+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
+ "System.err");\r
+ ap.setName("JalviewLogger");\r
+\r
+ laxis.addAppender(ap);\r
+ lcastor.addAppender(ap);\r
+ log.addAppender(ap);\r
+ }\r
+\r
+ /**\r
+ * main class for Jalview application\r
+ *\r
+ * @param args open <em>filename</em>\r
+ */\r
+ public static void main(String[] args)\r
+ {\r
+ System.out.println("Java version: "+System.getProperty("java.version"));\r
+ System.out.println(System.getProperty("os.arch")+" "\r
+ +System.getProperty("os.name")+" "\r
+ +System.getProperty("os.version"));\r
+\r
+\r
+ ArgsParser aparser = new ArgsParser(args);\r
+ boolean headless = false;\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
+ System.setProperty("java.awt.headless", "true");\r
+\r
+ if (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true"))\r
+ {\r
+ headless = true;\r
+ }\r
+\r
+ Cache.loadProperties(aparser.getValue("props"));\r
+\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
+ Desktop desktop = null;\r
+ if( !headless )\r
+ {\r
+ try\r
+ {\r
+ UIManager.setLookAndFeel(\r
+ UIManager.getSystemLookAndFeelClassName()\r
+ // UIManager.getCrossPlatformLookAndFeelClassName()\r
+//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
+//"javax.swing.plaf.metal.MetalLookAndFeel"\r
+//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
+//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
+\r
+ );\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ desktop = new Desktop();\r
+ desktop.setVisible(true);\r
+ desktop.discoverer.start();\r
+ }\r
+\r
+\r
+ String file = null, protocol = null, format = null, groups=null;\r
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();\r
+\r
+ file = aparser.getValue("open");\r
+\r
+ if (file == null && desktop==null)\r
+ {\r
+ System.out.println("No files to open!");\r
+ System.exit(1);\r
+ }\r