[Biococoa-dev] I/O classes

Peter Schols peter.schols at bio.kuleuven.be
Sat Apr 30 10:35:17 EDT 2005

Hi Koen,

Good point about the datastructure discussion. Most of the I/O formats 
we support now, don't have annotation possibilities, but we should 
definitely think about a way to handle sequence sets, as most of these 
file formats are just that. I'll see what I can come up with and I'll 
post any ideas on the list.

Best wishes,


On 29 Apr 2005, at 02:10, Koen van der Drift wrote:

> Hi Peter,
> Good to see you back!
> Right now BCSequenceReader is far from finished, I only added a few 
> methods (for the simple file formats ;-). The other methods in that 
> class are still from the old BCReader class. I think we still need to 
> carefully decide on how we are going to implement the datastructure, 
> regarding annotations, features, and sequence sets. Feel free to start 
> implementing the new methods, but I think we should also revive that 
> discussion here. It would be a waste of efforts if you did a lot of 
> work, but then later found that you are using a different datastorage 
> approach.
> cheers,
> - Koen.
> On Apr 28, 2005, at 12:35 PM, Peter Schols wrote:
>> Dear listers,
>> In the coming weeks, I'll finally have some time to resume my 
>> BioCocoa work. Much has changed since I checked out the project last 
>> time and I must say that I'm very impressed with the quality and the 
>> amount of work being done. Congratulations on a job well done!
>> I've started BioCocoa as a very small framework just to parse and 
>> write sequence file formats, so the main focus of my BC work will be 
>> on the I/O classes. I have noticed that Koen has already updated 
>> BCReader to the new architecture and it's now aptly called 
>> BCSequenceReader. If I'm right, BCCreator has not been modified yet 
>> so it seems that I'll be doing this. As some of you may know, I 
>> recently implemented Cocoa code for a lot more bioinformatics file 
>> formats (such as BEAST XML, Hennig86, Nona, Plain/Raw and TNT). If 
>> it's OK with you guys, I could add this implementation to the I/O 
>> classes. Any ideas/comments are welcome. Most of these formats are 
>> from the Phylogeny world, the area I'm working in.
>> Additionally, for one of my own projects, I'm working on classes to 
>> perform BLAST queries and return the results. They are far from 
>> finished but if they seem useful, I'm willing to 'donate' them to the 
>> BC project.
>> Anyway, as soon as I have done some real work, I'll post the .h and 
>> .m files on the list so everyone can review them as I don't want to 
>> mess with the CVS repository and commit something that breaks 
>> existing code ;-)
>> Peter
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