-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.bin;\r
\r
import jalview.gui.*;\r
+\r
import javax.swing.*;\r
\r
+import java.util.Vector;\r
+\r
+\r
+/**\r
+ * Main class for Jalview Application\r
+ * <br>\r
+ * <br>start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class Jalview\r
{\r
\r
- public static void main(String[] args) {\r
- try{\r
- UIManager.setLookAndFeel //("javax.swing.plaf.metal.MetalLookAndFeel");\r
- ( UIManager.getCrossPlatformLookAndFeelClassName() );\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
+ +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"\r
+ +"-features FILE\tUse the given file to mark features on the alignment.\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
+ +"\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");\r
+ System.exit(0);\r
+ }\r
+\r
+ Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!\r
+\r
+ if (aparser.contains("nodisplay"))\r
+ {\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
+ try\r
+ {\r
+ Cache.initLogger();\r
+ }\r
+ catch (java.lang.NoClassDefFoundError error)\r
+ {\r
+ error.printStackTrace();\r
+ System.out.println(\r
+ "\nEssential logging libraries not found."\r
+ +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");\r
+ System.exit(0);\r
+ }\r
+\r
+ Desktop desktop = null;\r
+\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
+ if (!headless)\r
+ {\r
+ desktop = new Desktop();\r
+ desktop.setVisible(true);\r
+ desktop.discoverer.start();\r
+ }\r
+\r
+\r
+ String file = null, protocol = null, format = null, data=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
+\r
+ if(file!=null)\r
+ {\r
+ System.out.println("Opening file: " + file);\r
+\r
+ if (!file.startsWith("http://"))\r
+ {\r
+ if (! (new java.io.File(file)).exists())\r
+ {\r
+ System.out.println("Can't find " + file);\r
+ if(headless)\r
+ System.exit(1);\r
+ }\r
+ }\r
+\r
+ protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)\r
+ {\r
+ protocol = "URL";\r
+ }\r
+\r
+\r
+\r
+ if (file.endsWith(".jar"))\r
+ format = "Jalview";\r
+ else\r
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
+\r
\r
- // ("com.sun.java.swing.plaf.windows.WindowsLookAndFeel");\r
- // ("com.sun.java.swing.plaf.motif.MotifLookAndFeel" );\r
- }\r
- catch (Exception ex)\r
- {}\r
\r
- // JFrame.setDefaultLookAndFeelDecorated(true);\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
\r
+ if(af==null)\r
+ {\r
+ System.out.println("error");\r
+ return;\r
+ }\r
\r
- if(args!=null && args.length>0)\r
+ data = aparser.getValue("colour");\r
+ if(data!=null)\r
+ {\r
+ data.replaceAll("%20", " ");\r
+\r
+ jalview.schemes.ColourSchemeI cs =\r
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().\r
+ getAlignment(), data);\r
+\r
+ if(cs == null)\r
+ {\r
+ jalview.schemes.UserColourScheme ucs\r
+ = new jalview.schemes.UserColourScheme("white");\r
+ ucs.parseAppletParameter(data);\r
+ cs = ucs;\r
+ }\r
+\r
+ System.out.println("colour is " + data);\r
+ af.changeColour( cs );\r
+ }\r
+\r
+\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 file = args[0];\r
- jalview.bin.Cache.LAST_DIRECTORY = file;\r
- String protocol = "File";\r
- if(file.indexOf("http:")>-1)\r
- protocol = "URL";\r
+ String arg = args[i].trim();\r
+ if (arg.charAt(0) == '-')\r
+ arg = arg.substring(1);\r
+ vargs.addElement(arg);\r
+ }\r
+ }\r
\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ public String getValue(String arg)\r
+ {\r
+ int index = vargs.indexOf(arg);\r
+ String ret = null;\r
+ if (index != -1)\r
+ {\r
+ ret = vargs.elementAt(index + 1).toString();\r
+ vargs.removeElementAt(index);\r
+ vargs.removeElementAt(index);\r
+ }\r
+ return ret;\r
+ }\r
\r
- frame.LoadFile(file, protocol, format);\r
+ public boolean contains(String arg)\r
+ {\r
+ if(vargs.contains(arg))\r
+ {\r
+ vargs.removeElement(arg);\r
+ return true;\r
}\r
+ else\r
+ return false;\r
+ }\r
\r
+ public String nextValue()\r
+ {\r
+ return vargs.remove(0).toString();\r
}\r
\r
-}\r
+ public int getSize()\r
+ {\r
+ return vargs.size();\r
+ }\r
+\r
+ }\r
git://source.jalview.org / jalview.git / blobdiff