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  1. Jalview
  2. JAL-4353

Cannot output individual images of more than one structure view attached to one open alignment

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.3.2
    • Fix Version/s: 2.11.3.3
    • Component/s: Command Line Interface
    • Labels:
      None
    • Urgency:
      Urgent
    • Sprint:
      2.11.3.3 release

      Description

      When attempting to output structure images of multiple structures opened for one or more sequences in a single alignment, each structure has its image written over all of the output structure image filenames.

      e.g.
      jalview --open alignment.fa \
      --structure struc1.pdb --seqid 101 --structureimage struc1.png \
      --srtucture struc2.pdb --seqid 101 --structureimage struc2.png \
      --all --overwrite

      will result in the image of struc1.pdb first being written to BOTH struc1.png and struc2.png, and THEN
      the image of struc2.pdb will be written to BOTH struc1.png and struc2.png.

      --structureimage should be limited after a --structure argument up to the next --structureimage, or next --open.

      This can probably be done relatively easily by adding a Type.STRUCTURE (like the Type.IMAGE, although --structureimage will be both, with Opt.PRIMARY applying to both -- might be worth adding an Opt.STRUCTUREPRIMARY, Opt.IMAGEPRIMARY though this becomes slightly less generic).

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            Assignee:
            soares Ben Soares
            Reporter:
            soares Ben Soares
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              Updated:
              Resolved: