[Biojava-l] Re: problem with accessing the fasta format files written using biojava

Thomas Down td2@sanger.ac.uk
Wed, 20 Jun 2001 14:51:27 +0100

On Wed, Jun 20, 2001 at 03:52:08PM +0200, Sarath wrote:
> hi
>   has anybody encountered a problem while accessing files written in fasta
> format using biojava .. following is a piece a code which i used
> in a program to redirect a sequence to a text file and then when i try to
> use the file it gives exceptions
> while (stream.hasNext()) {
> 	    Sequence seq = stream.nextSequence();
>         SequenceFormat seqFormat=new FastaFormat();
>         PrintStream str = new PrintStream(System.out);
>         seqFormat.writeSequence(seq, str);
>         str.println(seq);
>  }

That last line `str.println(seq)' is your problem.  You're
writing the sequence in Fasta format in the normal BioJava-ish
way.  You then try to write the Sequence object directly to
the output stream.  Since the Java I/O code doesn't know any
special behaviour for printing BioJava sequences, it calls
the toString() method, which gives you a string like:

> org.biojava.bio.seq.impl.SimpleSequence@2697a1

(which isn't hugely helpful -- we  should override toString
to return something a bit more useful.  But this isn't
strictly speaking a bug).

If you remove that `println' call, you'll get the output you