LIBMCS 05 crash on some NCI smiles

LIBMCS 0.5 crash on some files (NCI1000 sort.smi)


http://fiehnlab.ucdavis.edu/staff/kind/Collector/libmcs-benchmark.zip





Another weird behavior is, sometimes it asks : should I merge into current cluster, sometimes not?


Tobias





java.lang.ArrayIndexOutOfBoundsException: 9990


at chemaxon.clustering.LibraryMCS.mergeFailed(LibraryMCS.java:721)


at chemaxon.clustering.LibraryMCS.merge(LibraryMCS.java:692)


at chemaxon.clustering.LibraryMCS.clusterOneLevel(LibraryMCS.java:628)


at chemaxon.clustering.LibraryMCS.search(LibraryMCS.java:469)


at chemaxon.clustering.gui.JKlustorImport$SearchTask.<init>(JKlustorImport.java:273)


at chemaxon.clustering.gui.JKlustorImport$2.construct(JKlustorImport.java:254)


at chemaxon.clustering.gui.SwingWorker$2.run(SwingWorker.java:120)


at java.lang.Thread.run(Thread.java:595)


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:67)


at chemaxon.clustering.gui.JKlustor.setGraph(JKlustor.java:247)


at chemaxon.clustering.gui.JKlustorImport$2.finished(JKlustorImport.java:264)


at chemaxon.clustering.gui.SwingWorker$1.run(SwingWorker.java:114)


at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)


at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)


at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)


at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)


at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

Ok,


after hours and hours of testing (in a stupid way) instead


of creating multiple random datasets, I found its due to


several problems.





1) Its good if structures are canonized and duplicates


removed, although this is not a real problem, because


LibMCS 5.0 clusters all duplicates into the correct branches.





Ok this applies only for standard settings, any changes will also crash libmcs 5.0.


Tobias





See the three files (all same content, only one without duplicates)

Thanks Tobias, useful as always!!! I'll check these issues and we'll fix them asap.


Miklos