[Biojava-l] Question on FlexibleAlignment

[Russ Kepler]

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...