[Biojava-l] Getting a Slice of an Alignment

[Richard Holland]

Dear list... if I haven't heard any arguments to the contrary by 9am
Monday 3rd July (UK time), I'll make the changes described below.

cheers,
Richard

On Tue, 2006-06-27 at 12:57 -0700, Dexter Riley wrote:
> 
> Richard Holland-2 wrote:
> > 
> > Ah...
> > 
> > I just read the source code for the symbolListForLabel() method on sub
> > alignments, and found what may well be a bug.
> > 
> > BioJava list people, your help please! In my understanding,
> > symbolListForLabel() should return the symbols from the given label that
> > fall within the alignment. This is the case in all except sub
> > alignments. Sub alignments, for whatever reason, are returning the
> > symbols from the given label that fall within the parent alignment upon
> > which the sub alignment is based, NOT just those that fall within the
> > sub alignment itself.
> > 
> > Is this a bug? I think it is.
> > 
> > The solution would be for me to alter
> > AbstractULAlignment.SubULAlignment.symbolListForLabel() to restrict the
> > returned symbols to only include those in the area covered by the sub
> > alignment. It would return EMPTY_SEQUENCE if the label didn't cover the
> > area of the sub alignment, and it would return a truncated symbol list
> > if it only partially covered it.
> > 
> > Would this be acceptable?
> > 
> > If so, once this change was made, it would fix Ed's problems below as
> > subAlignment() would start returning vertical slices as I think it
> > should probably have done so from the start, rather than the horizontal
> > slices it is returning at present.
> > 
> > cheers,
> > Richard
> > 
> 
> I think that would provide just the functionality I was looking for!  Thanks
> very much for all your help.
> All the best,
> Ed
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416