Biojava doesn't attempt to recusivley remove features by itself. It relies
on cascading deletes in the database. I know Oracle can be set to do this
(and it works very well). If MySQL has equivalent functionality you may
need to turn it on. I'm pretty sure it does but you need to set it up.
- Mark
Martina <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/20/2005 05:43 PM
To: [EMAIL PROTECTED], BioJava <biojava-l@biojava.org>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [BioSQL-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
_______________________________________________
BioSQL-l mailing list
[EMAIL PROTECTED]
http://open-bio.org/mailman/listinfo/biosql-l
_______________________________________________
Biojava-l mailing list - Biojava-l@biojava.org
http://biojava.org/mailman/listinfo/biojava-l
