[Biojava-l] _removeSequence

[mark.schreiber at novartis.com]

To remove the database completely (while still keeping the tables etc) you 
would again need to turn on cascading deletes and delete the appropriate 
biodatabase row from the biodatabase table (or all of them if you have 
more than one).

You cannot currently do this using the biojava interface. You would need 
to code a JDBC statement to do it for you, or connect to the DB and issue 
the SQL statement yourself.

- Mark





Martina <boehme at mpiib-berlin.mpg.de>
Sent by: biojava-l-bounces at portal.open-bio.org
06/20/2005 05:43 PM

 
        To:     biosql-l at open-bio.org, BioJava <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] _removeSequence


Hi,

Im trying to delete a sequence and recursivly all its features.

So:

for (SequenceIterator si = db.sequenceIterator(); si.hasNext();) {
                 Sequence s = si.nextSequence();
                 String name = s.getName();
                 s = null;
                 db.removeSequence(name);
}

But if I look in the database (MySQL  4.1.12) I can still see plenty 
of entries and I have problems entering the same features again, 
because of dublicate key error. I would like to know if 
_removeSequence(String) in BioSQLSequenceDB is supposed to remove 
features recursivly or just the features of the removed sequence?
If so - what is the best way do delete the features of the features 
(and so on)? And how to empty the db completly?

Martina

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