From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 8 Sep 2023 13:43:09 +0000 (+0100)
Subject: JAL-4262 Dialog for GUI and WARN for CLI of old style arguments, or mixed arguments... 
X-Git-Tag: Release_2_11_3_0~8^2~5^2~30^2~2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=985d5f40db480896f550db914297cf948a32e963

JAL-4262 Dialog for GUI and WARN for CLI of old style arguments, or mixed arguments \(with exit\). Changed Jalview.exit to use an enum for exit code to avoid collisions.
---

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 0c4f165..eafabb2 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1464,3 +1464,6 @@ action.cluster_matrix = Cluster matrix
 action.clustering_matrix_for = Calculating tree for matrix {0} and clustering at {1}
 action.cluster_matrix_tooltip = Computes an average distance tree for the matrix and displays it
 label.all_known_alignment_files = All known alignment files
+label.command_line_arguments = Command Line Arguments
+warning.using_old_command_line_arguments = It looks like you are using old command line arguments.  These are now deprecated and will be removed in a future release of Jalview.\nFind out about the new command line arguments at\n
+warning.using_mixed_command_line_arguments = Jalview cannot use both old (-arg) and new (--arg) command line arguments.  Please check your command line arguments.\ne.g. {0} and {1}
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 1f256cb..72b49f8 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1438,3 +1438,6 @@ label.nothing_selected = Nada seleccionado
 prompt.analytics_title = Jalview Estadísticas de Uso
 prompt.analytics = ¿Quiere ayudar a mejorar Jalview habilitando la recopilación de estadísticas de uso con análisis Plausible?\nPuede habilitar o deshabilitar el seguimiento de uso en las preferencias.
 label.all_known_alignment_files = Todos los archivos de alineación conocidos
+label.command_line_arguments = Argumentos de línea de comando
+warning.using_old_command_line_arguments = Parece que estás utilizando argumentos antiguos de línea de comando. Estos ahora están en desuso y se eliminarán en una versión futura de Jalview.\nObtenga más información sobre los nuevos argumentos de la línea de comando en\n
+warning.using_mixed_command_line_arguments = Jalview no puede utilizar argumentos de línea de comando antiguos (-arg) y nuevos (--arg). Verifique los argumentos de su línea de comando.\ne.g. {0} y {1}
diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 8164182..d910819 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,6 +14,7 @@ import java.util.Map;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Jalview.ExitCode;
 import jalview.bin.argparser.Arg;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.ArgParser.Position;
@@ -140,7 +141,9 @@ public class Commands
     }
     if (argParser.getBoolean(Arg.QUIT))
     {
-      Jalview.getInstance().quit();
+      Jalview.getInstance().exit(
+              "Exiting due to " + Arg.QUIT.argString() + " argument.",
+              ExitCode.OK);
       return true;
     }
     // carry on with jalview.bin.Jalview
@@ -249,21 +252,24 @@ public class Commands
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
-          boolean xception=false;
-          try {
+          boolean xception = false;
+          try
+          {
             af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                     format);
           } catch (Throwable thr)
           {
-            xception=true;
-            Console.error("Couldn't open '"+openFile+"' as "+format+" "+thr.getLocalizedMessage()+ " (Enable debug for full stack trace)");
-            Console.debug("Exception when opening '"+openFile+"'",thr);
-          }
-          finally
+            xception = true;
+            Console.error("Couldn't open '" + openFile + "' as " + format
+                    + " " + thr.getLocalizedMessage()
+                    + " (Enable debug for full stack trace)");
+            Console.debug("Exception when opening '" + openFile + "'", thr);
+          } finally
           {
-            if (af==null && !xception)
+            if (af == null && !xception)
             {
-              Console.info("Ignoring '"+openFile+"' - no alignment data found.");
+              Console.info("Ignoring '" + openFile
+                      + "' - no alignment data found.");
               continue;
             }
           }
@@ -410,7 +416,8 @@ public class Commands
       {
         if (headless)
         {
-          Jalview.exit("Could not open any files in headless mode", 1);
+          Jalview.exit("Could not open any files in headless mode",
+                  ExitCode.NO_FILES);
         }
         else
         {
@@ -946,7 +953,7 @@ public class Commands
 
