X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=cb26fb5dc5374aceb1383e45a84194cf90558d31;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=48e9d643ab12f25d6c7e3e4cd3e05d04788b8720;hpb=be27d7b3cadbfb5c488066034c48b1735799b429;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 48e9d64..cb26fb5 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -51,8 +51,8 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
-public class TreeCanvas extends Panel implements MouseListener,
-        MouseMotionListener
+public class TreeCanvas extends Panel
+        implements MouseListener, MouseMotionListener
 {
   TreeModel tree;
 
@@ -210,8 +210,9 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
-              .getName()) : node.getName();
+      String name = (markPlaceholders && node.isPlaceholder())
+              ? (PLACEHOLDER + node.getName())
+              : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
@@ -261,10 +262,10 @@ 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)
-              + offy;
+      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);
@@ -490,7 +491,8 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.setColor(Color.gray);
       }
 
-      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
+      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx)
+              + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
@@ -629,7 +631,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
 
-      Vector<SequenceI> sequences = new Vector<SequenceI>();
+      Vector<SequenceI> sequences = new Vector<>();
       for (int j = 0; j < l.size(); j++)
       {
         SequenceI s1 = (SequenceI) l.elementAt(j).element();
@@ -655,9 +657,9 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColourScheme(sg,
-                  ColourSchemeProperty.getColourName(av
-                          .getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(av, sg,
+                  ColourSchemeProperty
+                  .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
         // if (cs != null)