Incorrect return of ArrayList

[Gunner 1]

Hello!
I'm manipulating ArrayList <monObjet>. I want to create an ArrayList "molecule" containing amino acids. Each amino acid is an ArrayList of atoms. My problem, c "is that when I do a display at the end of treatment, the ArrayList" molecule ", contains only copies of a AcideAmine the last set. I think my program is returning a incorrect arraylist
Here's the code:

while (Onln! = null) {
  if (condition){
    / / New amino acid
    AcideAmine cur = new AcideAmine(row.substring(17,20).toCharArray());
    while (autreCondition){ 
      / / Creating an object Atom	 
      atnm = ln.substring(13,16).toCharArray();
      Atom atomTrouve = new Atom(atnm);
      / / Add the atom in the current AA
      cur.addAtom(atomTrouve);
      ln = br.readLine();
    } 
    System.out.print("CurrentAA =");
    cur.print();
    arls.add(cur);
    cur = null ;  / / In case
  }
}
}

[HardWeaR]

Hello,
In your code you have provided, you can create. AcideAmine one with an ArrayList of atoms, right? So if you want you see something wrong because maybe he would have given the rest, Pointers in java . In java pointers exist but you can not handle them. Basically, we talk but no pointer reference object. I hope you are getting my point what I am trying to explain you.

[Gunner 1]

Hello,
In fact, what I do is I read a file organized as follows, On each line, there is an atom, and a number corresponding to the amino acid to which it belongs.
Every time I go in the first while,

 AcideAmine cur = new AcideAmine("name")

or AcideAmine is an ArrayList with methods defined

As is the same amino acid, add to currentAA atoms that I read,
with the method of ArrayList: add (); Now, when I found a different amino acid, add amino acid to an ArrayList aaArrayList by the method add () and I return to the first while. So logically, in my aaArrayList, I have an ArrayList with all the amino acids that I read, right?

[InterNetWorKed]

Hello,
Just have a look at the following code

AcideAmine cur = new AcideAmine(row.substring(17,20).toCharArray());
    while (autreCondition){ 
      / / Creating an object Atom	 
      atomname = ln.substring(13,16).toCharArray();
      Atom attrv = new Atom(atomname);
      / / Add the atom in the current AA
      cur.addAtom(attrv);
      ln = br.readLine();
    }

you do not forget to make a line br.readLine = (); before entering the loop?

[Linux-Us]

Hello
You create many new AA at every turn, there is no doubt. To be sure he is not the same object, you can make a display of hashCode () in the print method of AcidAmine (if hashCode is not redefined in class AcidAmine). Otherwise, I hope that the attributes of class AcidAmine are not static (indeed it is not possible what I just said).

[GlassFish]

Hello,

Public static char[] nm;
Public static ArrayList <Atom> atls;
Public static ArrayList <int[]> bnls;

Putting static variables that are the same for all instances of the class (hence the name variable class).
Replaces by

private static char[] nm;
private static ArrayList <Atom> atls;
private static ArrayList <int[]> bnls;

The private I do not know if it will pass to compile because I have not all your code. Take some reading on the OOP.