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