             Jalview.exit("No valid format specified for "
                     + Arg.OUTPUT.argString() + ". Valid formats are "
-                    + validSB.toString() + ".", 1);
+                    + validSB.toString() + ".", ExitCode.INVALID_FORMAT);
             // this return really shouldn't happen
             return false;
           }
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index eabad91..51e8a82 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -426,7 +426,7 @@ public class Jalview
     // stop now if only after --version
     if (bootstrapArgs.contains(Arg.VERSION))
     {
-      Jalview.exit(null, 0);
+      Jalview.exit(null, ExitCode.OK);
     }
 
     // old ArgsParser
@@ -458,7 +458,7 @@ public class Jalview
       error.printStackTrace();
       String message = "\nEssential logging libraries not found."
               + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
-      Jalview.exit(message, 0);
+      Jalview.exit(message, ExitCode.OK);
     }
 
     // register SIGTERM listener
@@ -545,7 +545,7 @@ public class Jalview
                 .getList(Arg.HELP);
         Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
                 .collect(Collectors.toList())));
-        Jalview.exit(null, 0);
+        Jalview.exit(null, ExitCode.OK);
       }
       if (aparser.contains("help") || aparser.contains("h"))
       {
@@ -554,7 +554,7 @@ public class Jalview
         showUsage();
         */
         Console.outPrintln(Arg.usage());
-        Jalview.exit(null, 0);
+        Jalview.exit(null, ExitCode.OK);
       }
 
       // new CLI
@@ -648,7 +648,7 @@ public class Jalview
       error.printStackTrace();
       String message = "\nEssential logging libraries not found."
               + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
-      Jalview.exit(message, 0);
+      Jalview.exit(message, ExitCode.OK);
     }
     desktop = null;
 
@@ -809,6 +809,30 @@ public class Jalview
         }
       }
     }
+    else
+    {
+
+      if (getArgParser().isMixedStyle())
+      {
+        String warning = MessageManager.formatMessage(
+                "warning.using_mixed_command_line_arguments",
+                getArgParser().getMixedExamples());
+        Console.warn(warning);
+        Jalview.exit(
+                "Exiting due to mixed old and new command line arguments",
+                ExitCode.INVALID_ARGUMENT);
+      }
+      if (getArgParser().isOldStyle())
+      {
+        String warning = MessageManager
+                .getString("warning.using_old_command_line_arguments")
+                .replace("\n", " ")
+                + "https://www.jalview.org/help/html/features/commandline.html";
+        Console.warn(warning);
+      }
+
+    }
+
     // Run Commands from cli
     cmds = new Commands(argparser, headlessArg);
     cmds.processArgs();
@@ -827,7 +851,7 @@ public class Jalview
         else
         {
           Jalview.exit("Successfully completed commands in headless mode",
-                  0);
+                  ExitCode.OK);
         }
       }
       Console.info("Successfully completed commands");
@@ -836,7 +860,8 @@ public class Jalview
     {
       if (headlessArg)
       {
-        Jalview.exit("Error when running Commands in headless mode", 1);
+        Jalview.exit("Error when running Commands in headless mode",
+                ExitCode.ERROR_RUNNING_COMMANDS);
       }
       Console.warn("Error when running commands");
     }
@@ -867,7 +892,7 @@ public class Jalview
 
     if (file == null && desktop == null && !commandsSuccess)
     {
-      Jalview.exit("No files to open!", 1);
+      Jalview.exit("No files to open!", ExitCode.NO_FILES);
     }
 
     long progress = -1;
@@ -897,7 +922,8 @@ public class Jalview
             if (headless)
             {
               Jalview.exit(
-                      "Can't find file '" + file + "' in headless mode", 1);
+                      "Can't find file '" + file + "' in headless mode",
+                      ExitCode.FILE_NOT_FOUND);
             }
             Console.warn("Can't find file'" + file + "'");
           }
@@ -1769,7 +1795,7 @@ public class Jalview
   public void quit()
   {
     // System.exit will run the shutdownHook first
-    Jalview.exit("Quitting now. Bye!", 0);
+    Jalview.exit("Quitting now. Bye!", ExitCode.OK);
   }
 
   public static AlignFrame getCurrentAlignFrame()
@@ -1787,8 +1813,9 @@ public class Jalview
     return cmds;
   }
 
