[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...

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 **
               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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