[Biococoa-dev] reading large fasta files

Charles Parnot charles.parnot at gmail.com
Sun Oct 21 11:22:49 EDT 2007

In general, it would be best to have the implementation hidden, so  
that indeed, the framework decides when to use one subclass or  
another. Just like NSString, NSData, or NSArray use different  
underlying data structures depending on the size of the data (I  
think). This is of course all hidden behind the class cluster design...

I also don't know how things are already implemented, maybe things are  
already addressed this way?


On Oct 21, 2007, at 6:13 AM, Koen van der Drift wrote:

> Hi,
> I was trying to load a large fasta file (2 MB) in the Translation  
> demo, and right now it takes a long time. Scott recently added  
> BCCachedFastaFile for exactly this purpose, but the code in  
> BCSequenceReader doesn't use it yet. How could we implement this in  
> BCSequenceReader? One possibility is to always use BCCachedFastaFile  
> for any fasta file. Or should we set a datasize limit in  
> readFastaFile that determines when to use BCCachedFastaFile or the  
> regular code? In the latter case, what would be a reasonable value  
> for this?  For now I will implement to always use BCCachedFastaFile,  
> but this can be change later, I will not delete any code ;-)
> cheers,
> - Koen.
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Help science move fast forward:

Charles Parnot
charles.parnot at gmail.com

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