JAL-2446 merged to spike branch

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 39c0a5b..954bb34 100755 (executable)
--- 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;
@@ -511,16 +510,10 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(af
+          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);