[Biojava-dev] Sequence and Feature

[Richard Holland]

Yes, Feature.getSequence() is intended only to return the sequence of  
the feature itself - so it would be fine not to store the whole  
genomic sequence, and instead just store locations referring to it.

Have you looked into the existing Alignment classes in BioJava? They  
might be of some help to you.

cheers,
Richard

On 2 Aug 2009, at 20:28, Micha Sammeth wrote:

> Hi,
>
> I am writing a parser for aligned sequencing reads and I plan to  
> separate the read information (sequence, qualities) from the  
> alignment information by reasons of redundancy and sortings.
>
> I planned the following classes:
>
> Read extends AbstractChangeable implements Sequence, Qualitative
>
> Alignment extends AbstractChangeable implements Feature
>
> Alignment I put directly as inner class of Read, to delegate the  
> Feature.getSequence() directly via the outer Object. I also have  
> sort of alignment groups which are inserted as additional Feature in  
> between these two, but I think for the sketched toy example they are  
> not important.
>
> One doubt is: Alignment links a subpart of the read with a subpart  
> of the genomic sequence, which is big and probably I will never hold  
> an instance of it. So, getSequence() here refers to the subpart of  
> the read that gets aligned and I have a couple of custom attributes  
> that annotate the location in the genome. Is this in the philosophy  
> of the class hierachy design?
>
> It would be nice if someone with a bit more experience in Biojava  
> could leave a comment if I go the right direction, or if there is a  
> more natural way to get my hierachy into biojava.
>
> Thanks and cheers!
>
> micha.
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/