[Biojava-dev] bjv2

[Michael Heuer]

Hello Matthew,

I tried a subversion update this morning and got

$ cd bjv2
$ svn update .
...
A  trunk/doc/text.css
A  trunk/doc/javadoc.css
svn: REPORT request failed on '/svn/repos/!svn/vcc/default'
svn: REPORT of '/svn/repos/!svn/vcc/default': Could not read response
body: connection was closed by server. (http://www.derkholm.net)

   michael


On Wed, 21 Jul 2004, Matthew Pocock wrote:

> Hi,
>
> I've had a fairly serious hack arround with bjv2 over the last 2 weeks.
> I will put in a tag before BOSC. The code triggers a bug in javac or
> javadoc with beta2 build from the sun website, but this is fixed in the
> beta3 pre-release.
>
> I've concentrated on core genomics so far, but we can start adding APIs
> for other things as soon as the core is out of alpha. So, wish-lists or
> use-cases or stories would be great.
>
> Matthew
>
>
> New since the last release:
>
> Documentation of often-used features
>   general IO
>   sequence IO
>   symbols and strings
>   controling data integration & memory
>
> Complete re-working of the APIs for biological symbols
>   type-safe
>   supports windowed views
>   supports convertions to/from strings using trivial syntax
>   supports systematic mappings of symbols e.g. dna->rna translations
>
> Data projection and integration
>   we can now map from underlying data to a 'view' bean based upon
>     javabean properties
>     annotations and map values
>     rdf properties
>   performance and scaleability fixes
>   support for agregate functions
>     min, max, average, all identical values
>
> RDF
>   there is a closer integration between RDFS data-models and bjv2
> introspection
>   RDF is fully supported in the query language
>
> New file formats
>   now cover Embl, Fasta, Gff, Blast (not tested on many blast flavors)
>
> Taverna plugin bridge
>   uses the @Utility hooks to expose all facades as taverna processors
>   same APIs could be used to expose all facades as web services, or whatever
>
> Todo before ISMB
>   swissprot IO
>   alignments + alignment IO
>   similarity search data model (populated from blast?)
>   protein alphabet
>   assemblies
>
> Todo soon after ISMB
>   wire RDF into the parser event framework propperly
>   bridge RDFS and Annotation
>   RDFS -> data model compiler
>   RDF -> file format parser, and write the RDF for /lots/ of SRS-able
> formats
>   use the RDF support to give us stable serialization, for RMI and for
> web services
>
> Todo slightly later ISMB
>   support data modification, transactions, set() methods.
>   add APIs for common areas
>     metabolomics
>     trees
>     snp analysis
>     linkage
>     ...
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