X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=44494e2db9672a947195c2ff898eae24394ae07f;hb=f52d881ba992cf5d4570d487f6319666f13263a9;hp=87c4ad5301279a8f0a7ed19cf07942f3a51e4b0d;hpb=20d904c8e71db456b1a1cf1f80ff75f8bc42d245;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 87c4ad5..44494e2 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -39,7 +39,9 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 import java.util.Properties;
@@ -64,8 +66,9 @@ import com.threerings.getdown.util.LaunchUtil;
 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
-import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.BootstrapArgs;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -126,6 +129,8 @@ public class Jalview
 
   private Desktop desktop;
 
+  protected Commands cmds;
+
   public static AlignFrame currentAlignFrame;
 
   static
@@ -284,6 +289,25 @@ public class Jalview
       System.setSecurityManager(null);
     }
 
+    // Move any new getdown-launcher-new.jar into place over old
+    // getdown-launcher.jar
+    String appdirString = System.getProperty("getdownappdir");
+    if (appdirString != null && appdirString.length() > 0)
+    {
+      final File appdir = new File(appdirString);
+      new Thread()
+      {
+        @Override
+        public void run()
+        {
+          LaunchUtil.upgradeGetdown(
+                  new File(appdir, "getdown-launcher-old.jar"),
+                  new File(appdir, "getdown-launcher.jar"),
+                  new File(appdir, "getdown-launcher-new.jar"));
+        }
+      }.start();
+    }
+
     // get args needed before proper ArgParser
     BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
 
@@ -363,9 +387,9 @@ 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
@@ -394,6 +418,8 @@ public class Jalview
     String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
             ? bootstrapArgs.get(Arg.PROPS)
             : aparser.getValue("props");
+    // if usrPropsFile == null, loadProperties will use the Channel
+    // preferences.file
     Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
@@ -406,12 +432,14 @@ public class Jalview
     // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
-      argparser = ArgParser
-              .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+      argparser = ArgParser.parseArgFiles(
+              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
     else
     {
-      argparser = new ArgParser(args);
+      argparser = new ArgParser(args,
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
 
     if (!Platform.isJS())
@@ -421,14 +449,18 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      if (aparser.contains("help") || aparser.contains("h")
-              || argparser.getBool(Arg.HELP))
+      if (bootstrapArgs.contains(Arg.HELP))
+      {
+        System.out.println(Arg.usage());
+        Jalview.exit(null, 0);
+      }
+      if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
-        System.exit(0);
+        Jalview.exit(null, 0);
       }
 
-      if (argparser.isSet(Arg.HEADLESS))
+      if (bootstrapArgs.contains(Arg.HEADLESS))
       {
         System.setProperty("java.awt.headless", "true");
         // new
@@ -462,26 +494,40 @@ public class Jalview
       }
     }
 
-    String defs = aparser.getValue("setprop");
-    while (defs != null)
+    List<String> setprops = new ArrayList<>();
+    if (bootstrapArgs.contains(Arg.SETPROP))
+    {
+      setprops = bootstrapArgs.getList(Arg.SETPROP);
+    }
+    else
+    {
+      String sp = aparser.getValue("setprop");
+      while (sp != null)
+      {
+        setprops.add(sp);
+        sp = aparser.getValue("setprop");
+      }
+    }
+    for (String setprop : setprops)
     {
-      int p = defs.indexOf('=');
+      int p = setprop.indexOf('=');
       if (p == -1)
       {
-        System.err.println("Ignoring invalid setprop argument : " + defs);
+        System.err
+                .println("Ignoring invalid setprop argument : " + setprop);
       }
       else
       {
-        System.out.println("Executing setprop argument: " + defs);
+        System.out.println("Executing setprop argument: " + setprop);
         if (Platform.isJS())
         {
-          Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+          Cache.setProperty(setprop.substring(0, p),
+                  setprop.substring(p + 1));
         }
         // DISABLED FOR SECURITY REASONS
         // TODO: add a property to allow properties to be overriden by cli args
-        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+        // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
       }
-      defs = aparser.getValue("setprop");
     }
     if (System.getProperty("java.awt.headless") != null
             && System.getProperty("java.awt.headless").equals("true"))
@@ -499,9 +545,9 @@ 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;
 
@@ -520,7 +566,8 @@ public class Jalview
 
     if (!(headless || headlessArg))
     {
-      Desktop.nosplash = aparser.contains("nosplash");
+      Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+              || aparser.contains("nosplash");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -627,32 +674,39 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews")
-                || Cache.getProperty("NONEWS") == null)
+        if ((!aparser.contains("nonews")
+                && Cache.getProperty("NONEWS") == null
+                && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
+                || "true".equals(bootstrapArgs.get(Arg.NEWS)))
         {
           desktop.checkForNews();
         }
 
         if (!aparser.contains("nohtmltemplates")
-                || Cache.getProperty("NOHTMLTEMPLATES") == null)
+                && Cache.getProperty("NOHTMLTEMPLATES") == null)
         {
           BioJsHTMLOutput.updateBioJS();
         }
       }
     }
     // Run Commands from cli
-    boolean commandsSuccess = Commands.processArgs(argparser, headlessArg);
+    cmds = new Commands(argparser, headlessArg);
+    boolean commandsSuccess = cmds.argsWereParsed();
     if (commandsSuccess)
     {
-      Console.info("Successfully completed commands");
       if (headlessArg)
-        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
@@ -665,25 +719,6 @@ public class Jalview
               + LaunchUtils.getJavaCompileVersion() + ".");
     }
 
-    // Move any new getdown-launcher-new.jar into place over old
-    // getdown-launcher.jar
-    String appdirString = System.getProperty("getdownappdir");
-    if (appdirString != null && appdirString.length() > 0)
-    {
-      final File appdir = new File(appdirString);
-      new Thread()
-      {
-        @Override
-        public void run()
-        {
-          LaunchUtil.upgradeGetdown(
-                  new File(appdir, "getdown-launcher-old.jar"),
-                  new File(appdir, "getdown-launcher.jar"),
-                  new File(appdir, "getdown-launcher-new.jar"));
-        }
-      }.start();
-    }
-
     String file = null, data = null;
 
     FileFormatI format = null;
@@ -698,10 +733,9 @@ public class Jalview
     groovyscript = aparser.getValue("groovy", true);
     file = aparser.getValue("open", true);
 
-    if (file == null && desktop == null)
+    if (file == null && desktop == null && !commandsSuccess)
     {
-      System.out.println("No files to open!");
-      System.exit(1);
+      Jalview.exit("No files to open!", 1);
     }
 
     long progress = -1;
@@ -728,11 +762,12 @@ 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 + "'");
           }
         }
       }
@@ -971,7 +1006,7 @@ public class Jalview
 
     if (!Platform.isJS() && !headless && file == null
             && Cache.getDefault("SHOW_STARTUP_FILE", true)
-            && !Commands.commandArgsProvided())
+            && !cmds.commandArgsProvided())
     // don't open the startup file if command line args have been processed
     // (&& !Commands.commandArgsProvided())
     /**
@@ -1572,7 +1607,7 @@ public class Jalview
   public void quit()
   {
     // System.exit will run the shutdownHook first
-    System.exit(0);
+    Jalview.exit("Quitting now. Bye!", 0);
   }
 
   public static AlignFrame getCurrentAlignFrame()
@@ -1584,4 +1619,21 @@ public class Jalview
   {
     Jalview.currentAlignFrame = currentAlignFrame;
   }
+
+  protected Commands getCommands()
+  {
+    return cmds;
+  }
+
+  public static void exit(String message, int exitcode)
+  {
+    Console.debug("Using Jalview.exit");
+    if (message != null)
+      if (exitcode == 0)
+        Console.info(message);
+      else
+        Console.error(message);
+    if (exitcode > -1)
+      System.exit(exitcode);
+  }
 }