[Biojava-l] ComponentFeature.Template

[Dr S.M. Huen]

>From what I can discern from the specs and the sources, the component and
the sequence onto which it is mapped must be collinear (ie. same size
and sense).  Have I understood that correctly?
 
I would like to propose an extension to allow the sequences to either be
parallel or antiparallel.  This has utility where the components were
annotated prior to the sense of that component being determined on the
tiling path.  Would there be objections to such an extension?
 
If the latter is to be permitted, we will need a means to indicate the
sense of the mapping.  We could either do that thru' inverting the start
and end coordinates of the component or by introducing a new field
corresponding to StrandedFeature.Strand.  The former is easier and won't
break existing code but less consistent with the convention within Biojava
insofar as I can discern.  The latter is a greater change to the API.
 
Could I have an indication of whether such a change would be accepted and
if so which route would we want?
 
Regards,
David Huen, Dept. of Genetics, Univ. of Cambridge.

P.S. Thomas, sorry for the duplicates, I got the cc wrong!