[Biococoa-dev] Sequence factory

[Koen van der Drift]

On Dec 23, 2004, at 7:49 PM, Alexander Griekspoor wrote:

> Now, coming back to your remark about the code. My proposal was (and 
> still is) to add these kind of (standard apple-like) methods to the 
> BCSequence class as convenience methods. You would simply call:
> 	mySeq=[BCSequence sequenceWithString:@"AGTAGATTTGAGGT"];
> and behind the scene this (in this case class) method would invoke:
> 	factory=[BCSequenceFactory sharedSequenceFactory];
> 	mySeq=[factory sequenceWithString:@"AGTAGATTTGAGGT"];
>

I thought a little bit more about how to implement this. Which class 
should actually contain this code? Right now the code

  + (BCSequenceDNA *) dnaSequenceWithString: (NSString *)entry 
skippingNonBases: (BOOL)skip {
      BCSequenceDNA *theReturn = [[BCSequenceDNA alloc] initWithString: 
entry skippingNonBases: skip];
      return [theReturn autorelease];
  }


is already in place in BCSequenceDNA (and similar ones in other 
subclasses of BCSequence). Alex, are you proposing to replace this with 
somthing like:

  + (BCSequenceDNA *) dnaSequenceWithString: (NSString *)entry 
skippingNonBases: (BOOL)skip
  {
	BCSequenceFactory	*factory = [BCSequenceFactory sharedSequenceFactory];
	
	BCSequenceDNA *theReturn = [factory 
sequenceWithString:@"AGTAGATTTGAGGT"];
      	
	return [theReturn autorelease];
  }


Sound fine with me, just checking if that is what you had in mind :)  
Although I am not sure how to deal with the skippingNonBases part. 
Probably that should be replaced by passing the right symbol set 
instead?

- Koen.