dont add sequence twice to new group

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 2864eb4..1fddc5b 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -414,6 +414,7 @@ public class TreeCanvas
 \r
   public void paintComponent(Graphics g)\r
   {\r
+    super.paintComponent(g);\r
     font = new Font("Verdana", Font.PLAIN, fontSize);\r
     g.setFont(font);\r
 \r
@@ -563,9 +564,12 @@ public class TreeCanvas
                                      new Vector());\r
 \r
          Vector sequences = new Vector();\r
-          for (int j = 0; j < l.size(); j++)\r
-          {\r
-            sequences.add( (Sequence)((SequenceNode) l.elementAt(j)).element());\r
+         for (int j = 0; j < l.size(); j++)\r
+         {\r
+           SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
+           if (!sequences.contains(s1))\r
+             sequences.addElement(s1);\r
+\r
           }\r
 \r
           ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
@@ -575,12 +579,10 @@ public class TreeCanvas
                            cs, true, true,\r
                            false, 0, av.alignment.getWidth());\r
 \r
-\r
+          if(sg.cs !=null)\r
            ( (ResidueColourScheme) sg.cs).setThreshold(25);\r
 \r
 \r
-\r
-\r
           if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
           {\r
             ConservationColourScheme ccs = (ConservationColourScheme) av.\r