Issues to implement at WormBase

[scottcain]

In order to implement JBrowse 2 at WormBase, I need a few items implemented:

Need to have:

1. A lib that provides programmatic access to the functions that make jb2export work. This is needed to create a web service that can return an SVG for inlining in feature pages.
2. Ability to resize track height in response to the “internal” height of the track. (Essentially Auto-adjust track heights to their current layout height #534) I would like to have this for both:

• LGV so that the embedded view could optionally automatically scale in height.
• For the lib that would be used for a svg web service.

Nice to have:

3. “Universal” NClist support (LGV and lib that would be used for a web service); probably useful for other sites looking to migration from 1 to 2.
4. Track content filtering (Allow custom filtering expressions to be applied to state or configuration of tracks #1988); would allow more general GFF use rather than requiring a GFF per track (example: at WormBase, we have multiple “Gene” tracks (all, coding, noncoding, pseudo, and historical) and it would nice to just use one GFF all of these tracks).
5. A final thing that I just thought about and don’t know much about is plugin support for LGV and the web service lib: I’d like to be able to use the simple jexl plugin that generates score-based color gradients.

For (2), I don't know that it has to be a complete, system wide option. I imagine that, somewhere in the code, it is known what the height of the internal track is (during layout of features, you can keep the largest value, right?). Couldn't this be passed back up the chain to somewhere that it could be exposed via a method call? Then one could issue the command to draw the layout again, but this time with the height that was determined before. It might be nice if the previous layout were cached, but that can be a problem for later.

[cmdcolin]

probably the (2) we will make a specialized flag for the exporter that makes it adjust the height of the tracks to the layout height

[cmdcolin]

I think these features all refer to other issue threads, if interested can tag them