Hi Lauren
I've taken a look at what you checked in for last week - generally it looks good! Thanks for rearranging the nucleotide stuff in the jbgui.GAlignFrame method.. it makes it much clearer when related menu option definitions are grouped together.
Two comments:
1. It doesn't look like the purine/pyrimidine colourscheme is added to the list of colourschemes provided for the Jmol menu (not a huge priority, but could be useful to Kersten).
2. I managed to get a flood of exceptions when testing the colourscheme with the vault protein example:
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 10
at jalview.schemes.PurinePyrimidineColourScheme.findColour(PurinePyrimidineColourScheme.java:49)
at jalview.gui.AnnotationPanel.drawBarGraph(AnnotationPanel.java:1433)
at jalview.gui.AnnotationPanel.drawComponent(AnnotationPanel.java:1214)
at jalview.gui.AnnotationPanel.paintComponent(AnnotationPanel.java:679)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
From your weekly update email, it looks like you're still finishing the colourscheme, so I guess it's not surprising that it threw exceptions 
I've got one other comment, but its mainly stylistic. However, I've hit an eclipse svn commit issue with googlecode, so I've not added it yet. Watch out for an incoming change later today, though.
Finally, can you remind me when we planned to talk this week ? I seem to remember suggesting we talk tomorrow afternoon (BST).. is that right ?
Cheers
Jim.
ps.
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