-  public static void exit(String message, int exitcode)
+  public static void exit(String message, ExitCode ec)
   {
+    int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1;
     if (Console.log == null)
     {
       // Don't start the logger just to exit!
@@ -1825,6 +1852,14 @@ public class Jalview
     }
   }
 
+  public enum ExitCode
+  {
+    // only add new ones to the end of the list (to preserve ordinal values)
+    OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
+    INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
+    ERROR_RUNNING_COMMANDS;
+  }
+
   /******************************
    * 
    * TEST OUTPUT METHODS
@@ -1844,7 +1879,7 @@ public class Jalview
    * @param a
    *          - Arg currently being processed
    * @param s1
-   *          - expected 
+   *          - expected
    * @param s2
    */
   protected static void testoutput(ArgParser ap, Arg a, String s1,
@@ -1900,7 +1935,8 @@ public class Jalview
   }
 
   /**
-   * conditionally (on @param yes) report that expected value s1 was set during CommandsTest tests
+   * conditionally (on @param yes) report that expected value s1 was set during
+   * CommandsTest tests
    */
   private static void testoutput(boolean yes, Arg a, String s1, String s2)
   {
@@ -1980,7 +2016,8 @@ public class Jalview
 
   public static boolean isBatchMode()
   {
-    return getInstance()!=null && (getInstance().desktop == null || getInstance().desktop.isInBatchMode());
+    return getInstance() != null && (getInstance().desktop == null
+            || getInstance().desktop.isInBatchMode());
   }
 
 }
diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 3862375..6e53770 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -37,6 +37,7 @@ import java.util.Map;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
 import jalview.bin.argparser.Arg.Opt;
 import jalview.bin.argparser.Arg.Type;
 import jalview.util.FileUtils;
@@ -177,6 +178,15 @@ public class ArgParser
 
   private BootstrapArgs bootstrapArgs = null;
 
+  private boolean oldArguments = false;
+
+  private boolean mixedArguments = false;
+
+  /**
+   * saved examples of mixed arguments
+   */
+  private String[] mixedExamples = new String[] { null, null };
+
   static
   {
     argMap = new HashMap<>();
@@ -241,19 +251,39 @@ public class ArgParser
       if (arg.startsWith(DOUBLEDASH))
       {
         dd = true;
-        break;
+        if (mixedExamples[1] == null)
+        {
+          mixedExamples[1] = arg;
+        }
       }
       else if (arg.startsWith("-") || arg.equals("open"))
       {
         d = true;
+        if (mixedExamples[0] == null)
+        {
+          mixedExamples[0] = arg;
+        }
+      }
+    }
+    if (d)
+    {
+      if (dd)
+      {
+        mixedArguments = true;
+      }
+      else
+      {
+        oldArguments = true;
       }
     }
-    if (d && !dd)
+
+    if (oldArguments || mixedArguments)
     {
       // leave it to the old style -- parse an empty list
       parse(new ArrayList<String>(), false, false);
       return;
     }
+
     if (bsa != null)
       this.bootstrapArgs = bsa;
     else
@@ -379,10 +409,12 @@ public class ArgParser
         {
           // arg not found
           Console.error("Argument '" + arg + "' not recognised.  Exiting.");
-          Jalview.exit("Invalid argument used." + System.lineSeparator()
-                  + "Use" + System.lineSeparator() + "jalview "
-                  + Arg.HELP.argString() + System.lineSeparator()
-                  + "for a usage statement.", 13);
+          Jalview.exit(
+                  "Invalid argument used." + System.lineSeparator() + "Use"
+                          + System.lineSeparator() + "jalview "
+                          + Arg.HELP.argString() + System.lineSeparator()
+                          + "for a usage statement.",
+                  ExitCode.INVALID_ARGUMENT);
           continue;
         }
         if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
@@ -915,7 +947,7 @@ public class ArgParser
       {
         String message = Arg.ARGFILE.argString() + EQUALS + "\""
                 + argFile.getPath() + "\": File does not exist.";
-        Jalview.exit(message, 2);
+        Jalview.exit(message, ExitCode.FILE_NOT_FOUND);
       }
       try
       {
@@ -929,7 +961,7 @@ public class ArgParser
       {
         String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
                 + "\": File could not be read.";
-        Jalview.exit(message, 3);
+        Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
       }
     }
     // Third param "true" uses Opt.PRIVATE args --setargile=argfile and
@@ -955,7 +987,7 @@ public class ArgParser
         String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
                 + "\": File could not be read.";
         Console.debug(message, e);
-        Jalview.exit(message, 3);
+        Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
       }
     }
     return args;
@@ -1341,4 +1373,18 @@ public class ArgParser
     return linkedArgs.get(linkedId);
   }
 
