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  1. Jalview
  2. JAL-1316

Support '' style escaping of quotes in Newick files

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    Details

    • Type: Improvement
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.8.0b1
    • Component/s: file format issue
    • Labels:
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      Description


      Newick tree files that contain nodes that include two consecutive single or double quotes in their names are currently not properly imported by Jalview.

      For example:

      'Syn_RCC307_5.3_3d''|CK_Syn_RCC307_2042'

      raises an exception in the jalview.io.NewickFile parser.

      The "''" in this case is generated by the NewickFile.print() method to escape node names that contain a ' - it's worth noting that this 'double-quote' escape convention (where a '' should be interpreted as a single ' in the name) is not necessarily standard procedure for NHX format, and it should be verified/qualified in the documentation.

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