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  1. Bug Repository
  2. BUG-26

Sequence viewer can be made to select past the end of the sequence.

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Major
          • Resolution: Fixed
          • Labels:
            None
          • Environment:

            OS X: 10.6
            Java: "1.6.0_24"
            IGB: SVN Version 7791

            Description

            In the sequence viewer, the user can select a character beyond the end of the sequence.
            The save and copy function do not handle this correctly and cause exceptions.
            The file save option still works correctly, but the edit drop down either does not show up or has the copy command grayed out.

            Exception in comments.

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                Issue Links

                relates to

                Task - A task that needs to be done. BUG-608 Sequence viewer bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

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                  adam Adam Baxter (Inactive) added a comment -

                  My test sequence was chr1: 17841987 - 17842032. In interbase, this is 46 characters long, not 47.

                  exception in Sequence.getResidues(start, end)
                  start = 16, end = 47
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.view.SequenceViewer.menuSelected(SequenceViewer.java:706)
                  at javax.swing.JMenu.fireMenuSelected(JMenu.java:1028)
                  at javax.swing.JMenu$MenuChangeListener.stateChanged(JMenu.java:1107)
                  at javax.swing.DefaultButtonModel.fireStateChanged(DefaultButtonModel.java:333)
                  at javax.swing.DefaultButtonModel.setSelected(DefaultButtonModel.java:215)
                  at javax.swing.JMenu.setSelected(JMenu.java:294)
                  at javax.swing.JMenu.menuSelectionChanged(JMenu.java:1175)
                  at javax.swing.MenuSelectionManager.setSelectedPath(MenuSelectionManager.java:100)
                  at javax.swing.plaf.basic.BasicMenuUI$Handler.mousePressed(BasicMenuUI.java:434)
                  at javax.swing.plaf.basic.BasicMenuUI$MouseInputHandler.mousePressed(BasicMenuUI.java:326)
                  at java.awt.Component.processMouseEvent(Component.java:6371)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6139)
                  at java.awt.Container.processEvent(Container.java:2085)
                  at java.awt.Component.dispatchEventImpl(Component.java:4736)
                  at java.awt.Container.dispatchEventImpl(Container.java:2143)
                  at java.awt.Component.dispatchEvent(Component.java:4566)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
                  at java.awt.Container.dispatchEventImpl(Container.java:2129)
                  at java.awt.Window.dispatchEventImpl(Window.java:2478)
                  at java.awt.Component.dispatchEvent(Component.java:4566)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
                  at java.awt.EventQueue.access$000(EventQueue.java:86)
                  at java.awt.EventQueue$1.run(EventQueue.java:639)
                  at java.awt.EventQueue$1.run(EventQueue.java:637)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
                  at java.awt.EventQueue$2.run(EventQueue.java:653)
                  at java.awt.EventQueue$2.run(EventQueue.java:651)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
                  exception in Sequence.getResidues(start, end)
                  start = 16, end = 47
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.view.SequenceViewer.menuSelected(SequenceViewer.java:706)
                  at javax.swing.JMenu.fireMenuSelected(JMenu.java:1028)
                  at javax.swing.JMenu$MenuChangeListener.stateChanged(JMenu.java:1107)
                  at javax.swing.DefaultButtonModel.fireStateChanged(DefaultButtonModel.java:333)
                  at javax.swing.DefaultButtonModel.setSelected(DefaultButtonModel.java:215)
                  at javax.swing.JMenu.setSelected(JMenu.java:294)
                  at javax.swing.JMenu.menuSelectionChanged(JMenu.java:1175)
                  at javax.swing.MenuSelectionManager.setSelectedPath(MenuSelectionManager.java:100)
                  at com.apple.laf.AquaMenuUI$AquaMouseInputHandler.mouseEntered(AquaMenuUI.java:134)
                  at java.awt.Component.processMouseEvent(Component.java:6383)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6139)
                  at java.awt.Container.processEvent(Container.java:2085)
                  at java.awt.Component.dispatchEventImpl(Component.java:4736)
                  at java.awt.Container.dispatchEventImpl(Container.java:2143)
                  at java.awt.Component.dispatchEvent(Component.java:4566)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
                  at java.awt.LightweightDispatcher.trackMouseEnterExit(Container.java:4410)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4264)
                  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
                  at java.awt.Container.dispatchEventImpl(Container.java:2129)
                  at java.awt.Window.dispatchEventImpl(Window.java:2478)
                  at java.awt.Component.dispatchEvent(Component.java:4566)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
                  at java.awt.EventQueue.access$000(EventQueue.java:86)
                  at java.awt.EventQueue$1.run(EventQueue.java:639)
                  at java.awt.EventQueue$1.run(EventQueue.java:637)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
                  at java.awt.EventQueue$2.run(EventQueue.java:653)
                  at java.awt.EventQueue$2.run(EventQueue.java:651)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

