updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.
[jalview.git] / src / jalview / util / BrowserLauncher.java
index bba5727..2fa3b97 100755 (executable)
@@ -1,19 +1,25 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
+ * 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.util;
 
-import java.io.File;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
+import java.io.*;
+import java.lang.reflect.*;
 
 /**
  * BrowserLauncher is a class that provides one static method, openURL, which opens the default
@@ -43,7 +49,7 @@ import java.lang.reflect.Method;
  * back from the inherently platform-sensitive concept of a default browser and simply attempts
  * to launch Netscape via a shell command.
  * <p>
- * This code is Copyright 1999-2001 by Eric Albert (ejalbert@cs.stanford.edu) and may be
+ * This code is Copyright 1999-2001 by Eric Albert (ejalbert\@cs.stanford.edu) and may be
  * redistributed or modified in any form without restrictions as long as the portion of this
  * comment from this paragraph through the end of the comment is not removed.  The author
  * requests that he be notified of any application, applet, or other binary that makes use of
@@ -59,539 +65,864 @@ import java.lang.reflect.Method;
  * @author Eric Albert (<a href="mailto:ejalbert@cs.stanford.edu">ejalbert@cs.stanford.edu</a>)
  * @version 1.4b1 (Released June 20, 2001)
  */
-public class BrowserLauncher {
-
-        /**
-         * The Java virtual machine that we are running on.  Actually, in most cases we only care
-         * about the operating system, but some operating systems require us to switch on the VM. */
-        private static int jvm;
-
-        /** The browser for the system */
-        private static Object browser;
-
-        /**
-         * Caches whether any classes, methods, and fields that are not part of the JDK and need to
-         * be dynamically loaded at runtime loaded successfully.
-         * <p>
-         * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
-         * IOException.
-         */
-        private static boolean loadedWithoutErrors;
+public class BrowserLauncher
+{
+  /**
+   * The Java virtual machine that we are running on.  Actually, in most cases we only care
+   * about the operating system, but some operating systems require us to switch on the VM. */
+  private static int jvm;
 
-        /** The com.apple.mrj.MRJFileUtils class */
-        private static Class mrjFileUtilsClass;
+  /** The browser for the system */
+  private static Object browser;
 
-        /** The com.apple.mrj.MRJOSType class */
-        private static Class mrjOSTypeClass;
+  /**
+   * Caches whether any classes, methods, and fields that are not part of the JDK and need to
+   * be dynamically loaded at runtime loaded successfully.
+   * <p>
+   * Note that if this is <code>false</code>, <code>openURL()</code> will always return an
+   * IOException.
+   */
+  private static boolean loadedWithoutErrors;
 
-        /** The com.apple.MacOS.AEDesc class */
-        private static Class aeDescClass;
+  /** The com.apple.mrj.MRJFileUtils class */
+  private static Class mrjFileUtilsClass;
 
-        /** The <init>(int) method of com.apple.MacOS.AETarget */
-        private static Constructor aeTargetConstructor;
+  /** The com.apple.mrj.MRJOSType class */
+  private static Class mrjOSTypeClass;
 
-        /** The <init>(int, int, int) method of com.apple.MacOS.AppleEvent */
-        private static Constructor appleEventConstructor;
+  /** The com.apple.MacOS.AEDesc class */
+  private static Class aeDescClass;
 
-        /** The <init>(String) method of com.apple.MacOS.AEDesc */
-        private static Constructor aeDescConstructor;
+  /** The &lt;init&gt;(int) method of com.apple.MacOS.AETarget */
+  private static Constructor aeTargetConstructor;
 
-        /** The findFolder method of com.apple.mrj.MRJFileUtils */
-        private static Method findFolder;
+  /** The &lt;init&gt;(int, int, int) method of com.apple.MacOS.AppleEvent */
+  private static Constructor appleEventConstructor;
 
-        /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
-        private static Method getFileCreator;
+  /** The &lt;init&gt;(String) method of com.apple.MacOS.AEDesc */
+  private static Constructor aeDescConstructor;
 
-        /** The getFileType method of com.apple.mrj.MRJFileUtils */
-        private static Method getFileType;
+  /** The findFolder method of com.apple.mrj.MRJFileUtils */
+  private static Method findFolder;
 
-        /** The openURL method of com.apple.mrj.MRJFileUtils */
-        private static Method openURL;
+  /** The getFileCreator method of com.apple.mrj.MRJFileUtils */
+  private static Method getFileCreator;
 
-        /** The makeOSType method of com.apple.MacOS.OSUtils */
-        private static Method makeOSType;
+  /** The getFileType method of com.apple.mrj.MRJFileUtils */
+  private static Method getFileType;
 
-        /** The putParameter method of com.apple.MacOS.AppleEvent */
-        private static Method putParameter;
+  /** The openURL method of com.apple.mrj.MRJFileUtils */
+  private static Method openURL;
 
-        /** The sendNoReply method of com.apple.MacOS.AppleEvent */
-        private static Method sendNoReply;
+  /** The makeOSType method of com.apple.MacOS.OSUtils */
+  private static Method makeOSType;
 
-        /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
-        private static Object kSystemFolderType;
+  /** The putParameter method of com.apple.MacOS.AppleEvent */
+  private static Method putParameter;
 
-        /** The keyDirectObject AppleEvent parameter type */
-        private static Integer keyDirectObject;
+  /** The sendNoReply method of com.apple.MacOS.AppleEvent */
+  private static Method sendNoReply;
 
-        /** The kAutoGenerateReturnID AppleEvent code */
-        private static Integer kAutoGenerateReturnID;
+  /** Actually an MRJOSType pointing to the System Folder on a Macintosh */
+  private static Object kSystemFolderType;
 
