[Biococoa-dev] BCCachedSequenceFile

Scott Christley schristley at mac.com
Mon Sep 24 12:20:36 EDT 2007

The meta-data is essentially just information about the sequences in  
the file, so it is standard BCAnnotation stuff like the sequence  
identifier, but it is also info that BCCachedSequenceFile needs to  
work, like where does each sequence start in the file, how long is  
the sequence, etc.  Then it can calculate a position directly into  
the file, and read the data from disk.  This meta-data is internal to  
the concrete implementation class, BCCachedFastaFile, as the type of  
information needed to be stored may be different from file format to  
file format.

So the design I was thinking of is BCCachedSequence would have a  
reference to its BCCachedSequenceFile, then when it needs data, it  
asks BCCachedSequenceFile for the data from disk.  The difficulty is  
that many of the BCSequence methods perform operations or return data  
on the complete sequence, which is difficult when you cannot read the  
whole sequence in memory because it is cached on disk ...


On Sep 22, 2007, at 5:13 PM, Koen van der Drift wrote:

> On Sep 22, 2007, at 11:36 AM, Scott Christley wrote:
>> For example, should each BCCachedSequence hold meta-data about  
>> that particular sequence (or all the sequences) in the file,  
>> should all of its interaction go strictly through  
>> BCCachedSequenceFile?
> I am not sure if I understand what you mean by meta-data. But we  
> have been talking on the list about adding a BCAnnotation and/or  
> BCFeature class to hold additional information about a particular  
> sequence. Actually, BCAnnotation is already a part of the  
> framework, albeit non functional.
> - Koen.

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