Conservation colour scheme is no more

[jalview.git] / src / jalview / appletgui / TreeCanvas.java

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 136be52..a6bc5df 100755 (executable)
--- 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();\r
           for (int j = 0; j < l.size(); j++)\r
           {\r
-            sequences.addElement( (Sequence) ( (SequenceNode) l.elementAt(j)).element());\r
+            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
+            if(!sequences.contains(s1))\r
+              sequences.addElement(s1);\r
           }\r
 \r
           ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
@@ -488,10 +490,8 @@ System.out.println("called here");
                                                false, 0, av.alignment.getWidth());\r
 \r
 \r
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+          if (av.getGlobalColourScheme().conservationApplied())\r
           {\r
-            ConservationColourScheme ccs = (ConservationColourScheme) av.\r
-                getGlobalColourScheme();\r
             Conservation c = new Conservation("Group",\r
                                               ResidueProperties.propHash, 3,\r
                                               sg.sequences, sg.getStartRes(),\r
@@ -499,9 +499,9 @@ System.out.println("called here");
 \r
             c.calculate();\r
             c.verdict(false, av.ConsPercGaps);\r
-            ccs = new ConservationColourScheme(c, ccs.cs);\r
+            cs.setConservation(c);\r
 \r
-            sg.cs = ccs;\r
+            sg.cs = cs;\r
 \r
           }\r
 \r