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 -- View this message in context: http://www.nabble.com/Getting-a-Slice-of-an-Alignment-tf1849222.html#a5072893 Sent from the BioJava forum at Nabble.com. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
