Knowtator / Discussion / Knowtator help/discussion: knowtator/protege stalling

Audra Browne - 2009-06-19

I'm sorry, I meant to add this, better maybe that this is a problem of its own accord rather than being grouped with the last subject.

I am having a serious problem getting protege to perform any annotation task in a timely manner, and I am also having a problem where, when I pull up the find/annotate box, and enter a search parameter, nothing ever happens, and for a minute or so, I am unable to click on anything within the program.

Any ideas or suggestions to stop this would be greatly appreciated, as it makes it almost impossible to annotate anything!

~Audra

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Philip Ogren - 2009-06-19
  
  Can you tell me a little bit about your computing environment? Are you using a Mac of PC? How much memory (RAM) does your machine have?
  
  Also, if you are getting a stack trace, then being able to see this would be very helpful. If you don't see a stack trace, then I can help you depending on your operating system.
  
  Thanks,
  Philip
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Audra Browne - 2009-06-20
  
  Philip,
  
  thanks for your reply. To answer your question, I am using a PC laptop running Vista, and my system info tells me that I have 893 mb available. I am shocked! Thought I had a lot more available RAM than that, but I must be maxxing this computer's memory. Maybe this is a large part of the problem!!!
  
  I am assuming that the stack trace is the message "stack" that appears in the protege background box, the one that looks a lot like a CMD black screen, right? If so, can you tell me how I copy and paste from this box? Maybe it says something about my understanding of these things, but I have no idea how to even get the cursor to move within the box.
  
  thanks!
  
  ~Audra
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - Philip Ogren - 2009-06-22
    
    "I am assuming that the stack trace is the message "stack" that appears in the protege background box, the one that looks a lot like a CMD black screen, right? "
    
    Yes - the "message stack" is another name for it.
    
    "If so, can you tell me how I copy and paste from this box?"
    
    You may need to turn on the edit mode for the protege background box. Here's how (on Windows):
    
    - bring the protege background box to the foreground
    - click on the protege "blender" icon (white background, three colored concentric blades)
    - select "properties" from the popup menu
    - from the "Properties" dialog choose the tab labeled "Options"
    - In the lower right-hand corner select "QuickEdit Mode"
    - click ok
    - choose "modify shortcut that started this window"
    - click ok
    
    Now to select some text from this window do the following:
    - highlight text with the cursor using your mouse
    - press enter on your keyboard to copy the text
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Audra Browne - 2009-06-20
  
  Philip,
  
  thanks for these instructions! I am going to try to increase the heap size max, and see if this doesn't help optimize performance.
  
  ~Audra
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Audra Browne - 2009-06-24
  
  ok, here's some text from the stack after the browser started to stall, and protege bagan to slow down. Background info: I had a window open in the browser, had protege half-screen and this half screen, a script was running at this address:http://blip.fm/mmemaledicta
  
  INFO: Load time for file:\C:\Users\Audra%20Browne\Desktop\Biomed%20co%20ref\audr
  a_practice_115321192%20.pprj = 10 sec (project) + 16 sec (ui)
  Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findNext(FindAnnot
  ateDialog.java:315)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:468)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.AbstractButton.doClick(Unknown Source)
          at javax.swing.plaf.basic.BasicRootPaneUI$Actions.actionPerformed(Unknow
  n Source)
          at javax.swing.SwingUtilities.notifyAction(Unknown Source)
          at javax.swing.JComponent.processKeyBinding(Unknown Source)
          at javax.swing.KeyboardManager.fireBinding(Unknown Source)
          at javax.swing.KeyboardManager.fireKeyboardAction(Unknown Source)
          at javax.swing.JComponent.processKeyBindingsForAllComponents(Unknown Sou
  rce)
          at javax.swing.JComponent.processKeyBindings(Unknown Source)
          at javax.swing.JComponent.processKeyEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
          at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(Unknown Source)
  
          at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(Unknown Sour
  ce)
          at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Sour
  ce)
          at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)
  
  maybe this will give a clue as to what's happening. Happy to report that though protege slows down and the browser stalls out, nothing has crashed so far today. If or when that happens, I'll make sure to copy the stack trace so you can see what's happening there.
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Audra Browne - 2009-06-24
  
  here's some more of the stack trace that appears when I attempt to use the find/annotate function (which is not working for me at all these days)
  
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findNext(FindAnnot
  ateDialog.java:315)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:468)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findNext(FindAnnot
  ateDialog.java:315)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:468)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findPrevious(FindA
  nnotateDialog.java:320)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:471)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findPrevious(FindA
  nnotateDialog.java:320)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:471)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findPrevious(FindA
  nnotateDialog.java:320)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:471)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Audra Browne - 2009-06-25
  
  ok, so the browser started crashing on me again, and here's the stack message:
  
  Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findPrevious(FindA
  nnotateDialog.java:320)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:471)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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.NoClassDefFoundError: java/util
  /regex/Pattern$SliceA
          at java.util.regex.Pattern.newSlice(Unknown Source)
          at java.util.regex.Pattern.escape(Unknown Source)
          at java.util.regex.Pattern.atom(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.group0(Unknown Source)
          at java.util.regex.Pattern.sequence(Unknown Source)
          at java.util.regex.Pattern.expr(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at java.util.regex.Pattern.<init>(Unknown Source)
          at java.util.regex.Pattern.compile(Unknown Source)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.preparePattern(Fin
  dAnnotateDialog.java:311)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.reset(FindAnnotate
  Dialog.java:326)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.findPrevious(FindA
  nnotateDialog.java:320)
          at edu.uchsc.ccp.knowtator.wizards.FindAnnotateDialog.actionPerformed(Fi
  ndAnnotateDialog.java:471)
          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
          at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
  ce)
          at java.awt.Component.processMouseEvent(Unknown Source)
          at javax.swing.JComponent.processMouseEvent(Unknown Source)
          at java.awt.Component.processEvent(Unknown Source)
          at java.awt.Container.processEvent(Unknown Source)
          at java.awt.Component.dispatchEventImpl(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
          at java.awt.Container.dispatchEventImpl(Unknown Source)
          at java.awt.Window.dispatchEventImpl(Unknown Source)
          at java.awt.Component.dispatchEvent(Unknown Source)
          at java.awt.EventQueue.dispatchEvent(Unknown Source)
          at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Philip Ogren - 2009-06-26
  
  Audra,
  
  I can't make any sense out of the stack trace that you sent me (no fault of yours!) I think what would be helpful is to tell me exactly how you are configuring the Find/Annotate dialog. Please tell me what your search string is and what checkboxes are checked.
  
  Also, could you send me the version of the java you are using? You should be able to type "java -version" from a shell prompt.
  
  Thanks,
  Philip
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Audra Browne - 2009-07-18
  
  philip, sorry for the delay. It could be any search string, whole words or partial, and none of the boxes are checked.
  
  Here's the java info:
  C:\Windows\system32>java -version
  java version "1.6.0_11"
  Java(TM) SE Runtime Environment (build 1.6.0_11-b03)
  Java HotSpot(TM) Client VM (build 11.0-b16, mixed mode, sharing)
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

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