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  1. Jalview
  2. JAL-4186

Making a mistake in renaming a sequence crashes Jalview

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 2.11.3
    • Fix Version/s: 2.11.3.0
    • Component/s: None
    • Environment:
      Slackware linux, OSX
    • Urgency:
      Urgent

      Description

      Hi, where a common mistake like this (keeping a space in the sequence name) used to be automatically repaired with an underscore (_) now a unrecoverable error occurs and all ongoing stuff will be lost.

      stack output:

      Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on -Dswing.aatext=true -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel
      Running jalview.bin.Jalview with memory setting -Xmx15766658048
      Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on -Dswing.aatext=true -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel
      Java version: 11.0.17
      Java home: /usr/lib64/java
      Java arch: amd64 Linux 6.1.28
      Jalview Develop version: 2.11.3.0-d20230517 (Source git-commit:b3fb6325a8 [develop])
      Setting initial log level to INFO
      WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
      SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
      SLF4J: Defaulting to no-operation (NOP) logger implementation
      SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
      INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (150ms)
      INFO - Getting messages for lang: en_GB
      Linux platform only! You may have the following warning next: "WARNING: An illegal reflective access operation has occurred"
      This is expected and cannot be avoided, sorry about that.
      WARNING: An illegal reflective access operation has occurred
      WARNING: Illegal reflective access by jalview.gui.Desktop (file:/home/rob/WORK/BIOINFO/JALVIEW/jalview-all-2.11.3.0-d20230517-j11.jar) to field sun.awt.X11.XToolkit.awtAppClassName
      WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
      WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
      WARNING: All illegal access operations will be denied in a future release
      WARN - Error when running commands
      May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
      WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
      May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
      WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
      May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
      WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
      May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
      WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
      May 19, 2023 1:39:14 PM compbio.ws.client.Jws2Client connectToRegistry
      INFO: Connected to RegistryWS successfully!
      registry.getSupportedServices: [AAConWS, DisemblWS, MSAprobsWS, GLprobsWS, ProbconsWS, GlobPlotWS, MafftWS, ClustalWS, RNAalifoldWS, TcoffeeWS, MuscleWS, JronnWS, IUPredWS, ClustalOWS]
      Attempting to connect with MafftWS...
      May 19, 2023 1:39:15 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2adf9390
      Attempting to connect with MuscleWS...
      May 19, 2023 1:39:16 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3f79e7cf
      Attempting to connect with ClustalWS...
      May 19, 2023 1:39:17 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@58b3502d
      Attempting to connect with ClustalOWS...
      May 19, 2023 1:39:19 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@b44920e
      Attempting to connect with TcoffeeWS...
      May 19, 2023 1:39:19 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@645490cb
      Attempting to connect with ProbconsWS...
      May 19, 2023 1:39:20 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@47778f15
      Attempting to connect with MSAprobsWS...
      May 19, 2023 1:39:21 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6d114f49
      Attempting to connect with GLprobsWS...
      May 19, 2023 1:39:22 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@456acf0d
      Attempting to connect with AAConWS...
      May 19, 2023 1:39:23 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@610580d2
      Attempting to connect with RNAalifoldWS...
      May 19, 2023 1:39:24 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@ae5d1a9
      Attempting to connect with JronnWS...
      May 19, 2023 1:39:25 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@68155115
      Attempting to connect with DisemblWS...
      May 19, 2023 1:39:26 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5e6ce4ac
      Attempting to connect with GlobPlotWS...
      May 19, 2023 1:39:27 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3baa15d0
      Attempting to connect with IUPredWS...
      May 19, 2023 1:39:28 PM compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!
      Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@533a0d1
      INFO - I18N missing key with root label.colourScheme_: en_GB label.colourScheme_rgg
      Serious - RSBS descriptions in user preferences are corrupt!
      java.lang.NullPointerException
      at jalview.ws.rest.RestServiceDescription.parseServiceList(RestServiceDescription.java:566)
      at jalview.ws.rest.RestServiceDescription.parseDescriptions(RestServiceDescription.java:892)
      at jalview.ws.rest.RestClient.getRestClients(RestClient.java:414)
      at jalview.gui.AlignFrame.build_urlServiceMenu(AlignFrame.java:4484)
      at jalview.gui.AlignFrame$14$1.run(AlignFrame.java:4428)
      at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
      at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
      at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
      at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
      at java.base/java.security.AccessController.doPrivileged(Native Method)
      at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
      at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
      at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
      at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
      at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
      at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
      at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
      at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)



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            Assignee:
            soares Ben Soares
            Reporter:
            brobr Rob v N
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              Dates

              Created:
              Updated:
              Resolved: