[Biojava-l] deprecating some SymbolList methods

[Keith James]

>>>>> "David" == David Waring <dwaring@u.washington.edu> writes:

    David> I would be strongly against it.

[...]

I agree with David. Please don't do it. I haven't seen anyone offer a
reason for deprecating the methods yet. A quick straw poll here found
that everyone I asked expected these methods (or their equivalents) to
be where they are.

    David> I'm not sure why you would want to deprecate methods that
    David> are as obvious to have on a SymbolList.  I agree that the
    David> Tokenization code is a great way to handle the intricacies
    David> of multiple alphabets. Yes it is possible to use this
    David> whenever you want to get a String, after all that is what
    David> AbstractSymbolList does! I would say that seqString() is as
    David> obviously necessary to an object representing a DNA or
    David> protein sequence, as toString() is to an Object.

Exactly. It will always end up being implemented somewhere - where
better than in AbstractSymbolList?. SymbolLists and Sequences are
being stringified all over the place here e.g. for peptides and oligos
-> JTextFields etc it's the quickest way.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -