I've introduced myself to the jalview-discuss list! Hopefully I won't be flooded with requests.
I had a meeting with Jim today and he went over some of the details on how Jmol is embedded into Jalview. This will help me add VARNA to Jalview, if possible. The main places I will need to look for inspiration (or modify) will be the
StructureSelectionManager class in the jalview.structurepackage
AppJmol class in jalview.gui package
PopupMenu class in jalview.gui package
I emailed Yann Ponty, one of the VARNA authors and he responded very warmly. He took a brief look at my goals and wrote that VARNAPanel does not support mouseover events. I need to look more closely at the code to see if this will make my job difficult.
I also added Jalview ver. 2.5 source code to Google's open source project hosting site, code.google.com. I used svn:
svn import jalview-2.5 https://jalview.googlecode.com/svn/trunk/ -m "First import" --username lauren.ucsc
Right now only Jim and I can add code. I added a project description but I need to figure out what needs to be on the wiki.