[Biojava-l] ComponentFeature.Template

[Thomas Down]

On Mon, Jun 04, 2001 at 08:49:30PM +0100, Dr S.M. Huen wrote:
> >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?

The requirements are that both location and componentLocation
are contiguous and of equal length.  I guess `colinear'
probably isn't the right way to put this.  I'll take a look.

> 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?

That's already supported.  If you look at ComponentFeature, it's
a sub-interface of StrandedFeature.  The `strand' property
indicates whether or not the component is `flipped' in the
assembly.  You can see the support code for how this all works
in AssembledSymbolList and ProjectedFeatureHolder.

Does this do the sort of things you require?

   Thomas