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 b00d6cc..a6bc5df 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -70,7 +70,7 @@ public class TreeCanvas
     longestName = label;\r
     setLayout(null);\r
 \r
-    PaintRefresher.Register(this);\r
+    PaintRefresher.Register(this, av.alignment);\r
   }\r
 \r
   public void TreeSelectionChanged(Sequence sequence)\r
@@ -85,7 +85,8 @@ public class TreeCanvas
     selected.setEndRes(av.alignment.getWidth());\r
     selected.addOrRemove(sequence, true);\r
 \r
-    PaintRefresher.Refresh(this);\r
+System.out.println("called here");\r
+    PaintRefresher.Refresh(this, av.alignment);\r
     repaint();\r
   }\r
 \r
@@ -424,7 +425,6 @@ public class TreeCanvas
 \r
   public void mousePressed(MouseEvent e)\r
   {\r
-\r
     av.setCurrentTree(tree);\r
 \r
     int x = e.getX();\r
@@ -472,18 +472,26 @@ public class TreeCanvas
 \r
           Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(\r
               i), new Vector());\r
-          SequenceGroup sg = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true, false,\r
-                                     0, av.alignment.getWidth());\r
+\r
+          Vector sequences = new Vector();\r
           for (int j = 0; j < l.size(); j++)\r
           {\r
-            SequenceNode sn = (SequenceNode) l.elementAt(j);\r
-            sg.addSequence( (Sequence) sn.element(), false);\r
+            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();\r
+            if(!sequences.contains(s1))\r
+              sequences.addElement(s1);\r
           }\r
 \r
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)\r
+          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),\r
+              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));\r
+\r
+\r
+          SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",\r
+                                               cs, true, true,\r
+                                               false, 0, av.alignment.getWidth());\r
+\r
+\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
@@ -491,9 +499,9 @@ public class TreeCanvas
 \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
@@ -503,7 +511,7 @@ public class TreeCanvas
       }\r
     }\r
 \r
-    PaintRefresher.Refresh(this);\r
+    PaintRefresher.Refresh(this, av.alignment);\r
     repaint();\r
 \r
   }\r