On Wed Jul 18 02:16:12 2012, Nicee Srivastava wrote: > > any suggestions as how to highlight/colour the columns. sorry for not answering your quetion 'in turn' - I was travelling at the time, didn't have time to properly think about your code.
Generally, to colour parts of the alignment, you'd create a sequence group (jalview.datamodel.SequenceGroup), which holds a set of references to SequenceI objects in the alignment, a start/end column range, and has its own colourscheme and other display attributes. Then, simply add the sequence group to the AlignmentI (there's a method for this). if you're doing this on a panel that's already displayed, then you can call repaint(true) to tell the AlignPanel that the view has changed. If you want to colour whole columns of the alignment, rather than create a column selection, you could add a series of groups containing all sequences, and where the start/end are contiguous columns that you want to highlight. Set the cs field with a colourscheme to control colour of each group (you can create new colourschemes where every residue gets the same colour with jalview.schemes.ColourSchemeProperty.getColour(AlignmentI alignment,"<red/green/etc colour name>") (note - this is the method signature for version 2.8 - the v2.7 code method doesn't need the alignment reference, IIRC). Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
