I've re-encountered something that has always puzzled me - I'm building a FlexibleAlignment with a bunch of SimpleAlignmentElements composed of SimpleGappedSequences. The SimpleAlignmentElement wants a RangeLocation, but insists that the max()-min()+1 be sequence.length(). But the sequence.length() includes any gap placed at the start of the sequence, so necessarily you include any offseting gap to make the alignment. This means that FlexibleAlignment.getLabelsAt(1) will always return the list of all the SimpleAlignmentElements. It seems that either the getLabelsAt() should exclude the elements that don't have sequence at the position (yet) or the SimpleAlignmentElement shouldn't be using the length of the sequence in testing the RangeLocation.
Any comments? I hope this makes sense to someone... _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
