[Biojava-l] deprecating some SymbolList methods

[Matthew Pocock]

Fine. They stay in.

Matthew

Keith James wrote:
>>>>>>"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
>