Hi guys,
SeqIOTools.writeSwissprot(OutputStream, SequenceIterator) goes like
this:
SequenceFormat former = new EmblLikeFormat();
PrintStream ps = new PrintStream(os);
while (in.hasNext()) {
former.writeSequence(in.nextSequence(), ps);
}
and EmblLikeFormat.writeSequence(Sequence, PrintStream) does one of
these:
writeSequence(seq, getDefaultFormat(), os);
but getDefaultFormat() returns "EMBL".
I'm not sure what the actual differences between these formats is, but
I would imagine that writeSwissprot should be explicitly setting the
format to "SWISSPROT".
A related note, I was hoping that if I annotated a sequence with a
Taxon keyed off OrganismParser.PROPERTY_ORGANISM, the Swissprot format
would magically convert this to OC and OS output lines, but nay. If I
want this to happen, is extending SwissprotFileFormer the right way to
go about it? Does anybody actually link Sequences with Taxons?
Cheers,
Len.
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