-        /** The kAnyTransactionID AppleEvent code */
-        private static Integer kAnyTransactionID;
+  /** The keyDirectObject AppleEvent parameter type */
+  private static Integer keyDirectObject;
 
-        /** The linkage object required for JDirect 3 on Mac OS X. */
-        private static Object linkage;
+  /** The kAutoGenerateReturnID AppleEvent code */
+  private static Integer kAutoGenerateReturnID;
 
-        /** The framework to reference on Mac OS X */
-        private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
+  /** The kAnyTransactionID AppleEvent code */
+  private static Integer kAnyTransactionID;
 
-        /** JVM constant for MRJ 2.0 */
-        private static final int MRJ_2_0 = 0;
+  /** The linkage object required for JDirect 3 on Mac OS X. */
+  private static Object linkage;
 
-        /** JVM constant for MRJ 2.1 or later */
-        private static final int MRJ_2_1 = 1;
+  /** The framework to reference on Mac OS X */
+  private static final String JDirect_MacOSX = "/System/Library/Frameworks/Carbon.framework/Frameworks/HIToolbox.framework/HIToolbox";
 
-        /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
-        private static final int MRJ_3_0 = 3;
+  /** JVM constant for MRJ 2.0 */
+  private static final int MRJ_2_0 = 0;
 
-        /** JVM constant for MRJ 3.1 */
-        private static final int MRJ_3_1 = 4;
+  /** JVM constant for MRJ 2.1 or later */
+  private static final int MRJ_2_1 = 1;
 
-        /** JVM constant for any Windows NT JVM */
-        private static final int WINDOWS_NT = 5;
+  /** JVM constant for Java on Mac OS X 10.0 (MRJ 3.0) */
+  private static final int MRJ_3_0 = 3;
 
-        /** JVM constant for any Windows 9x JVM */
-        private static final int WINDOWS_9x = 6;
+  /** JVM constant for MRJ 3.1 */
+  private static final int MRJ_3_1 = 4;
 
-        /** JVM constant for any other platform */
-        private static final int OTHER = -1;
+  /** JVM constant for any Windows NT JVM */
+  private static final int WINDOWS_NT = 5;
 
-        /**
-         * The file type of the Finder on a Macintosh.  Hardcoding "Finder" would keep non-U.S. English
-         * systems from working properly.
-         */
-        private static final String FINDER_TYPE = "FNDR";
+  /** JVM constant for any Windows 9x JVM */
+  private static final int WINDOWS_9x = 6;
 
-        /**
-         * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
-         * application.
-         */
-        private static final String FINDER_CREATOR = "MACS";
+  /** JVM constant for any other platform */
+  private static final int OTHER = -1;
 
-        /** The name for the AppleEvent type corresponding to a GetURL event. */
-        private static final String GURL_EVENT = "GURL";
+  /**
+   * The file type of the Finder on a Macintosh.  Hardcoding "Finder" would keep non-U.S. English
+   * systems from working properly.
+   */
+  private static final String FINDER_TYPE = "FNDR";
 
-        /**
-         * The first parameter that needs to be passed into Runtime.exec() to open the default web
-         * browser on Windows.
-         */
-    private static final String FIRST_WINDOWS_PARAMETER = "/c";
+  /**
+   * The creator code of the Finder on a Macintosh, which is needed to send AppleEvents to the
+   * application.
+   */
+  private static final String FINDER_CREATOR = "MACS";
 
-    /** The second parameter for Runtime.exec() on Windows. */
-    private static final String SECOND_WINDOWS_PARAMETER = "start";
+  /** The name for the AppleEvent type corresponding to a GetURL event. */
+  private static final String GURL_EVENT = "GURL";
 
-    /**
-     * The third parameter for Runtime.exec() on Windows.  This is a "title"
-     * parameter that the command line expects.  Setting this parameter allows
-     * URLs containing spaces to work.
-     */
-    private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
+  /**
+   * The first parameter that needs to be passed into Runtime.exec() to open the default web
+   * browser on Windows.
+   */
+  private static final String FIRST_WINDOWS_PARAMETER = "/c";
 
-        /**
-         * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
-         * on many command-line systems.
-         */
-        private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
-        private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
-        private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
-        private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
+  /** The second parameter for Runtime.exec() on Windows. */
+  private static final String SECOND_WINDOWS_PARAMETER = "start";
 
-        /**
-         * The message from any exception thrown throughout the initialization process.
-         */
-        private static String errorMessage;
+  /**
+   * The third parameter for Runtime.exec() on Windows.  This is a "title"
+   * parameter that the command line expects.  Setting this parameter allows
+   * URLs containing spaces to work.
+   */
+  private static final String THIRD_WINDOWS_PARAMETER = "\"\"";
 
-        /**
-         * An initialization block that determines the operating system and loads the necessary
-         * runtime data.
-         */
-        static {
-                loadedWithoutErrors = true;
-                String osName = System.getProperty("os.name");
-                if (osName.startsWith("Mac OS")) {
-                        String mrjVersion = System.getProperty("mrj.version");
-                        String majorMRJVersion = mrjVersion.substring(0, 3);
-                        try {
-                                double version = Double.valueOf(majorMRJVersion).doubleValue();
-                                if (version == 2) {
-                                        jvm = MRJ_2_0;
-                                } else if (version >= 2.1 && version < 3) {
-                                        // Assume that all 2.x versions of MRJ work the same.  MRJ 2.1 actually
-                                        // works via Runtime.exec() and 2.2 supports that but has an openURL() method
-                                        // as well that we currently ignore.
-                                        jvm = MRJ_2_1;
-                                } else if (version == 3.0) {
-                                        jvm = MRJ_3_0;
-                                } else if (version >= 3.1) {
-                                        // Assume that all 3.1 and later versions of MRJ work the same.
-                                        jvm = MRJ_3_1;
-                                } else {
-                                        loadedWithoutErrors = false;
-                                        errorMessage = "Unsupported MRJ version: " + version;
-                                }
-                        } catch (NumberFormatException nfe) {
-                                loadedWithoutErrors = false;
-                                errorMessage = "Invalid MRJ version: " + mrjVersion;
-                        }
-                } else if (osName.startsWith("Windows")) {
-                        if (osName.indexOf("9") != -1) {
-                                jvm = WINDOWS_9x;
-                        } else {
-                                jvm = WINDOWS_NT;
-                        }
-                } else {
-                        jvm = OTHER;
-                }
+  /**
+   * The shell parameters for Netscape that opens a given URL in an already-open copy of Netscape
+   * on many command-line systems.
+   */
+  private static final String NETSCAPE_REMOTE_PARAMETER = "-remote";
+  private static final String NETSCAPE_OPEN_PARAMETER_START = "openURL(";
+  private static final String NETSCAPE_OPEN_NEW_WINDOW = ", new-window";
+  private static final String NETSCAPE_OPEN_PARAMETER_END = ")";
 
-                if (loadedWithoutErrors) {     // if we haven't hit any errors yet
-                        loadedWithoutErrors = loadClasses();
-                }
+  /**
+   * The message from any exception thrown throughout the initialization process.
+   */
+  private static String errorMessage;
+
+  /**
+   * An initialization block that determines the operating system and loads the necessary
+   * runtime data.
+   */
+  static
+  {
+    loadedWithoutErrors = true;
+
+    String osName = System.getProperty("os.name");
+
+    if (osName.startsWith("Mac OS"))
+    {
+      String mrjVersion = System.getProperty("mrj.version");
+      String majorMRJVersion = mrjVersion.substring(0, 3);
+
+      try
+      {
+        double version = Double.valueOf(majorMRJVersion).doubleValue();
+
+        if (version == 2)
+        {
+          jvm = MRJ_2_0;
+        }
+        else if ( (version >= 2.1) && (version < 3))
+        {
+          // Assume that all 2.x versions of MRJ work the same.  MRJ 2.1 actually
+          // works via Runtime.exec() and 2.2 supports that but has an openURL() method
+          // as well that we currently ignore.
+          jvm = MRJ_2_1;
+        }
+        else if (version == 3.0)
+        {
+          jvm = MRJ_3_0;
+        }
+        else if (version >= 3.1)
+        {
+          // Assume that all 3.1 and later versions of MRJ work the same.
+          jvm = MRJ_3_1;
         }
+        else
+        {
+          loadedWithoutErrors = false;
+          errorMessage = "Unsupported MRJ version: " + version;
+        }
+      }
+      catch (NumberFormatException nfe)
+      {
+        loadedWithoutErrors = false;
+        errorMessage = "Invalid MRJ version: " + mrjVersion;
+      }
+    }
+    else if (osName.startsWith("Windows"))
+    {
+      if (osName.indexOf("9") != -1)
+      {
+        jvm = WINDOWS_9x;
+      }
+      else
+      {
+        jvm = WINDOWS_NT;
+      }
+    }
+    else
+    {
+      jvm = OTHER;
+    }
+
+    if (loadedWithoutErrors)
+    { // if we haven't hit any errors yet
+      loadedWithoutErrors = loadClasses();
+    }
+  }
+
+  /**
+   * This class should be never be instantiated; this just ensures so.
+   */
+  private BrowserLauncher()
+  {
+  }
+
+  /**
+   * Called by a static initializer to load any classes, fields, and methods required at runtime
+   * to locate the user's web browser.
+   * @return <code>true</code> if all intialization succeeded
+   *                        <code>false</code> if any portion of the initialization failed
+   */
+  private static boolean loadClasses()
+  {
+    switch (jvm)
+    {
+      case MRJ_2_0:
+
+        try
+        {
+          Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
+          Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
+          Class appleEventClass = Class.forName(
+              "com.apple.MacOS.AppleEvent");
+          Class aeClass = Class.forName("com.apple.MacOS.ae");
+          aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
+
+          aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class[]
+              {
+              int.class
+          });
+          appleEventConstructor = appleEventClass.getDeclaredConstructor(new
+              Class[]
+              {
+              int.class, int.class, aeTargetClass, int.class,
+              int.class
+          });
+          aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[]
+              {
+              String.class
+          });
+
+          makeOSType = osUtilsClass.getDeclaredMethod("makeOSType",
+              new Class[]
+              {String.class});
+          putParameter = appleEventClass.getDeclaredMethod("putParameter",
+              new Class[]
+              {int.class, aeDescClass});
+          sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply",
+              new Class[]
+              {});
+
+          Field keyDirectObjectField = aeClass.getDeclaredField(
+              "keyDirectObject");
+          keyDirectObject = (Integer) keyDirectObjectField.get(null);
+
+          Field autoGenerateReturnIDField = appleEventClass.getDeclaredField(
+              "kAutoGenerateReturnID");
+          kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
+
+          Field anyTransactionIDField = appleEventClass.getDeclaredField(
+              "kAnyTransactionID");
+          kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
 
-        /**
-         * This class should be never be instantiated; this just ensures so.
-         */
-        private BrowserLauncher() { }
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
 
-        /**
-         * Called by a static initializer to load any classes, fields, and methods required at runtime
-         * to locate the user's web browser.
-         * @return <code>true</code> if all intialization succeeded
-         *                     <code>false</code> if any portion of the initialization failed
-         */
-        private static boolean loadClasses() {
-                switch (jvm) {
-                        case MRJ_2_0:
-                                try {
-                                        Class aeTargetClass = Class.forName("com.apple.MacOS.AETarget");
-                                        Class osUtilsClass = Class.forName("com.apple.MacOS.OSUtils");
-                                        Class appleEventClass = Class.forName("com.apple.MacOS.AppleEvent");
-                                        Class aeClass = Class.forName("com.apple.MacOS.ae");
-                                        aeDescClass = Class.forName("com.apple.MacOS.AEDesc");
-
-                                        aeTargetConstructor = aeTargetClass.getDeclaredConstructor(new Class [] { int.class });
-                                        appleEventConstructor = appleEventClass.getDeclaredConstructor(new Class[] { int.class, int.class, aeTargetClass, int.class, int.class });
-                                        aeDescConstructor = aeDescClass.getDeclaredConstructor(new Class[] { String.class });
-
-                                        makeOSType = osUtilsClass.getDeclaredMethod("makeOSType", new Class [] { String.class });
-                                        putParameter = appleEventClass.getDeclaredMethod("putParameter", new Class[] { int.class, aeDescClass });
-                                        sendNoReply = appleEventClass.getDeclaredMethod("sendNoReply", new Class[] { });
-
-                                        Field keyDirectObjectField = aeClass.getDeclaredField("keyDirectObject");
-                                        keyDirectObject = (Integer) keyDirectObjectField.get(null);
-                                        Field autoGenerateReturnIDField = appleEventClass.getDeclaredField("kAutoGenerateReturnID");
-                                        kAutoGenerateReturnID = (Integer) autoGenerateReturnIDField.get(null);
-                                        Field anyTransactionIDField = appleEventClass.getDeclaredField("kAnyTransactionID");
-                                        kAnyTransactionID = (Integer) anyTransactionIDField.get(null);
-                                } catch (ClassNotFoundException cnfe) {
-                                        errorMessage = cnfe.getMessage();
-                                        return false;
-                                } catch (NoSuchMethodException nsme) {
-                                        errorMessage = nsme.getMessage();
-                                        return false;
-                                } catch (NoSuchFieldException nsfe) {
-                                        errorMessage = nsfe.getMessage();
-                                        return false;
-                                } catch (IllegalAccessException iae) {
-                                        errorMessage = iae.getMessage();
-                                        return false;
-                                }
-                                break;
-                        case MRJ_2_1:
-                                try {
-                                        mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
-                                        mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
-                                        Field systemFolderField = mrjFileUtilsClass.getDeclaredField("kSystemFolderType");
-                                        kSystemFolderType = systemFolderField.get(null);
-                                        findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder", new Class[] { mrjOSTypeClass });
-                                        getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator", new Class[] { File.class });
-                                        getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType", new Class[] { File.class });
-                                } catch (ClassNotFoundException cnfe) {
-                                        errorMessage = cnfe.getMessage();
-                                        return false;
-                                } catch (NoSuchFieldException nsfe) {
-                                        errorMessage = nsfe.getMessage();
-                                        return false;
-                                } catch (NoSuchMethodException nsme) {
-                                        errorMessage = nsme.getMessage();
-                                        return false;
-                                } catch (SecurityException se) {
-                                        errorMessage = se.getMessage();
-                                        return false;
-                                } catch (IllegalAccessException iae) {
-                                        errorMessage = iae.getMessage();
-                                        return false;
-                                }
-                                break;
-                        case MRJ_3_0:
-                            try {
-                                        Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
-                                        Constructor constructor = linker.getConstructor(new Class[]{ Class.class });
-                                        linkage = constructor.newInstance(new Object[] { BrowserLauncher.class });
-                                } catch (ClassNotFoundException cnfe) {
-                                        errorMessage = cnfe.getMessage();
-                                        return false;
-                                } catch (NoSuchMethodException nsme) {
-                                        errorMessage = nsme.getMessage();
-                                        return false;
-                                } catch (InvocationTargetException ite) {
-                                        errorMessage = ite.getMessage();
-                                        return false;
-                                } catch (InstantiationException ie) {
-                                        errorMessage = ie.getMessage();
-                                        return false;
-                                } catch (IllegalAccessException iae) {
-                                        errorMessage = iae.getMessage();
-                                        return false;
-                                }
-                                break;
-                        case MRJ_3_1:
-                                try {
-                                        mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
-                                        openURL = mrjFileUtilsClass.getDeclaredMethod("openURL", new Class[] { String.class });
-                                } catch (ClassNotFoundException cnfe) {
-                                        errorMessage = cnfe.getMessage();
-                                        return false;
-                                } catch (NoSuchMethodException nsme) {
-                                        errorMessage = nsme.getMessage();
-                                        return false;
-                                }
-                                break;
-                        default:
-                            break;
-                }
-                return true;
+          return false;
         }
+        catch (NoSuchFieldException nsfe)
+        {
+          errorMessage = nsfe.getMessage();
 
