[Biococoa-dev] Using an untyped class sequence

[Koen van der Drift]

On Jul 6, 2005, at 3:53 AM, Alexander Griekspoor wrote:

> I agree that in some cases tools are the way to go, but one of the 
> things I dislike most of the biojava project (and I remember from 
> previous discussions that I was not alone) is in fact that you can't 
> do a thing without needing a bunch of helper, factory, and/or tool 
> objects. Please, let us stay far from that. It's really un-cocoa like, 
> imagine NSString and you would need a "exporter tool" to save it to 
> file, a "converter tool" to return it in a different encoding etc etc. 
> Help!!
>
>> BCSequenceTool -> MW, ...
>> BCProteinTool -> pI, digest, ...
>> BCDNATool -> translate, ...
>> BCRNATool -> transcribe, ...
> Please not, the names of these tools alone are terrible!!!! I agree 
> that for some relatively difficult things like a translation, digests 
> or alignments, we need a tool, but even then I would like to have 
> convenience methods that do the job of creating and handling the tool 
> object in the background. For the rest, a simple MW should be one call 
> and not need a tool! And IF we need a tool, make it specialized: 
> BCDigester or what else instead of BCSequenceTool.

These names were only put in as an example, not a proposal :)

Anyway, using tools classes makes the framework very modular and 
maintainable, in fact we are already using them. So I am not sure what 
your objection is against tools classes? Do you want to put all code in 
the subclasses?

cheers,

- Koen.