From: Rajarshi G. <rx...@ps...> - 2006-03-14 21:32:04
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Hi, I'm working with v2.2.0 of jchempaint (synced with the latest CVS). When I draw a single bond and then click on it again to try and get a double bond I get an exception: Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError at java.util.Hashtable.getEnumeration(Hashtable.java:547) at java.util.Hashtable.keys(Hashtable.java:233) at org.openscience.cdk.ChemObject.clone(ChemObject.java:303) at org.openscience.cdk.Element.clone(Element.java:158) at org.openscience.cdk.Isotope.clone(Isotope.java:240) at org.openscience.cdk.Atom.clone(Atom.java:617) at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1332) at org.openscience.cdk.Molecule.clone(Molecule.java:91) at org.openscience.cdk.ChemObject.clone(ChemObject.java:314) at org.openscience.cdk.Element.clone(Element.java:158) at org.openscience.cdk.Isotope.clone(Isotope.java:240) at org.openscience.cdk.Atom.clone(Atom.java:617) [snip] I'm running JDK 1.5.0. Fedora Core 4. Does anybody know why this might be happening? Thanks, ------------------------------------------------------------------- Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- After an instrument has been assembled, extra components will be found on the bench. |
From: Christoph S. <c.s...@un...> - 2006-03-15 15:05:36
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Rajarshi Guha wrote: > Hi, > I'm working with v2.2.0 of jchempaint (synced with the latest CVS). > When I draw a single bond and then click on it again to try and get a > double bond I get an exception: >=20 > Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError > at java.util.Hashtable.getEnumeration(Hashtable.java:547) > at java.util.Hashtable.keys(Hashtable.java:233) > at org.openscience.cdk.ChemObject.clone(ChemObject.java:303) > at org.openscience.cdk.Element.clone(Element.java:158) > at org.openscience.cdk.Isotope.clone(Isotope.java:240) > at org.openscience.cdk.Atom.clone(Atom.java:617) > at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1= 332) > at org.openscience.cdk.Molecule.clone(Molecule.java:91) > at org.openscience.cdk.ChemObject.clone(ChemObject.java:314) > at org.openscience.cdk.Element.clone(Element.java:158) > at org.openscience.cdk.Isotope.clone(Isotope.java:240) > at org.openscience.cdk.Atom.clone(Atom.java:617) > [snip] >=20 > I'm running JDK 1.5.0. Fedora Core 4. Does anybody know why this might > be happening? I have been encountering the same problem and I have no idea why that is. Especially, I don't understand why cloning should be involved when drawin= g a=20 double bond. Maybe this is due to redo/undo, but the stacktrace doesn't r= eally=20 say something about the origin of the error. Cheers, Christoph. --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Stefan K. <ste...@un...> - 2006-03-16 15:03:26
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This should be solved in HEAD. Stefan Am Tuesday 14 March 2006 22:32 schrieb Rajarshi Guha: > Hi, > I'm working with v2.2.0 of jchempaint (synced with the latest CVS). > When I draw a single bond and then click on it again to try and get a > double bond I get an exception: > > Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError > at java.util.Hashtable.getEnumeration(Hashtable.java:547) > at java.util.Hashtable.keys(Hashtable.java:233) > at org.openscience.cdk.ChemObject.clone(ChemObject.java:303) > at org.openscience.cdk.Element.clone(Element.java:158) > at org.openscience.cdk.Isotope.clone(Isotope.java:240) > at org.openscience.cdk.Atom.clone(Atom.java:617) > at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1= 332) > at org.openscience.cdk.Molecule.clone(Molecule.java:91) > at org.openscience.cdk.ChemObject.clone(ChemObject.java:314) > at org.openscience.cdk.Element.clone(Element.java:158) > at org.openscience.cdk.Isotope.clone(Isotope.java:240) > at org.openscience.cdk.Atom.clone(Atom.java:617) > [snip] > > I'm running JDK 1.5.0. Fedora Core 4. Does anybody know why this might > be happening? > > Thanks, > > ------------------------------------------------------------------- > Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net> > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > After an instrument has been assembled, extra components will be found > on the bench. > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking scripting lang= uage > that extends applications into web and mobile media. Attend the live > webcast and join the prime developer group breaking into this new codin= g > territory! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat= =3D121642 > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel --=20 Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=C3=BClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 My public PGP key is available at http://pgp.mit.edu |
From: Rajarshi G. <rx...@ps...> - 2006-03-16 15:15:15
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On Thu, 2006-03-16 at 16:36 +0100, Stefan Kuhn wrote: > This should be solved in HEAD. > Stefan Thanks, it works now. However another (similar) problem. I draw a molecule and then Ctrl-A to select it all and then I click on 'clean up' from the menu bar. The menu option stays highlighted and no clean up occurs. I also get a stack trace, part of which is below: Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1324) at org.openscience.cdk.Molecule.clone(Molecule.java:91) at org.openscience.cdk.ChemObject.clone(ChemObject.java:314) at org.openscience.cdk.Element.clone(Element.java:158) at org.openscience.cdk.Isotope.clone(Isotope.java:240) at org.openscience.cdk.Atom.clone(Atom.java:617) at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1332) at org.openscience.cdk.Molecule.clone(Molecule.java:91) at org.openscience.cdk.ChemObject.clone(ChemObject.java:314) at org.openscience.cdk.Element.clone(Element.java:158) at org.openscience.cdk.Isotope.clone(Isotope.java:240) at org.openscience.cdk.Atom.clone(Atom.java:617) at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1332) [snip] I'm running JDK 1.5.0, Fedora Core 4 and the latest CVS versions of CDK and JChempaint ------------------------------------------------------------------- Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- The only perfect science is hindsight. |