[Biojava-l] A little (??!!!) stress test.

[Thomas Down]

On Sun, Jul 02, 2000 at 11:22:24PM +0200, Gerald Loeffler wrote:
> Hi thomas,
> 
> can you please be more more specific about the "trouble" the big
> ArrayList causes?! Does it throw an Out of Memory exception, which could
> be  solved with the -Xmx argument to "java"? Or does it throw any other
> exception? Or does it hang?...

No, nothing like that (well, actually the first time I tried
I /did/ get an OutOfMemoryError, but as you say that's easy to
fix).  The real problem comes with code like:

  int BIG_NUM = 20000000;
  List myList = Collections.nCopies(BIG_NUM, "blah");
  List myListCopy = new ArrayList(myList);

The final like throws a NegativeArraySizeException -- this
must be a bug in the ArrayList copy constructor (not that
it's entirely possible to build an ArrayList of that size
by other means, it's just the copy constructor that causes
problems).

Of course, /why/ BioJava was needing to copy the sequence at
all is another question entirely, but I have a fix for that now
(Constructing a SimpleSequence from a SymbolList now delegates
to the SymbolList rather than copying its contents).

Hope this makes things clearer,

Thomas.
-- 
He looked up with big brown eyes.  ``They're really only
tiny little A-bombs, honest.''
                                     -- David Brin.