Details
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Type: Story
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Status: Resolved
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Priority: Major
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Resolution: Fixed
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Affects Version/s: 2.8
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Fix Version/s: 2.8.0b1
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Component/s: file format issue
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Labels:None
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Sprint:2.8.1 annotation gui
Description
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
- depends on
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JAL-1297 Grouped line graph annotation rows are not exported to annotation file
- Resolved
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JAL-1299 Cannot create multiple groups of line graphs with several 'combine' statements in annotation file
- Resolved
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JAL-1295 test for export/reimport of annotation created by web service jobs
- Resolved
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JAL-1325 export/import group and sequence associated line graph thresholds
- Resolved
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JAL-1103 extend annotation format to support specifying calculation IDs for groups of annotation
- Open
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JAL-1300 COMBINE statement uses current SEQUENCE_REF and GROUP_REF scope to group annotation rows
- Resolved
- related with
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JAL-1296 example annotation file in documentation is invalid
- Resolved
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JAL-1305 Allow distinct sets of annotation for a sequence to be propagated and visually compared
- Open