interpret jbrowse-style category look and feel on the Track Panel

[childers]

Currently the tracks panel is a straightforward listing of available tracks, with a developer centric Details panel at the bottom (Fig 1). Are there plans to support organization via categories in the new UI? Clicking the "Full-screen view" does pop it out into a new JBrowse window, with all of the 'classic' settings intact.

Do you envision people working from new UI in general (all of the other screenshots I've seen use it), or popping out to the 'traditional' view for working? The users are free to adopt whatever methods that work best for them, but I am very interested in how you see this tool being used.

We've spent a good amount of time creating a system for managing larger numbers of tracks, and I'd like to know the best ways for making use of them moving forward (Fig 2).

Thanks for reading all the way to the bottom!

[nathandunn]

Replaces #227 because this has nicer pictures.

[nathandunn]

We definitely did plan to add it back after the initial release. @cmdcolin that could even be an HTML Panel and utilize much the same code . . or it could be rendered in GWT.

[nathandunn]

@childers We support the users using whatever work-flow works for them, so we support both of the models you mentioned above. If there was a simple way to put the old tracks in the new side-bar, I think we would do that. A more likely solution will be creating an HTML view of the page and using largely the same code from the existing JBrowse side-bar.

[childers]

@nathandunn This project has been great about being flexible to support different usage scenarios; I'm interested in how the vision for using Web Apollo is changing to reflect the significant new features and interfaces. It's a complicated question that I found myself pondering as I interacted with the new UI. I imagine you've had the same questions, and would love to hear your thoughts, especially if there are tips and tricks for building a better experience for the end users.

[nathandunn]

@childers Sorry, I lost all of these emails in an over-zealous junk folder. I would love to chat about this (this Thursday). My original plan was to put the other track window back on the other side using largely the same code.

[childers]

@nathandunn No worries, we've all got a lot of irons in the fire. I look forward to talking more with you about it on Thursday.

[nathandunn]

• add / exposed faceted to add (if exists)
• add configurable tracks as well (re-parse the current)

[nathandunn]

FYI @cmdcolin / @monicacecilia

[cmdcolin]

Technically we are just using "&tracklist=0" on the jbrowse frame which suppresses the native tracklist. We could re-enable it but at the cost of screen real estate

[cmdcolin]

In the email thread we said that we can basically add a category falg to the track selector

I think this is pretty much the best stop gap solution because if it goes further than that, then there are screen real estate issues

[nathandunn]

I think category selector is good.

If there is a way we could trigger the facet selector (if it is there) that would be good as well. If you know what the hook is there, I can register the function.

Nathan

On Oct 7, 2015, at 2:16 PM, Colin Diesh notifications@github.com wrote:

In the email thread we said that we can basically add a category falg to the track selector

I think this is pretty much the best stop gap solution because if it goes further than that, then there are screen real estate issues

—
Reply to this email directly or view it on GitHub #536 (comment).

[nathandunn]

So . . to paraphrase what we discussed today:

• provide a way to show facets (i.e, tracklist=1 instead of 0) from Apollo if JBrowse is configured as faceted
• for category tracks, expose the additional emulation data to expose the tracks

I was looking at the differences between the faceted and category, but they seem very different beasts. Looking at the categories, though I don't think that emulation will be too bad.

[nathandunn]

Added discussion note that the facet button can be close, but not in the exact place as above:

• move / update "JBrowse-style track selector button"

[hexylena]

Another +1 for this. I've basically settled on automatically hiding apollo panel + forcing JBrowse selector on as a result of this issue. This was mildly annoying before (and some users were happy to scroll through the unsorted apollo track list in preference to the JBrowse list), but now it is an actual issue as there are multiple identically named tracks that are in different (meaningful) places in the hierarchy

As you can see in the picture, we re-run our functional annotation workflow every so often which generates another set of duplicately named tracks. Users cannot tell which "TMHMM" named track is the correct (i.e. latest) one in the apollo panel.

[nathandunn]

@erasche Do you have a trackList.json or tracks.conf file (obscured is fine) that I could look at to make sure I could support this?

I think if I just convert it to a tree widget it should be fine. The category functionality is relatively straight-forward.

[nathandunn]

The use-cases are just:

• layered (A/B/C, etc.)

@erasche If its pretty easy (like a couple of hours), I'll see if I can't get something done, otherwise it may be for another time/ day.

[hexylena]

Sure thing @nathandunn. This link should work: trackList.json

As per usual, no pressure / rush from me on this. I have a work around that's fine for the foreseeable future.

[nathandunn]

No worries. I thought I'd have a couple of hours, I wanted to take a crack at it. Wanted to pull some nice stuff with projection.

I could use another tree item, but I think the collapse panels actually look better (if I can appropriately size them):

https://gwtbootstrap3.github.io/gwtbootstrap3-demo/#collapse

[nathandunn]

Closing for now per #1526. If we need more depth or other features, we can open another issue.