[Biococoa-dev] I/O classes
peter.schols at bio.kuleuven.be
Sat Apr 30 10:35:17 EDT 2005
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.
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
> - 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 ;-)
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
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