X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=954bb34bd63bc94e4eedfc845a59a073c7a0500a;hb=fcb68d2ebaf7ebdde2bf6e857de856dc7f46a8da;hp=c52b5622b6ec2db4fe401fafe6bbe170442a276b;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index c52b562..954bb34 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -40,7 +40,6 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -514,13 +513,7 @@ public class Jalview
           ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af
                   .getViewport().getAlignment(), data);
 
-          if (cs == null)
-          {
-            UserColourScheme ucs = new UserColourScheme("white");
-            ucs.parseAppletParameter(data);
-            cs = ucs;
-          }
-          else
+          if (cs != null)
           {
             System.out.println("CMD [-color " + data
                     + "] executed successfully!");
@@ -585,18 +578,14 @@ public class Jalview
         data = aparser.getValue("tree", true);
         if (data != null)
         {
-          jalview.io.NewickFile fin = null;
           try
           {
             System.out.println("CMD [-tree " + data
                     + "] executed successfully!");
-            fin = new NewickFile(data,
+            NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
-            if (fin != null)
-            {
-              af.getViewport().setCurrentTree(
-                      af.ShowNewickTree(fin, data).getTree());
-            }
+            af.getViewport().setCurrentTree(
+                    af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
             System.err.println("Couldn't add tree " + data);