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: 2.8.2, 2.8.2b1
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Component/s: file format issue
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Labels:None
Description
Reported by Kazutaka Katoh - sequence ID lines with angle brackets cause VARNA exceptions to be thrown. Most likely cause is angle-brackets match the jalview.io.Identify pattern for an RNAML file, so Jalview attempts to call the VARNA rnaml parser.
Importing this:
>aseq 5 soso <>[some reference]
MSTFMSTF
Results in the following stacktrace:
Exception in thread "AWT-EventQueue-2" java.lang.NoClassDefFoundError: fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax
at jalview.g.e.a(Unknown Source)
at jalview.appletgui.A.a(Unknown Source)
at jalview.appletgui.A.actionPerformed(Unknown Source)
Unobfuscated:
Exception in thread "AWT-EventQueue-3" java.lang.NoClassDefFoundError: fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:273)
at jalview.appletgui.CutAndPasteTransfer.ok(CutAndPasteTransfer.java:237)
at jalview.appletgui.CutAndPasteTransfer.actionPerformed(CutAndPasteTransfer.java:98)
Importing this:
>aseq 5 soso <>[some reference]
MSTFMSTF
Results in the following stacktrace:
Exception in thread "AWT-EventQueue-2" java.lang.NoClassDefFoundError: fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax
at jalview.g.e.a(Unknown Source)
at jalview.appletgui.A.a(Unknown Source)
at jalview.appletgui.A.actionPerformed(Unknown Source)
Unobfuscated:
Exception in thread "AWT-EventQueue-3" java.lang.NoClassDefFoundError: fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:273)
at jalview.appletgui.CutAndPasteTransfer.ok(CutAndPasteTransfer.java:237)
at jalview.appletgui.CutAndPasteTransfer.actionPerformed(CutAndPasteTransfer.java:98)