Within the class ToggleShowAsPairedAction, David Norris left a comment about needing to register state in the java preferences. Looking at the ToggleToolTipAction class file, this may be a couple lines of code to save to preferences in the PreferenceUtils.

Need first level review for the branch
https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1442-sc-settings

Thanks

Looks like this got forgotten. Someone should pick it up - please grab the code, rebase, test, and move into 1st level review. Please consult with Dr. Freese as required.

I have merged the latest changes with this branch.

Testing Steps followed:

1. Loaded a bam file and changed the soft clips settings.
2.Saved the session
3.Re-loaded the session and the settings were restored.

Working as expected.

Since I do not have write access to kiran korey's fork I have pulled the changes from his fork to mine

https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-1442#diff

Noor Zahara, it is working as expcted. Code level review has been done for the same. You can now submit a pull request for it.

Needed two small changes in TrackStyle.java. There were two places where the boolean values for soft clipped custom color were being incorrectly assigned by the default color.

Made changes and issued pull request .

The soft clip settings are otherwise being correctly saved in the session xml, and between IGB sessions.

Noor Zahara, I have followed the steps mentioned above to test the ticket i.e. I have changed the soft clicked settings to use the custom color and then I saved the session. When I loaded the same saved session then the setting which was done previously was preserved.
Working as expected. Moving the ticket to DONE.