libmcs 0.7 - java.lang.NullPointerException

Hi,

I used libmcs with 0.7 with Marvin 5.2.2

I attached the SMILES file

Warning! Non exact integer match for property value: 2.280000000000001e+002
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at chemaxon.clustering.gui.component.TreeTableModel.<init>(TreeTableModel.java:66)
        at chemaxon.clustering.gui.component.TreeTable.setGraph(TreeTable.java:132)
        at chemaxon.clustering.gui.component.ClusterViewer.setGraph(ClusterViewer.java:72)
        at chemaxon.clustering.gui.JKlustor.setGraph(JKlustor.java:314)
        at chemaxon.clustering.JKlustorImport$2.finished(JKlustorImport.java:349)
        at chemaxon.clustering.gui.SwingWorker$1.run(SwingWorker.java:114)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at chemaxon.clustering.gui.component.TreeRendererModel.sortBySize(TreeRendererModel.java:174)
        at chemaxon.clustering.gui.component.TreeTable.sortBySize(TreeTable.java:248)
        at chemaxon.clustering.gui.component.ClusterViewer.setTreeTableMode(ClusterViewer.java:193)
        at chemaxon.clustering.gui.component.ClusterViewer.setMode(ClusterViewer.java:162)
        at chemaxon.clustering.gui.component.ClusterViewer.setProgressMode(ClusterViewer.java:136)
        at chemaxon.clustering.JKlustorImport.stopProgress(JKlustorImport.java:393)
        at chemaxon.clustering.JKlustorImport.access$1000(JKlustorImport.java:51)
        at chemaxon.clustering.JKlustorImport$TimerListener.actionPerformed(JKlustorImport.java:494)
        at javax.swing.Timer.fireActionPerformed(Unknown Source)
        at javax.swing.Timer$DoPostEvent.run(Unknown Source)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)

 

Dear Tobias,

 

I was unable to reproduce the exception. Which java version do you use? Could you describe which steps resulted in the exception?

 

Thanks in advance,

Regards,

Gabor

Hi Gabor,

I repeated it and could not see the error, actually I dont remember what I did, I just wanted to cluster those cmpds.

 

Another big issue is the scroll graph in

Marvin View MODE

select the second ord third cluster level (to see multiple cmpds)

try to scroll the lower large molecule window with the right slider ,

it will grow like hell and can not be resized or adjusted.

 

On the upper ones it works, the lower window it does not work.

 

Actually, after just selecting different view modes and just playing here and there

I got this similar error (same dataset). But I did not record all my clicks.

 

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at chemaxon.clustering.gui.component.RGroupTablePanel.getSelectedParentOfNode(RGroupTablePanel.java:192)
at chemaxon.clustering.gui.component.RGroupTablePanel.setNode(RGroupTablePanel.java:183)
at chemaxon.clustering.gui.component.DendogramViewer.updateRGroupPanel(DendogramViewer.java:297)
at chemaxon.clustering.gui.component.ClusterViewer.update(ClusterViewer.java:96)
at chemaxon.clustering.gui.component.ClusterViewer.setGraph(ClusterViewer.java:73)
at chemaxon.clustering.gui.JKlustor.setGraph(JKlustor.java:314)
at chemaxon.clustering.JKlustorImport$2.finished(JKlustorImport.java:349)
at chemaxon.clustering.gui.SwingWorker$1.run(SwingWorker.java:114)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at chemaxon.clustering.gui.component.RGroupTablePanel.getSelectedParentOfNode(RGroupTablePanel.java:192)
at chemaxon.clustering.gui.component.RGroupTablePanel.setNode(RGroupTablePanel.java:183)
at chemaxon.clustering.gui.component.DendogramViewer.updateRGroupPanel(DendogramViewer.java:297)
at chemaxon.clustering.gui.component.ClusterViewer.update(ClusterViewer.java:96)
at chemaxon.clustering.gui.component.ClusterViewer.setRGroupMode(ClusterViewer.java:184)
at chemaxon.clustering.gui.component.ClusterViewer.setMode(ClusterViewer.java:165)
at chemaxon.clustering.gui.component.ClusterViewer.setProgressMode(ClusterViewer.java:136)
at chemaxon.clustering.JKlustorImport.stopProgress(JKlustorImport.java:393)
at chemaxon.clustering.JKlustorImport.access$1000(JKlustorImport.java:51)
at chemaxon.clustering.JKlustorImport$TimerListener.actionPerformed(JKlustorImport.java:494)
at javax.swing.Timer.fireActionPerformed(Unknown Source)
at javax.swing.Timer$DoPostEvent.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

Cheers

Tobias

 

 

Dear Tobias,


We are already aware that the slider can behave dodgy. As a dirty workaround resizing the windows vertical size fixes it. We are working on the new version of the clustering gui, this bug probably will be fixed in it.

The exception was not thrown for me, anyway thanks for the report.


regards,

Gabor