12)
Add the "real length" to the file.

Overrides:

to_File in class Palindrome1

See Also:

ADN1cible.to_File(String)

load_File

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

"Following methods sorted by use order in ADN1 Class". (13)
"This method create an _object_ (palindrome tab) from data in a file. "

Overrides:

load_File in class Palindrome1

Parameters:

entree - (BufferedReader)

Throws:

java.lang.Exception - e

See Also:

ADN1cible.load_File(BufferedReader), Interface12.setInterface(Profil, String, Palindrome1cible, int)

rechercher

public int rechercher(java.util.Vector tabPal)

"Following methods sorted by use order in ADN1 Class". (14)
"to find a palindrome in a Vector of palindromes"

Parameters:

tabPal - (Vector)

Returns:

(int) position

See Also:

ADN1cible.resultat_commun(Vector)

rechercher_approx

public int rechercher_approx(java.util.Vector tabPal)

"Following methods sorted by use order in ADN1 Class". (15)
"to find an approximate palindrome in a vector of palindromes."

Parameters:

tabPal - (Vector)

Returns:

(int) position

See Also:

ADN1cible.resultat_commun(Vector)

egaux

private boolean egaux(Palindrome1cible p)

"Following methods sorted by use order in ADN1 Class". (14')
"equals method"

Parameters:

p - (Palindrome1cible)

Returns:

boolean

See Also:

rechercher(Vector)

inclu_dans

public boolean inclu_dans(Palindrome1cible p)

"Following methods sorted by use order in ADN1 Class". (16)
"this method to know if current instance is included in argument with common pairwise "

Parameters:

p - (Palindrome1cible)

Returns:

(boolean)

See Also:

ADN1cible.palindromes_communs(Palindrome1cible[], Palindrome1cible[], boolean), rechercher_approx(Vector), incompatibilite_plusieurs_choix(Vector, int, int, int, double, boolean, int), incompatibilite_un_choix(Palindrome1cible[], int, int)

chevauchant

public boolean chevauchant(Palindrome1cible p)

"Following methods sorted by use order in ADN1 Class". (17)
"to know if two palindrome are crossed together"

Parameters:

p - (Palindrome1cible)

Returns:

(boolean)

See Also:

ADN1cible.resultat_commun(Vector)

vec_to_tab

public static Palindrome1cible[] vec_to_tab(java.util.Vector vec)

"Following methods sorted by use order in ADN1 Class". (18)
"transform a vector of palindromes to a vector of palindroms"

Parameters:

vec - (Vector)

Returns:

(Palindrome1cible[])

See Also:

ADN1cible.resultat_commun(Vector)

toString

public java.lang.String toString()

"This method to permit show of characteristiks of each palindromeof sequence. "

Overrides:

toString in class Palindrome1

See Also:

ADN1cible.afficher_Caracteristique(), toString()

toString_web

public java.lang.String toString_web()

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

Overrides:

toString_web in class Palindrome1

Returns:

(String) HTML view.

Since:

August 2008

See Also:

ADN1cible.afficher_Caracteristique_Web()