                  Show
                  adam Adam Baxter (Inactive) added a comment - My test sequence was chr1: 17841987 - 17842032. In interbase, this is 46 characters long, not 47. exception in Sequence.getResidues(start, end) start = 16, end = 47 Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.SequenceViewer.menuSelected(SequenceViewer.java:706) at javax.swing.JMenu.fireMenuSelected(JMenu.java:1028) at javax.swing.JMenu$MenuChangeListener.stateChanged(JMenu.java:1107) at javax.swing.DefaultButtonModel.fireStateChanged(DefaultButtonModel.java:333) at javax.swing.DefaultButtonModel.setSelected(DefaultButtonModel.java:215) at javax.swing.JMenu.setSelected(JMenu.java:294) at javax.swing.JMenu.menuSelectionChanged(JMenu.java:1175) at javax.swing.MenuSelectionManager.setSelectedPath(MenuSelectionManager.java:100) at javax.swing.plaf.basic.BasicMenuUI$Handler.mousePressed(BasicMenuUI.java:434) at javax.swing.plaf.basic.BasicMenuUI$MouseInputHandler.mousePressed(BasicMenuUI.java:326) at java.awt.Component.processMouseEvent(Component.java:6371) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6139) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4736) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212) at java.awt.Container.dispatchEventImpl(Container.java:2129) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680) at java.awt.EventQueue.access$000(EventQueue.java:86) at java.awt.EventQueue$1.run(EventQueue.java:639) at java.awt.EventQueue$1.run(EventQueue.java:637) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:653) at java.awt.EventQueue$2.run(EventQueue.java:651) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:650) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) exception in Sequence.getResidues(start, end) start = 16, end = 47 Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.SequenceViewer.menuSelected(SequenceViewer.java:706) at javax.swing.JMenu.fireMenuSelected(JMenu.java:1028) at javax.swing.JMenu$MenuChangeListener.stateChanged(JMenu.java:1107) at javax.swing.DefaultButtonModel.fireStateChanged(DefaultButtonModel.java:333) at javax.swing.DefaultButtonModel.setSelected(DefaultButtonModel.java:215) at javax.swing.JMenu.setSelected(JMenu.java:294) at javax.swing.JMenu.menuSelectionChanged(JMenu.java:1175) at javax.swing.MenuSelectionManager.setSelectedPath(MenuSelectionManager.java:100) at com.apple.laf.AquaMenuUI$AquaMouseInputHandler.mouseEntered(AquaMenuUI.java:134) at java.awt.Component.processMouseEvent(Component.java:6383) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6139) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4736) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.trackMouseEnterExit(Container.java:4410) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4264) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212) at java.awt.Container.dispatchEventImpl(Container.java:2129) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680) at java.awt.EventQueue.access$000(EventQueue.java:86) at java.awt.EventQueue$1.run(EventQueue.java:639) at java.awt.EventQueue$1.run(EventQueue.java:637) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:653) at java.awt.EventQueue$2.run(EventQueue.java:651) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:650) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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                  vbishnoi vbishnoi added a comment -

                  On selecting the empty space after the last character would not cause exception now, but still the empty space would remain, this is an existing problem in basic classes and can not be fixed now without creating many other unknown issues.

                  Show
                  vbishnoi vbishnoi added a comment - On selecting the empty space after the last character would not cause exception now, but still the empty space would remain, this is an existing problem in basic classes and can not be fixed now without creating many other unknown issues.
                  Hide
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                  adam Adam Baxter (Inactive) added a comment -

                  I just tested on IGB 7807 and I still receive an exception when the last space is selected. Has this been committed to SVN yet?

                  Show
                  adam Adam Baxter (Inactive) added a comment - I just tested on IGB 7807 and I still receive an exception when the last space is selected. Has this been committed to SVN yet?
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  It was not merged in branch. Should work now.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - It was not merged in branch. Should work now.
                  Hide
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                  adam Adam Baxter (Inactive) added a comment -

                  Problem resolved as of SVN version: 7811

                  Show
                  adam Adam Baxter (Inactive) added a comment - Problem resolved as of SVN version: 7811
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9808 Windows

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                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9808 Windows
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed 6.7.0 (9891) on Mac

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                  anuj Anuj Puram (Inactive) added a comment - Passed 6.7.0 (9891) on Mac
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  orignially reported by Adam Baxter

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                  alyssa Alyssa Gulledge (Inactive) added a comment - orignially reported by Adam Baxter
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                  darius darius added a comment -

                  Passed 7.0 (11806)

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                  darius darius added a comment - Passed 7.0 (11806)
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Sequence Viewer bugs

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                  alyssa Alyssa Gulledge (Inactive) added a comment - Sequence Viewer bugs
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed, 13526, Mac, Java 1.060_37

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed, 13526, Mac, Java 1.060_37

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: