It works as expected. No pop-up is shown with the error but is logged on the consoled.

Merged and ready for testing.

PR submitted

https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/772/igbf-2270-replace-call-to-errorpanel-with/diff

I just reviewed the changes that are made for the same in order to remove the error panel that was showing message: "The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix.". A logger is added instead of the error panel which is showing the same message in the console.
I have also tested it with IGB and it looks fine. Attaching screenshot for the reference.
Please submit a PR for the same.

Thank you!

Branch with changes: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2270-manySeqMessage

To test:
In IGB, open Xenopus tropicalis Nov 2009. The console should log the warning:
"The file contains data for too many sequences; some may not be shown. If this is a problem, please compress and index the file using tabix."
No popups regarding the warning should occur.

I changed the handling of the issue so that instead of presenting the user with a popup it is logged to the console.

There seems to be several things going on with this issue.
1) The X tropicalis Nov 2009 refgene file (X_tropicalis_Nov_2009_refGene.bed.gz) is gzipped, but does not have a tabix index.
2) This issue is related to https://jira.transvar.org/browse/IGBF-33. However, IGBF-33 did not fully address the original issue, which was meant to be addressed by additional refactoring that never occurred (https://jira.transvar.org/browse/DB-166).