[Biococoa-dev] BCSequenceCluster

Charles Parnot charles.parnot at gmail.com
Thu Oct 6 17:45:58 EDT 2005

At this point, given that I don't know that much about the fine  
details of sequence clusters and sequence groups, could you, Peter,  
take some time to explain exactly what the concept is, and also maybe  
come up with some examples of what it can be used for and how a user  
of the framework would want to use it. This way, we can define a  
header that does the job, and then worry about the implementation. In  
fact, I should have asked that question in the first place instead of  
pretending I understood what it was all about!

Sorry maybe this is a quite wide question. We don't have to go too  
deep at this point, as we merely want some I/O to work. However, in  
'I/O', there is 'O' for output, so the question is: after loading a  
sequence from disk, what information will the user want to retrieve?  
Or will she just want to perform some operations on the sequence  
group and then move on?



On Oct 6, 2005, at 5:26 AM, Peter Schols wrote:

> Hi Koen,
>> In the case where the input sequences are already aligned, we're  
>> ready to go, I guess. Also note we already have a BCAlignment  
>> class which we could use. However, I have not yet adapted that to  
>> use the NSData structure. I didn't write the alignment code, and I  
>> don't want to mess up someone elses work ;-)
>> I added the representative sequence after looking up some info  
>> about sequence clusters (see eg http://en.wikipedia.org/wiki/ 
>> Sequence_clustering). But if you suggest it is not needed in this  
>> case, I'll be happy to remove it!
> I don't think we need the sequence cluster functionality for the  
> BCSequenceGroup class. We could reserve the name BCSequenceCluster  
> for such a class we could eventually create in the future (if there  
> is any need for this). The BCSequenceCluster class could then  
> inherit from BCSequenceGroup.
> Peter
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Help science move fast forward:

Charles Parnot
charles.parnot at gmail.com

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