-        /**
-         * Attempts to locate the default web browser on the local system.  Caches results so it
-         * only locates the browser once for each use of this class per JVM instance.
-         * @return The browser for the system.  Note that this may not be what you would consider
-         *                     to be a standard web browser; instead, it's the application that gets called to
-         *                     open the default web browser.  In some cases, this will be a non-String object
-         *                     that provides the means of calling the default browser.
-         */
-        private static Object locateBrowser() {
-                if (browser != null) {
-                        return browser;
-                }
-                switch (jvm) {
-                        case MRJ_2_0:
-                                try {
-                                        Integer finderCreatorCode = (Integer) makeOSType.invoke(null, new Object[] { FINDER_CREATOR });
-                                        Object aeTarget = aeTargetConstructor.newInstance(new Object[] { finderCreatorCode });
-                                        Integer gurlType = (Integer) makeOSType.invoke(null, new Object[] { GURL_EVENT });
-                                        Object appleEvent = appleEventConstructor.newInstance(new Object[] { gurlType, gurlType, aeTarget, kAutoGenerateReturnID, kAnyTransactionID });
-                                        // Don't set browser = appleEvent because then the next time we call
-                                        // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
-                                        // added the relevant parameter. Instead, regenerate the AppleEvent every time.
-                                        // There's probably a way to do this better; if any has any ideas, please let
-                                        // me know.
-                                        return appleEvent;
-                                } catch (IllegalAccessException iae) {
-                                        browser = null;
-                                        errorMessage = iae.getMessage();
-                                        return browser;
-                                } catch (InstantiationException ie) {
-                                        browser = null;
-                                        errorMessage = ie.getMessage();
-                                        return browser;
-                                } catch (InvocationTargetException ite) {
-                                        browser = null;
-                                        errorMessage = ite.getMessage();
-                                        return browser;
-                                }
-                        case MRJ_2_1:
-                                File systemFolder;
-                                try {
-                                        systemFolder = (File) findFolder.invoke(null, new Object[] { kSystemFolderType });
-                                } catch (IllegalArgumentException iare) {
-                                        browser = null;
-                                        errorMessage = iare.getMessage();
-                                        return browser;
-                                } catch (IllegalAccessException iae) {
-                                        browser = null;
-                                        errorMessage = iae.getMessage();
-                                        return browser;
-                                } catch (InvocationTargetException ite) {
-                                        browser = null;
-                                        errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
-                                        return browser;
-                                }
-                                String[] systemFolderFiles = systemFolder.list();
-                                // Avoid a FilenameFilter because that can't be stopped mid-list
-                                for(int i = 0; i < systemFolderFiles.length; i++) {
-                                        try {
-                                                File file = new File(systemFolder, systemFolderFiles[i]);
-                                                if (!file.isFile()) {
-                                                        continue;
-                                                }
-                                                // We're looking for a file with a creator code of 'MACS' and
-                                                // a type of 'FNDR'.  Only requiring the type results in non-Finder
-                                                // applications being picked up on certain Mac OS 9 systems,
-                                                // especially German ones, and sending a GURL event to those
-                                                // applications results in a logout under Multiple Users.
-                                                Object fileType = getFileType.invoke(null, new Object[] { file });
-                                                if (FINDER_TYPE.equals(fileType.toString())) {
-                                                        Object fileCreator = getFileCreator.invoke(null, new Object[] { file });
-                                                        if (FINDER_CREATOR.equals(fileCreator.toString())) {
-                                                                browser = file.toString();     // Actually the Finder, but that's OK
-                                                                return browser;
-                                                        }
-                                                }
-                                        } catch (IllegalArgumentException iare) {
-                                                browser = browser;
-                                                errorMessage = iare.getMessage();
-                                                return null;
-                                        } catch (IllegalAccessException iae) {
-                                                browser = null;
-                                                errorMessage = iae.getMessage();
-                                                return browser;
-                                        } catch (InvocationTargetException ite) {
-                                                browser = null;
-                                                errorMessage = ite.getTargetException().getClass() + ": " + ite.getTargetException().getMessage();
-                                                return browser;
-                                        }
-                                }
-                                browser = null;
-                                break;
-                        case MRJ_3_0:
-                        case MRJ_3_1:
-                                browser = "";  // Return something non-null
-                                break;
-                        case WINDOWS_NT:
-                                browser = "cmd.exe";
-                                break;
-                        case WINDOWS_9x:
-                                browser = "command.com";
-                                break;
-                        case OTHER:
-                        default:
-                                browser = jalview.bin.Cache.applicationProperties.getProperty("jalview.browser");
-                                if (browser==null) {
-                                  // hope netscape exists :-/
-                                  browser = "netscape";
-                                }
-                                break;
-                }
-                return browser;
+          return false;
         }
+        catch (IllegalAccessException iae)
+        {
+          errorMessage = iae.getMessage();
 
-        /**
-         * Attempts to open the default web browser to the given URL.
-         * @param url The URL to open
-         * @throws IOException If the web browser could not be located or does not run
-         */
-        public static void openURL(String url) throws IOException {
-                if (!loadedWithoutErrors) {
-                        throw new IOException("Exception in finding browser: " + errorMessage);
-                }
-                Object browser = locateBrowser();
-                if (browser == null) {
-                        throw new IOException("Unable to locate browser: " + errorMessage);
-                }
+          return false;
+        }
+
+        break
+            ;
+
+      case MRJ_2_1:
+
+        try
+        {
+          mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
+          mrjOSTypeClass = Class.forName("com.apple.mrj.MRJOSType");
+
+          Field systemFolderField = mrjFileUtilsClass.getDeclaredField(
+              "kSystemFolderType");
+          kSystemFolderType = systemFolderField.get(null);
+          findFolder = mrjFileUtilsClass.getDeclaredMethod("findFolder",
+              new Class[]
+              {mrjOSTypeClass});
+          getFileCreator = mrjFileUtilsClass.getDeclaredMethod("getFileCreator",
+              new Class[]
+              {File.class});
+          getFileType = mrjFileUtilsClass.getDeclaredMethod("getFileType",
+              new Class[]
+              {File.class});
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
+
+          return false;
+        }
+        catch (NoSuchFieldException nsfe)
+        {
+          errorMessage = nsfe.getMessage();
+
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
+
+          return false;
+        }
+        catch (SecurityException se)
+        {
+          errorMessage = se.getMessage();
+
+          return false;
+        }
+        catch (IllegalAccessException iae)
+        {
+          errorMessage = iae.getMessage();
+
+          return false;
+        }
+
+        break
+            ;
+
+      case MRJ_3_0:
+
+        try
+        {
+          Class linker = Class.forName("com.apple.mrj.jdirect.Linker");
+          Constructor constructor = linker.getConstructor(new Class[]
+              {
+              Class.class
+          });
+          linkage = constructor.newInstance(new Object[]
+                                            {
+                                            BrowserLauncher.class
+          });
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
+
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
+
+          return false;
+        }
+        catch (InvocationTargetException ite)
+        {
+          errorMessage = ite.getMessage();
 
