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  1. Jalview
  2. JAL-4593

Fileformat Exception reported for retrieval of a nonexistant PFAM accession rather than recognising when entry 'Does not exist'

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Trivial
    • Resolution: Unresolved
    • Affects Version/s: 2.11.5.0
    • Fix Version/s: 2.12.0
    • Component/s: web service bug
    • Labels:
      None

      Description

      Noticed the output below in the log for a non-existent PFAM retrieval. The dialog reports 'Couldn't retrieve PF0200008' - might be nicer to detect when we get a 'does not exist' response.

      INFO - Error retrieving PF020008 from PFAM (Full)
      jalview.io.FileFormatException: Formats currently supported are
      Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, and Jalview.
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:252) ~[jalview.jar:2.11.5.0-test]
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:236) ~[jalview.jar:2.11.5.0-test]
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:161) ~[jalview.jar:2.11.5.0-test]
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:154) ~[jalview.jar:2.11.5.0-test]
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:245) ~[jalview.jar:2.11.5.0-test]
      at jalview.ws.dbsources.Xfam.getSequenceRecords(Xfam.java:70) ~[jalview.jar:2.11.5.0-test]
      at jalview.gui.SequenceFetcher.fetchSingleAccession(SequenceFetcher.java:841) [jalview.jar:2.11.5.0-test]
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:623) [jalview.jar:2.11.5.0-test]
      at java.lang.Thread.run(Thread.java:750) [?:1.8.0_372]

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: