X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=87bacc15af3fbf4c4d54002eecc0b2b1ab7bdadb;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=bdfe3aedfcb50e37ed89433144d1690fa1ee1153;hpb=5874ca652d08909c74d422552eb03a996112316d;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bdfe3ae..87bacc1 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -105,8 +105,8 @@ public class Jalview
           try
           {
             UIManager.setLookAndFeel(
-                   UIManager.getSystemLookAndFeelClassName()
-            //        UIManager.getCrossPlatformLookAndFeelClassName()
+                UIManager.getSystemLookAndFeelClassName()
+                //        UIManager.getCrossPlatformLookAndFeelClassName()
 //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
 //"javax.swing.plaf.metal.MetalLookAndFeel"
 //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
@@ -150,7 +150,7 @@ public class Jalview
 
             protocol = "File";
 
-            if (file.indexOf("http:") > -1)
+            if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)
             {
               protocol = "URL";
             }
@@ -164,17 +164,39 @@ public class Jalview
 
             AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
 
+            data = aparser.getValue("colour");
+            if(data!=null)
+            {
+              data.replaceAll("%20", " ");
+
+              jalview.schemes.ColourSchemeI cs =
+                  jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
+                  getAlignment(), data);
+
+              if(cs == null)
+              {
+                jalview.schemes.UserColourScheme ucs
+                    = new jalview.schemes.UserColourScheme("white");
+                ucs.parseAppletParameter(data);
+                cs = ucs;
+              }
+
+              System.out.println("colour is " + data);
+              af.changeColour( cs );
+            }
+
+
             // Must maintain ability to use the groups flag
             data = aparser.getValue("groups");
             if (data != null)
             {
-              af.parseGroupsFile(data);
+              af.parseFeaturesFile(data, protocol);
               System.out.println("Added "+data);
             }
             data = aparser.getValue("features");
             if (data != null)
             {
-              af.parseGroupsFile(data);
+              af.parseFeaturesFile(data, protocol);
               System.out.println("Added "+data);
             }
 
@@ -228,9 +250,11 @@ public class Jalview
           }
 
         // We'll only open the default file if the desktop is visible.
+        // And the user
         //////////////////////
           if (
               !headless
+          && file==null
           && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
                     )
           {