origincomment
Class ADN1

java.lang.Object
  origincomment.ADN1

Direct Known Subclasses:

ADN1cible, ADN1test

public class ADN1
extends java.lang.Object

The main class for sequences.

Author:

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

Field Summary

protected java.lang.String

nom name of the sequence.

Constructor Summary

protected	ADN1() Default constructor : nothing happend.
protected	ADN1(java.lang.String nomFichier, java.lang.String sequence) Constructor with name and aligned sequence...

Method Summary

protected java.lang.String	afficher_Caracteristique_Web() Some changes to this procedure to make results appears for web / HTML.
protected java.lang.String	afficher_Caracteristique() "Methode pour l'affichage des resultat sur une sequence d'ADN cible."
void	change_nom(java.lang.String nom)
boolean	est_Une_Base(char base) "Methode qui teste si un caractere est une base" "This method test if a character is a base
protected void	load_File(java.io.BufferedReader entree) To read the name of a sequence using a BufferedReader input (first line).
boolean	match(char x, char y) "Methode qui teste si deux bases peuvent s'apparier"
java.lang.String	quel_nom()
protected void	to_File(java.io.PrintWriter sortie) To print the name of the sequence in a PrintWriter output.

Methods inherited from class java.lang.Object

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

Field Detail

nom

protected java.lang.String nom

name of the sequence. Can be read by inheritant classes.

Constructor Detail

ADN1

protected ADN1()

Default constructor : nothing happend.

See Also:

ADN1cible.ADN1cible(), ADN1cible.sequenceCible(String, boolean)

ADN1

protected ADN1(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 [unused]

Method Detail

quel_nom

public java.lang.String quel_nom()

change_nom

public void change_nom(java.lang.String nom)

match

public boolean match(char x,
                     char y)

"Methode qui teste si deux bases peuvent s'apparier"

Parameters:

x - (char)

y - (char)

Returns:

(boolean)

See Also:

ADN1test.match(char, char), ADN1cible.recherche_Point_Ancrage(ADN1cible, int, int, int, double, ADN1test[], int), ADN1test.score(char, char), ADN1cible.verifier_Conservation_Commune(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[]), ADN1cible.verifier_Conservation(Palindrome1cible, Palindrome1test, double, double, int, ADN1test[])

est_Une_Base

public boolean est_Une_Base(char base)

"Methode qui teste si un caractere est une base"
"This method test if a character is a base. "

Parameters:

base - (char)

Returns:

(boolean)

See Also:

ADN1cible.ADN1cible(String, String), ADN1test.ADN1test(String, String), ADN1cible.calcul_Taille(Palindrome1cible), ADN1cible.est_Une_Base_Test(char), ADN1test.est_Une_Base(char), TODO use regexp

afficher_Caracteristique

protected java.lang.String afficher_Caracteristique()

"Methode pour l'affichage des resultat sur une sequence d'ADN cible."
This method return "la sequence "+(the name of the sequence)

Returns:

(String)

See Also:

ADN1cible.afficher_Caracteristique(), Interface3.setInterface(ADN1cible, java.util.Vector)

afficher_Caracteristique_Web

protected java.lang.String afficher_Caracteristique_Web()

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

Returns:

(String) HTML view.

Since:

August 2008

See Also:

Palindrome1cible.toString_web(), ADN1cible.afficher_Caracteristique_Web()

to_File

protected void to_File(java.io.PrintWriter sortie)

To print the name of the sequence in a PrintWriter output.

Parameters:

sortie - (PrintWriter)

See Also:

ADN1cible.to_File(String)

load_File

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

To read the name of a sequence using a BufferedReader input (first line).

Parameters:

entree - (BufferedReader)

Throws:

java.lang.Exception - e

See Also:

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