X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=f965ff4686b41d79f7209b7e2b36e76c61736447;hb=3d998cf52e272c70873c44c7672bc1270cafbf10;hp=1355916b0d8d7066f3355607992d8dd1d12015a2;hpb=fe68da05540c32386ec63bd3beeadf8b9d624a16;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 1355916..f965ff4 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -87,7 +87,7 @@ public class TreeCanvas extends Panel
 
   Hashtable nodeHash = new Hashtable();
 
-  SequenceNode highlightNode;
+  BinaryNode highlightNode;
 
   AlignmentPanel ap;
 
@@ -123,15 +123,15 @@ public class TreeCanvas extends Panel
     tree2.findHeight(tree2.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector<SequenceNode> leaves = tree2.findLeaves(tree2.getTopNode());
+    Vector<BinaryNode> leaves = tree2.findLeaves(tree2.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
     for (int i = 0; i < leaves.size(); i++)
     {
-      SequenceNode lf = leaves.elementAt(i);
+      BinaryNode lf = leaves.elementAt(i);
 
-      if (lf.isPlaceholder())
+      if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
       {
         has_placeholders = true;
       }
@@ -147,7 +147,7 @@ public class TreeCanvas extends Panel
     setMarkPlaceholders(has_placeholders);
   }
 
-  public void drawNode(Graphics g, SequenceNode node, float chunk,
+  public void drawNode(Graphics g, BinaryNode node, float chunk,
           double scale, int width, int offx, int offy)
   {
     if (node == null)
@@ -211,9 +211,10 @@ public class TreeCanvas extends Panel
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder())
-              ? (PLACEHOLDER + node.getName())
-              : node.getName();
+      String name = (markPlaceholders && node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())
+                      ? (PLACEHOLDER + node.getName())
+                      : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
@@ -238,9 +239,9 @@ public class TreeCanvas extends Panel
     }
     else
     {
-      drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx,
+      drawNode(g, (BinaryNode) node.left(), chunk, scale, width, offx,
               offy);
-      drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
+      drawNode(g, (BinaryNode) node.right(), chunk, scale, width, offx,
               offy);
 
       double height = node.height;
@@ -385,8 +386,8 @@ public class TreeCanvas extends Panel
     }
     else
     {
-      pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width,
-              offx, offy);
+      pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx,
+              offy);
       pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width,
               offx, offy);
     }
@@ -528,7 +529,7 @@ public class TreeCanvas extends Panel
       }
       else
       {
-        Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
+        Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
 
         for (int i = 0; i < leaves.size(); i++)
         {
@@ -555,9 +556,9 @@ public class TreeCanvas extends Panel
 
     Object ob = findElement(evt.getX(), evt.getY());
 
-    if (ob instanceof SequenceNode)
+    if (ob instanceof BinaryNode)
     {
-      highlightNode = (SequenceNode) ob;
+      highlightNode = (BinaryNode) ob;
       repaint();
     }
     else
@@ -597,7 +598,7 @@ public class TreeCanvas extends Panel
         threshold = (float) (x - offx)
                 / (float) (getSize().width - labelLength - 2 * offx);
 
-        List<SequenceNode> groups = tree.groupNodes(threshold);
+        List<BinaryNode> groups = tree.groupNodes(threshold);
         setColor(tree.getTopNode(), Color.black);
 
         av.setSelectionGroup(null);
@@ -621,7 +622,7 @@ public class TreeCanvas extends Panel
 
   }
 
-  void colourGroups(List<SequenceNode> groups)
+  void colourGroups(List<BinaryNode> groups)
   {
     for (int i = 0; i < groups.size(); i++)
     {
@@ -630,7 +631,7 @@ public class TreeCanvas extends Panel
               (int) (Math.random() * 255), (int) (Math.random() * 255));
       setColor(groups.get(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
+      Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
 
       Vector<SequenceI> sequences = new Vector<>();
       for (int j = 0; j < l.size(); j++)