JAL-2428 separate TreeModel from TreeBuilder/NJTree/AverageDistanceTree

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index eb4253f..3730b56 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -21,7 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -53,6 +53,7 @@ import java.awt.print.PrinterException;
 import java.awt.print.PrinterJob;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JColorChooser;
@@ -73,7 +74,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   /** DOCUMENT ME!! */
   public static final String PLACEHOLDER = " * ";
 
-  NJTree tree;
+  TreeModel tree;
 
   JScrollPane scrollPane;
 
@@ -168,7 +169,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setTree(NJTree tree)
+  public void setTree(TreeModel tree)
   {
     this.tree = tree;
     tree.findHeight(tree.getTopNode());
@@ -929,8 +930,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         threshold = (float) (x - offx)
                 / (float) (getWidth() - labelLength - (2 * offx));
 
-        tree.getGroups().removeAllElements();
-        tree.groupNodes(tree.getTopNode(), threshold);
+        List<SequenceNode> groups = tree.groupNodes(threshold);
         setColor(tree.getTopNode(), Color.black);
 
         AlignmentPanel[] aps = getAssociatedPanels();
@@ -950,7 +950,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             aps[a].av.getCodingComplement().clearSequenceColours();
           }
         }
-        colourGroups();
+        colourGroups(groups);
       }
 
       PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
@@ -959,17 +959,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
   }
 
-  void colourGroups()
+  void colourGroups(List<SequenceNode> groups)
   {
     AlignmentPanel[] aps = getAssociatedPanels();
-    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>();