[Biojava-l] memory leak while reading nr.fasta

[Gem Yang]

Hi,

I am new to Biojava.  
I have the following program, which is copied from ReadFaster2 in the
cookbook.

public static void main(String[] args) {
        try {
                // args[0] is nr.fasta
          BufferedReader br = new BufferedReader(new FileReader(args[0]));

          String format = "FASTA";
          String alphabet = "PROTEIN";

          SequenceIterator iter =
quenceIterator)SeqIOTools.fileToBiojava(format,alphabet, br);

          int count =0; 
          long start = System.currentTimeMillis();
          while(iter.hasNext())
          {
                        Sequence s = iter.nextSequence();
                        String name = s.getName();
                        
                        //System.out.println(name);
                        s.getAnnotation();
                        //System.out.println(s.seqString());
                        count ++;
                        System.out.println(count);
                        
          }
          long end = System.currentTimeMillis();
          System.out.println("number of sequence " + count);
          System.out.println("time used" + (end-start)/1000 + "seconds");
          System.out.println((end-start)/1000/60 + "minutes");
        }
        catch (FileNotFoundException ex) {
          //can't find file specified by args[0]
          ex.printStackTrace();
        }catch (BioException ex) {
          //error parsing requested format
          ex.printStackTrace();
        }
  }

When running this code, I got out of memory error in about half an hour and
1.5GB memory allocated.  My workstation is a Windows XP with 2 GB of memory.
My biojava version is 1.3. My JRE is one came with Websphere application
developer.

Thanks.
Gem
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