JAL-3224 Tidied up Network installers in install4j template. Moved getdown-launcher...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cd7d1af..ece610a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -52,11 +52,6 @@ import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
-import java.security.AllPermission;
-import java.security.CodeSource;
-import java.security.PermissionCollection;
-import java.security.Permissions;
-import java.security.Policy;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
@@ -64,6 +59,8 @@ import java.util.Vector;
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
+import com.sun.xml.ws.policy.Policy;
+
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 
@@ -96,6 +93,8 @@ public class Jalview
   static
   {
     // grab all the rights we can the JVM
+    Policy.createEmptyPolicy();
+    /*
     Policy.setPolicy(new Policy()
     {
       @Override
@@ -105,12 +104,13 @@ public class Jalview
         perms.add(new AllPermission());
         return (perms);
       }
-
+    
       @Override
       public void refresh()
       {
       }
     });
+    */
   }
 
   /**
@@ -335,6 +335,18 @@ public class Jalview
     {
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
+
+      try
+      {
+        JalviewTaskbar.setTaskbar(this);
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      } catch (Throwable t)
+      {
+        t.printStackTrace();
+      }
+
       desktop.setVisible(true);
       desktop.startServiceDiscovery();
       if (!aparser.contains("nousagestats"))
@@ -538,7 +550,8 @@ public class Jalview
           data.replaceAll("%20", " ");
 
           ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport().getAlignment(), data);
+                  .getColourScheme(af.getViewport(),
+                          af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {
@@ -828,9 +841,6 @@ public class Jalview
                     // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
                     // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
-                    + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
-                    + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
-                    + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     // +
                     // "-vdoc vamsas-document\tImport vamsas document into new
@@ -965,7 +975,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<>();
+      Map<String, java.lang.Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {