Details
Description
While testing JAL-2665 I picked up some exceptions while working with wrapped alignments. I was unable to reproduce any of these. Also see attached screenshot which occurred after printing (to pdf) the wrapped alignment - no exceptions were thrown and the alignment was printed correctly.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at jalview.renderer.AnnotationRenderer.drawComponent(AnnotationRenderer.java:655)
at jalview.gui.SeqCanvas.drawWrappedPanel(SeqCanvas.java:725)
at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:401)
at javax.swing.JComponent.paint(JComponent.java:1056)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
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.awt.EventQueue.dispatchEvent(EventQueue.java:726)
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)
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.Vector$Itr.checkForComodification(Vector.java:1184)
at java.util.Vector$Itr.remove(Vector.java:1150)
at sun.java2d.Spans.sortAndCollapse(Spans.java:186)
at sun.java2d.Spans.add(Spans.java:77)
at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1801)
at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1777)
at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1767)
at sun.print.PeekGraphics.drawString(PeekGraphics.java:1470)
at sun.print.PeekGraphics.drawString(PeekGraphics.java:861)
at jalview.gui.SequenceRenderer.drawText(SequenceRenderer.java:423)
at jalview.gui.SequenceRenderer.drawSequence(SequenceRenderer.java:186)
at jalview.gui.SeqCanvas.draw(SeqCanvas.java:941)
at jalview.gui.SeqCanvas.drawPanel(SeqCanvas.java:837)
at jalview.gui.SeqCanvas.drawWrappedPanel(SeqCanvas.java:715)
at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:401)
at javax.swing.JComponent.paint(JComponent.java:1056)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
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.awt.EventQueue.dispatchEvent(EventQueue.java:726)
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)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at jalview.renderer.AnnotationRenderer.drawComponent(AnnotationRenderer.java:655)
at jalview.gui.SeqCanvas.drawWrappedPanel(SeqCanvas.java:725)
at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:401)
at javax.swing.JComponent.paint(JComponent.java:1056)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
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.awt.EventQueue.dispatchEvent(EventQueue.java:726)
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)
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.Vector$Itr.checkForComodification(Vector.java:1184)
at java.util.Vector$Itr.remove(Vector.java:1150)
at sun.java2d.Spans.sortAndCollapse(Spans.java:186)
at sun.java2d.Spans.add(Spans.java:77)
at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1801)
at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1777)
at sun.print.PeekGraphics.addDrawingRect(PeekGraphics.java:1767)
at sun.print.PeekGraphics.drawString(PeekGraphics.java:1470)
at sun.print.PeekGraphics.drawString(PeekGraphics.java:861)
at jalview.gui.SequenceRenderer.drawText(SequenceRenderer.java:423)
at jalview.gui.SequenceRenderer.drawSequence(SequenceRenderer.java:186)
at jalview.gui.SeqCanvas.draw(SeqCanvas.java:941)
at jalview.gui.SeqCanvas.drawPanel(SeqCanvas.java:837)
at jalview.gui.SeqCanvas.drawWrappedPanel(SeqCanvas.java:715)
at jalview.gui.SeqCanvas.paintComponent(SeqCanvas.java:401)
at javax.swing.JComponent.paint(JComponent.java:1056)
at javax.swing.JComponent.paintChildren(JComponent.java:889)
at javax.swing.JComponent.paint(JComponent.java:1065)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1579)
at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1502)
at javax.swing.RepaintManager.paint(RepaintManager.java:1272)
at javax.swing.JComponent._paintImmediately(JComponent.java:5158)
at javax.swing.JComponent.paintImmediately(JComponent.java:4969)
at javax.swing.RepaintManager$4.run(RepaintManager.java:831)
at javax.swing.RepaintManager$4.run(RepaintManager.java:814)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:814)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:789)
at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:738)
at javax.swing.RepaintManager.access$1200(RepaintManager.java:64)
at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1732)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
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.awt.EventQueue.dispatchEvent(EventQueue.java:726)
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)