+ /**\r
+ * main class for Jalview application\r
+ *\r
+ * @param args open <em>filename</em>\r
+ */\r
+ public static void main(String[] args)\r
+ {\r
+ ArgsParser aparser = new ArgsParser(args);\r
+\r
+ try\r
+ {\r
+ UIManager.setLookAndFeel(\r
+ // "javax.swing.plaf.metal.MetalLookAndFeel"\r
+ // "javax.swing.plaf.multi.MultiLookAndFeel"\r
+ UIManager.getSystemLookAndFeelClassName());\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ Cache.loadProperties(aparser.getValue("props"));\r
+ jalview.gui.Preferences.initPreferences();\r
+ try\r
+ {\r
+ initLogger();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Problems initializing the log4j system\n");\r
+ }\r
+\r
+\r
+ String file = null, protocol = null, format = null, groups=null;\r
+ Desktop desktop = new Desktop();\r
+\r
+\r
+ if(args==null || args.length==0)\r
+ {\r
+ desktop.setVisible(true);\r
+ }\r
+ else\r
+ {\r
+ if( aparser.contains("help") || aparser.contains("h") )\r
+ {\r
+ System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"\r
+ +"-nodisplay\tRun Jalview without User Interface.\n"\r
+ +"-props FILE\tUse the given Jalview properties file instead of users default.\n"\r
+ +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"\r
+ +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"\r
+ +"SequenceID is used in preference to SequenceIndex if both are provided.\n"\r
+ +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"\r
+ +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"\r
+ +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"\r
+ +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"\r
+ +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"\r
+ +"-msf FILE\tCreate alignment file FILE in MSF format.\n"\r
+ +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"\r
+ +"-pir FILE\tCreate alignment file FILE in PIR format.\n"\r
+ +"-blc FILE\tCreate alignment file FILE in BLC format.\n"\r
+ +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"\r
+ +"-png FILE\tCreate PNG image FILE from alignment.\n"\r
+ +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"\r
+ +"-eps FILE\tCreate EPS file FILE from alignment.");\r
+ System.exit(0);\r
+\r
+ }\r
+\r
+ if (!aparser.contains("nodisplay"))\r
+ desktop.setVisible(true);\r
+\r
+ file = aparser.getValue("open");\r
+\r
+ if (file == null && !desktop.isVisible())\r
+ {\r
+ System.out.println("No files to open!");\r
+ System.exit(1);\r
+ }\r
+ else if(!file.startsWith("http://"))\r
+ {\r
+ if (!(new java.io.File(file)).exists())\r
+ {\r
+ System.out.println("Can't find " + file);\r
+ System.exit(1);\r
+ }\r
+ }\r
+\r
+ protocol = "File";\r