X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=b29d9d72cc2d70e92729b7d3e6c0835fe7db6c32;hb=65ed1da9a1710a9ce132c7edfce54955dc1ddf99;hp=159cf7593db0616b3a54f231765fe586d8f90b3e;hpb=4fd4608b88401dbb1a86a29f8d607c7481145e27;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 159cf75..b29d9d7 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -343,6 +343,25 @@ public class Jalview
       }
     }
 
+    // set individual session preferences
+    if (bootstrapArgs.contains(Arg.P))
+    {
+      for (String kev : bootstrapArgs.getValueList(Arg.P))
+      {
+        if (kev == null)
+        {
+          continue;
+        }
+        int equalsIndex = kev.indexOf(ArgParser.EQUALS);
+        if (equalsIndex > -1)
+        {
+          String key = kev.substring(0, equalsIndex);
+          String val = kev.substring(equalsIndex + 1);
+          Cache.setSessionProperty(key, val);
+        }
+      }
+    }
+
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");
@@ -396,7 +415,7 @@ public class Jalview
 
     // get bootstrap properties (mainly for the logger level)
     Properties bootstrapProperties = Cache
-            .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
+            .bootstrapProperties(bootstrapArgs.getValue(Arg.PROPS));
 
     // report Jalview version
     Cache.loadBuildProperties(
@@ -451,11 +470,14 @@ public class Jalview
                 .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false)
                 || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false);
         StructureViewerBase.setQuitClose(closeExternal);
-        for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+        if (desktop != null)
         {
-          if (frame instanceof StructureViewerBase)
+          for (JInternalFrame frame : Desktop.desktop.getAllFrames())
           {
-            ((StructureViewerBase) frame).closeViewer(closeExternal);
+            if (frame instanceof StructureViewerBase)
+            {
+              ((StructureViewerBase) frame).closeViewer(closeExternal);
+            }
           }
         }
 
@@ -479,7 +501,7 @@ public class Jalview
     });
 
     String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
-            ? bootstrapArgs.get(Arg.PROPS)
+            ? bootstrapArgs.getValue(Arg.PROPS)
             : aparser.getValue("props");
     // if usrPropsFile == null, loadProperties will use the Channel
     // preferences.file
@@ -533,7 +555,7 @@ public class Jalview
       }
 
       // new CLI
-      headlessArg = isHeadless(bootstrapArgs);
+      headlessArg = bootstrapArgs.isHeadless();
       if (headlessArg)
       {
         System.setProperty("java.awt.headless", "true");
@@ -550,7 +572,7 @@ public class Jalview
       // allow https handshakes to download intermediate certs if necessary
       System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
 
-      String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+      String jabawsUrl = bootstrapArgs.getValue(Arg.JABAWS);
       if (jabawsUrl == null)
         jabawsUrl = aparser.getValue("jabaws");
       if (jabawsUrl != null)
@@ -642,7 +664,7 @@ public class Jalview
 
     if (!(headless || headlessArg))
     {
-      Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+      Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
               || aparser.contains("nosplash")
               || Cache.getDefault("SPLASH", "true").equals("false");
       desktop = new Desktop();
@@ -717,18 +739,18 @@ public class Jalview
           testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
         }
 
-        boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+        boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
         if (aparser.contains("nousagestats"))
           usagestats = false;
         if (usagestats)
         {
           startUsageStats(desktop);
-          testoutput(argparser, Arg.USAGESTATS);
+          testoutput(argparser, Arg.NOUSAGESTATS);
         }
         else
         {
           System.out.println("CMD [-nousagestats] executed successfully!");
-          testoutput(argparser, Arg.USAGESTATS);
+          testoutput(argparser, Arg.NOUSAGESTATS);
         }
 
         boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
@@ -771,8 +793,8 @@ public class Jalview
 
         if ((!aparser.contains("nonews")
                 && Cache.getProperty("NONEWS") == null
-                && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
-                || "true".equals(bootstrapArgs.get(Arg.NEWS)))
+                && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
+                || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
         {
           desktop.checkForNews();
         }
@@ -1111,7 +1133,8 @@ public class Jalview
 
     if (!Platform.isJS() && !headless && file == null
             && Cache.getDefault("SHOW_STARTUP_FILE", true)
-            && !cmds.commandArgsProvided())
+            && !cmds.commandArgsProvided()
+            && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
     // don't open the startup file if command line args have been processed
     // (&& !Commands.commandArgsProvided())
     /**
@@ -1837,7 +1860,7 @@ public class Jalview
   }
 
   /*
-   * testoutput for boolean values
+   * testoutput for boolean and unary values
    */
   protected static void testoutput(ArgParser ap, Arg a)
   {
@@ -1880,29 +1903,15 @@ public class Jalview
 
   private static void testoutput(boolean yes, Arg a)
   {
-    System.out.println("[TESTOUTPUT] arg "
-            + (yes ? a.argString() : a.negateArgString()) + " was set");
-  }
-
-  private static boolean isHeadless(BootstrapArgs bootstrapArgs)
-  {
-    if (bootstrapArgs == null)
-    {
-      return false;
-    }
-    boolean isHeadless = false;
-    if (bootstrapArgs.contains(Arg.GUI))
-    {
-      isHeadless = !bootstrapArgs.getBoolean(Arg.GUI);
-    }
-    else if (bootstrapArgs.contains(Arg.HEADLESS))
+    String message = null;
+    if (a.hasOption(Opt.BOOLEAN))
     {
-      isHeadless = bootstrapArgs.getBoolean(Arg.HEADLESS);
+      message = (yes ? a.argString() : a.negateArgString()) + " was set";
     }
-    else if (bootstrapArgs.argsHaveOption(Opt.OUTPUTFILE))
+    else if (a.hasOption(Opt.UNARY))
     {
-      isHeadless = true;
+      message = a.argString() + (yes ? " was set" : " was not set");
     }
-    return isHeadless;
+    System.out.println("[TESTOUTPUT] arg " + message);
   }
 }