[Biococoa-dev] Using an untyped class sequence
Koen van der Drift
kvddrift at earthlink.net
Wed Jul 6 05:51:44 EDT 2005
On Jul 6, 2005, at 4:41 AM, Alexander Griekspoor wrote:
> I don't have any objection against tool classes, but I have a lot of
> problems with the way things got out of hand in BioJava, there you
> can't do ANYTHING without tools. So names aside, I don't get what pI
> and digest do in 1 protein tool object. I plea to do very simplethings
> like MW and pI inside BCSequence where ever possible, and use
> specialized tools like a BCTranslatorTool and BCDigesterTool instead
> of one Proteintool and one DNAtool that bundle a lot of non-related
> stuff...
I see now what you mean. Yes, I also think the BioJava class structure
is way too complicated, and we should avoid that absolutely. Their way
of using one general tool class at first seems logical, but you are
right, it just add some extra steps.
However, I still like the idea of separating structure and
functionality classes, we can always use convenience methods to call
the tools. Even for 'simple' operations such as MW and pI calculations.
cheers,
- Koen.
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