Good catch.

Please review the adjusted code:
https://bitbucket.org/anhmoss/integrated-genome-browser/branch/IGBF-1308-ProtAnnotWindowTitle

I found the code that was affecting the title of the ProtAnnot window, which was adding 'chr' as a prefix to any title that did not already start with 'chr'. This was an issue because not all titles started with the lowercase prefix 'chr', so it was appearing twice 'chrChr1' in chromosome titles. Other genomes, such as the blueberry genome, have scaffolds titled as 'scaffold00001'. Others are contigs, and etc. I fixed this error by deleting the code that was adding this prefix.

To test:
• I cleaned and rebuilt the ProtAnnot project.
• Since the ProtAnnot app was still showing version 9.0.0, we removed the default remote repository, and then created, added and installed a local repository, which then reflected app version 9.0.1. This indicated that the ProtAnnot repo had a separate update cycle from IGB.
• We talked to Kiran, and he said he had submitted a recent fix that might've interfered our code change, so we reverted my repo copy to an earlier commit (commit id: 5748edd7f) before his changes, rebuilt the ProtAnnot project, and was able to see our code changes reflected in ProtAnnot window.

Thank you.

Recent fix by Kiran blocks user from installing plug-ins (Apps) from local repository. Commit link:
https://bitbucket.org/lorainelab/integrated-genome-browser/commits/bec9bf3567dd6370239ea136e6455491d6ff1275
IGBF-1108:Added condition to check network connection before installing plugin

Found Anh's branch:
https://bitbucket.org/anhmoss/integrated-genome-browser/branch/IGBF-1308-ProtAnnotWindowTitle

Since there is a recent commit that would make it hard to test this, I am using the released version installed on my machine.
This shortly after the 9.0.1 release that is really close to the current master.

functional test
I checked out Anh's branch. I removed the target directory in the ProtAnnot module and then built the ProtAnnot module. I opened IGB (the released version). I added my local copy of the ProtAnnot target directory as an app repository, and disabled the bioviz one. installed protannot, selected a gene model, started protannot. The sequence name looks correct (no added "chr"). Then I uninstalled protannot, disabled the local app repo, re-enabled the bioviz app rep, and installed protannot (from bioviz). I selected the same gene model and started protannot. Now the sequence is incorrect, it displays as "chrChr1". This confirms that the Anh's changes removed the 'chr' that appears when you install protannot from bioviz.

code review,
Looking at the changes in bitbucket, the change is very minor, and I do not see any potential for side effects.

git review
All changes are in a single commit with an appropriate message.
The branch is currently two commits behind Anh's master, so it needs to be rebased.

I am reassigning this to Anh to do the rebase and then submit a pull request.
Anh, be sure to update your local master from upstream master, then rebase this branch onto your master, and push both master and this branch to your remote. Check that the branch says 'ahead by 1 commit' relative to your master.

Pull request merged.

I am not currently seeing this issue as resolved. When I open ProtAnnot using the IGB App Manager, I am seeing content in the title bar such as "chrChr1". Should I be testing this story a different way besides using the App Manager? For now, I am re-assigning this story to Ann and moving to To-Do.

After clarifying the testing protocol, I am moving this back to Needs Testing and assigning it to Mason.

My testing confirms that the contig name error is fixed in ProtAnnot. I am no longer seeing the additional "chr" text in the window title. I am also not experiencing any side effects related to this change, so the story will now be closed.