X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=87bacc15af3fbf4c4d54002eecc0b2b1ab7bdadb;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=3e8018bfc44d155f5a50bb1d0d791d8c6904b898;hpb=aca26588a9857a2b71d7ca2450676521ca874eae;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3e8018b..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)
                     )
           {
@@ -252,7 +276,7 @@ public class Jalview
             else
             {
               format = new jalview.io.IdentifyFile().Identify(file, protocol);
-              desktop.LoadFile(file, protocol, format);
+              new jalview.io.FileLoader().LoadFile(file, protocol, format);
             }
           }
     }