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

[Gem Yang]

I have just a couple of typos in my previous post.

Sorry about that.

Gem

-----Original Message-----
From: Gem Yang [mailto:cyang27 at bme.jhu.edu] 
Sent: Thursday, June 30, 2005 2:30 PM
To: 'biojava-l at biojava.org'
Subject: memory leak while reading nr.fasta

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