JAL-4023 store distances as doubles

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0c11808..fc4c821 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -49,6 +49,7 @@ import javax.swing.UIManager.LookAndFeelInfo;
 
 import com.threerings.getdown.util.LaunchUtil;
 
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.ext.so.SequenceOntology;
@@ -95,6 +96,10 @@ public class Jalview
   static
   {
     Platform.getURLCommandArguments();
+    Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+    Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
   }
 
   /*
@@ -471,12 +476,17 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews"))
+        if (!aparser.contains("nonews")
+                || Cache.getProperty("NONEWS") == null)
         {
           desktop.checkForNews();
         }
 
-        BioJsHTMLOutput.updateBioJS();
+        if (!aparser.contains("nohtmltemplates")
+                || Cache.getProperty("NOHTMLTEMPLATES") == null)
+        {
+          BioJsHTMLOutput.updateBioJS();
+        }
       }
     }
 
@@ -1112,7 +1122,8 @@ public class Jalview
               @Override
               public void run()
               {
-                Console.debug("Initialising googletracker for usage stats.");
+                Console.debug(
+                        "Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
                 Console.debug("Tracking enabled.");
               }