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  1. Jalview
  2. JAL-2954

select highlighted columns slow for very large alignments

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 2.10.3, 2.10.3b1
    • Fix Version/s: 2.10.4
    • Component/s: Efficiency
    • Labels:
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      Description

      Import a large (>1000 sequence) alignment and create a find expression to select two or three positions. Hit B - note in profile that jalview.datamodel.Alignment.getWidth() is called multiple times via getEndRes and SearchResults.markColumns(). This is expensive - getWidth() could cache results but it's recommended to just call it once and cache before any looping over sequences.

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter Jim Procter
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