+\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
+ String imageName = "unnamed.png";\r
+ while (aparser.getSize() > 1)\r
+ {\r
+ format = aparser.nextValue();\r
+ file = aparser.nextValue();\r
+\r
+ if (format.equalsIgnoreCase("png"))\r
+ {\r
+ af.createPNG(new java.io.File(file));\r
+ imageName = (new java.io.File(file)).getName();\r
+ System.out.println("Creating PNG image: " + file);\r
+ continue;\r
+ }\r
+ else if (format.equalsIgnoreCase("imgMap"))\r
+ {\r
+ af.createImageMap(new java.io.File(file), imageName);\r
+ System.out.println("Creating image map: " + file);\r
+ continue;\r
+ }\r
+ else if (format.equalsIgnoreCase("eps"))\r
+ {\r
+ System.out.println("Creating EPS file: " + file);\r
+ af.createEPS(new java.io.File(file));\r
+ continue;\r
+ }\r
+\r
+ if (af.saveAlignment(file, format))\r
+ System.out.println("Written alignment in " + format +\r
+ " format to " + file);\r
+ else\r
+ System.out.println("Error writing file " + file + " in " + format +\r
+ " format!!");\r
+\r
+ }\r
+\r
+ while (aparser.getSize() > 0)\r
+ {\r
+ System.out.println("Unknown arg: " + aparser.nextValue());\r
+ }\r
+ }\r
+\r
+ // We'll only open the default file if the desktop is visible.\r
+ // And the user\r
+ //////////////////////\r
+ if (\r
+ !headless\r
+ && file==null\r
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)\r
+ )\r
+ {\r
+\r
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",\r
+ "http://www.jalview.org/examples/exampleFile.jar");\r
+\r
+ protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1)\r
+ {\r
+ protocol = "URL";\r
+ }\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ format = "Jalview";\r
+ }\r
+ else\r
+ {\r
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
+ }\r
+\r
+ fileLoader.LoadFile(file, protocol, format);\r
+\r
+ }\r
+ }\r
+}\r
+\r
+ class ArgsParser\r
+ {\r
+ Vector vargs = null;\r
+ public ArgsParser(String [] args)\r
+ {\r
+ vargs = new Vector();\r
+ for (int i = 0; i < args.length; i++)\r
+ {\r
+ String arg = args[i].trim();\r
+ if (arg.charAt(0) == '-')\r
+ arg = arg.substring(1);\r
+ vargs.addElement(arg);\r