On Mon, 25 Aug 2003 16:05:20 +0100, Derek Gatherer wrote: > Hi > A couple of related questions about adding codon usage plots to the > Graph menu.
> I notice that /diana/components/BasePlotGroup.java has a line > // addAlgorithm (new CodonUsageAlgorithm (forward_strand)); > but that uncommenting this line causes BasePlotGroup.java to give an error > on compile. Is CodonUsageAlgorithm about to be phased in, or is it > something from the past that has been abandoned? I can't find that line in BasePlotGroup.java: http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/powmap/diana/components/BasePlotGroup.java?rev=1.30&content-type=text/x-cvsweb-markup&cvsroot=Pathogen&f=h Which version of Artemis are you looking at? > I'd like to know if Artemis will soon have a standard class for accessing > codon usage values, Artemis has this class: http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/powmap/diana/plot/CodonUsageWeight.java?rev=1.9&content-type=text/x-cvsweb-markup&cvsroot=Pathogen&f=h which is able to read codon usage files from this web site: http://www.kazusa.or.jp/codon/ The "Write Codon Usage of Selected Features" function in the Write menu also creates file in this format. > This works but is painfully slow when implemented, especially when > changing window size or zooming up and down in the genome. It occurs > to me that perhaps I am (badly) reinventing the wheel here and should > avoid TreeMaps. What do you recommend? I would imagine that there's some free code in Java on the internet that will do what you need. Kim.
