Design pattern question

Karl Schmid schmid at ice.mpg.de
Wed Aug 21 09:59:56 CEST 2002


Hi Markus,

I know of the biopython project and use their tools extensively ;-)

I am trying to learn design patterns and they may be useful in this project.

The goal is to separate the abstraction of a sequence assembler from its 
partiular implementation. The abstraction is expressed by the abstract 
class SequenceAssembly() and when it is instantiated, it is given a 
parameter (which, for example, is set in the configuration file for a 
particular project) that determines which implementation (the actual 
assembly algorithm) is used. The switch between implementations is then in 
the abstract class and not in the client program that calls the 
SequenceAssembly() instance. The client then does not need to know anything 
about the particular implementation (this is called loose coupling, I 
believe) which makes it very easy to add additional assembly algorithms.

In python, the return statement is not allowed in the __init__ function, 
which could be used to return instances of particular implementations 
(e.g., the Cap3Assembler), so a different solution has to be found, which 
is what I am looking for.

Karl 

Markus von Ehr wrote:

> Hi Karl,
> 
> I don't understand what you wanna do exactly, but do you know the
> BioPython project? Maybe there's already something inside matching
> your problem.
> 
> http://biopython.org
> 
> Markus
> 
> 
> Karl Schmid schrieb:
>> 
>> Hi,
>> 
>> I would like to separate an abstraction from its implementation. I think
>> this is called the Bridge pattern by Gamma et al. (or at least it is a
>> part of a bridge pattern).
>> 
>> In particular, I would like to assemble a set of DNA sequences and have
>> the option to chose among different assembly algorithms. I am not sure
>> what the best way to do this would be:
>> 
>> class SequenceAssembler:
>> 
>>     def __init__(self,assembler_type):
>> 
>>         if assembler_type == 'cap3':
>>             # What should I do here?
>>         elif assembler_type == 'phrap':
>>             # What should I do here?
>> 
>>     def save_sequences():
>>         pass
>> 
>> class Cap3Assembler(SequenceAssembler):
>> 
>>     def run_assembler():
>>         # Cap3 specific instructions
>>         pass
>> 
>> class PhrapAssembler(SequenceAssembler):
>> 
>>     def run_assembler():
>>         # Phrap specific instructions
>>         pass
>> 
>> Now I would like to instantiate the abstract class, but to obtain an
>> instance of either the Cap3Assembler or PhrapAssembler class depending on
>> the assembler_type variable.
>> 
>> >>> assembler = SequenceAssembler(assembler_type)
>> 
>> Is this possible?
>> 
>> Thank you in advance.
>> 
>> -- Karl Schmid




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