origincomment
Class Appariement

java.lang.Object
  origincomment.Appariement

public class Appariement
extends java.lang.Object

Class about pairwise and pair bases arrangement.

Author:

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

See Also:

Alignement, Palindrome1cible.en_appariements(Vector)

Field Summary

private int	pos3prime 3' position.
private int	pos5prime 5' position.
private double	taux_mut Mutation rate.

Constructor Summary

Appariement(int pos5, int pos3, double taux_mut)
Constructor.

Method Summary

void	change_app3prime(int pos3)
void	change_app5prime(int pos5)
void	change_taux_mut(double taux)
boolean	egaux_inverse(Appariement a) Equals method with reverse positions.
boolean	egaux(Appariement a) Equals method.
static java.util.Vector	en_paire_de_bases(java.io.BufferedReader entree) "Get the pairwises contain in a ct format file"
int	quel_pos3prime()
int	quel_pos5prime()
double	quel_taux_mut()
int	rechercher(java.util.Vector appariements)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

pos5prime

private int pos5prime

5' position.

pos3prime

private int pos3prime

3' position.

taux_mut

private double taux_mut

Mutation rate.

Constructor Detail

Appariement

public Appariement(int pos5,
                   int pos3,
                   double taux_mut)

Constructor.

Parameters:

pos5 - (int) 5' position

pos3 - (int) 3' position

taux_mut - (int) mutation rate

See Also:

Palindrome1cible.en_appariements(Vector)

Method Detail

quel_pos5prime

public int quel_pos5prime()

quel_pos3prime

public int quel_pos3prime()

quel_taux_mut

public double quel_taux_mut()

change_app5prime

public void change_app5prime(int pos5)

change_app3prime

public void change_app3prime(int pos3)

change_taux_mut

public void change_taux_mut(double taux)

egaux

public boolean egaux(Appariement a)

Equals method.

Parameters:

a - (Appariement) other instance to compare with...

Returns:

(boolean)

See Also:

ADN1cible.calcul_score_structure(Vector, Vector), rechercher(Vector)

egaux_inverse

public boolean egaux_inverse(Appariement a)

Equals method with reverse positions.

Parameters:

a - (Appariement) other instance to compare with...

Returns:

(boolean)

See Also:

en_paire_de_bases(BufferedReader)

rechercher

public int rechercher(java.util.Vector appariements)

en_paire_de_bases

public static java.util.Vector en_paire_de_bases(java.io.BufferedReader entree)
                                          throws java.lang.Exception

"Get the pairwises contain in a ct format file"

Parameters:

entree - (BufferedReader)

Returns:

(Vector)

Throws:

java.lang.Exception - e

See Also:

ADN1cible.calcul_score_structure(String, String)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object