Hello Paolo. On 07/04/2012 12:13, Paolo Di Tommaso wrote: > I see quite clear. I will give a look how it could be implemented. ace. > It would the nice also to render somehow the msa consensus scores. I > mean the last colored row you see in each block in the T-Coffee html > result, identified by with sequence id 'cons'. Ideally it should be > rendered as a colored line under the MSA redered by Jalview. This > would be a third new feature. there are two ways you can do this. The easy one is to simply add the consensus scores as a new histogram style plot. You can see examples of code that does this in jalview.io.AnnotationFile, and JPredAnnotationMaker (which is a bit more complex).
> I use Eclipse, but for Git I'm more confident with the cmdline tool. Would > not be easier that I create a new local branch and then I push it to the > remote repository. Like explained here http://goo.gl/fpkzU > > What do you think? yep - that's the safer way - sorry - couldn't remember if you were doing everything with egit or not. I was actually pretty impressed with egit when I took a look today, it's almost as good as gitx now.. but still way slower. >>> I more thing, how do you report error messages in Jalview? do you a >>> particular method? syso.println ? >> Depends on the error and also where it occurs. The basic philosophy is >> to throw 'Error' objects for implementation problems, throw exceptions >> which get dumped to System.err if there are unexpected errors due to >> input, and try to give an informative message to the user. >> >> For alignment input files, there is a standard method for raising >> dialogs for the user, but there isn't anything yet for importing >> annotation files (something for my TODO list), so for the moment, send >> errors to System.err and I'll take a look and see if there's a better way. >> > OK! glad that made sense ;) happy Easter! Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
