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  1. Jalview
  2. JAL-3851

Prototype comms for JBrowse(2)

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    Details

    • Type: New Feature
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2
    • Fix Version/s: None
    • Component/s: REST-API
    • Labels:
      None

      Description

      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 ?

        Attachments

        1. notes.odt
          14 kB
          Ben Soares
        2. Screenshot_20210721_180643.png
          144 kB
          Ben Soares

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              Assignee:
              soares Ben Soares
              Reporter:
              soares Ben Soares
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                Dates

                Created:
                Updated: