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: 2.11.1.7, 2.11.2.0
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Fix Version/s: 2.11.2.1
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Component/s: data retrieval services, Datamodel, gui
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Labels:None
Description
When retrieving crossreferences for ENA entries with many database crossrefs, moving the mouse over the sequence ID panel can trigger an exception:
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.base/java.util.ArrayList.sort(ArrayList.java:1752)
at jalview.io.SequenceAnnotationReport.appendDbRefs(SequenceAnnotationReport.java:548)
at jalview.io.SequenceAnnotationReport.createSequenceAnnotationReport(SequenceAnnotationReport.java:510)
at jalview.io.SequenceAnnotationReport.createTooltipAnnotationReport(SequenceAnnotationReport.java:630)
at jalview.gui.IdPanel.mouseMoved(IdPanel.java:130)
It turns out that the SequenceAnnotationReport code applies an in place sort to the list of database references - causing the exception.
Solution 0: defensive copy prior to sorting for display.
Solution 1: maintain the dbrefs as a sorted list ?
Solution 2: store references indexed by provider, each sorted by accession.
See JAL-3979 for other optimisations
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.base/java.util.ArrayList.sort(ArrayList.java:1752)
at jalview.io.SequenceAnnotationReport.appendDbRefs(SequenceAnnotationReport.java:548)
at jalview.io.SequenceAnnotationReport.createSequenceAnnotationReport(SequenceAnnotationReport.java:510)
at jalview.io.SequenceAnnotationReport.createTooltipAnnotationReport(SequenceAnnotationReport.java:630)
at jalview.gui.IdPanel.mouseMoved(IdPanel.java:130)
It turns out that the SequenceAnnotationReport code applies an in place sort to the list of database references - causing the exception.
Solution 0: defensive copy prior to sorting for display.
Solution 1: maintain the dbrefs as a sorted list ?
Solution 2: store references indexed by provider, each sorted by accession.
See JAL-3979 for other optimisations
Attachments
Issue Links
- related with
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JAL-3981 Sequence Details takes a long time to be displayed
- In Progress