X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=5b2116a5d907b1bdc26c03201c3fae427455497b;hb=6312ff96a7669b59327d583d1dc64b0b96647d67;hp=136be529298649cd2ca432758121e9b21e25c6ee;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 136be52..5b2116a 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -476,7 +476,9 @@ System.out.println("called here");
           Vector sequences = new Vector();
           for (int j = 0; j < l.size(); j++)
           {
-            sequences.addElement( (Sequence) ( (SequenceNode) l.elementAt(j)).element());
+            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+            if(!sequences.contains(s1))
+              sequences.addElement(s1);
           }
 
           ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
@@ -485,13 +487,12 @@ System.out.println("called here");
 
           SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
                                                cs, true, true,
-                                               false, 0, av.alignment.getWidth());
+                                               false, 0, av.alignment.getWidth()-1);
 
 
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-          {
-            ConservationColourScheme ccs = (ConservationColourScheme) av.
-                getGlobalColourScheme();
+          if (  av.getGlobalColourScheme()!=null
+             && av.getGlobalColourScheme().conservationApplied())
+            {
             Conservation c = new Conservation("Group",
                                               ResidueProperties.propHash, 3,
                                               sg.sequences, sg.getStartRes(),
@@ -499,9 +500,9 @@ System.out.println("called here");
 
             c.calculate();
             c.verdict(false, av.ConsPercGaps);
-            ccs = new ConservationColourScheme(c, ccs.cs);
+            cs.setConservation(c);
 
-            sg.cs = ccs;
+            sg.cs = cs;
 
           }