[Biojava-dev] Sequence and Feature

[Micha Sammeth]

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.