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  1. Bug Repository
  2. BUG-507

NPE, if fixed causes looping

          Details

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

            Description

            • Load h_sapiens
            • chr1
            • Data Access tab selected
            • select top 3 icons (forward strand) at 145,413,190 (see attached)
            • select Selection Info tab
            • select Sliced View tab

            it throws a NPE. I fixed it in two places

            GileTypeHolder.java
            public FileTypeHandler getFileTypeHandlerForURI(String uri) {
            if (uri == null)

            { // added code return null; // added code }

            // code
            . . .

            and

            GeneralUtils.java
            public static String stripEndings(String name) {
            for (int i=0; i<compression_endings.length; i++) {
            String ending = compression_endings[i].toLowerCase();
            if (name != null && name.toLowerCase().endsWith(ending)) { // "name != null && " added

            when I make these changes, then try again, the Alt Splice View loops

              Attachments

              1. alt_slice.png
                250 kB
                Lance Frohman
              2. load.PNG
                68 kB
                Katharine Kubiak

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-661 Sliced View

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

                  Activity

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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed. Test it out.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed. Test it out.
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Did as directed, threw these errors:

                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.setColorCombobox(TrackAdjusterTab.java:704)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.trackstylePropertyChanged(TrackAdjusterTab.java:898)
                  at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:45)
                  at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:28)
                  at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280)
                  at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182)
                  at com.affymetrix.igb.prefs.TierPrefsView.refreshList(TierPrefsView.java:233)
                  at com.affymetrix.igb.prefs.TierPreferencesPanel.mapRefresh(TierPreferencesPanel.java:37)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:846)
                  at com.affymetrix.igb.action.SeqMapViewActionA.refreshMap(SeqMapViewActionA.java:62)
                  at com.affymetrix.igb.action.TransformAction.actionPerformed(TransformAction.java:30)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
                  at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:291)
                  at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
                  at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
                  at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
                  at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
                  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
                  at java.awt.Component.processMouseEvent(Component.java:6373)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6138)
                  at java.awt.Container.processEvent(Container.java:2085)
                  at java.awt.Component.dispatchEventImpl(Component.java:4735)
                  at java.awt.Container.dispatchEventImpl(Container.java:2143)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
                  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:4565)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:638)
                  at java.awt.EventQueue$1.run(EventQueue.java:636)
                  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:652)
                  at java.awt.EventQueue$2.run(EventQueue.java:650)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
                  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 thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.setColorCombobox(TrackAdjusterTab.java:704)
                  at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.trackstylePropertyChanged(TrackAdjusterTab.java:898)
                  at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:45)
                  at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:28)
                  at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280)
                  at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182)
                  at com.affymetrix.igb.prefs.TierPrefsView.refreshList(TierPrefsView.java:233)
                  at com.affymetrix.igb.prefs.TierPreferencesPanel.mapRefresh(TierPreferencesPanel.java:37)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:846)
                  at com.affymetrix.igb.tiers.SeqMapViewPopup.refreshMap(SeqMapViewPopup.java:80)
                  at com.affymetrix.igb.view.load.DataManagementTableModel.setValueAt(DataManagementTableModel.java:367)
                  at javax.swing.JTable.setValueAt(JTable.java:2710)
                  at com.jidesoft.grid.JideTable.editingStopped(Unknown Source)
                  at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:125)
                  at javax.swing.DefaultCellEditor$EditorDelegate.stopCellEditing(DefaultCellEditor.java:350)
                  at javax.swing.DefaultCellEditor.stopCellEditing(DefaultCellEditor.java:215)
                  at javax.swing.DefaultCellEditor$EditorDelegate.actionPerformed(DefaultCellEditor.java:367)
                  at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
                  at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
                  at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
                  at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:291)
                  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
                  at java.awt.Component.processMouseEvent(Component.java:6373)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6138)
                  at java.awt.Container.processEvent(Container.java:2085)
                  at java.awt.Component.dispatchEventImpl(Component.java:4735)
                  at java.awt.Container.dispatchEventImpl(Container.java:2143)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:918)
                  at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1134)
                  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:273)
                  at java.awt.Component.processMouseEvent(Component.java:6373)
                  at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
                  at java.awt.Component.processEvent(Component.java:6138)
                  at java.awt.Container.processEvent(Container.java:2085)
                  at java.awt.Component.dispatchEventImpl(Component.java:4735)
                  at java.awt.Container.dispatchEventImpl(Container.java:2143)
                  at java.awt.Component.dispatchEvent(Component.java:4565)
                  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
                  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
                  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:4565)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:638)
                  at java.awt.EventQueue$1.run(EventQueue.java:636)
                  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:652)
                  at java.awt.EventQueue$2.run(EventQueue.java:650)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
                  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
                  alyssa Alyssa Gulledge (Inactive) added a comment - Did as directed, threw these errors: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.setColorCombobox(TrackAdjusterTab.java:704) at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.trackstylePropertyChanged(TrackAdjusterTab.java:898) at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:45) at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:28) at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280) at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182) at com.affymetrix.igb.prefs.TierPrefsView.refreshList(TierPrefsView.java:233) at com.affymetrix.igb.prefs.TierPreferencesPanel.mapRefresh(TierPreferencesPanel.java:37) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:846) at com.affymetrix.igb.action.SeqMapViewActionA.refreshMap(SeqMapViewActionA.java:62) at com.affymetrix.igb.action.TransformAction.actionPerformed(TransformAction.java:30) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:291) at javax.swing.AbstractButton.doClick(AbstractButton.java:389) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6373) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6138) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4735) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4565) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282) 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:4565) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) 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:652) at java.awt.EventQueue$2.run(EventQueue.java:650) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:649) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.setColorCombobox(TrackAdjusterTab.java:704) at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.trackstylePropertyChanged(TrackAdjusterTab.java:898) at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:45) at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:28) at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280) at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182) at com.affymetrix.igb.prefs.TierPrefsView.refreshList(TierPrefsView.java:233) at com.affymetrix.igb.prefs.TierPreferencesPanel.mapRefresh(TierPreferencesPanel.java:37) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:846) at com.affymetrix.igb.tiers.SeqMapViewPopup.refreshMap(SeqMapViewPopup.java:80) at com.affymetrix.igb.view.load.DataManagementTableModel.setValueAt(DataManagementTableModel.java:367) at javax.swing.JTable.setValueAt(JTable.java:2710) at com.jidesoft.grid.JideTable.editingStopped(Unknown Source) at javax.swing.AbstractCellEditor.fireEditingStopped(AbstractCellEditor.java:125) at javax.swing.DefaultCellEditor$EditorDelegate.stopCellEditing(DefaultCellEditor.java:350) at javax.swing.DefaultCellEditor.stopCellEditing(DefaultCellEditor.java:215) at javax.swing.DefaultCellEditor$EditorDelegate.actionPerformed(DefaultCellEditor.java:367) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:291) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.Component.processMouseEvent(Component.java:6373) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6138) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4735) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4565) at javax.swing.plaf.basic.BasicTableUI$Handler.repostEvent(BasicTableUI.java:918) at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1134) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:273) at java.awt.Component.processMouseEvent(Component.java:6373) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6138) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4735) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4565) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282) 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:4565) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) 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:652) at java.awt.EventQueue$2.run(EventQueue.java:650) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:649) 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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                  hiralv Hiral Vora (Inactive) added a comment -

                  Cannot reproduce.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Cannot reproduce.
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Windows v12026

                  No errors or exceptions thrown. However the loading bar in the status bar appears and never goes away. I try to click cancel and the bar is just stuck (attached photo load.png).

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Windows v12026 No errors or exceptions thrown. However the loading bar in the status bar appears and never goes away. I try to click cancel and the bar is just stuck (attached photo load.png).
                  Hide
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Fixed in 12228.

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - Fixed in 12228.
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed Windows v12265

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed Windows v12265

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      lfrohman Lance Frohman (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: