[Biojava-dev] biojava 3 progress

[Andy Yates]

It's getting ready very slowly. Currently we need:

* Locations correctly implemented
** There's no way of requesting subseqs from them atmo
* Feature on sequences support
* Extra attributes which do not fit into top-level attributes
* Mapping between sequences/assemblies
* circular location support
** so no checks on start being less than end
* Documentation

Think that's it off the top of my head

Andy

On 16 Mar 2010, at 15:57, Andreas Prlic wrote:

> Hi,
> 
> ISMB/BOSC is coming up rapidly and we should start to prepare for the annual
> BioJava release. As such it would be a good moment to discuss the current
> status of the various new BioJava 3 modules.
> 
> The biojava-structure, biojava-structure-gui modules are essentially ready
> for release and I started to update the Cookbook with the latest features
> http://biojava.org/wiki/BioJava:CookBook:PDB:align
> 
> Some of the re-factored modules based on biojava 1.7 could be released
> anytime soon as well. The documentation just needs to be updated to explain
> where the functionality can be found now (e.g. alignment module)
> 
> What about the new code that has been under development since the hackathon?
> Is it getting release ready slowly? Any plans for documentation? What is
> missing before we can make the first Biojava 3 release?
> 
> Andreas
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/