Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-1294

Cannot export and re-import IUPred protein disorder predictions as annotation file

    XMLWordPrintable

    Details

    • Type: Story
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.8
    • Fix Version/s: 2.8.0b1
    • Component/s: file format issue
    • Labels:
      None
    • Sprint:
      2.8.1 annotation gui

      Description

      Protein disorder predictions made with IUPred result in a set of grouped line graphs for each sequence. Attempting to export these linegraphs to a jalview alignment annotation file, then re-import them to a fresh version of the alignment results in an error dialog box.

      Exception shown in logs:
      java.util.NoSuchElementException
      at java.util.StringTokenizer.nextToken(StringTokenizer.java:332)
      at jalview.io.AnnotationFile.parseAnnotationFrom(AnnotationFile.java:777)
      at jalview.io.AnnotationFile.readAnnotationFile(AnnotationFile.java:575)
      at jalview.gui.AlignFrame.loadJalviewDataFile(AlignFrame.java:4893)
      at jalview.gui.AlignFrame.associatedData_actionPerformed(AlignFrame.java:1258)
      at jalview.jbgui.GAlignFrame$96.actionPerformed(GAlignFrame.java:1506)
      at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
      at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
      at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
      at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
      at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
      at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
      at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
      at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
      at java.awt.Component.processMouseEvent(Component.java:6382)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
      at java.awt.Component.processEvent(Component.java:6147)
      at java.awt.Container.processEvent(Container.java:2083)
      at java.awt.Component.dispatchEventImpl(Component.java:4744)
      at java.awt.Container.dispatchEventImpl(Container.java:2141)
      at java.awt.Component.dispatchEvent(Component.java:4572)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
      at java.awt.Container.dispatchEventImpl(Container.java:2127)
      at java.awt.Window.dispatchEventImpl(Window.java:2489)
      at java.awt.Component.dispatchEvent(Component.java:4572)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:710)
      at java.awt.EventQueue.access$400(EventQueue.java:82)
      at java.awt.EventQueue$2.run(EventQueue.java:669)
      at java.awt.EventQueue$2.run(EventQueue.java:667)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$3.run(EventQueue.java:683)
      at java.awt.EventQueue$3.run(EventQueue.java:681)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:680)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
      Problem reading annotation file: java.util.NoSuchElementException

      ( line numbers generated from dev version, so won't match release )

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: