JAL-629 All applications System.exits going through Jalview.exit

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index 14785ea..fca2320 100644 (file)
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -1199,20 +1199,20 @@ public class ArgParser
     {
       if (!argFile.exists())
       {
-        System.err.println(DOUBLEDASH
+        String message = DOUBLEDASH
                 + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
-                + argFile.getPath() + "\": File does not exist.");
-        System.exit(2);
+                + argFile.getPath() + "\": File does not exist.";
+        Jalview.exit(message, 2);
       }
       try
       {
         argsList.addAll(Files.readAllLines(Paths.get(argFile.getPath())));
       } catch (IOException e)
       {
-        System.err.println(DOUBLEDASH
+        String message = DOUBLEDASH
                 + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
-                + argFile.getPath() + "\": File could not be read.");
-        System.exit(3);
+                + argFile.getPath() + "\": File could not be read.";
+        Jalview.exit(message, 3);
       }
     }
     return new ArgParser(argsList);

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 26ce8c3..f71ebf3 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -374,8 +374,7 @@ public class Commands
       {
         if (headless)
         {
-          Console.error("Could not open any files in headless mode");
-          System.exit(1);
+          Jalview.exit("Could not open any files in headless mode", 1);
         }
         else
         {

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index a728bc8..fbbb16c 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -365,9 +365,9 @@ public class Jalview
     } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
-      System.out.println("\nEssential logging libraries not found."
-              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
-      System.exit(0);
+      String message = "\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+      Jalview.exit(message, 0);
     }
 
     // register SIGTERM listener
@@ -427,7 +427,7 @@ public class Jalview
               || argparser.getBool(Arg.HELP))
       {
         showUsage();
-        System.exit(0);
+        Jalview.exit(null, 0);
       }
 
       if (bootstrapArgs.contains(Arg.HEADLESS))
@@ -501,9 +501,9 @@ public class Jalview
     NoClassDefFoundError error)
     {
       error.printStackTrace();
-      System.out.println("\nEssential logging libraries not found."
-              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
-      System.exit(0);
+      String message = "\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+      Jalview.exit(message, 0);
     }
     desktop = null;
 
@@ -647,18 +647,19 @@ public class Jalview
     boolean commandsSuccess = cmds.argsWereParsed();
     if (commandsSuccess)
     {
-      Console.info("Successfully completed commands");
       if (headlessArg)
       {
-        System.out.println("#### EXITING");
-        System.exit(0);
+        Jalview.exit("Successfully completed commands in headless mode", 0);
       }
+      Console.info("Successfully completed commands");
     }
     else
     {
-      Console.warn("Error when running commands");
       if (headlessArg)
-        System.exit(1);
+      {
+        Jalview.exit("Error when running Commands in headless mode", 1);
+      }
+      Console.warn("Error when running commands");
     }
 
     // Check if JVM and compile version might cause problems and log if it
@@ -706,8 +707,7 @@ public class Jalview
 
     if (file == null && desktop == null)
     {
-      System.out.println("No files to open!");
-      System.exit(1);
+      Jalview.exit("No files to open!", 1);
     }
 
     long progress = -1;
@@ -734,11 +734,12 @@ public class Jalview
         {
           if (!(new File(file)).exists())
           {
-            System.out.println("Can't find " + file);
             if (headless)
             {
-              System.exit(1);
+              Jalview.exit(
+                      "Can't find file '" + file + "' in headless mode", 1);
             }
+            Console.warn("Can't find file'" + file + "'");
           }
         }
       }
@@ -1578,8 +1579,7 @@ public class Jalview
   public void quit()
   {
     // System.exit will run the shutdownHook first
-    System.out.println("Quitting now. Bye!");
-    System.exit(0);
+    Jalview.exit("Quitting now. Bye!", 0);
   }
 
   public static AlignFrame getCurrentAlignFrame()
@@ -1596,4 +1596,17 @@ public class Jalview
   {
     return cmds;
   }
+
+  public static void exit(String message, int exitcode)
+  {
+    System.err.println("####### EXITING HERE!");
+    Console.debug("Using Jalview.exit");
+    if (message != null)
+      if (exitcode == 0)
+        Console.info(message);
+      else
+        Console.error(message);
+    if (exitcode > -1)
+      System.exit(exitcode);
+  }
 }

diff --git a/src/jalview/bin/Launcher.java b/src/jalview/bin/Launcher.java
index 9e1fb51..cab2c00 100644 (file)
--- a/src/jalview/bin/Launcher.java
+++ b/src/jalview/bin/Launcher.java
@@ -254,7 +254,6 @@ public class Launcher
     {
       e.printStackTrace();
     }
-    // System.exit(0);
   }
 
 }

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ba7665b..981a060 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1436,8 +1436,7 @@ 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).
-    System.out.println("Desktop exiting.");
-    System.exit(0);
+    Jalview.exit("Desktop exiting.", 0);
   }
 
   private void storeLastKnownDimensions(String string, Rectangle jc)

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 027390a..98978d0 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,19 +26,19 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.util.Locale;
-
-import jalview.datamodel.SequenceNode;
-import jalview.util.MessageManager;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Jalview;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
  * tree distances and topology are unreliable when they are parsed. TODO: on
@@ -487,7 +487,8 @@ public class NewickFile extends FileParse
         {
           try
           {
-            distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+            distance = (Double.valueOf(ndist.stringMatched(1)))
+                    .floatValue();
             HasDistances = true;
             nodehasdistance = true;
           } catch (Exception e)
@@ -944,9 +945,8 @@ public class NewickFile extends FileParse
     {
       if (args == null || args.length != 1)
       {
-        System.err.println(
-                "Takes one argument - file name of a newick tree file.");
-        System.exit(0);
+        Jalview.exit(
+                "Takes one argument - file name of a newick tree file.", 0);
       }
 
       File fn = new File(args[0]);

diff --git a/src/jalview/util/AWTConsole.java b/src/jalview/util/AWTConsole.java
index ab049a3..cf44dcb 100644 (file)
--- a/src/jalview/util/AWTConsole.java
+++ b/src/jalview/util/AWTConsole.java
@@ -48,6 +48,8 @@ import java.io.PipedInputStream;
 import java.io.PipedOutputStream;
 import java.io.PrintStream;
 
+import jalview.bin.Jalview;
+
 public class AWTConsole extends WindowAdapter
         implements WindowListener, ActionListener, Runnable
 {
@@ -174,8 +176,7 @@ public class AWTConsole extends WindowAdapter
     } catch (Exception e)
     {
     }
-    System.out.println("Window closing. Bye!");
-    System.exit(0);
+    Jalview.exit("Window closing. Bye!", 0);
   }
 
   @Override