+  public boolean isOldStyle()
+  {
+    return oldArguments;
+  }
+
+  public boolean isMixedStyle()
+  {
+    return mixedArguments;
+  }
+
+  public String[] getMixedExamples()
+  {
+    return mixedExamples;
+  }
 }
\ No newline at end of file
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 035da25..6b2044c 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -87,9 +87,11 @@ import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
+import javax.swing.JTextArea;
 import javax.swing.JTextField;
 import javax.swing.KeyStroke;
 import javax.swing.SwingUtilities;
@@ -106,6 +108,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
@@ -635,6 +638,62 @@ public class Desktop extends jalview.jbgui.GDesktop
       // used for jalviewjsTest
       jalview.bin.Console.info("JALVIEWJS: CREATED DESKTOP");
     }
+
+    cliWarning();
+  }
+
+  /**
+   * Warning about old or mixed command line arguments
+   */
+  private void cliWarning()
+  {
+    Jalview j = Jalview.getInstance();
+    boolean oldStyle = j.getArgParser() != null
+            && j.getArgParser().isOldStyle();
+    boolean mixedStyle = j.getArgParser() != null
+            && j.getArgParser().isMixedStyle();
+
+    String title = MessageManager.getString("label.command_line_arguments");
+    if (mixedStyle)
+    {
+      String warning = MessageManager.formatMessage(
+              "warning.using_mixed_command_line_arguments",
+              j.getArgParser().getMixedExamples());
+      String quit = MessageManager.getString("action.quit");
+      JvOptionPane jvp = JvOptionPane.newOptionDialog(this);
+      jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> {
+      });
+      jvp.showDialogOnTopAsync(this, warning, title, JOptionPane.YES_OPTION,
+              JOptionPane.WARNING_MESSAGE, null, new Object[]
+              { quit }, quit, true, null, false);
+
+      Jalview.getInstance().exit(
+              "Exiting due to mixed old and new command line arguments.",
+              ExitCode.MIXED_CLI_ARGUMENTS);
+      return;
+    }
+    if (oldStyle)
+    {
+      String warning = MessageManager
+              .getString("warning.using_old_command_line_arguments")
+              + "https://www.jalview.org/help/html/features/commandline.html";
+
+      JTextArea jta = new JTextArea(2, 32);
+      // jta.setLineWrap(true);
+      jta.setEditable(false);
+      jta.setWrapStyleWord(true);
+      jta.setAutoscrolls(true);
+      jta.setText(warning);
+
+      String ok = MessageManager.getString("label.continue");
+      JvOptionPane jvp = JvOptionPane.newOptionDialog(this);
+      jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> {
+      });
+      jvp.showDialogOnTopAsync(this, jta, title, JOptionPane.YES_OPTION,
+              JOptionPane.WARNING_MESSAGE, null, new Object[]
+              { ok }, ok, false, null, false);
+    }
+
   }
 
   /**
@@ -1081,23 +1140,23 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     setKeyBindings(frame);
 
-    // Since the latest FlatLaf patch, we occasionally have problems showing structureViewer frames...
-    int tries=3;
-    boolean shown=false;
-    Exception last=null;
+    // Since the latest FlatLaf patch, we occasionally have problems showing
+    // structureViewer frames...
+    int tries = 3;
+    boolean shown = false;
+    Exception last = null;
     do
     {
       try
       {
         desktop.add(frame);
-        shown=true;
+        shown = true;
       } catch (IllegalArgumentException iaex)
       {
-        last=iaex;
+        last = iaex;
         tries--;
-        jalview.bin.Console.info(
-                "Squashed IllegalArgument Exception (" + tries + " left) for "+frame.getTitle(),
-                iaex);
+        jalview.bin.Console.info("Squashed IllegalArgument Exception ("
+                + tries + " left) for " + frame.getTitle(), iaex);
         try
         {
           Thread.sleep(5);
@@ -1109,7 +1168,9 @@ public class Desktop extends jalview.jbgui.GDesktop
     } while (!shown && tries > 0);
     if (!shown)
     {
-      jalview.bin.Console.error("Serious Problem whilst showing window "+frame.getTitle(),last);
+      jalview.bin.Console.error(
+              "Serious Problem whilst showing window " + frame.getTitle(),
+              last);
     }
 
     windowMenu.add(menuItem);
@@ -1522,7 +1583,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // this will run the shutdownHook but QuitHandler.getQuitResponse() should
     // not run a second time if gotQuitResponse flag has been set (i.e. user
     // confirmed quit of some kind).
-    Jalview.exit("Desktop exiting.", 0);
+    Jalview.exit("Desktop exiting.", ExitCode.OK);
   }
 
   private void storeLastKnownDimensions(String string, Rectangle jc)
@@ -1635,7 +1696,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     } catch (Exception ex)
     {
-      jalview.bin.Console.errPrintln("Error opening help: " + ex.getMessage());
+      jalview.bin.Console
+              .errPrintln("Error opening help: " + ex.getMessage());
     }
   }
 
@@ -1866,7 +1928,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     boolean autoSave = projectFile != null && !saveAs
             && BackupFiles.getEnabled();
 
-    // jalview.bin.Console.outPrintln("autoSave="+autoSave+", projectFile='"+projectFile+"',
+    // jalview.bin.Console.outPrintln("autoSave="+autoSave+",
+    // projectFile='"+projectFile+"',
     // saveAs="+saveAs+", Backups
     // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
@@ -3660,14 +3723,16 @@ public class Desktop extends jalview.jbgui.GDesktop
       Desktop us = Desktop.instance;
       Desktop.instance = null;
       // call dispose in a separate thread - try to avoid indirect deadlocks
-      new Thread(new Runnable() {
+      new Thread(new Runnable()
+      {
         @Override
         public void run()
         {
           ExecutorService dex = us.dialogExecutor;
-          if (dex!=null) {
+          if (dex != null)
+          {
             dex.shutdownNow();
-            us.dialogExecutor=null;
+            us.dialogExecutor = null;
             us.block.drainPermits();
           }
           us.dispose();
diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java
index 5b926c3..3f5de0a 100644
--- a/src/jalview/gui/JvOptionPane.java
+++ b/src/jalview/gui/JvOptionPane.java
@@ -722,7 +722,8 @@ public class JvOptionPane extends JOptionPane
 
   private static void outputMessage(Object message)
   {
-    jalview.bin.Console.outPrintln(">>> JOption Message : " + message.toString());
+    jalview.bin.Console
+            .outPrintln(">>> JOption Message : " + message.toString());
   }
 
   public static Object getMockResponse()
@@ -1264,6 +1265,17 @@ public class JvOptionPane extends JOptionPane
           int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
           Object initialValue, boolean modal, JButton[] buttons)
   {
+    showDialogOnTopAsync(dialogParent, label, actionString,
+            JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+            initialValue, modal, buttons, true);
+  }
+
+  public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+          String actionString, int JOPTIONPANE_OPTION,
+          int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+          Object initialValue, boolean modal, JButton[] buttons,
+          boolean dispose)
+  {
     if (!isInteractiveMode())
     {
       handleResponse(getMockResponse());
@@ -1285,8 +1297,11 @@ public class JvOptionPane extends JOptionPane
             JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal,
             buttons);
 
-    dialogParent.setAlwaysOnTop(false);
-    dialogParent.dispose();
+    if (dispose)
+    {
+      dialogParent.setAlwaysOnTop(false);
+      dialogParent.dispose();
+    }
   }
 
   /**
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 38ee9ca..a43dc42 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -36,6 +36,7 @@ import java.util.StringTokenizer;
 import com.stevesoft.pat.Regex;
 
 import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
@@ -324,7 +325,7 @@ public class NewickFile extends FileParse
         {
           c.setRight(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (BinaryNode) c.right();
+          c = c.right();
         }
         else
         {
@@ -338,7 +339,7 @@ public class NewickFile extends FileParse
 
           c.setLeft(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (BinaryNode) c.left();
+          c = c.left();
         }
 
         if (realroot == null)
@@ -579,7 +580,7 @@ public class NewickFile extends FileParse
               // Just advance focus, if we need to
               if ((c.left() != null) && (!c.left().isLeaf()))
               {
-                c = (BinaryNode) c.left();
+                c = c.left();
               }
             }
           }
@@ -617,7 +618,7 @@ public class NewickFile extends FileParse
     }
     // THe next line is failing for topali trees - not sure why yet. if
     // (root.right()!=null && root.isDummy())
-    root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+    root = root.right().detach(); // remove the imaginary root.
 
     if (!RootHasDistance)
     {
@@ -947,7 +948,8 @@ public class NewickFile extends FileParse
       if (args == null || args.length != 1)
       {
         Jalview.exit(
-                "Takes one argument - file name of a newick tree file.", 0);
+                "Takes one argument - file name of a newick tree file.",
+                ExitCode.INVALID_ARGUMENT);
       }
 
       File fn = new File(args[0]);
@@ -969,20 +971,24 @@ public class NewickFile extends FileParse
       jalview.bin.Console.outPrintln("Original file :\n");
 
       Regex nonl = new Regex("\n+", "");
-      jalview.bin.Console.outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
+      jalview.bin.Console
+              .outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
 
       jalview.bin.Console.outPrintln("Parsed file.\n");
-      jalview.bin.Console.outPrintln("Default output type for original input.\n");
+      jalview.bin.Console
+              .outPrintln("Default output type for original input.\n");
       jalview.bin.Console.outPrintln(trf.print());
       jalview.bin.Console.outPrintln("Without bootstraps.\n");
       jalview.bin.Console.outPrintln(trf.print(false));
       jalview.bin.Console.outPrintln("Without distances.\n");
       jalview.bin.Console.outPrintln(trf.print(true, false));
-      jalview.bin.Console.outPrintln("Without bootstraps but with distanecs.\n");
+      jalview.bin.Console
+              .outPrintln("Without bootstraps but with distanecs.\n");
       jalview.bin.Console.outPrintln(trf.print(false, true));
       jalview.bin.Console.outPrintln("Without bootstraps or distanecs.\n");
       jalview.bin.Console.outPrintln(trf.print(false, false));
-      jalview.bin.Console.outPrintln("With bootstraps and with distances.\n");
+      jalview.bin.Console
+              .outPrintln("With bootstraps and with distances.\n");
       jalview.bin.Console.outPrintln(trf.print(true, true));
     } catch (java.io.IOException e)
     {
diff --git a/src/jalview/util/AWTConsole.java b/src/jalview/util/AWTConsole.java
index f6145c2..6fa7c5c 100644
--- a/src/jalview/util/AWTConsole.java
+++ b/src/jalview/util/AWTConsole.java
@@ -49,6 +49,7 @@ import java.io.PipedOutputStream;
 import java.io.PrintStream;
 
 import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
 
 public class AWTConsole extends WindowAdapter
         implements WindowListener, ActionListener, Runnable
@@ -176,7 +177,7 @@ public class AWTConsole extends WindowAdapter
     } catch (Exception e)
     {
     }
-    Jalview.exit("Window closing. Bye!", 0);
+    Jalview.exit("Window closing. Bye!", ExitCode.OK);
   }
 
   @Override