[Owl-devel] Refactoring of SiftsConnection and SiftsFeature

[Henning Stehr]

Dear developers,

I did some refactoring in

owl.core.connection.SiftsConnection
and
owl.core.features.SiftsFeature.

Basically, I needed the mapping from Uniprot to Pdb (previously, it
was only Pdb to Uniprot), so I implemented this and made some changes
to the existing code:

1. To make method names consistent, I renamed the method
'getMappings(String pdbCode, String pdbChainCode)' to 'getPdb2Uniprot'
to distinguish it from the new method 'getUniprot2Pdb(String
uniprotId)'.

2. I realized that SiftsFeature was implemented as a feature of a Pdb
chain. I would like to change this so that SiftsFeature is a feature
of a Uniprot entry. To me it makes more sense because Pdb chains are
usually subdomains of a Uniprot gene. Is that ok for everyone? If it
breaks existing code, I can also revert this for the moment.

3. I added to the constructor of SiftsFeature the missing fields
pdbBeg and pdbEnd.

If you use these classes in your projects, please update your code or
let me know if you disagree with any of these changes.

Cheers,
Henning