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  1. Jalview
  2. JAL-4216

chains in PDB or mmCIF files with negative RESNUMs for their whole sequence extent throw exceptions

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Incomplete
    • Affects Version/s: 2.11.2.6
    • Fix Version/s: 2.11.3.0
    • Component/s: Structures
    • Labels:

      Description

      Retrieval of a structure like 7W5B - an em structure - fails in the PDB fetcher.

      Culprit in this case is a chain with authornum running from -13 to -1 for modelled coordinates in chain 4 (author provided chain numbering).

      java.lang.NegativeArraySizeException
      at jalview.ext.jmol.JmolParser.addSecondaryStructureAnnotation(JmolParser.java:437)
      at jalview.ext.jmol.JmolParser.createAnnotation(JmolParser.java:414)
      at jalview.ext.jmol.JmolParser.transformJmolModelToJalview(JmolParser.java:277)
      at jalview.ext.jmol.JmolParser.parse(JmolParser.java:125)
      at jalview.io.AlignFile.doParse(AlignFile.java:208)
      at jalview.io.AlignFile.doParse(AlignFile.java:196)
      at jalview.io.AlignFile.<init>(AlignFile.java:143)
      at jalview.io.AlignFile.<init>(AlignFile.java:120)
      at jalview.io.StructureFile.<init>(StructureFile.java:74)
      at jalview.ext.jmol.JmolParser.<init>(JmolParser.java:78)
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:184)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:241)
      at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:168)
      at jalview.gui.SequenceFetcher.fetchSingleAccession(SequenceFetcher.java:800)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:582)
      at java.lang.Thread.run(INFO - Error retrieving 7w5b from PDB
      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:245) ~[jalview.jar:2.11.2.6]
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:241) ~[jalview.jar:2.11.2.6]
      at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:168) ~[jalview.jar:2.11.2.6]
      at jalview.gui.SequenceFetcher.fetchSingleAccession(SequenceFetcher.java:800) [jalview.jar:2.11.2.6]
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:582) [jalview.jar:2.11.2.6]
      at java.lang.Thread.run(Thread.java:748) [?:1.8.0_202]
      Thread.java:748)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated:
              Resolved: