JAL-629 Opening files in new windows. not working yet

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 046ad90..bc8c997 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -64,8 +64,9 @@ 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;
@@ -415,9 +416,9 @@ public class Jalview
     String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
             ? bootstrapArgs.get(Arg.PROPS)
             : aparser.getValue("props");
-    Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
+      Cache.loadProperties(usrPropsFile);
       System.out.println(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
@@ -648,14 +649,16 @@ 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();
         }
@@ -1599,7 +1602,6 @@ public class Jalview
 
   public static void exit(String message, int exitcode)
   {
-    System.err.println("####### EXITING HERE!");
     Console.debug("Using Jalview.exit");
     if (message != null)
       if (exitcode == 0)