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: 2.9.0b2
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Fix Version/s: 2.10.0
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Component/s: None
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Labels:None
Description
An exception is raised and rendering of the alignment window breaks when trying to define subgroups on an alignment when t-coffee shading is enabled.
To reproduce:
1. import examples/uniref50.fa
2. Add examples/uniref50.score_ascii (drag and drop or load annotations)
3. Calculate a tree
4. click on the tree to create subgroups.
Exception is:
Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
at jalview.schemes.TCoffeeColourScheme.alignmentChanged(TCoffeeColourScheme.java:90)
at jalview.schemes.TCoffeeColourScheme.<init>(TCoffeeColourScheme.java:71)
at jalview.schemes.ColourSchemeProperty.getColour(ColourSchemeProperty.java:514)
at jalview.schemes.ColourSchemeProperty.getColour(ColourSchemeProperty.java:428)
at jalview.gui.TreeCanvas.colourGroups(TreeCanvas.java:962)
at jalview.gui.TreeCanvas.mousePressed(TreeCanvas.java:913)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
at java.awt.Component.processMouseEvent(Component.java:6530)
To reproduce:
1. import examples/uniref50.fa
2. Add examples/uniref50.score_ascii (drag and drop or load annotations)
3. Calculate a tree
4. click on the tree to create subgroups.
Exception is:
Exception in thread "AWT-EventQueue-2" java.lang.NullPointerException
at jalview.schemes.TCoffeeColourScheme.alignmentChanged(TCoffeeColourScheme.java:90)
at jalview.schemes.TCoffeeColourScheme.<init>(TCoffeeColourScheme.java:71)
at jalview.schemes.ColourSchemeProperty.getColour(ColourSchemeProperty.java:514)
at jalview.schemes.ColourSchemeProperty.getColour(ColourSchemeProperty.java:428)
at jalview.gui.TreeCanvas.colourGroups(TreeCanvas.java:962)
at jalview.gui.TreeCanvas.mousePressed(TreeCanvas.java:913)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
at java.awt.Component.processMouseEvent(Component.java:6530)