Jalview REST API for Interoperation with Genome Browsers

This is an issue to hang prototyping live comms between Jalview and JBrowse onto.

Jim's notes (see attached odt and screenshot):
Jalview <> JBrowse2
Take a look at the 2.11.2 code for spinning up rest servers to communicate with structure viewers
Create prototype
HTTP Interface with endpoints for
Initiate a session
/viewgene
Ensembl:geneid
Jalview retrieves Gene from Ensembl
(optionally) Jalview shows gene as splitframe
Return an ID that client can use to
Check whether jalview has finished loading
https://www.jalview.org/old/v2_5_1/applet/formComplete.html
(extensions would be to post files, sequence db
Given a loaded dataset/session
For a specific alignment view/data OR ‘general broadcast’
Highlight region
{ID + position/range}..
Select region
{ID + position/range}...
Prototype stage 2
POST to JBrowse2 for
View Gene ID in JBrowse2
Once opened, mouse overs and selections would be propagated
Demo
Jalview launched from JBrowse2
Passes in JBrowse2 API port as an argument ?