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.
>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
>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
>> 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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