[Biojava-dev] BioJava 3 code usage examples

[mark.schreiber at novartis.com]

biojava-dev-bounces at lists.open-bio.org wrote on 11/21/2008 09:02:37 AM:

> Hello. Thanks for spending the time looking into the code. It's a bit
> like a virtual code review session for me... you've made some very
> useful comments.
> 
> > 1) It doesn't seem that you want to avoid name conflicts with the old
> > version because you are continuing using the package name 
"org.biojava.*"
> > instead of "org.biojava3.*"
> 
> Yes, I agree, I think they should be changed to org.biojava3. I will
> do this when I get 5 minutes spare. They should be in org.biojava3
> because one of the stated goals was to be able to write a
> biojava-biojava3 mapper module if someone needed that to happen, and
> the use of org.biojava in the new code would preclude that.
> 

I think it would be a very good idea to differentiate this from old code 
via the packages. Strictly speaking you are supposed to use a domain that 
you own. I don't know if biojava3.org is available or if open-bio wants to 
obtain it. It's not critical but it would prevent possible issues.

Alternatives would be to use org.biojava.v3.*

or you could use the open-bio domain as in org.open-bio.biojava3

- Mark

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