Bioperl: Boulderio 1.14 released

[Ewan Birney]

On Tue, 30 Nov 1999, Lincoln Stein wrote:

> Hi All,
> 
> I've just released version 1.14 of the BoulderIO parser libraries.
> These libraries provide easy access to hierarchical tag/value data,
> such as GenBank, XML and BLAST documents.  New in this version:
> 
>      1) Support for Boulder->XML and back again.

Cool. Much needed/wanted. Do you use your own parser, or are there XML::
dependencies?

>      2) Much improved support for Genbank Entrez access:
> 	a) uses batch entrez for big performance increases
> 	b) provides access to features tables -- for example,
> 	you can ask for all features that overlap a specified
> 	region.
>      3) Support for both WU-Blast and NCBI Blast outputs.
>      4) Improved support for SwissProt, Unigene, Medline, and 
> 	OMIM, thanks to Luca Toldo.
> 
> Luca is currently working on the Java port of Boulder, which compiles
> on some systems and not on others (due to libdb incompatibilities),
> and on a LocusLink parser.  I am working on integrating Boulder with
> the main bioperl distribution, and finding it very hard to reconcile
> the data-oriented and object-oriented views of the world!
> 

I know this is tough! I thought it would be a challenge... 

My view on how to do this is that objects should subscribe to a
data-orientated interface that allows a data-orientated view of the
object. This interface should be defined somewhere off in Bio::Root::
stuff. 

This means that you shift the mapping problem of objects<->data to the
object authors, which is where I think it belongs (realistically, only
they know what their object is doing), but this means that there is
alot of code duplication, and as deep down in the objects, there *is* a
data orientated view (being the hashes kepts by the object) one might
want to do something cleverer, which would prevent authors having to
write something.

Possible there is some middle ground, where if it has the interface, it
uses that, but otherwise is does something a little like data::dumper.


But - as you know - I'm one of the object-orientated types out here.

> You can find Boulder in CPAN in the LDS directory, or at:
> 
>     http://stein.cshl.org/software/boulder
> 
> The Java version is also available at the above URL.
> 
> Lincoln
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
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