-/*\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
-\r
-package jalview.bin;\r
-\r
-import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import jalview.io.*;\r
-\r
-import org.apache.log4j.*;\r
-\r
-public class Jalview extends JApplet\r
-{\r
- public static JApplet applet;\r
- Desktop frame;\r
- public void init()\r
- {\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
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- applet.stop();\r
- applet.destroy();\r
- }\r
- });\r
-\r
- String file = getParameter("alignment");\r
-\r
- if(file!=null)\r
- {\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
- String protocol = "File";\r
- if (file.indexOf("http:") > -1)\r
- protocol = "URL";\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
- {\r
- if(applet!=null)\r
- applet.stop();\r
- else\r
- System.exit(0);\r
- frame.setVisible(false);\r
- }\r
-\r
- private static void initLogger() {\r
- Logger l = Logger.getLogger("org.apache.axis");\r
- if (Cache.getProperty("logs.Axis.Level")==null) {\r
- Cache.setProperty("logs.Axis.Level", Level.INFO.toString());\r
- }\r
-\r
- l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));\r
- ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");\r
- ap.setName("Axis");\r
- l.addAppender(ap);\r
- }\r
- public static void main(String[] args) {\r
-\r
- Cache.loadProperties();\r
- jalview.gui.Preferences.initPreferences();\r
- try {\r
- initLogger();\r
- } catch (Exception e) {\r
- System.err.println("Problems initializing the log4j system\n");\r
- e.printStackTrace();\r
- }\r
- try{\r
- UIManager.setLookAndFeel(\r
- // "javax.swing.plaf.metal.MetalLookAndFeel"\r
- // "javax.swing.plaf.multi.MultiLookAndFeel"\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
- );\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
-\r
-\r
-\r
- if(args!=null && args.length>0)\r
- {\r
- String file=null;\r
- if(args[0].equals("-open"))\r
- file = args[1];\r
- else\r
- file = args[0];\r
-\r
- String protocol = "File";\r
- if(file.indexOf("http:")>-1)\r
- protocol = "URL";\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
- }\r
-\r
- if(jalview.gui.Preferences.showStartupFile &&\r
- jalview.gui.Preferences.startupFile!=null)\r
- {\r
- String file = jalview.gui.Preferences.startupFile;\r
- String protocol = "File";\r
- if (file.indexOf("http:") > -1)\r
- protocol = "URL";\r
-\r
- if(file.endsWith(".jar"))\r
- Jalview2XML.LoadJalviewAlign(file);\r
- else\r
- {\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
- frame.LoadFile(file, protocol, format);\r
- }\r
- }\r
-\r
-\r
-\r
- }\r
-\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.bin;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.gui.*;
+
+/**
+ * Main class for Jalview Application
+ * <br>
+ * <br>start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview
+{
+
+ /**
+ * main class for Jalview application
+ *
+ * @param args open <em>filename</em>
+ */
+ public static void main(String[] args)
+ {
+ System.out.println("Java version: " + System.getProperty("java.version"));
+ System.out.println(System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ ArgsParser aparser = new ArgsParser(args);
+ boolean headless = false;
+
+ if (aparser.contains("help") || aparser.contains("h"))
+ {
+ System.out.println(
+ "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ + "-nodisplay\tRun Jalview without User Interface.\n"
+ +
+ "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ +
+ "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ +
+ "-features FILE\tUse the given file to mark features on the alignment.\n"
+ + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ + "-png FILE\tCreate PNG image FILE from alignment.\n"
+ +
+ "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ + "-eps FILE\tCreate EPS file FILE from alignment."
+ + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
+ + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ System.exit(0);
+ }
+
+ Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
+
+ if (aparser.contains("nodisplay"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ }
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ headless = true;
+ }
+
+ try
+ {
+ Cache.initLogger();
+ }
+ catch (java.lang.NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out.println(
+ "\nEssential logging libraries not found."
+ + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.exit(0);
+ }
+
+ Desktop desktop = null;
+
+ try
+ {
+ UIManager.setLookAndFeel(
+ UIManager.getSystemLookAndFeelClassName()
+ // UIManager.getCrossPlatformLookAndFeelClassName()
+ //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
+ //"javax.swing.plaf.metal.MetalLookAndFeel"
+ //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
+ //"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
+ );
+ }
+ catch (Exception ex)
+ {}
+ if (!headless)
+ {
+ desktop = new Desktop();
+ desktop.setVisible(true);
+ desktop.discoverer.start();
+ String url = aparser.getValue("questionnaire");
+ if (url != null)
+ {
+ // Start the desktop questionnaire prompter with the specified questionnaire
+ Cache.log.debug("Starting questionnaire url at " + url);
+ desktop.checkForQuestionnaire(url);
+ }
+ else
+ {
+ if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+ {
+ // Start the desktop questionnaire prompter with the specified questionnaire
+ // String defurl = "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; //
+ String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+ Cache.log.debug("Starting questionnaire with default url: " + defurl);
+ desktop.checkForQuestionnaire(defurl);
+
+ }
+ }
+
+ }
+
+ String file = null, protocol = null, format = null, data = null;
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+
+ file = aparser.getValue("open");
+
+ if (file == null && desktop == null)
+ {
+ System.out.println("No files to open!");
+ System.exit(1);
+ }
+
+ if (file != null)
+ {
+ System.out.println("Opening file: " + file);
+
+ if (!file.startsWith("http://"))
+ {
+ if (! (new java.io.File(file)).exists())
+ {
+ System.out.println("Can't find " + file);
+ if (headless)
+ {
+ System.exit(1);
+ }
+ }
+ }
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = "Jalview";
+ }
+ else
+ {
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ }
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+
+ if (af == null)
+ {
+ System.out.println("error");
+ return;
+ }
+
+ data = aparser.getValue("colour");
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
+
+ jalview.schemes.ColourSchemeI cs =
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
+ getAlignment(), data);
+
+ if (cs == null)
+ {
+ jalview.schemes.UserColourScheme ucs
+ = new jalview.schemes.UserColourScheme("white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
+ }
+
+ System.out.println("colour is " + data);
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups");
+ if (data != null)
+ {
+ af.parseFeaturesFile(data, protocol);
+ System.out.println("Added " + data);
+ }
+ data = aparser.getValue("features");
+ if (data != null)
+ {
+ af.parseFeaturesFile(data, protocol);
+ System.out.println("Added " + data);
+ }
+
+ data = aparser.getValue("annotations");
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data);
+ System.out.println("Added " + data);
+ }
+
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new java.io.File(file));
+ imageName = (new java.io.File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ System.out.println("Creating EPS file: " + file);
+ af.createEPS(new java.io.File(file));
+ continue;
+ }
+
+ if (af.saveAlignment(file, format))
+ {
+ System.out.println("Written alignment in " + format +
+ " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in " + format +
+ " format!!");
+ }
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
+ }
+
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ //////////////////////
+ if (
+ !headless
+ && file == null
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
+ )
+ {
+
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+ "http://www.jalview.org/examples/exampleFile_2_3.jar");
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ // if (file.endsWith(".jar"))
+ {
+ // format = "Jalview";
+ }
+ // else
+ {
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ }
+
+ fileLoader.LoadFile(file, protocol, format);
+
+ }
+ }
+}
+
+class ArgsParser
+{
+ Vector vargs = null;
+ public ArgsParser(String[] args)
+ {
+ vargs = new Vector();
+ for (int i = 0; i < args.length; i++)
+ {
+ String arg = args[i].trim();
+ if (arg.charAt(0) == '-')
+ {
+ arg = arg.substring(1);
+ }
+ vargs.addElement(arg);
+ }
+ }
+
+ public String getValue(String arg)
+ {
+ int index = vargs.indexOf(arg);
+ String ret = null;
+ if (index != -1)
+ {
+ ret = vargs.elementAt(index + 1).toString();
+ vargs.removeElementAt(index);
+ vargs.removeElementAt(index);
+ }
+ return ret;
+ }
+
+ public boolean contains(String arg)
+ {
+ if (vargs.contains(arg))
+ {
+ vargs.removeElement(arg);
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ public String nextValue()
+ {
+ return vargs.remove(0).toString();
+ }
+
+ public int getSize()
+ {
+ return vargs.size();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff