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  1. Jalview
  2. JAL-3240

Remove gaps / gapped columns doesn't adjust hidden or selected columns

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    Details

    • Type: Bug
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.3, 2.10.5
    • Fix Version/s: None
    • Component/s: editing
    • Labels:
      None
    • Environment:
      Jalview Installation: installAnywhere git-commit:5610d0f
      Java version: 1.8.0_92
      x86_64 Mac OS X 10.14.4

      Description

      I'm attempting to refine an alignment to create a figure containing just a region of interest, so have many columns of the alignment and some sequences hidden. If I now attempt to remove empty columns, with nothing selected, all columns are removed from the alignment.

      The previous attempt at removing empty columns prior to hiding a further sequence showed similar but less dramatic effects, with all columns up to 964 (I think) being removed, some of which are clearly not empty.

      I've attached screenshots from before I attempt to remove empty columns (and a matching project), and following removal of 'empty' columns...

      It appears possible to work round the issue by filtering by occupancy, although this results in the hidden columns becoming unhidden again

        Attachments

        1. remove_empty_gaps.jvp
          58 kB
          James Abbott
        2. Screenshot 2019-04-29 at 11.41.49.png
          156 kB
          James Abbott
        3. Screenshot 2019-04-29 at 11.42.12.png
          52 kB
          James Abbott

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              j.abbott@dundee.ac.uk James Abbott
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                Dates

                Created:
                Updated: