[IGBF-4314] Rename titles and variable names for Color by and Filter of SAMtags - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Minor
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.2.0
Labels:
None

Story Points:
0.5
Epic Link:
Do Ph.D. research in visualization
Sprint:
Fall 2, Fall 3, Fall 4, Fall 5, Fall 6

Description

Color by and Filter Functions for SAMtools Tags UI will look similar in the near future with a dialog for tables to add tag values/cluster names. This ticket is to change the titles of the dialog and some variables names as needed to differentiate clearly for the user and future developers.

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Activity

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Karthik Raveendran added a comment - 04/Sep/25 3:01 PM

See commit

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Karthik Raveendran added a comment - 04/Sep/25 3:01 PM See commit

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Paige Kulzer (Inactive) added a comment - 11/Sep/25 12:08 PM

I tested by fetching Karthik's branch and running it on my Mac. I'm seeing errors in the Log when I attempt to open the Color by table:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.util.List.add(Object)" because "tags" is null
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.refreshSAMTAGS(ConfigureOptionsPanel.java:199)
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.init(ConfigureOptionsPanel.java:129)
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.<init>(ConfigureOptionsPanel.java:99)
	at com.affymetrix.igb.util.ConfigureOptionsDialog$1.<init>(ConfigureOptionsDialog.java:65)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.init(ConfigureOptionsDialog.java:65)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:57)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:44)
	at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:71)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029)
	at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
	at java.desktop/java.awt.Component.processEvent(Component.java:6386)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

I'm seeing the same error when clicking the "Add" button in the Filter by table. I'm guessing there were some inconsistencies with variable names when making these changes.

Additionally, I have a few picky comments:

In ToolTipConstants.java, I think "SAMTags" should be "SAMtags" for consistency with other instances of this word in IGB.
In SAMtagsTable.java, should "SAMtools Tag Color Mapping" be "SAMtags Color Mapping"?

Show

Paige Kulzer (Inactive) added a comment - 11/Sep/25 12:08 PM I tested by fetching Karthik's branch and running it on my Mac. I'm seeing errors in the Log when I attempt to open the Color by table: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.util.List.add( Object )" because "tags" is null at com.affymetrix.igb.shared.ConfigureOptionsPanel.refreshSAMTAGS(ConfigureOptionsPanel.java:199) at com.affymetrix.igb.shared.ConfigureOptionsPanel.init(ConfigureOptionsPanel.java:129) at com.affymetrix.igb.shared.ConfigureOptionsPanel.<init>(ConfigureOptionsPanel.java:99) at com.affymetrix.igb.util.ConfigureOptionsDialog$1.<init>(ConfigureOptionsDialog.java:65) at com.affymetrix.igb.util.ConfigureOptionsDialog.init(ConfigureOptionsDialog.java:65) at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:57) at com.affymetrix.igb.util.ConfigureOptionsDialog.<init>(ConfigureOptionsDialog.java:44) at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:71) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) I'm seeing the same error when clicking the "Add" button in the Filter by table. I'm guessing there were some inconsistencies with variable names when making these changes. Additionally, I have a few picky comments: In ToolTipConstants.java, I think " SAMTags " should be " SAMtags " for consistency with other instances of this word in IGB. In SAMtagsTable.java, should " SAMtools Tag Color Mapping " be " SAMtags Color Mapping "?

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Karthik Raveendran added a comment - 15/Oct/25 10:34 AM

Fix the errors mentioned above. See commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/92b6b8d7f96f8803441a530c2af1c0dce0c0a071

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Karthik Raveendran added a comment - 15/Oct/25 10:34 AM Fix the errors mentioned above. See commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/92b6b8d7f96f8803441a530c2af1c0dce0c0a071

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Paige Kulzer (Inactive) added a comment - 15/Oct/25 11:15 AM

I am no longer seeing an error when clicking the "Add" button in the Filter by table. However, I am seeing an error when working with the Color by table:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.lang.Class.isInstance(Object)" because the return value of "java.util.Map.get(Object)" is null
	at com.affymetrix.genometry.general.Parameters.setParameterValue(Parameters.java:44)
	at com.affymetrix.genometry.general.Parameters.setParametersValue(Parameters.java:37)
	at com.affymetrix.genometry.color.ColorProvider.setParametersValue(ColorProvider.java:30)
	at com.affymetrix.igb.shared.ConfigureOptionsPanel.getReturnValue(ConfigureOptionsPanel.java:565)
	at com.affymetrix.igb.util.ConfigureOptionsDialog.showDialog(ConfigureOptionsDialog.java:124)
	at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:76)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029)
	at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
	at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
	at java.desktop/java.awt.Component.processEvent(Component.java:6386)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

To reproduce, add the 10X_PMBC3k QL and zoom to chr21:27,484,286-27,484,423. Add an entry to the SAMtools Tag Color Mapping window (e.g., TGTACTCAGA), assign it a color, and select the UB SAMtag. Then, click Save and Apply, click OK, and observe the error.

