[Biococoa-dev] BCCachedSequenceFile

Koen van der Drift kvddrift at earthlink.net
Mon Sep 24 12:57:59 EDT 2007

The nice thing about BCSequence is that it can hold any (part of a) sequence, not necessarily a complete one. There are a bunch of methods available that will allow to create a subsequence, maybe you can use that?

I also noticed that your BCCachedSequenceFile class creates a reverse sequence. FYI, BCSequence can already do this.

- Koen.

-----Original Message-----
>From: Scott Christley <schristley at mac.com>
>Sent: Sep 24, 2007 12:20 PM
>To: Koen van der Drift <kvddrift at earthlink.net>
>Cc: biococoa-dev at bioinformatics.org
>Subject: Re: [Biococoa-dev] BCCachedSequenceFile
>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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