[Biococoa-dev] New Structure for BioCocoa

Koen van der Drift kvddrift at earthlink.net
Sun Jul 3 07:45:12 EDT 2005

On Jul 3, 2005, at 6:12 AM, Philipp Seibel wrote:

>> I like the parser idea, particularly if it is already written by you 
>> ;-)
>> I won't be of any help with C++, though!
> this is no problem, because there is no much need of c++ except from 
> expression templates.
> The parser isn't allready written by me sorry ;-), but i'm working on 
> it.
> I'd like to know the different sequence formats i should implement, 
> that i can finish the parsers for the sequence io first.

Check out BCSequenceReader and BCReader (deprecated, but still in the 
project for reference) for some formats, just note that these methods 
still need a lot of work, annotations and features are still not 
completely implemented. Note that there a re already various parsers 
out there that could be of help, eg lucegene, bioperl and more.

What I don't understand yet is why the sequence parser framework is at 
the bottom of your picture. This implies to me that it is the basis for 
all the other frameworks? Why not put BCFoundation with BCSymbol and 
BCSequence there, that seems much more logical to me.

> Very good summary of the discussion. 
> I think we should try to implement the string thing in different ways 
> and test the performance, to see which one is the best.

Maybe you can already post some sample code here, so we can get an idea 
what you have in mind.


- Koen.

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