/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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 jalview.io.*;\r
-\r
import org.apache.log4j.*;\r
\r
-import java.awt.event.*;\r
-\r
import javax.swing.*;\r
\r
-\r
-public class Jalview extends JApplet {\r
- public static JApplet applet;\r
- Desktop frame;\r
-\r
- public void init() {\r
- applet = this;\r
- Cache.loadProperties();\r
- jalview.gui.Preferences.initPreferences();\r
-\r
- frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);\r
- frame.addWindowListener(new WindowAdapter() {\r
- public void windowClosing(WindowEvent e) {\r
- applet.stop();\r
- applet.destroy();\r
- }\r
- });\r
-\r
- String file = getParameter("alignment");\r
-\r
- if (file != null) {\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
-\r
- String protocol = "File";\r
-\r
- if (file.indexOf("http:") > -1) {\r
- protocol = "URL";\r
- }\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
- }\r
- }\r
-\r
- public void destroy() {\r
- if (applet != null) {\r
- applet.stop();\r
- } else {\r
- System.exit(0);\r
- }\r
-\r
- frame.setVisible(false);\r
- }\r
-\r
- private static void initLogger() {\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
+ * Initialises the Apache Axis logger\r
+ */\r
+ private static void initLogger()\r
+ {\r
Logger laxis = Logger.getLogger("org.apache.axis");\r
Logger lcastor = Logger.getLogger("org.exolab.castor");\r
- if (Cache.getProperty("logs.Axis.Level") == null) {\r
+\r
+ if (Cache.getProperty("logs.Axis.Level") == null)\r
+ {\r
Cache.setProperty("logs.Axis.Level", Level.INFO.toString());\r
}\r
- if (Cache.getProperty("logs.Castor.Level") == null) {\r
+\r
+ if (Cache.getProperty("logs.Castor.Level") == null)\r
+ {\r
Cache.setProperty("logs.Castor.Level", Level.INFO.toString());\r
}\r
\r
lcastor.addAppender(ap);\r
}\r
\r
- public static void main(String[] args) {\r
- Cache.loadProperties();\r
- jalview.gui.Preferences.initPreferences();\r
-\r
- try {\r
- initLogger();\r
- } catch (Exception e) {\r
- System.err.println("Problems initializing the log4j system\n");\r
- e.printStackTrace();\r
- }\r
-\r
- try {\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
+ ArgsParser aparser = new ArgsParser(args);\r
+\r
+ try\r
+ {\r
UIManager.setLookAndFeel(\r
- // "javax.swing.plaf.metal.MetalLookAndFeel"\r
+ // "javax.swing.plaf.metal.MetalLookAndFeel"\r
// "javax.swing.plaf.multi.MultiLookAndFeel"\r
UIManager.getSystemLookAndFeelClassName());\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\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
\r
- if ((args != null) && (args.length > 0)) {\r
- String file = null;\r
+ file = aparser.getValue("open");\r
\r
- if (args[0].equals("-open")) {\r
- file = args[1];\r
- } else {\r
- file = args[0];\r
+ if (file == null)\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
+ if (!aparser.contains("nodisplay"))\r
+ desktop.setVisible(true);\r
+\r
+ protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1)\r
+ {\r
+ protocol = "URL";\r
+ }\r
\r
- String protocol = "File";\r
+ if(file.endsWith(".jar"))\r
+ format = "Jalview";\r
+ else\r
+ format = jalview.io.IdentifyFile.Identify(file, protocol);\r
\r
- if (file.indexOf("http:") > -1) {\r
- protocol = "URL";\r
+ System.out.println("Opening: " + format + " file " + file);\r
+\r
+ AlignFrame af = desktop.LoadFileWaitTillLoaded(file, protocol, format);\r
+\r
+ groups = aparser.getValue("groups");\r
+ if(groups!=null)\r
+ {\r
+ af.parseGroupsFile(groups);\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
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ }\r
\r
- frame.LoadFile(file, protocol, format);\r
+ while (aparser.getSize() > 0)\r
+ {\r
+ System.out.println("Unknown arg: " + aparser.nextValue());\r
+ }\r
}\r
\r
- if (jalview.gui.Preferences.showStartupFile &&\r
- (jalview.gui.Preferences.startupFile != null)) {\r
- String file = jalview.gui.Preferences.startupFile;\r
- String protocol = "File";\r
+ if (jalview.gui.Preferences.showStartupFile &&\r
+ (jalview.gui.Preferences.startupFile != null))\r
+ {\r
\r
- if (file.indexOf("http:") > -1) {\r
- protocol = "URL";\r
+ file = jalview.gui.Preferences.startupFile;\r
+ protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1)\r
+ {\r
+ protocol = "URL";\r
}\r
\r
- if (file.endsWith(".jar")) {\r
- Jalview2XML.LoadJalviewAlign(file);\r
- } else {\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
- frame.LoadFile(file, protocol, format);\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ Jalview2XML.LoadJalviewAlign(file);\r
}\r
- }\r
+ else\r
+ {\r
+ format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ desktop.LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+\r
+ if (!desktop.isVisible())\r
+ System.exit(0);\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
+ }\r
+ }\r
+\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
+ 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
+ public int getSize()\r
+ {\r
+ return vargs.size();\r
+ }\r
+\r
+ }\r
git://source.jalview.org / jalview.git / blobdiff