Drag-and-drop to associate pdb files with sequences of same name is broken

The current development build doesn't seem to support mass association of PDB files (JAL-732). When I try to drop a PDB file named the same way as a sequence onto an alignment, I get the following exception:


Exceptions from Jmol when processing data in pdb file
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at jalview.io.StructureFile.processWithJmolParser(StructureFile.java:285)
at jalview.io.StructureFile.addSecondaryStructure(StructureFile.java:251)
at MCview.PDBfile.parse(PDBfile.java:187)
at jalview.io.AlignFile.doParse(AlignFile.java:170)
at MCview.PDBfile.<init>(PDBfile.java:54)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:395)
at jalview.gui.AssociatePdbFileWithSeq.associatePdbWithSeq(AssociatePdbFileWithSeq.java:53)
at jalview.gui.AlignFrame.drop(AlignFrame.java:5227)
at java.awt.dnd.DropTarget.drop(DropTarget.java:455)
at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538)
at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143)
at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852)
at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776)
at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48)
at java.awt.Component.dispatchEventImpl(Component.java:4746)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.NullPointerException
at MCview.PDBChain.<init>(PDBChain.java:85)
at jalview.ext.jmol.JmolParser.transformJmolModelToJalview(JmolParser.java:162)
at jalview.ext.jmol.JmolParser.parse(JmolParser.java:109)
at jalview.io.AlignFile.doParse(AlignFile.java:170)
at jalview.io.AlignFile.<init>(AlignFile.java:152)
at jalview.io.AlignFile.<init>(AlignFile.java:134)
at jalview.io.StructureFile.<init>(StructureFile.java:56)
at jalview.ext.jmol.JmolParser.<init>(JmolParser.java:72)
... 45 more
java.lang.NullPointerException
at jalview.structure.StructureSelectionManager.setProgressBar(StructureSelectionManager.java:1293)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:525)
at jalview.gui.AssociatePdbFileWithSeq.associatePdbWithSeq(AssociatePdbFileWithSeq.java:53)
at jalview.gui.AlignFrame.drop(AlignFrame.java:5227)
at java.awt.dnd.DropTarget.drop(DropTarget.java:455)
at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538)
at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143)
at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852)
at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776)
at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48)
at java.awt.Component.dispatchEventImpl(Component.java:4746)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)