[Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB

[mark.schreiber at novartis.com]

Very cool use of reflection in there!

I don't see how commits and rollbacks are handled though??

- Mark





"Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
Sent by: biojava-dev-bounces at portal.open-bio.org
01/24/2006 10:51 AM

 
        To:     <biojava-dev at biojava.org>
        cc:     Mark Schreiber/GP/Novartis at PH
        Subject:        [Biojava-dev] BioSQLRichSequenceDB and BioSQLBioEntryDB


We've added two new modules to BioJavaX that allow you to wrap a 
BioSQL/Hibernate database in a SequenceDB compatible wrapper. More for 
convenience sake than anything else (its not foolproof) but it might be 
useful. 

They are:

                 org.biojavax.bio.db.biosql.BioSQLBioEntryDB
                 org.biojavax.bio.db.biosql.BioSQLRichSequenceDB

The code depends on you having unique values in the 'name' column of the 
BioEntry table in your BioSQL database. You'll get 'IllegalIDExceptions' 
thrown all over the place if this does not hold true. If this is the case, 
you should use Hibernate directly rather than this convenience wrapper 
code.

To use it, make sure Hibernate is on your classpath. Then you can do 
things like this:

                 Session session = ...;  // get a Hibernate session from 
somewhere

                 RichObjectFactory.connectToHibernate(session); // bind 
BioJavaX to the hibernate session
                 RichSequenceDB db = new BioSQLRichSequenceDB(session); // 
connect the hibernate session to our SequenceDB

                 System.out.println(db.ids()); // prints out a list of all 
the values in the 'name' column of the BioEntry table in the database  

                 for (Iterator i = db.getRichSequences("bloggs"); 
i.hasNext(); ) {  // retrieve all sequences where the name is 'bloggs'
                     RichSequence seq = (RichSequence)i.next(); // get the 
next one
                     ... // do something with it here
                 }

To add sequences to your database:

                 RichSequence seq = ...; // get a RichSequence from 
somewhere
                 db.addRichSequence(seq);

To remove them again:

                 db.removeRichSequence("bloggs"); // removes the sequence 
with the name 'bloggs'

The BioSQLBioEntryDB works in exactly the same way but returns only 
BioEntry objects - ie. sequences without the sequence data attached. This 
might help with performance in some cases.

Finally, we also added a GenbankRichSequenceDB object that behaves much 
like the old GenbankSequenceDB object but returns RichSequence objects 
instead.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
Genome Institute of Singapore
60 Biopolis Street, #02-01 Genome, Singapore 138672
Tel: (65) 6478 8000   DID: (65) 6478 8199
Email: hollandr at gis.a-star.edu.sg
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