X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1116fe404ec5733ba508dbdae70a5513b3b29d4f;hb=bc39ee8df9694f820a8a8bd2430f527b87c07f31;hp=3e8018bfc44d155f5a50bb1d0d791d8c6904b898;hpb=aca26588a9857a2b71d7ca2450676521ca874eae;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3e8018b..1116fe4 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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"
@@ -137,6 +137,7 @@ public class Jalview
 
           if(file!=null)
           {
+            System.out.println("Opening file: " + file);
 
             if (!file.startsWith("http://"))
             {
@@ -150,31 +151,61 @@ public class Jalview
 
             protocol = "File";
 
-            if (file.indexOf("http:") > -1)
+            if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)
             {
               protocol = "URL";
             }
 
+
+
             if (file.endsWith(".jar"))
               format = "Jalview";
             else
               format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
-            System.out.println("Opening: " + format + " file " + file);
+
 
             AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
 
+            if(af==null)
+            {
+              System.out.println("error");
+              return;
+            }
+
+            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 +259,11 @@ 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)
                     )
           {
@@ -247,13 +280,15 @@ public class Jalview
 
             if (file.endsWith(".jar"))
             {
-              new Jalview2XML().LoadJalviewAlign(file);
+              format = "Jalview";
             }
             else
             {
               format = new jalview.io.IdentifyFile().Identify(file, protocol);
-              desktop.LoadFile(file, protocol, format);
             }
+
+            fileLoader.LoadFile(file, protocol, format);
+
           }
     }
 }