[Biojava-l] ComponentFeature `feature' ;-)

[Thomas Down]

Hi...


Just been looking at the ComponentFeature code, and I've
noticed an interesting quirk.  Normally, reverse-strand
features have a getSymbols() method which returns the
reverse-complement of the symbols which are covered by
that feature (so far so good...).  However, out implementations
of ComponentFeature don't do this -- they all return forward-
strand symbols.

The reason this has been hidden for so long is that there's
a compensating bug in AssembledSymbolList, so the assemblies
still work out properly!

I'd like to fix this this afternoon (and yes, I'll check
in fixes for both the bug and the counter-bug at the same
time :-).  This shouldn't affect anyone unless you've
written a custom implementation of ComponentFeature, in which
case you might have to update getSymbols().

At the same time, I'll be adding an extra method, 
getComponentSequenceName(), which will be useful in DAS-type
environements.

Is this going to cause trouble for anyone?

   Thomas.