JAL-629 Add --nowebdiscovery. Distinguish arg=="open" as old style. Increase timeout...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 689080e..e384a0b 100755 (executable)
--- 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;
@@ -281,12 +283,14 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-
     if (!Platform.isJS())
     {
       System.setSecurityManager(null);
     }
 
+    if (args == null)
+      args = new String[] {};
+
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");
@@ -430,12 +434,14 @@ 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())
@@ -445,8 +451,12 @@ 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();
         Jalview.exit(null, 0);
@@ -486,26 +496,40 @@ 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"))
@@ -545,7 +569,8 @@ public class Jalview
     if (!(headless || headlessArg))
     {
       Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
-              || aparser.contains("nosplash");
+              || aparser.contains("nosplash")
+              || Cache.getDefault("SPLASH", "true").equals("false");
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -605,7 +630,12 @@ public class Jalview
           }
         }
 
-        if (!aparser.contains("nowebservicediscovery"))
+        boolean doWebServiceDiscovery = !aparser
+                .contains("nowebservicediscovery");
+        if (bootstrapArgs.contains(Arg.WEBSERVICEDISCOVERY))
+          doWebServiceDiscovery = bootstrapArgs
+                  .getBoolean(Arg.WEBSERVICEDISCOVERY);
+        if (doWebServiceDiscovery)
         {
           desktop.startServiceDiscovery();
         }