origincomment
Class Palindrome1test

java.lang.Object
  origincomment.Palindrome1
      origincomment.Palindrome1test

public class Palindrome1test
extends Palindrome1

This define palindromes of test sequences ??

Author:

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

See Also:

ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[])

Field Summary

private boolean	conservation Is the palindrome conserved in this test sequence ?
private int	longueur1 Length of complementary reverse 5' repetition.
private int	longueur2 Length of complementary reverse 3' repetition.
private int	nberreur Number of errors.
private int	nbmutdouble Number of double mutations (compensatory).
private int	nbmutsimple Number of single mutations.
private int	score Weight of test palindrome (function of compensatory mutations).

Fields inherited from class origincomment.Palindrome1

positionDebut, positionFin

Constructor Summary

Palindrome1test(int debut, int fin, int longueur1, int longueur2)
Constructor with given begin, end and two lengths.

Method Summary

void	changer_conservation(boolean conservation)
void	changer_nberreur(int nberreur)
void	changer_nbmutdouble(int nbmutdouble)
void	changer_nbmutsimple(int nbmutsimple)
void	changer_score(int score)
static Palindrome1test[]	choisir_meilleur(int nb, Palindrome1test[] tabpal) "This method choose the best _nb_ test palindromes"
boolean	conservation()
int	quel_nb_mut_double()
int	quel_nb_mut_simple()
int	quel_score()
int	quelle_longueur1()
int	quelle_longueur2()
int	quelle_nb_erreur()

Methods inherited from class origincomment.Palindrome1

change_position_debut, change_position_fin, load_File, quelle_position_debut, quelle_position_fin, to_File, toString_web, toString

Methods inherited from class java.lang.Object

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

Field Detail

longueur1

private int longueur1

Length of complementary reverse 5' repetition.

longueur2

private int longueur2

Length of complementary reverse 3' repetition.

nberreur

private int nberreur

Number of errors.

nbmutdouble

private int nbmutdouble

Number of double mutations (compensatory).

nbmutsimple

private int nbmutsimple

Number of single mutations.

score

private int score

Weight of test palindrome (function of compensatory mutations).

conservation

private boolean conservation

Is the palindrome conserved in this test sequence ?

Constructor Detail

Palindrome1test

public Palindrome1test(int debut,
                       int fin,
                       int longueur1,
                       int longueur2)

Constructor with given begin, end and two lengths.
score is set to -100, conservation to false and numbers to 0.

Parameters:

debut - (int) begin

fin - (int) end

longueur1 - (int) length 1

longueur2 - (int) length 2

See Also:

choisir_meilleur(int, Palindrome1test[]), TestAln.main(String[]), ADN1cible.recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]), Interface5.setInterface(ADN1cible, ADN1test[], int, int, int, int, int)

Method Detail

quelle_longueur1

public int quelle_longueur1()

quelle_longueur2

public int quelle_longueur2()

quel_nb_mut_simple

public int quel_nb_mut_simple()

quel_nb_mut_double

public int quel_nb_mut_double()

quelle_nb_erreur

public int quelle_nb_erreur()

quel_score

public int quel_score()

conservation

public boolean conservation()

changer_nbmutsimple

public void changer_nbmutsimple(int nbmutsimple)

changer_nbmutdouble

public void changer_nbmutdouble(int nbmutdouble)

changer_nberreur

public void changer_nberreur(int nberreur)

changer_score

public void changer_score(int score)

changer_conservation

public void changer_conservation(boolean conservation)

choisir_meilleur

public static Palindrome1test[] choisir_meilleur(int nb,
                                                 Palindrome1test[] tabpal)

"This method choose the best _nb_ test palindromes"

Parameters:

nb - (int) number of palindrome to choose

tabpal - (Palindromes1test[])

Returns:

(Palindrome1tets[])

See Also:

ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[])