[BUG-26] Sequence viewer can be made to select past the end of the sequence. - JIRA UNCC

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

BUG-608 Sequence viewer bugs

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Adam Baxter (Inactive) added a comment - 21/Mar/11 8:04 AM

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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Adam Baxter (Inactive) added a comment - 21/Mar/11 8:04 AM 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)

5 older comments

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Anuj Puram (Inactive) added a comment - 20/Jan/12 6:32 AM

Passed 6.7.0 (9891) on Mac

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Anuj Puram (Inactive) added a comment - 20/Jan/12 6:32 AM Passed 6.7.0 (9891) on Mac

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Alyssa Gulledge (Inactive) added a comment - 30/Apr/12 8:27 AM

orignially reported by Adam Baxter

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Alyssa Gulledge (Inactive) added a comment - 30/Apr/12 8:27 AM orignially reported by Adam Baxter

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darius added a comment - 05/Jun/12 9:19 AM

Passed 7.0 (11806)

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darius added a comment - 05/Jun/12 9:19 AM Passed 7.0 (11806)

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Alyssa Gulledge (Inactive) added a comment - 13/Nov/12 9:59 AM

Sequence Viewer bugs

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Alyssa Gulledge (Inactive) added a comment - 13/Nov/12 9:59 AM Sequence Viewer bugs

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Richard Linchangco (Inactive) added a comment - 14/Nov/12 7:07 AM

Passed, 13526, Mac, Java 1.060_37

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Richard Linchangco (Inactive) added a comment - 14/Nov/12 7:07 AM Passed, 13526, Mac, Java 1.060_37

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

Votes:

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Dates

Created:

21/Mar/11 8:03 AM

Updated:

14/Nov/12 7:08 AM

Resolved:

14/Nov/12 7:08 AM