X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=272a2b3f172cfc536289690cd4de34fcdba2fd74;hb=613818a08b858e3fe0dd778c738a362b3a4a0882;hp=7040c42f26aaf554723f5e4508233b44944194f3;hpb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 7040c42..272a2b3 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -21,7 +21,7 @@
 package jalview.appletgui;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -48,12 +48,13 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class TreeCanvas extends Panel implements MouseListener,
         MouseMotionListener
 {
-  NJTree tree;
+  TreeModel tree;
 
   ScrollPane scrollPane;
 
@@ -115,13 +116,13 @@ public class TreeCanvas extends Panel implements MouseListener,
     selected.addOrRemove(sequence, true);
   }
 
-  public void setTree(NJTree tree)
+  public void setTree(TreeModel tree2)
   {
-    this.tree = tree;
-    tree.findHeight(tree.getTopNode());
+    this.tree = tree2;
+    tree2.findHeight(tree2.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+    Vector<SequenceNode> leaves = tree2.findLeaves(tree2.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
@@ -260,10 +261,11 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.fillRect(xend - 2, ypos - 2, 4, 4);
       }
 
-      int ystart = (int) (((SequenceNode) node.left()).ycount * chunk)
-              + offy;
-      int yend = (int) (((SequenceNode) node.right()).ycount * chunk)
+      int ystart = (int) (node.left() == null ? 0 : (((SequenceNode) node
+              .left()).ycount * chunk))
               + offy;
+      int yend = (int) (node.right() == null ? 0 : (((SequenceNode) node
+              .right()).ycount * chunk)) + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
@@ -593,8 +595,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         threshold = (float) (x - offx)
                 / (float) (getSize().width - labelLength - 2 * offx);
 
-        tree.getGroups().removeAllElements();
-        tree.groupNodes(tree.getTopNode(), threshold);
+        List<SequenceNode> groups = tree.groupNodes(threshold);
         setColor(tree.getTopNode(), Color.black);
 
         av.setSelectionGroup(null);
@@ -608,7 +609,7 @@ public class TreeCanvas extends Panel implements MouseListener,
           codingComplement.clearSequenceColours();
         }
 
-        colourGroups();
+        colourGroups(groups);
 
       }
     }
@@ -618,17 +619,16 @@ public class TreeCanvas extends Panel implements MouseListener,
 
   }
 
-  void colourGroups()
+  void colourGroups(List<SequenceNode> groups)
   {
-    for (int i = 0; i < tree.getGroups().size(); i++)
+    for (int i = 0; i < groups.size(); i++)
     {
 
       Color col = new Color((int) (Math.random() * 255),
               (int) (Math.random() * 255), (int) (Math.random() * 255));
-      setColor(tree.getGroups().elementAt(i), col.brighter());
+      setColor(groups.get(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
-              .elementAt(i));
+      Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
 
       Vector<SequenceI> sequences = new Vector<SequenceI>();
       for (int j = 0; j < l.size(); j++)