[Biojava-l] Parsing ClustalW output

[Johan Hattne]

On Wed, 25 Jul 2001, Simon Brocklehurst wrote:

> > Has anybody had any luck in parsing output from ClustalW using biojava's
> > ClustalWAlignmentSAXParser? I can get it to return the sequences' names,
> > but I'm hoping to get at the sequence's symbols. I've looped through the
> > attribute lists sent to my handler's startElement() method, but there only
> > seems to be one attribute: the name.
>
> *Hopefully*, this is an easy one to solve.  The sequence symbols
> themselves are returned as PCDATA - i.e. they aren't returned as
> attributes.  You can get at the PCData in the characters method (as
> opposed to the startElement method) in your ContentHandler.
>
> Let me know if it works.

Yes, it works. And is _was_ easy, too. I had completely overlooked
the characters method. Thanks a lot for your help!

// Johan


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