[Biojava-l] Integrating Biojava into an organism Database System

Arnaud Kerhornou axk@sanger.ac.uk
Tue, 23 Jan 2001 11:00:55 +0000


I work for the Pathogen Sequencing Unit at the Sanger Centre. One of our
projects is to set a database. This database will store publicly
available data regarding several organisms.
We are interested in implementing the Database Interface  with Java.

So I was thinking how to integrate BioJava, in other words our objects
would behave as BioJava objects, following two ways :

The first one is our own objects would inherit from the BioJava
Interface. This implies to implement them, and thus we'll have
difficulties to keep them compliant iwth the future development within
Another solution is to inherit from your own object implementation, but
in that case we won't be able to set a hierarcherical class inheritance
tree of our own (no multiple inheritance).

The second solution, our objects would wrap Biojava objects, thus
delegating the implementation of Biojava behaviours to objects, part of
the Biojava project.

Does this solution sound better ?

I started implementing my own Sequence object which wraps a
SimpleSequence Object.

Our objects are designed as Persistent and the storage will be in a
relational database. Instead of mapping the Biojava design into a
Relational Design, I tried to store the wrapped SimpleSequence object
into a MySQL Blob data type.
    => An exception has been raised because SimpleFeatureHolder is not
serializable !

But actually I'm not sure we need to make Biojava Objects persistent, we
would have our own object design. These objects will just be able to
behave as biojava objects, delegating the behaviour implementation to a
transient biojava object.

Does it make any sense ?

Arnaud Kerhornou

The Sanger Centre
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax:  +44 (0) 1223 494919