The user has also requested that we add the ability to persist "filter by" options for tracks as well. We should discuss what other aspects of IGB should be persisted to increase usability for people who work often with IGB.

Mason, please create a separate issue for the request to persist filter-by options between sessions. Also, please provide a link to the BioStars post, if there was one.

3/8/17 discussion - Ann & Devdatta:

We discussed how to implement this. IGB already has a system for persisting track sessions between sessions using a preferences sub-system within IGB.
Also, we noted that IGB previously had a feature that enabled users to "Export Preferences" and "Import Preferences." Go to the on-line User's Guide and search "Export Preferences" to find documentation.
In addition, Devdatta noted that there is an "action" object in IGB that performs export of preferences, but this action is not reachable within the GUI, although the Preferences Toolbar window refers to it. (See attachment.)

Probably the safest, smartest, most robust approach will be to use the current preferences subsystem architecture in IGB to save heatmap settings. However, we imagine there will be many parameters to capture from a session. One challenge will be ensuring synchronization between the heatmap editor GUI widget and tracks that have been configured with heatmap settings.

Requirement:

If a track has been configured to use a heatmap, its heatmap settings should be preserved between sessions, even if the user has changed from heatmap visualization to something else.

After reading notes from the discussion above, I understand that you are planning to use the existing preferences sub-system for the heatmap persistence feature. I wanted to point out that the session saving feature currently does not work for custom genomes. Do you think that may mean heatmap settings may not be persisted for custom genome tracks with this planned implementation? If you think that is a major problem, we may need to figure out another way to implement persistence of heatmap settings or we could plan to make session saving work for custom genomes instead.

Good question. I think actually it will be fine — I've shown Devdatta how IGB "remembers" color and other track settings between sessions. This works quite well – everything you configure (except Color by.. settings) for a track is "remembered" in future sessions. I believe this is using a sub-system in IGB that is different from the session saving and session reloading feature. (Which is buggy, as you mentioned.)

My testing verifies that this story has been resolved. Heatmap settings are now being persisted between sessions for each track, until IGB Preferences are reset to default. Also, several heatmap settings may be stored for each track depending on the field being colored by, which is excellent. The color by feature must still be applied each session, but I am assuming that this is expected. If we wish for the saved colors to be automatically applied upon loading a track with color data, I can create a new story to track this, but I will wait until I hear that the behavior is desired. The heatmap setting persistence is also working for custom genome tracks, which is excellent. Since this story has been resolved, it will now be closed. Great work!