I changed the position of the View menu to be in between Bookmarks and Help menus.

This is how it looks:

It no longer covers up the filter symbol or the "collapse option" button.

To achieve this, the method called initializeParentMenuEntries() in MenuBarManager.java was changed from:

parentMenuEntries.put(0, fileMenu);
parentMenuEntries.put(1, editMenu);
parentMenuEntries.put(5, viewMenu);
parentMenuEntries.put(10, toolsMenu);
parentMenuEntries.put(100, helpMenu);

to

parentMenuEntries.put(0, fileMenu);
parentMenuEntries.put(1, editMenu);
parentMenuEntries.put(5, toolsMenu);
parentMenuEntries.put(20, viewMenu);
parentMenuEntries.put(100, helpMenu);

After implementing it, I realized that the menu can still cover the "collapse option" button if the user stretches the label window of the track to the right, so it's right under the menu.
The filter mark however is always present on the far left of the track label window, so it does not get affected when the user stretches the track label window to the right.

In addition, I have seen Chirag's changes of moving the icons of the button to the right of the text and enabling the check mark to be visible, and his changes can be applied over my current changes of moving the View menu's position to make the user experience much better.

Please see the following commit for changing the View menu position:
https://bitbucket.org/Gchamma/integrated-genome-browser/commits/2393ea815983dddb015aa01f8a9e05785d62e6c5

Branch: https://bitbucket.org/chirag06/integrated-genome-browser/src/IGBF-2465/

Please submit PR.

Pull request submitted:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/815/change-view-menu-position-to-be-after/diff

I merged this before I noticed a problem with the commit message: It needs to contain the Jira ticket number to ensure that we can easily find the ticket from the ticket commit message. It is too late to fix this now because I've already merged it. Please make note Jay Chamma to include the Jira ticket number in future commit messages.

pull request submitted:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/816

[~aloraine] My mistake. I will make sure to include the ticket number for future pull requests.

Both branches are now merged. Master branch installers are building.

Tested this ticket. The position of the View menu is now between Bookmarks and Help menus. The checkmarks are now visible and the icons are shifted to right. Also, there exists a horizontal line separator between MenuItems 'Show All Visual Tools' and 'Show Zoom Stripe' and also between 'Show Full File Path in Track' and 'Set AutoLoad Threshold to Current View'.

For the next steps, Logan Weidenhammer - could you run the new master branch installers (from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/) and comment on the change in usability?

If at all possible, please do this today (Wed).

I have run IGB off of the newest master branch installers from earlier today. It appears that this version, versus the one we were testing off of previously from last week, has a new issue where clicking on "Show all visual tools" or "Hide Visual Tools" is not switching the state of "Show Data Tooltip" and "Show Full File Path In Track" submenu options. Chirag has been able to reproduce this on his machine as well.

All of Shamika's findings from her previous comment are still accurate: New location of view menu, checkmarks are visible, horizontal separator is present.

Otherwise the usability is improved. Some items relevant to the functionality affected by the options within the View menu are now visible. The separators also help with understanding how each option differs in it's type of functionality (e.g. on or off). The checkmarks are now present, creating a common look across the options and reducing confusion.

Going forward, I think we should investigate what has caused the change in function of the "Show All Visual Tools" and "Hide Visual Tools" options in the View menu between this week's installers and last week's installers.

Moving back to To-Do and requesting investigation into this issue.

Chirag Chandrahas Shetty,
Per Dr. Freese, since the options in question do not act on the main canvas in IGB, they do not need to be toggled by the "Show all visual tools" or "Hide Visual Tools" options.

The "Show Data Tooltip" and "Show Full File Path In Track" options should be moved to below the dividing line within the View menu.

Branch: https://bitbucket.org/chirag06/integrated-genome-browser/branch/IGBF-2465

Tested on Windows

View menu is in the correct position between “Bookmarks” and “Help”.
Submenu items are divided by separator lines.
Check marks are present.
All items affected by “Show All Visual Tools” and “Hide Visual Tools” are grouped together.
“Show data tooltip” and “Show Full File Path In Track” are moved to the grouping below.
Code changes appear appropriate.

Ready for Pull Request

Submitted Pull Request:

https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/819

Merged and master branch installers are built. Ready for testing.

Working as expected. Moving it to done.