[Biococoa-dev] Using an untyped class sequence
Alexander Griekspoor
mek at mekentosj.com
Wed Jul 6 04:41:18 EDT 2005
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...
Alex
On 6-jul-2005, at 10:34, Koen van der Drift wrote:
>
> 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.
>
>
>
*********************************************************
** Alexander Griekspoor **
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The Netherlands Cancer Institute
Department of Tumorbiology (H4)
Plesmanlaan 121, 1066 CX, Amsterdam
Tel: + 31 20 - 512 2023
Fax: + 31 20 - 512 2029
AIM: mekentosj at mac.com
E-mail: a.griekspoor at nki.nl
Web: http://www.mekentosj.com
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