- // Must maintain ability to use the groups flag
- data = aparser.getValue("groups");
- if (data != null)
- {
- af.parseFeaturesFile(data, checkProtocol(data));
- System.out.println("Added " + data);
- }
- data = aparser.getValue("features");
- if (data != null)
- {
- af.parseFeaturesFile(data, checkProtocol(data));
- System.out.println("Added " + data);
- }
-
- data = aparser.getValue("annotations");
- if (data != null)
- {
- af.loadJalviewDataFile(data);
- System.out.println("Added " + data);
- }
- // set or clear the sortbytree flag.
- if (aparser.contains("sortbytree"))
- {
- af.getViewport().setSortByTree(true);
- }
- if (aparser.contains("nosortbytree"))
- {
- af.getViewport().setSortByTree(false);
- }
- data = aparser.getValue("tree");
- if (data != null)
- {
- jalview.io.NewickFile fin = null;
- try
- {
- fin = new jalview.io.NewickFile(data, checkProtocol(data));
- if (fin != null)