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  1. Jalview
  2. JAL-1841

RNA structure consensus is only calculated for base pairs marked with (), and counts are buggy

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.8.2, 2.9
    • Fix Version/s: 2.10.0
    • Component/s: jvdesktop, jvlite, na
    • Labels:
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      Description

      Import some RNA and manually create base pairs by adding an annotation row and right clicking a region, and set the symbol to be either '<' or '>'.

      Jalview will show arrows for these regions, but once the structure consensus row has been created (currently via creating a new view - see JAL-1577), no base pair logo will be shown, even though the Helix colouring will highlight these regions as paired. Conversely, importing a file with base pairs marked in this way works fine - Jalview translates them to an internal representation that is recognised by the calculation routine.

        Attachments

          Issue Links

          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2214 Distinguish between canonical and WC dominated base-pair patterns in StructureConsensus annotation

          • Major - Major loss of function.
          • Closed
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2118 annotation sorting reorders annotation row after it is created and placed

          • Blocker - Blocks development and/or testing work, production could not run.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-1577 colour by RNA Helices not enabled when user created annotation added to alignment

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2171 Default RNA SS to 'matching bracket' for manual entry

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-2215 Modifying the ignore gaps in consensus setting for a view doesn't refresh annotation panel

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: