[Biococoa-dev] Compilation warnings with tools
Koen van der Drift
kvddrift at earthlink.net
Mon Feb 7 22:52:06 EST 2005
On Feb 7, 2005, at 8:05 PM, Charles PARNOT wrote:
>> I don't understand why there have to be two methods, instead of one
>> general like this:
>> -(NSArray *) translateSequence: (BCSequence *)sequence
>> usingGeneticCode: code
> This works fine if you only use BCSequence and never relies on the
> other sequence classes. But if you use a BCSequenceDNA on the above
> method, you get a compiler warning.
> Just to let the possibility for strong typing. e.g. if John wants to
> enforce the use of a BCSequenceDNA for that method, then we need a
> separate method with the BCSequenceDNA typing. An alternative is to
> use the BCAbstractSequence type and have only one method. But then it
> would also accept BCSequenceProtein, etc...
> An alternative is to define a 'BCSequenceDNA' protocol, that both
> BCSequence and BCSequenceDNA would follow. I am not a big fan of
> protocols, but that may be a nice use of them. Importantly, the user
> would not have to worry about the protocol.
> Bottom line: it might be best to have both methods. The 'generic' one
> would test for the sequence type, and return an empty array if
> non-relevant type, or call the method for BCSequenceDNA if the
> sequence is indeed of that type.
Or have one weak typed method as I suggested in a previous post, and
test for the type in that method. Then either return an empty or useful
>> I still believe that we should keep the BCSequence class et al as
>> clean as possible, and put all the manipulations in a separate class.
>> The way I see it to use the tools classes is as follows:
>> myTool = [BCSequenceToolFoo toolFooWithSequence: BCSequence];
>> [myTool setParameter1: param1];
>> [myTool setParameter:2 param2];
>> result = [myTool doSomethingWithSequence];
>> This way we keep the framework modular, and don't clog BCSequence
>> with code that works for some classes in one case, and other classes
>> in another case. It will also be more confusing for the user when
>> some methods are in BCSequence, other ones are in a separate
>> BCSequenceTool subclass. However, we can alsways have convenience
>> methods in the BCSequence classes to the BCSequenceTool classes that
>> takes care of some very general situations. If the user needs some
>> more special manipulations (s)he can always use the approach as I
>> sketched above. Also making some tools private and others not is
>> confusing, so we should stick with one approach, I think.
> I completely agree that there should only be one approach, so no tool
> should be private. I was foolish to imagine the other possibility...
> Now, what do you think of this other 'rule': to NOT have a convenience
> method both in the tool (+translateSequence:usingGeneticCode:) AND in
> the BCSequence (-translatedSequenceUsingGeneticCode:), but only in the
> BCSequence? I am not completely sure about all this and we may have to
> see how it works out in the long term...
That seems like a reasonable 'rule'. I don't see any problems when the
convenience method is only in BCSequence.
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