[Biococoa-dev] BCSequenceCluster

[Charles Parnot]

I think that returning the array of offset to the user is like giving  
the user the Bible not as a string, but as a list of positions of all  
the letters of the alphabet!!

The offset array should remain private, I think. We should return  
sequences with gaps (either generate them using the offsetArray, or  
use gaps symbols from the start).

what do you think?

charles




> Hi,
>
>
>> I suppose there would be some positional information, where the  
>> sequence are aligned in some specific ways, so an array of  
>> sequences + an array of offset should do. The best way to start is  
>> to agree on a good, simple but complete and consistent header and  
>> then the implementation almost does not matter and can always be  
>> modified in the future.
>>
>
> Here's a first attempt for an interface for a BCSequenceCluster  
> class :
>
> @interface BCSequenceCluster : NSObject
> {
>     BCSequence        *representativeSequence;      // the sequence  
> to which others are aligned, is 1st entry in sequenceArray
>
>     NSMutableArray     *sequenceArray;            // array of the  
> sequences
>     NSMutableArray    *offsetArray;            // array of NSRanges  
> that hold the offset information (position + length) of each  
> sequence relative to the representativeSequence. The sequenceArray  
> and offsetArray should be in sync, so the first entry in  
> offsetArray is [0,0]
>
>     NSString        *description;            // text to describe  
> the cluster
> }
>
> -(BCSequence *)representativeSequence;
>
> -(NSMutableArray *)sequenceArray;
> -(NSMutableArray *)offsetArray;
>
> -(void) addSequence: (BCSequence *) aSequence;
> -(void) removeSequence: (BCSequence *) aSequence;
>
> -(void) alignSequencesUsingSelector:(SEL)alignment;    // allows  
> for the use of all kind of alignments if needed
>
> @end
>
>
> Let me know what you guys think.
>
> cheers,
>
> - Koen.
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Charles Parnot
charles.parnot at gmail.com