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  1. Jalview
  2. JAL-4041

3D Beacons results in structure chooser don't include models if one of the selected sequences does not have a uniprot accession

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2.3, 2.11.2.4
    • Fix Version/s: 2.11.3
    • Labels:
      None

      Description

      An example:

      1) Open Jalview, load the uniref50.fa file.
      2) Right click on FER1_SPIOL and select 3D Structure Data...
      3) 3D-Beacons search finds four models.

      1) Open Jalview, load the uniref50.fa file.
      2) Select all sequences, right click and select 3D Structure Data...
      3) 3D-Beacons search finds nothing and is no longer an option in the Structure Chooser window.

      Java Console output _sometimes_ has an ArrayIndexOutOfBoundsException:
      https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(text:o80429_maize)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=overall_quality+desc
      query >>>>>>> jalview.fts.core.FTSRestRequest@7c26c22f
      Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 2 >= 2
      at java.base/java.util.Vector.elementAt(Vector.java:497)
      at java.desktop/javax.swing.table.DefaultTableColumnModel.getColumn(DefaultTableColumnModel.java:295)
      at java.desktop/javax.swing.plaf.basic.BasicTableUI.paintGrid(BasicTableUI.java:2044)
      at java.desktop/javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1880)
      at java.desktop/javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
      at java.desktop/javax.swing.JComponent.paintComponent(JComponent.java:797)
      at java.desktop/javax.swing.JComponent.paint(JComponent.java:1074)
      at java.desktop/javax.swing.JComponent.paintToOffscreen(JComponent.java:5255)
      at java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBufferedImpl(RepaintManager.java:1643)
      at java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1618)
      at java.desktop/javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1556)
      at javahttps://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=1&start=0&q=(uniprot_accession:P83527+OR+uniprot_id:P83527)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=overall_quality+desc

      Even though no 3D-Beacons models are presented in the Structure Chooser, if you then look at each sequence _individually_, there are 3D-Beacons models discovered for all sequences except for Q7XA98_TRIPR and O80429_MAIZE.

      When the ArrayIndexOutOfBoundsException is not observed (when searching across all sequences), there are still no 3D-Beacons models presented.

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              Assignee:
              jprocter Jim Procter
              Reporter:
              soares Ben Soares
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                Dates

                Created:
                Updated: