ArrayIndexOutOfBounds in writing assembly diagrams

[josemduarte]

An ArrayIndexOutOfBounds happens in a few entries, some examples: 4m4i, 3inc, 1z02

The stack trace for 4m4i

Exception in thread "main" com.github.mustachejava.MustacheException: Error invoking method eppic.assembly.gui.LatticeGUIMustache.getGraph2D() on eppic.assembly.gui.LatticeGUIMustache@2082545616 @[mustache/eppic/assembly/gui/AssemblyDiagramThumb.dot.mustache:25]
        at com.github.mustachejava.reflect.ReflectionWrapper.call(ReflectionWrapper.java:73)
        at com.github.mustachejava.reflect.ReflectionObjectHandler.find(ReflectionObjectHandler.java:85)
        at com.github.mustachejava.reflect.GuardedBinding.getWrapper(GuardedBinding.java:94)
        at com.github.mustachejava.reflect.GuardedBinding.createAndGet(GuardedBinding.java:79)
        at com.github.mustachejava.reflect.GuardedBinding.get(GuardedBinding.java:74)
        at com.github.mustachejava.codes.DefaultCode.get(DefaultCode.java:139)
        at com.github.mustachejava.codes.IterableCode.execute(IterableCode.java:40)
        at com.github.mustachejava.codes.DefaultMustache.run(DefaultMustache.java:32)
        at com.github.mustachejava.codes.DefaultCode.execute(DefaultCode.java:161)
        at com.github.mustachejava.codes.DefaultCode.execute(DefaultCode.java:150)
        at eppic.assembly.gui.LatticeGUIMustache.execute(LatticeGUIMustache.java:291)
        at eppic.GraphvizRunner.generateFromDot(GraphvizRunner.java:79)
        at eppic.Main.doWriteAssemblyDiagrams(Main.java:597)
        at eppic.Main.run(Main.java:945)
        at eppic.Main.run(Main.java:879)
        at eppic.Main.main(Main.java:853)
Caused by: java.lang.IndexOutOfBoundsException: Index: 6, Size: 1
        at java.util.ArrayList.rangeCheck(ArrayList.java:653)
        at java.util.ArrayList.get(ArrayList.java:429)
        at org.biojava.nbio.structure.symmetry.core.RotationGroup.getRotation(RotationGroup.java:53)
        at eppic.assembly.layout.QuaternaryOrientationLayout.projectLatticeGraph(QuaternaryOrientationLayout.java:52)
        at eppic.assembly.layout.ComboLayout.projectLatticeGraph(ComboLayout.java:34)
        at eppic.assembly.gui.LatticeGUIMustache.getGraph2D(LatticeGUIMustache.java:394)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at com.github.mustachejava.reflect.ReflectionWrapper.call(ReflectionWrapper.java:64)
        ... 15 more

[josemduarte]

This is probably some sort of bug in the quaternary symmetry code in biojava or in eppic.assembly.layout.QuaternaryOrientationLayout. Could you have a look @sbliven ? It must be an specific edge case not caught properly. It affects quite a lot of structures, I found the 3 above out of a random 1000.

[josemduarte]

I've tested it and the issue seems to be solved by biojava/biojava#634. Thanks @sbliven ! I'll produce a new biojava bugfix release soon and point eppic to it.