-                switch (jvm) {
-                        case MRJ_2_0:
-                                Object aeDesc = null;
-                                try {
-                                        aeDesc = aeDescConstructor.newInstance(new Object[] { url });
-                                        putParameter.invoke(browser, new Object[] { keyDirectObject, aeDesc });
-                                        sendNoReply.invoke(browser, new Object[] { });
-                                } catch (InvocationTargetException ite) {
-                                        throw new IOException("InvocationTargetException while creating AEDesc: " + ite.getMessage());
-                                } catch (IllegalAccessException iae) {
-                                        throw new IOException("IllegalAccessException while building AppleEvent: " + iae.getMessage());
-                                } catch (InstantiationException ie) {
-                                        throw new IOException("InstantiationException while creating AEDesc: " + ie.getMessage());
-                                } finally {
-                                        aeDesc = null; // Encourage it to get disposed if it was created
-                                        browser = null;        // Ditto
-                                }
-                                break;
-                        case MRJ_2_1:
-                                Runtime.getRuntime().exec(new String[] { (String) browser, url } );
-                                break;
-                        case MRJ_3_0:
-                                int[] instance = new int[1];
-                                int result = ICStart(instance, 0);
-                                if (result == 0) {
-                                        int[] selectionStart = new int[] { 0 };
-                                        byte[] urlBytes = url.getBytes();
-                                        int[] selectionEnd = new int[] { urlBytes.length };
-                                        result = ICLaunchURL(instance[0], new byte[] { 0 }, urlBytes,
-                                                                                        urlBytes.length, selectionStart,
-                                                                                        selectionEnd);
-                                        if (result == 0) {
-                                                // Ignore the return value; the URL was launched successfully
-                                                // regardless of what happens here.
-                                                ICStop(instance);
-                                        } else {
-                                                throw new IOException("Unable to launch URL: " + result);
-                                        }
-                                } else {
-                                        throw new IOException("Unable to create an Internet Config instance: " + result);
-                                }
-                                break;
-                        case MRJ_3_1:
-                                try {
-                                        openURL.invoke(null, new Object[] { url });
-                                } catch (InvocationTargetException ite) {
-                                        throw new IOException("InvocationTargetException while calling openURL: " + ite.getMessage());
-                                } catch (IllegalAccessException iae) {
-                                        throw new IOException("IllegalAccessException while calling openURL: " + iae.getMessage());
-                                }
-                                break;
-                    case WINDOWS_NT:
-                    case WINDOWS_9x:
-                            // Add quotes around the URL to allow ampersands and other special
-                            // characters to work.
-                                Process process = Runtime.getRuntime().exec(new String[] { (String) browser,
-                                                                                                                                FIRST_WINDOWS_PARAMETER,
-                                                                                                                                SECOND_WINDOWS_PARAMETER,
-                                                                                                                                THIRD_WINDOWS_PARAMETER,
-                                                                                                                                '"' + url + '"' });
-                                // This avoids a memory leak on some versions of Java on Windows.
-                                // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
-                                try {
-                                        process.waitFor();
-                                        process.exitValue();
-                                } catch (InterruptedException ie) {
-                                        throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
-                                }
-                                break;
-                        case OTHER:
-                                // Assume that we're on Unix and that Netscape is installed
-
-                                // First, attempt to open the URL in a currently running session of Netscape
-                                process = Runtime.getRuntime().exec(new String[] { (String) browser,
-                                                                                                        NETSCAPE_REMOTE_PARAMETER,
-                                                                                                        NETSCAPE_OPEN_PARAMETER_START +
-                                                                                                        url +
-                                                                                                        NETSCAPE_OPEN_NEW_WINDOW +
-                                                                                                        NETSCAPE_OPEN_PARAMETER_END });
-                                try {
-                                        int exitCode = process.waitFor();
-                                        if (exitCode != 0) {   // if Netscape was not open
-                                                Runtime.getRuntime().exec(new String[] { (String) browser, url });
-                                        }
-                                } catch (InterruptedException ie) {
-                                        throw new IOException("InterruptedException while launching browser: " + ie.getMessage());
-                                }
-                                break;
-                        default:
-                                // This should never occur, but if it does, we'll try the simplest thing possible
-                                Runtime.getRuntime().exec(new String[] { (String) browser, url });
-                                break;
+          return false;
+        }
+        catch (InstantiationException ie)
+        {
+          errorMessage = ie.getMessage();
+
+          return false;
+        }
+        catch (IllegalAccessException iae)
+        {
+          errorMessage = iae.getMessage();
+
+          return false;
+        }
+
+        break
+            ;
+
+      case MRJ_3_1:
+
+        try
+        {
+          mrjFileUtilsClass = Class.forName("com.apple.mrj.MRJFileUtils");
+          openURL = mrjFileUtilsClass.getDeclaredMethod("openURL",
+              new Class[]
+              {String.class});
+        }
+        catch (ClassNotFoundException cnfe)
+        {
+          errorMessage = cnfe.getMessage();
+
+          return false;
+        }
+        catch (NoSuchMethodException nsme)
+        {
+          errorMessage = nsme.getMessage();
+
+          return false;
+        }
+
+        break
+            ;
+
+      default:
+        break;
+    }
+
+    return true;
+  }
+
+  /**
+   * Attempts to locate the default web browser on the local system.    s results so it
+   * only locates the browser once for each use of this class per JVM instance.
+   * @return The browser for the system.  Note that this may not be what you would consider
+   *                        to be a standard web browser; instead, it's the application that gets called to
+   *                        open the default web browser.  In some cases, this will be a non-String object
+   *                        that provides the means of calling the default browser.
+   */
+  private static Object locateBrowser()
+  {
+    if (browser != null)
+    {
+      return browser;
+    }
+
+    switch (jvm)
+    {
+      case MRJ_2_0:
+
+        try
+        {
+          Integer finderCreatorCode = (Integer) makeOSType.invoke(null,
+              new Object[]
+              {FINDER_CREATOR});
+          Object aeTarget = aeTargetConstructor.newInstance(new Object[]
+              {
+              finderCreatorCode
+          });
+          Integer gurlType = (Integer) makeOSType.invoke(null,
+              new Object[]
+              {GURL_EVENT});
+          Object appleEvent = appleEventConstructor.newInstance(new Object[]
+              {
+              gurlType, gurlType, aeTarget, kAutoGenerateReturnID,
+              kAnyTransactionID
+          });
+
+          // Don't set browser = appleEvent because then the next time we call
+          // locateBrowser(), we'll get the same AppleEvent, to which we'll already have
+          // added the relevant parameter. Instead, regenerate the AppleEvent every time.
+          // There's probably a way to do this better; if any has any ideas, please let
+          // me know.
+          return appleEvent;
+        }
+        catch (IllegalAccessException iae)
+        {
+          browser = null;
+          errorMessage = iae.getMessage();
+
+          return browser;
+        }
+        catch (InstantiationException ie)
+        {
+          browser = null;
+          errorMessage = ie.getMessage();
+
+          return browser;
+        }
+        catch (InvocationTargetException ite)
+        {
+          browser = null;
+          errorMessage = ite.getMessage();
+
+          return browser;
+        }
+
+        case MRJ_2_1:
+
+          File systemFolder;
+
+          try
+          {
+            systemFolder = (File) findFolder.invoke(null,
+                new Object[]
+                {kSystemFolderType});
+          }
+          catch (IllegalArgumentException iare)
+          {
+            browser = null;
+            errorMessage = iare.getMessage();
+
+            return browser;
+          }
+          catch (IllegalAccessException iae)
+          {
+            browser = null;
+            errorMessage = iae.getMessage();
+
+            return browser;
+          }
+          catch (InvocationTargetException ite)
+          {
+            browser = null;
+            errorMessage = ite.getTargetException().getClass() + ": " +
+                ite.getTargetException().getMessage();
+
+            return browser;
+          }
+
+          String[] systemFolderFiles = systemFolder.list();
+
+          // Avoid a FilenameFilter because that can't be stopped mid-list
+          for (int i = 0; i < systemFolderFiles.length; i++)
+          {
+            try
+            {
+              File file = new File(systemFolder, systemFolderFiles[i]);
+
+              if (!file.isFile())
+              {
+                continue;
+              }
+
+              // We're looking for a file with a creator code of 'MACS' and
+              // a type of 'FNDR'.  Only requiring the type results in non-Finder
+              // applications being picked up on certain Mac OS 9 systems,
+              // especially German ones, and sending a GURL event to those
+              // applications results in a logout under Multiple Users.
+              Object fileType = getFileType.invoke(null,
+                  new Object[]
+                  {file});
+
+              if (FINDER_TYPE.equals(fileType.toString()))
+              {
+                Object fileCreator = getFileCreator.invoke(null,
+                    new Object[]
+                    {file});
+
+                if (FINDER_CREATOR.equals(fileCreator.toString()))
+                {
+                  browser = file.toString(); // Actually the Finder, but that's OK
+
+                  return browser;
                 }
+              }
+            }
+            catch (IllegalArgumentException iare)
+            {
+              errorMessage = iare.getMessage();
+
+              return null;
+            }
+            catch (IllegalAccessException iae)
+            {
+              browser = null;
+              errorMessage = iae.getMessage();
+
+              return browser;
+            }
+            catch (InvocationTargetException ite)
+            {
+              browser = null;
+              errorMessage = ite.getTargetException().getClass() + ": " +
+                  ite.getTargetException().getMessage();
+
+              return browser;
+            }
+          }
+
+          browser = null;
+
+          break;
+
+      case MRJ_3_0:
+      case MRJ_3_1:
+        browser = ""; // Return something non-null
+
+        break;
+
+      case WINDOWS_NT:
+        browser = "cmd.exe";
+
+        break;
+
+      case WINDOWS_9x:
+        browser = "command.com";
+
+        break;
+
+      case OTHER:
+      default:
+        browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
+
+        break;
+    }
+
+    return browser;
+  }
+  /**
+   * used to ensure that browser is up-to-date after a configuration
+   * change (Unix DEFAULT_BROWSER property change).
+   */
+  public static void resetBrowser() {
+    browser = null;
+  }
+  /**
+   * Attempts to open the default web browser to the given URL.
+   * @param url The URL to open
+   * @throws IOException If the web browser could not be located or does not run
+   */
+  public static void openURL(String url)
+      throws IOException
+  {
+    if (!loadedWithoutErrors)
+    {
+      throw new IOException("Exception in finding browser: " +
+                            errorMessage);
+    }
+
+    Object browser = locateBrowser();
+
+    if (browser == null)
+    {
+      throw new IOException("Unable to locate browser: " + errorMessage);
+    }
+
+    switch (jvm)
+    {
+      case MRJ_2_0:
+
+        Object aeDesc = null;
+
+        try
+        {
+          aeDesc = aeDescConstructor.newInstance(new Object[]
+                                                 {url});
+          putParameter.invoke(browser,
+                              new Object[]
+                              {keyDirectObject, aeDesc});
+          sendNoReply.invoke(browser, new Object[]
+                             {});
+        }
+        catch (InvocationTargetException ite)
+        {
+          throw new IOException(
+              "InvocationTargetException while creating AEDesc: " +
+              ite.getMessage());
+        }
+        catch (IllegalAccessException iae)
+        {
+          throw new IOException(
+              "IllegalAccessException while building AppleEvent: " +
+              iae.getMessage());
+        }
+        catch (InstantiationException ie)
+        {
+          throw new IOException(
+              "InstantiationException while creating AEDesc: " +
+              ie.getMessage());
+        }
+        finally
+        {
+          aeDesc = null; // Encourage it to get disposed if it was created
+          browser = null; // Ditto
+        }
+
+        break;
+
+      case MRJ_2_1:
+        Runtime.getRuntime().exec(new String[]
+                                  { (String) browser, url});
+
+        break;
+
+      case MRJ_3_0:
+
+        int[] instance = new int[1];
+        int result = ICStart(instance, 0);
+
+        if (result == 0)
+        {
+          int[] selectionStart = new int[]
+              {
+              0};
+          byte[] urlBytes = url.getBytes();
+          int[] selectionEnd = new int[]
+              {
+              urlBytes.length};
+          result = ICLaunchURL(instance[0], new byte[]
+                               {0}, urlBytes,
+                               urlBytes.length, selectionStart, selectionEnd);
+
+          if (result == 0)
+          {
+            // Ignore the return value; the URL was launched successfully
+            // regardless of what happens here.
+            ICStop(instance);
+          }
+          else
+          {
+            throw new IOException("Unable to launch URL: " + result);
+          }
+        }
+        else
+        {
+          throw new IOException(
+              "Unable to create an Internet Config instance: " + result);
+        }
+
+        break;
+
+      case MRJ_3_1:
+
+        try
+        {
+          openURL.invoke(null, new Object[]
+                         {url});
+        }
+        catch (InvocationTargetException ite)
+        {
+          throw new IOException(
+              "InvocationTargetException while calling openURL: " +
+              ite.getMessage());
+        }
+        catch (IllegalAccessException iae)
+        {
+          throw new IOException(
+              "IllegalAccessException while calling openURL: " +
+              iae.getMessage());
+        }
+
+        break
+            ;
+
+      case WINDOWS_NT:
+      case WINDOWS_9x:
+
+        // Add quotes around the URL to allow ampersands and other special
+        // characters to work.
+        Process process = Runtime.getRuntime().exec(new String[]
+            {
+            (String) browser, FIRST_WINDOWS_PARAMETER,
+            SECOND_WINDOWS_PARAMETER, THIRD_WINDOWS_PARAMETER,
+            '"' + url + '"'
+        });
+
+        // This avoids a memory leak on some versions of Java on Windows.
+        // That's hinted at in <http://developer.java.sun.com/developer/qow/archive/68/>.
+        try
+        {
+          process.waitFor();
+          process.exitValue();
+        }
+        catch (InterruptedException ie)
+        {
+          throw new IOException(
+              "InterruptedException while launching browser: " +
+              ie.getMessage());
         }
 
