[Biojava-l] Alignment files?

[Lehman, Jeff (SEA)]

Hello Everyone,
	I've got some msf alignment files (generated by clustalw) I'm trying
to parse, but org.biojava.bio.seq.io.MSFAlignmentFormat chokes on them and
org.biojava.bio.program.sax.SequenceAlignmentSAXParser doesn't parse MSF
files, it only parses Clustal and Needle.  I was thinking about contributing
some fixes to these parsers but I'm not really clear on which one is the
"current" version.  I've already tried out some fixes to the SAX parser
which seem to work pretty well, but I could fix MSFAlignmentFormat if that
would be more helpful.
			-Jeff Lehman
		Asst. Computational Scientist
			Celltech R&D


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