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  1. Jalview
  2. JAL-4333

error while using 'Calculate > Translate as cDNA'

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 2.11.2.7
    • Fix Version/s: 2.11.4.2
    • Component/s: None
    • Labels:
    • Environment:
      Debian GNU/Linux Sid - openjdk 17.0.9 (build 17.0.9+9-Debian-2)

      Description

      Hi,

      Here is the copy-paste from the Java console.

      Regards,
      Patrice

      Jalview non-release Version: 2.11.2.7+dfsg-1
      Jalview non-release Installation: deb
      Build Date: 21:17:17 08 October 2023
      Java version: 17.0.9
      amd64 Linux 6.5.0-2-amd64
      LookAndFeel: Metal (javax.swing.plaf.metal.MetalLookAndFeel)
      Channel: default
      Java home: /usr/lib/jvm/java-17-openjdk-amd64
      ERROR - Exception during translation. Please report this !
      java.lang.ArrayIndexOutOfBoundsException: Index 4066 out of bounds for length 4066
      at jalview.analysis.Dna.translateCodingRegion(Dna.java:595) ~[jalview-2.11.2.7.jar:2.11.2.7]
      at jalview.analysis.Dna.translateCdna(Dna.java:213) ~[jalview-2.11.2.7.jar:2.11.2.7]
      at jalview.gui.AlignFrame.showTranslation_actionPerformed(AlignFrame.java:4498) ~[jalview-2.11.2.7.jar:2.11.2.7]
      at jalview.jbgui.GAlignFrame$76.actionPerformed(GAlignFrame.java:1285) ~[jalview-2.11.2.7.jar:2.11.2.7]
      at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) ~[?:?]
      at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2313) ~[?:?]
      at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) ~[?:?]
      at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) ~[?:?]
      at javax.swing.AbstractButton.doClick(AbstractButton.java:374) ~[?:?]
      at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1028) ~[?:?]
      at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1072) ~[?:?]
      at java.awt.Component.processMouseEvent(Component.java:6626) ~[?:?]
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3389) ~[?:?]
      at java.awt.Component.processEvent(Component.java:6391) ~[?:?]
      at java.awt.Container.processEvent(Container.java:2266) ~[?:?]
      at java.awt.Component.dispatchEventImpl(Component.java:5001) ~[?:?]
      at java.awt.Container.dispatchEventImpl(Container.java:2324) ~[?:?]
      at java.awt.Component.dispatchEvent(Component.java:4833) ~[?:?]
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) ~[?:?]
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) ~[?:?]
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) ~[?:?]
      at java.awt.Container.dispatchEventImpl(Container.java:2310) ~[?:?]
      at java.awt.Window.dispatchEventImpl(Window.java:2780) ~[?:?]
      at java.awt.Component.dispatchEvent(Component.java:4833) ~[?:?]
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775) ~[?:?]
      at java.awt.EventQueue$4.run(EventQueue.java:720) ~[?:?]
      at java.awt.EventQueue$4.run(EventQueue.java:714) ~[?:?]
      at java.security.AccessController.doPrivileged(AccessController.java:399) ~[?:?]
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) ~[?:?]
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97) ~[?:?]
      at java.awt.EventQueue$5.run(EventQueue.java:747) ~[?:?]
      at java.awt.EventQueue$5.run(EventQueue.java:745) ~[?:?]
      at java.security.AccessController.doPrivileged(AccessController.java:399) ~[?:?]
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) ~[?:?]
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:744) ~[?:?]
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) ~[?:?]
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) ~[?:?]
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) ~[?:?]
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) ~[?:?]
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) ~[?:?]
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:90) ~[?:?]

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            Assignee:
            jprocter James Procter
            Reporter:
            pduroux Patrice Duroux
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              Updated:
              Resolved: