OMG John :). I had a live hacking session this morning and five people watching me messing all up....

Thank you for the information. Please send greetings to all at the EBI.

Regards,
Andreas

Am 22.01.2013 16:05, schrieb John May:
Hi Andreas,

Yep, patch from Stephan is waiting to be pulled: https://sourceforge.net/p/cdk/patches/600/

Basically when I updated the comparators for JDK 1.7 I put the null sorting the wrong way. Not a problem if you use collations but the ringset uses a fixed size array - hence: 

rings = [Ring,null,null,null,null,null,null,null,null]

when sorted becomes

rings = [null,null,null,null,null,null,null,null,Ring]

the renderer then does this without null checking…

rings[0].aMethod();

My bad as I said in the patch :(

Thanks,
J

On 22 Jan 2013, at 14:41, Andreas Truszkowski <at_lists@gmx.de> wrote:

Hi together,

I have a problem getting the CDK renderer working. It throws the
following nullpointer:
java.lang.NullPointerException
    at org.openscience.cdk.RingSet.getRings(RingSet.java:72)
    at
org.openscience.cdk.tools.manipulator.RingSetManipulator.getHeaviestRing(RingSetManipulator.java:154)
    at
org.openscience.cdk.renderer.generators.BasicBondGenerator.generate(BasicBondGenerator.java:276)
    at
org.openscience.cdk.renderer.generators.BasicBondGenerator.generate(BasicBondGenerator.java:262)
    at
org.openscience.cdk.renderer.generators.BasicBondGenerator.generate(BasicBondGenerator.java:63)
    at
org.openscience.cdk.renderer.AbstractRenderer.generateDiagram(AbstractRenderer.java:119)
    at
org.openscience.cdk.renderer.AtomContainerRenderer.paint(AtomContainerRenderer.java:203)
    at cdkhandson.Draw2DStructure.drawMolecule(Draw2DStructure.java:99)
    at cdkhandson.Draw2DStructure.drawMolecule(Draw2DStructure.java:82)
    at
cdkhandson.MainFrameController$2.actionPerformed(MainFrameController.java:68)

It seems that the ring finder got any troubles. Has got anyone an idea
what the problemcould be?
Many thanks it advance,

Regards,
Andreas

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