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  1. Jalview
  2. JAL-681

modifying start/end via the sequence ID edit box can cause exceptions and corrupt sequence feature display

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.6
    • Fix Version/s: None
    • Component/s: Datamodel, gui
    • Labels:
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      Description

      Modifications of the start/end numbering by inserting a new '/start-end' phrase at the end of a sequence's ID in the edit sequence ID text box are not properly validated (ie the stated length can be less or more than the actual number of symbols present in the sequence) - leading to exceptions and problems with feature display:

      1. Cigar based AlignmentView creation can fail with an exception raised about inconsistencies between the alignment's start/end position and the dataset sequence's start/end.
      2. If (end-start+1) is shorter than the actual non-gap character symbol string length then sequence features after the stated end position will not be rendered. If end<start then no sequence features are rendered at all.

      Workarounds - which will result in the displayed end position being re-calculated correctly:
      1. copy and paste the alignment into a new window.
      2. export the alignment to a flat file and re-import.


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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: