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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
