I'm trying to add gene names using the automatically create gene names function under the edit menu. Here's the process:
1. Select 4550 CDS features using the feature selector and choose to view them. 2. In the view, select all and choose automatically create gene names from the Edit menu. Answer yes to everything, except to adding a 'c' to complementary features. 3. Wait... On release 9 this locked up Artemis (no component painting) for >30 minutes before I killed it. Release 10 is better in that the paint thread is still working, but after >30 minutes the job is not done. I attached a profiler and most of the time is being spent in autonaming and autosaving. I wonder is there is some sort of bad interaction between the automatic edits and the autosaver? Here's the two relevant chunks of profiler output: Method: uk.ac.sanger.artemis.components.EditMenu$27.actionPerformed(java.awt.event.ActionEvent) Hits : 36 Total : 12273896.4ms Method: uk.ac.sanger.artemis.components.EditMenu.autoGeneName() Hits : 36 Total : 12273895.7ms Local : 0.0ms Method: uk.ac.sanger.artemis.components.EditMenu.autoGeneNameHelper(uk.ac.sanger.artemis.FeatureVector,java.lang.String,int,int,java.lang.String,boolean,int) Hits : 36 Total : 11734965.5ms Local : 0.0ms Method: uk.ac.sanger.artemis.Feature.addQualifierValues(uk.ac.sanger.artemis.io.Qualifier) Hits : 1043 Total : 975571.2ms Local : 0.0ms Method: uk.ac.sanger.artemis.Feature.setQualifier(uk.ac.sanger.artemis.io.Qualifier) Hits : 1043 Total : 974744.6ms Local : 0.0ms ... Method: uk.ac.sanger.artemis.io.DocumentEntryAutosaveThread.run() Hits : 36 Total : 11733928.6ms Local : 0.0ms ... -- - Keith James - Wellcome Trust Sanger Institute, UK - _______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
