[Biococoa-dev] Compilation warnings with tools

[Koen van der Drift]

On Feb 8, 2005, at 10:55 AM, John Timmer wrote:

>>
>>>>> ...<snip>... An alternative is to use the BCAbstractSequence type 
>>>>> and have
>>>>> only one method....
>>>>
>>>> Or have one weak typed method as I suggested in a previous post, 
>>>> and test
>>>> for
>>>> the type in that method. Then either return an empty or useful 
>>>> array.
>>>
>>> So, you mean 'BCAbstractSequence', right?
>>> I am completely OK with that! (I just wanted to make sure that 
>>> whatever we
>>> choose will please everybody).
>>
>> Sorry, have to chime in here - I'm not!  I thought the idea here was 
>> that
>> the convenience methods, which would be present only in classes that
>> actually should use that method, would be strictly typed.  That way, 
>> anybody
>> as uptight as I am can be using strict classes and have access to 
>> methods
>> with strict signatures in them.

As long as the use of strong typing remains in the convenience method, 
that that sounds fine to me too. What I mean is, that the use of strong 
tying should remain hidden from the user - he should only have to deal 
with BCSequence.



>
> Just an aside here - I'm assuming that since we aren't getting rid of 
> the
> subclasses, then it's probably worth my putting in a 
> BCSequenceNucleotide to
> hold a bunch of the convenience methods that will be common to the DNA 
> and
> RNA classes?
>
> I should also explicitly state that, as I want the convenience 
> methods, I'll
> put them in.  One thing that would help here is if the tools headers 
> were
> well commented - last I looked, some of them were and some weren't.  
> This
> may have changed, but I need to run Tiger for a while to get a project
> moving, and I don't want to risk incompatibilities by accessing CVS 
> from
> that environment.

I guess that would be my bad. Which classes in particular are you 
referring to?

- Koen.