Details
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Type: Bug
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Status: Open
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Priority: Blocker
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Resolution: Unresolved
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Affects Version/s: 2.11.2.3, 2.11.2.4, 2.11.2.5, 2.11.2.6, 2.11.2.7, 2.11.3.0, 2.11.3.1, 2.11.3.2, 2.11.3.3, 2.11.4.0
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Fix Version/s: 2.11.4.2
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Component/s: data retrieval services
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Labels:
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Epic Link:
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Urgency:Highest
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.
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.
Attachments
Issue Links
- related with
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JAL-4034 Make the 3D-Beacons Search button more buttony and logic for Uniprot search
- Closed