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  1. Jalview
  2. JAL-4563

cannot import structure via URL on command line

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    • Sprint:
      2.11.5.0 alpha

      Description

      This command (or variants of it) should open the example alignment with features and a structure view bound to a sequence.

      java -jar build/libs/jalview-all-TEST-j11.jar --open https://www.jalview.org/examples/plantfdx.fa --features https://www.jalview.org/examples/plantfdx.features --structure https://www.jalview.org/examples/1gaq.txt --seqid FER1_MAIZE

      In all released versions of Jalview, the structure is not loaded, with an error suggesting the URL has not been processed correctly:

      WARN - The following errors and warnings occurred whilst processing files:
      - Structure file '/Users/jprocter/uod-development/git/jalview-2025/https:/www.jalview.org/examples/1gaq.txt' not found.

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            Assignee:
            jprocter James Procter
            Reporter:
            jsutges Javier Sanchez Utges
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              Dates

              Created:
              Updated: