[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.


- Koen.

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