[Biococoa-dev] I/O classes

Koen van der Drift kvddrift at earthlink.net
Thu Apr 28 20:10:08 EDT 2005

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 


- 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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