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  1. Jalview
  2. JAL-703

CAth das server errors appear as features in the alignment

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: web service bug
    • Labels:
      None

      Description


      Fetching features using incorrectly formatted IDs from the cath DAS source results in features like the following being created on the alignment:

      STARTGROUP cath
      BAD PDB FORMAT (FER_CAPAA): try '1xxx', '1xxxA' or '1xxxA01' FER_CAPAA -1 0 0 0.0
      BAD PDB FORMAT (FER_CAPAN): try '1xxx', '1xxxA' or '1xxxA01' FER_CAPAN -1 0 0 0.0
      BAD PDB FORMAT (FER1_SOLLC): try '1xxx', '1xxxA' or '1xxxA01' FER1_SOLLC -1 0 0 0.0
      BAD PDB FORMAT (Q93XJ9_SOLTU): try '1xxx', '1xxxA' or '1xxxA01' Q93XJ9_SOLTU -1 0 0 0.0
      BAD PDB FORMAT (FER1_PEA): try '1xxx', '1xxxA' or '1xxxA01' FER1_PEA -1 0 0 0.0
      BAD PDB FORMAT (Q7XA98_TRIPR): try '1xxx', '1xxxA' or '1xxxA01' Q7XA98_TRIPR -1 0 0 0.0
      BAD PDB FORMAT (FER1_MESCR): try '1xxx', '1xxxA' or '1xxxA01' FER1_MESCR -1 0 0 0.0
      BAD PDB FORMAT (FER1_SPIOL): try '1xxx', '1xxxA' or '1xxxA01' FER1_SPIOL -1 0 0 0.0
      BAD PDB FORMAT (FER3_RAPSA): try '1xxx', '1xxxA' or '1xxxA01' FER3_RAPSA -1 0 0 0.0
      BAD PDB FORMAT (FER1_ARATH): try '1xxx', '1xxxA' or '1xxxA01' FER1_ARATH -1 0 0 0.0
      BAD PDB FORMAT (FER_BRANA): try '1xxx', '1xxxA' or '1xxxA01' FER_BRANA -1 0 0 0.0
      BAD PDB FORMAT (FER2_ARATH): try '1xxx', '1xxxA' or '1xxxA01' FER2_ARATH -1 0 0 0.0
      BAD PDB FORMAT (Q93Z60_ARATH): try '1xxx', '1xxxA' or '1xxxA01' Q93Z60_ARATH -1 0 0 0.0
      BAD PDB FORMAT (FER1_MAIZE): try '1xxx', '1xxxA' or '1xxxA01' FER1_MAIZE -1 0 0 0.0
      BAD PDB FORMAT (O80429_MAIZE): try '1xxx', '1xxxA' or '1xxxA01' O80429_MAIZE -1 0 0 0.0
      ENDGROUP cath

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated: