Hi Jim, I've just pushed the changes integrating the T-Coffee score in Jalview.
So, what's new: - A T-Coffee score file parser. - A new menu entry in the color menu "T-Coffee scores" both in the applet and desktop versions. - A new 'scoreFile' parameter in the applet to load the T-Coffee score file when including jalview into a web page. - A new menu entry in the file menu, named "Load T-Coffee scores", in the desktop version (maybe it would have sense to add also to the applet). - Updated the appletParameters.html page. What is missing: - JAL-1068 - T-Coffee consens score histogram - Updating the manual for the remaining features The new branch is named: origin/Tcoffee_JAL-1065 I will wait for your comment before continue with other developments Cheers, Paolo On Apr 8, 2012, at 1:53 AM, Jim Procter wrote: > 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
