Re: [artemis-users] Codon Usage plots in Graph menu

[Derek Gatherer]

Hi

> //  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:
Yes, sorry, I should have checked rather than relying on my memory.  What I 
should have written was, there is a line (116):

//    plot_algorithms_temp.add (new CAIWindowAlgorithm (forward_strand, 
cai_test));

which suggests that somebody was/is working on adding the Codon Adaptation 
Index.

and later (174), there is a method:

/**
   *  Return the first CodonUsageAlgorithm or null if there isn't one in the
   *  group.
   **/
  public CodonUsageAlgorithm getCodonUsageAlgorithm () {
What does this do?

Thanks for the pointers to the other code.

Cheers
Derek