[Biococoa-dev] more ramblings

Koen van der Drift kvddrift at earthlink.net
Fri Nov 26 08:16:03 EST 2004

On Nov 25, 2004, at 5:17 PM, Alexander Griekspoor wrote:

>> Thanks - that indeed sounds like a good plan. I was working a bit on 
>> readClustalFile and it would indeed make a lot of sense to keep the 
>> files together, including the line that indicates the alignment. Also 
>> so far readFile ignores all information but the sequence. Right now, 
>> readFile returns an NSArray with sequences from the same file, but 
>> that should be not too difficult change, maybe to an NSDictionary? Or 
>> are you guys talking about a complete wrapper class?
> Yes, because it would not only be a simple container of multiple 
> sequences, but would also contain "Metadata" about them, like 
> annotations, notes, relation parameters etc... A dictionary would be a 
> property of the wrapper class. But for the moment, if you return an 
> array of sequences it should be easily converted to use the wrappers 
> once they are there...

Right now, I am working on the clustal reading method. I could store 
the BCSequences in an NSArray, but then Ioose the info about which 
sequence is which. So one thing I could do is make an NSDictionary with 
a key for the ID, and a BCSequence for the value. However, the 'ID' is 
different for each file format. Sometimes it is easier to use the file 
name (eg in SwissProt). Peter's original solution, by storing an 
NSArray in the NSDictionary that only contains the ID's for lookup is 
also a possibility. I would like to move this forward, so we need to 
come up with a definitive structure for the wrapper. John, Alex, you 
proposed this, do you have a more concrete idea of what it should look 


- Koen.

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