-        /**
-         * Methods required for Mac OS X.  The presence of native methods does not cause
-         * any problems on other platforms.
+        break
+            ;
+
+      case OTHER:
+
+        // Assume that we're on Unix and that Netscape (actually Firefox) is installed
+        // First, attempt to open the URL in a currently running session of Netscape
+        // JBPNote log debug
+
+        /* System.out.println("Executing : "+browser+" "+
+         NETSCAPE_REMOTE_PARAMETER+" "+
+         NETSCAPE_OPEN_PARAMETER_START +
+         url +
+         NETSCAPE_OPEN_NEW_WINDOW +
+         NETSCAPE_OPEN_PARAMETER_END);
          */
-        private native static int ICStart(int[] instance, int signature);
-        private native static int ICStop(int[] instance);
-        private native static int ICLaunchURL(int instance, byte[] hint, byte[] data, int len,
-                                                                                        int[] selectionStart, int[] selectionEnd);
+        process = Runtime.getRuntime().exec(new String[]
+                                            {
+                                            (String) browser,
+                                            NETSCAPE_REMOTE_PARAMETER,
+
+                                            NETSCAPE_OPEN_PARAMETER_START + url +
+                                            NETSCAPE_OPEN_NEW_WINDOW +
+                                            NETSCAPE_OPEN_PARAMETER_END
+        });
+
+        try
+        {
+          int exitCode = process.waitFor();
+
+          if (exitCode != 0)
+          { // if Netscape was not open
+            Runtime.getRuntime().exec(new String[]
+                                      { (String) browser, url});
+          }
+        }
+        catch (InterruptedException ie)
+        {
+          throw new IOException(
+              "InterruptedException while launching browser: " +
+              ie.getMessage());
+        }
+
+        break
+            ;
+
+      default:
+
+        // This should never occur, but if it does, we'll try the simplest thing possible
+        Runtime.getRuntime().exec(new String[]
+                                  { (String) browser, url});
+
+        break;
+    }
+  }
+
+  /**
+   * Methods required for Mac OS X.  The presence of native methods does not cause
+   * any problems on other platforms.
+   */
+  private native static int ICStart(int[] instance, int signature);
+
+  private native static int ICStop(int[] instance);
+
+  private native static int ICLaunchURL(int instance, byte[] hint,
+                                        byte[] data, int len,
+                                        int[] selectionStart,
+                                        int[] selectionEnd);
 }