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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
