X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=94834363056bfa073c0acff835e1bf330022c8aa;hb=064f2fdaa463367f8bf7e6aea5e7fc6a32170138;hp=b00d6cc7bb45a5cd76bcdc58a9119ecc00862b76;hpb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index b00d6cc..9483436 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -70,7 +70,7 @@ public class TreeCanvas
     longestName = label;
     setLayout(null);
 
-    PaintRefresher.Register(this);
+    PaintRefresher.Register(this, av.alignment);
   }
 
   public void TreeSelectionChanged(Sequence sequence)
@@ -82,10 +82,10 @@ public class TreeCanvas
       av.setSelectionGroup(selected);
     }
 
-    selected.setEndRes(av.alignment.getWidth());
+    selected.setEndRes(av.alignment.getWidth()-1);
     selected.addOrRemove(sequence, true);
 
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
     repaint();
   }
 
@@ -424,7 +424,6 @@ public class TreeCanvas
 
   public void mousePressed(MouseEvent e)
   {
-
     av.setCurrentTree(tree);
 
     int x = e.getX();
@@ -472,18 +471,43 @@ public class TreeCanvas
 
           Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
               i), new Vector());
-          SequenceGroup sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true, false,
-                                     0, av.alignment.getWidth());
+
+          Vector sequences = new Vector();
           for (int j = 0; j < l.size(); j++)
           {
-            SequenceNode sn = (SequenceNode) l.elementAt(j);
-            sg.addSequence( (Sequence) sn.element(), false);
+            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+            if(!sequences.contains(s1))
+              sequences.addElement(s1);
           }
 
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
+          ColourSchemeI cs = null;
+
+          if (av.getGlobalColourScheme() != null)
           {
-            ConservationColourScheme ccs = (ConservationColourScheme) av.
-                getGlobalColourScheme();
+            if (av.getGlobalColourScheme() instanceof UserColourScheme)
+            {
+              cs = new UserColourScheme(
+                  ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+
+            }
+            else
+              cs = ColourSchemeProperty.getColour(sequences,
+                                                  av.alignment.getWidth(),
+                                                  ColourSchemeProperty.getColourName(
+                                                      av.getGlobalColourScheme()));
+
+              cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                                                   av.getIgnoreGapsConsensus());
+          }
+
+          SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
+                                               cs, true, true,
+                                               false, 0, av.alignment.getWidth()-1);
+
+
+          if (  av.getGlobalColourScheme()!=null
+             && av.getGlobalColourScheme().conservationApplied())
+            {
             Conservation c = new Conservation("Group",
                                               ResidueProperties.propHash, 3,
                                               sg.sequences, sg.getStartRes(),
@@ -491,9 +515,9 @@ public class TreeCanvas
 
             c.calculate();
             c.verdict(false, av.ConsPercGaps);
-            ccs = new ConservationColourScheme(c, ccs.cs);
+            cs.setConservation(c);
 
-            sg.cs = ccs;
+            sg.cs = cs;
 
           }
 
@@ -503,7 +527,7 @@ public class TreeCanvas
       }
     }
 
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
     repaint();
 
   }