Nowlan Freese added a comment - 15/Dec/25 3:56 PM Add/Remove/Edit button sometimes disappears from Filter by if the existing chain filter has long string values, Fix in commit

Nowlan Freese added a comment - 15/Dec/25 3:56 PM Seeing an error when exiting the Edit filter window via the Red X. 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:262) at com.affymetrix.igb.util.ConfigureFilters.editButtonActionPerformed(ConfigureFilters.java:158) 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) I'm not sure if this was a pre-existing issue because I do recall seeing this before but I can't find evidence of that in any related tickets. Otherwise, I am able to see and interact with the Add/Remove/Edit buttons even after adding a long string of values. The issue of those disappearing appears to have been fixed.

Nowlan Freese added a comment - 16/Dec/25 11:03 AM Testing the Add/Remove/Edit Filters window on Mac 10.1.0 - The window cannot be resized, if large number of values entered window remains the same size. Closing the Edit filter window using the red X on Mac causes an exception. 10.2.0 old commit - window can be resized, text box changes size with the window. If large number of values entered window remains the same size, but buttons disappear when window resized or clicking OK. 10.2.0 new commit - Window can be resized, but the text box remains the same size. If large number of values entered window remains the same size. Default window size cuts off right portion of buttons. The exception that Paige reported appears to be an existing issue. However, there are still some issues with the resizing of the Add/Remove/Edit Filters window, such as the sides of the buttons being cut off on Mac, and the resizing not working on the text box itself. After discussion with Karthik, he will attempt to rework the layout.

Karthik Raveendran added a comment - 17/Dec/25 10:24 AM Issue fixed in 43e676c

Paige Kulzer (Inactive) added a comment - 17/Dec/25 11:10 AM General testing procedure: Load the hg38 human genome Go to chr16:28,931,601-28,939,711 Add the 10k_PBMC_chr16.bam file (Download the file from Google Drive ) Click Load Data Right-click the BAM track label, select Filter... Click Add > Property For the value copy/paste the contents of 10k_PBMC_cluster10.txt Click OK Click OK Right-click the BAM track label, select Filter... Click Edit The Edit filter window is not formatting correctly, the comparator field is cut off as well as the OK and Cancel buttons. Moving back to To-Do.

Karthik Raveendran added a comment - 17/Dec/25 2:57 PM Issue fixed in b476849

Paige Kulzer (Inactive) added a comment - 17/Dec/25 3:16 PM I am still seeing this issue on Mac but have confirmed with Karthik that the issue is not occurring on Windows. Passing back to Karthik for further investigation into this issue.

Karthik Raveendran added a comment - 18/Dec/25 10:51 AM Paige Kulzer Please check if the issue persists in Mac fate the the new changes in 697f700

Paige Kulzer (Inactive) added a comment - 18/Dec/25 11:26 AM The comparator field is now visible in the Edit Filter window but the OK and Cancel buttons are not displayed when the window is pulled up. I can see and interact with them after expanding the Edit Filter window. Also, clicking the green + button to expand the Edit Filter window pushes the window to the bottom left of my screen and only expands it slightly, it doesn't expand it to fill my screen as I'd expect. This is true of the Add/Remove/Edit Filters window as well. Conversely, the Color by window does expand to fill my entire screen after clicking the green + button. Does this need to be fixed? Passing back to Karthik for further changes.

Paige Kulzer (Inactive) added a comment - 18/Dec/25 1:56 PM The Edit Filter window is now sized correctly and automatically displaying all of the buttons as expected. The expanding/collapsing of the window is not a priority issue so that can be something to be fixed down the road. These changes do not appear to be impacting the Filter by function and there are no errors in the Log. Recommending PR!

Karthik Raveendran added a comment - 18/Dec/25 2:55 PM - edited Squashed all prev commits to commit

Paige Kulzer (Inactive) added a comment - 18/Dec/25 3:02 PM Color by window is no longer opening in the top left corner. The Edit Filter window is formatted properly, no errors in the Log. Recommending PR!

Karthik Raveendran added a comment - 18/Dec/25 3:06 PM PR Submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1098

Ann Loraine added a comment - 18/Dec/25 3:08 PM PR is merged.

Ann Loraine added a comment - 18/Dec/25 3:31 PM Installers are built and deployed to the Early Access section of BioViz.org. Ready for testing.

Nowlan Freese added a comment - 19/Dec/25 1:38 PM Tested on main branch installer on Mac. Filter window appears normal, long user entered values do not cause the add/remove/edit buttons to disappear. Window is resizable to some extent. Closing ticket.