Hi Paolo On Tue Apr 10 13:19:27 2012, Paolo Di Tommaso wrote: > I've just pushed the changes integrating the T-Coffee score in Jalview. I took a look - it works pretty nicely.
> 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. OK - I'll raise a few issues on JIRA over the next few hours - mostly to do with reuse of existing code for doing things like resolving data URIs (its a bit of a pain in the applet to cover all bases and support legacy behaviour - so I might fix that patch). Your implementation also raises an interesting design question about attaching invariant indexes to sequences (as you do to index into the alignment scores matrix). > > What is missing: > - JAL-1068 > - T-Coffee consens score histogram > - Updating the manual for the remaining features OK - will also put some more comments on the bugs. > The new branch is named: origin/Tcoffee_JAL-1065 I'll start to merge this onto the develop branch, since that code is in flux. My initial experiments seem to suggest it should all be fine, but more testing will be needed. > I will wait for your comment before continue with other developments Thanks for taking the time to do this ! I also note that you have bravely checked in a directory of JUnit tests! This has forced me to think a bit about how to retrofit the legacy test data to this model. Most of our test data sits in the examples directory, so that we can get people to run import tests on their live Jalview installation if they run into problems (this is a nice way of checking that their local environment is good). Wonder if Groovy is the way to go here for a test harness ? Jim. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
