[Biococoa-dev] BCSequenceCluster

[Koen van der Drift]

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.