Fwd: [Biococoa-dev] more ramblings

[Alexander Griekspoor]

Op 21-nov-04 om 13:19 heeft Koen van der Drift het volgende geschreven:

>
> On Nov 19, 2004, at 5:41 AM, Alexander Griekspoor wrote:
>
>> It's an idea about how to further organize and extend the sequence 
>> classes to a higher level. Especially with regards to annotations. 
>> The sequence class which we all know and love (haha) would be the 
>> core which contains the actual symbol sequence. Above that would be a 
>> wrapper that contains this sequence, but also the accompanying 
>> annotations, metadata and notes. Certainly when processing data you 
>> don't always need the annotations and this way you can keep things 
>> lightweight if needed. Above that you can envision the need for 
>> sequence groups or clusters, related sequences for instance 
>> (translations/conversions), alignments, genomes etc.
>> So, these is not a class hierarchy rather a wrapper hierarchy (if 
>> that exist). How we practically implement and name this is another 
>> issue (and probably long debate ;-), but  I think it's a nice working 
>> model...
>> Hope I did makes clearer, and not even more fussy.
>>
>
> 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...

Alex

*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut
              http://www.mekentosj.com/enzymex

*********************************************************


*********************************************************
                       ** Alexander Griekspoor **
*********************************************************
                 The Netherlands Cancer Institute
                 Department of Tumorbiology (H4)
           Plesmanlaan 121, 1066 CX, Amsterdam
                     Tel:  + 31 20 - 512 2023
                     Fax:  + 31 20 - 512 2029
                    AIM: mekentosj at mac.com
                     E-mail: a.griekspoor at nki.nl
                 Web: http://www.mekentosj.com

           LabAssistant - Get your life organized!
           http://www.mekentosj.com/labassistant

*********************************************************