I'm also seeing an error that I believe is unrelated to these title/variable changes:

Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: class java.lang.String cannot be cast to class java.lang.Integer (java.lang.String and java.lang.Integer are in module java.base of loader 'bootstrap')
	at com.affymetrix.igb.util.ConfigureFilters.beginEditing(ConfigureFilters.java:256)
	at com.affymetrix.igb.util.ConfigureFilters.editButtonActionPerformed(ConfigureFilters.java:156)
	at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
	at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
	at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
	at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
	at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279)
	at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
	at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
	at java.desktop/java.awt.Component.processEvent(Component.java:6386)
	at java.desktop/java.awt.Container.processEvent(Container.java:2266)
	at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
	at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
	at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
	at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
	at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
	at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
	at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

To reproduce, add an entry to the filter by table (SAMtags or otherwise), then click Edit. Close the Edit Filter window using the red X and observe the error. Please disregard if I've already made note of this issue and a ticket has been made to address it.

Passing back to Karthik Raveendran for another round of changes.

Show

Paige Kulzer (Inactive) added a comment - 15/Oct/25 11:15 AM I am no longer seeing an error when clicking the "Add" button in the Filter by table. However, I am seeing an error when working with the Color by table: Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "java.lang. Class .isInstance( Object )" because the return value of "java.util.Map.get( Object )" is null at com.affymetrix.genometry.general.Parameters.setParameterValue(Parameters.java:44) at com.affymetrix.genometry.general.Parameters.setParametersValue(Parameters.java:37) at com.affymetrix.genometry.color.ColorProvider.setParametersValue(ColorProvider.java:30) at com.affymetrix.igb.shared.ConfigureOptionsPanel.getReturnValue(ConfigureOptionsPanel.java:565) at com.affymetrix.igb.util.ConfigureOptionsDialog.showDialog(ConfigureOptionsDialog.java:124) at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:76) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029) at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) To reproduce, add the 10X_PMBC3k QL and zoom to chr21:27,484,286-27,484,423. Add an entry to the SAMtools Tag Color Mapping window (e.g., TGTACTCAGA), assign it a color, and select the UB SAMtag. Then, click Save and Apply, click OK, and observe the error. I'm also seeing an error that I believe is unrelated to these title/variable changes: Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: class java.lang. String cannot be cast to class java.lang. Integer (java.lang. String and java.lang. Integer are in module java.base of loader 'bootstrap') at com.affymetrix.igb.util.ConfigureFilters.beginEditing(ConfigureFilters.java:256) at com.affymetrix.igb.util.ConfigureFilters.editButtonActionPerformed(ConfigureFilters.java:156) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398) at java.desktop/java.awt.Component.processEvent(Component.java:6386) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) at java.base/java.security.AccessController.doPrivileged(AccessController.java:400) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) To reproduce, add an entry to the filter by table (SAMtags or otherwise), then click Edit. Close the Edit Filter window using the red X and observe the error. Please disregard if I've already made note of this issue and a ticket has been made to address it. Passing back to Karthik Raveendran for another round of changes.

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Karthik Raveendran added a comment - 21/Oct/25 6:46 PM

One of the labels was still SAMtools which through the error above. Bug fixed in https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/9c89f86158058bd6677818624ff16ddbc2ad3e2d

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Karthik Raveendran added a comment - 21/Oct/25 6:46 PM One of the labels was still SAMtools which through the error above. Bug fixed in https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/9c89f86158058bd6677818624ff16ddbc2ad3e2d

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Paige Kulzer (Inactive) added a comment - 22/Oct/25 10:28 AM

I refetched this branch and tested for the above errors. All reported errors have been fixed and I am unable to find any new ones while using the Color and Filter by features. Looks good, ready for PR!

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Paige Kulzer (Inactive) added a comment - 22/Oct/25 10:28 AM I refetched this branch and tested for the above errors. All reported errors have been fixed and I am unable to find any new ones while using the Color and Filter by features. Looks good, ready for PR!

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Karthik Raveendran added a comment - 24/Oct/25 4:29 PM

PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1083

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Karthik Raveendran added a comment - 24/Oct/25 4:29 PM PR Submitted https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1083

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Ann Loraine added a comment - 29/Oct/25 10:04 AM

PR is merged, new installers are built and deployed to bioviz.org.
Read for final testing.

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Ann Loraine added a comment - 29/Oct/25 10:04 AM PR is merged, new installers are built and deployed to bioviz.org. Read for final testing.

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Paige Kulzer (Inactive) added a comment - 29/Oct/25 12:22 PM

Downloaded the early access release from bioviz.org and tested for any remaining issues related to variable names. I'm unable to find any errors, color and filter by functionality is working as expected.

Closing ticket.

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Paige Kulzer (Inactive) added a comment - 29/Oct/25 12:22 PM Downloaded the early access release from bioviz.org and tested for any remaining issues related to variable names. I'm unable to find any errors, color and filter by functionality is working as expected. Closing ticket.

People

Assignee:

Karthik Raveendran

Reporter:

Karthik Raveendran

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Watchers:

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Dates

Created:

04/Sep/25 1:47 PM

Updated:

02/Dec/25 10:31 AM

Resolved:

29/Oct/25 12:22 PM