[Biococoa-dev] Using an untyped class sequence

John Timmer jtimmer at bellatlantic.net
Wed Jul 6 08:33:32 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...
> 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.

I largely agree with Alex here, but I wonder where to reasonably draw the
line.  Something like complementation, which can be implemented in about 3
lines of code, shouldn't need to overhead of object creation and
configuration of a tool -  do it in BCNucleotide.  Translation, which is a
lot more annoying and can produce many different results based on the
configuration (range, reading frame, etc.) clearly does.  How do we choose
when there's something in between?  Set an arbitrary limit on number of
lines of code or possible configurations?


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