There is also the BS-zap-all script in the BioSQL distribution which will wipe the whole lot for you in one go. :)
Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > [EMAIL PROTECTED] > Sent: Monday, June 20, 2005 6:07 PM > To: Martina > Cc: [EMAIL PROTECTED]; BioJava; > [EMAIL PROTECTED] > Subject: [BioSQL-l] Re: [Biojava-l] _removeSequence > > > 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 <[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: [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 > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > > > > _______________________________________________ > 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
