+\r
+ // Must maintain ability to use the groups flag\r
+ data = aparser.getValue("groups");\r
+ if (data != null)\r
+ {\r
+ af.parseFeaturesFile(data, protocol);\r
+ System.out.println("Added "+data);\r
+ }\r
+ data = aparser.getValue("features");\r
+ if (data != null)\r
+ {\r
+ af.parseFeaturesFile(data, protocol);\r
+ System.out.println("Added "+data);\r
+ }\r
+\r
+ data = aparser.getValue("annotations");\r
+ if (data != null)\r
+ {\r
+ af.loadJalviewDataFile(data);\r
+ System.out.println("Added "+data);\r
+ }\r
+\r
+\r