arrayList in a while loop

[Lund01]

I got a little bit of code I am kinda stuck with.

I got this arrayList where we stored a fasta file.

 
Fasta file example: 
>seq1 
guguurguorgungun 
ionjlimlmo 
>seq2 
jjkliuihlni 
>seq3 
ppokkpdgstdcbch
mdhdgsvtxtgsgwd
jdbuydfyhedgy

Now I would like to make a while loop where he constantly takes the next >seq... (and the lines below) and do something with it.

But the problem is, how do I get it to take the next >seq...

I was thinking of letting it count++;
But overall, how can I find a certain ietm in the arrayList? (Like this ">")
I don't know if indexOf would help?

[Norm]

how can I find a certain ietm in the arrayList? (Like this ">")

If the ArrayList contains String objects, then you should be able to find the String: ">"
But if the '>' is embedded in a longer String or class, you will have to get each object in the list and look in the object's contents.

[Lund01]

We now made a function getProtein. And what getProtein does is he takes every >seq and the lines below.
Now the idea was something like this:

int count = 0;

// Do something to continue to the next with getProtein function (>seq2 etc.)

count++;

Do you maybe have any idea on this one?
Like how to get the next >seq...

[Norm]

Like how to get the next >seq...

To look at the contents of a String you could use the indexOf() method.