Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: 2.8.2b1, 2.9, 2.9.0b2
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Fix Version/s: 2.10.0
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Component/s: None
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Labels:None
Description
While executing the SIFTS N2NScan, I discovered that the PDBfile parser throws an Arithmetic exception caused by division by zero.
To reproduce, try fetching one of the following entries using the PDB sequence fetcher: 1a08; 1a09; 1a07; 1a1a; 1a1b; 1a1b; 1a1e.
Stack trace:
java.lang.ArithmeticException: / by zero
at MCview.PDBChain.makeCaBondList(PDBChain.java:255)
at MCview.PDBfile.makeCaBondList(PDBfile.java:518)
at MCview.PDBfile.parse(PDBfile.java:200)
at jalview.io.AlignFile.doParse(AlignFile.java:169)
at MCview.PDBfile.<init>(PDBfile.java:85)
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:281)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
at java.lang.Thread.run(Thread.java:745)
Failed to read alignment using the 'PDB' reader.
java.lang.ArithmeticException: / by zero
INFO : jalview.bin.Jalview - Error retrieving 1a08 from PDB
java.io.IOException: Formats currently supported are
BLC, CLUSTAL, FASTA, MSF, PileUp, PIR, PFAM, STH, PDB, JnetFile, RNAML, PHYLIP, JSON, GFF v2 or v3, and HTML.
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:350)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
at java.lang.Thread.run(Thread.java:745)
INFO - Error retrieving 1a08 from PDB
java.io.IOException: Formats currently supported are
BLC, CLUSTAL, FASTA, MSF, PileUp, PIR, PFAM, STH, PDB, JnetFile, RNAML, PHYLIP, JSON, GFF v2 or v3, and HTML.
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:350)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
at java.lang.Thread.run(Thread.java:745)
To reproduce, try fetching one of the following entries using the PDB sequence fetcher: 1a08; 1a09; 1a07; 1a1a; 1a1b; 1a1b; 1a1e.
Stack trace:
java.lang.ArithmeticException: / by zero
at MCview.PDBChain.makeCaBondList(PDBChain.java:255)
at MCview.PDBfile.makeCaBondList(PDBfile.java:518)
at MCview.PDBfile.parse(PDBfile.java:200)
at jalview.io.AlignFile.doParse(AlignFile.java:169)
at MCview.PDBfile.<init>(PDBfile.java:85)
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:281)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
at java.lang.Thread.run(Thread.java:745)
Failed to read alignment using the 'PDB' reader.
java.lang.ArithmeticException: / by zero
INFO : jalview.bin.Jalview - Error retrieving 1a08 from PDB
java.io.IOException: Formats currently supported are
BLC, CLUSTAL, FASTA, MSF, PileUp, PIR, PFAM, STH, PDB, JnetFile, RNAML, PHYLIP, JSON, GFF v2 or v3, and HTML.
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:350)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
at java.lang.Thread.run(Thread.java:745)
INFO - Error retrieving 1a08 from PDB
java.io.IOException: Formats currently supported are
BLC, CLUSTAL, FASTA, MSF, PileUp, PIR, PFAM, STH, PDB, JnetFile, RNAML, PHYLIP, JSON, GFF v2 or v3, and HTML.
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:350)
at jalview.io.FormatAdapter.readFile(FormatAdapter.java:311)
at jalview.ws.dbsources.Pdb.getSequenceRecords(Pdb.java:134)
at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:579)
at java.lang.Thread.run(Thread.java:745)
Attachments
Issue Links
- related with
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JAL-1979 SIFTS End-To-End scanning
- In Progress