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  1. Jalview
  2. JAL-629

create sequence/structure associations and add associated data via command line

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    • Sprint:
      2.11.3.0 release

      Description

      This was an outstanding feature for the original launchApp service - it is still relevant, so giving it a bump:

      Currently, PDB files cannot be associated with aligned sequences via the command line, which means Jalview cannot be used for batch generation of figures from alignments linked with structure data.

      The main thing that needs to be fixed for this to happen:

      * A new command line argument is needed so specific structure data files can be loaded onto the alignment being imported in to the application

      This CLI arg need to also allow additional data to be passed - e.g. pae files, reliability score data.

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          Epic - Created by Jira Software - do not edit or delete. Issue type for a big user story that needs to be broken down. JAL-2349 Contact prediction visualisation

          • Major - Major loss of function.
          • In Progress

          New Feature - A new feature of the product, which has yet to be developed. JAL-2382 Import and display sequence-associated contact predictions in CASP-RR format

          • Major - Major loss of function.
          • In Progress

          New Feature - A new feature of the product, which has yet to be developed. JAL-3858 Import and display alphafold predicted alignment error matrices from JSON

          • Major - Major loss of function.
          • Closed
          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-4312 concurrent modification exceptions during CLI tests

          • Major - Major loss of function.
          • Closed
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-4160 New command line argument framework

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-4187 Powershell launcher script fails when given no arguments with the old ArgsParser

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-4185 Add argument to allow concurrent AlignFrame operations when being run from the command line with batch processing

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • In Progress

          New Feature - A new feature of the product, which has yet to be developed. JAL-4167 Create separate gradle test task for some tests

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4121 Assume --headless when jalview is run with a command line argument that generates output

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed
          mentioned on

          GitLab Commit - JAL-4490 release notes for JAL-4491 JAL-4503 JAL-4504 JAL-629

          GitLab Commit - JAL-4503 patch regression introduced in JAL-629 by JBP...

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              Assignee:
              soares Ben Soares
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: