[Biococoa-dev] I/O classes

Peter Schols peter.schols at bio.kuleuven.be
Thu Apr 28 12:35:18 EDT 2005

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 


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