[Biojava-l] RevCompSequence - call for input

[David Waring]

I am creating a new class: RevCompSequence to allow reverse complementing of
Sequence with all of its Features. It uses a ProjectedFeatureHolder to
project the features. I have included a createFeature(Feature.Template)
method which gets the projected location and projected strand of a
Feature.Template and then creates a new feature on the original Sequence.
Anyone see any problem with that? Should I make it optional to reflect it
back onto the original? My choice is no but I am open to suggestions.

Another question. How should a reverse complement of a NON-stranded feature
behave? Specifically should getSymbols() return the same SymbolList as it
would on the original Sequence? For StrandedFeatures it is obvious, of
course it should. But I kind of feel that a NON-stranded feature should
return the rc view. Think about looking a Sequence, rc'ing it and selecting
a region for some non stranded feature. I think getSymbols() should show the
same sequence that you selected. Any opinions?

David