[Biojava-l] who uses seq.genomic?

[Matthew Pocock]

Hi,

I was wondering if anybody uses the interfaces in 
org.biojava.bio.seq.genomic to capture the actual types of features. At 
the moment, these interfaces are decoupled from the Feature.getType() 
property and there is no enforcement that children must be of the 
correct type.

We could add a feature types repository to biojava that would allow you 
to state that exons must have trancripts as parents, and that 
transcripts can have exons but not Genes as children, and so on. Then, 
the Feature.getType() could return a type ID that could be resolved to 
these rules. Feature types that don't look like IDs would continue to 
function as now.

So, does anyone use the seq.genomic classes, do people feel attached to 
them, and would you cry if they dissapeard?

-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

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