JAL-4034 add round corners to 3DB confirmation button with icon on a mac

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

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 7040c42..2e5f938 100755 (executable)
--- 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
+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 = "";
 
@@ -209,8 +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();
@@ -260,10 +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);
@@ -489,7 +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);
     }
@@ -593,8 +596,7 @@ 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 +610,7 @@ public class TreeCanvas extends Panel implements MouseListener,
           codingComplement.clearSequenceColours();
         }
 
-        colourGroups();
+        colourGroups(groups);
 
       }
     }
@@ -618,19 +620,18 @@ 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>();
+      Vector<SequenceI> sequences = new Vector<>();
       for (int j = 0; j < l.size(); j++)
       {
         SequenceI s1 = (SequenceI) l.elementAt(j).element();
@@ -656,9 +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)