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  1. Jalview
  2. JAL-1722

Jalview becomes slow when large numbers of columns are hidden

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.0
    • Component/s: Efficiency
    • Labels:
      None

      Description

      The 'hide gaps' command reference sequence allows lots of hidden regions to be created easily. This revealed that Jalview's redraw algorithm becomes very slow when working with lots of hidden regions.

      Need to take a look at the jalview.datamodel.ColumnSelection object and how it is used by the sequence renderer and alignment panel canvas and work out a way to make redraws occur in (near) constant time regardless of hidden regions. It may be that instead of the existing implementation (Integer object looked up in HashMap of integers), we will need to use a BitSet.

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          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2524 Too wide a region can be rendered if hidden columns present

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

          Task - A task that needs to be done. JAL-2001 Refactor ColumnSelection to store ranges rather than individual selected columns

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-926 Provide a rendering that indicates the size of hidden regions in figures

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

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2050 Hide introns in locus/transcript view

          • Major - Major loss of function.
          • Closed

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: