JAL-1421 add generics to NJTree, refactor recursive search

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 254d032..279d9ad 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -175,13 +175,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     tree.findHeight(tree.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
     for (int i = 0; i < leaves.size(); i++)
     {
-      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+      SequenceNode lf = leaves.elementAt(i);
 
       if (lf.isPlaceholder())
       {
@@ -748,10 +748,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Empty method to satisfy the MouseListener interface
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent e)
@@ -759,10 +758,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Empty method to satisfy the MouseListener interface
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseEntered(MouseEvent e)
@@ -770,10 +768,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Empty method to satisfy the MouseListener interface
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseExited(MouseEvent e)
@@ -781,10 +778,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Handles a mouse click on a tree node (clicks elsewhere are handled in
+   * mousePressed). Click selects the sub-tree, double-click swaps leaf nodes
+   * order, right-click opens a dialogue to choose colour for the sub-tree.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseClicked(MouseEvent evt)
@@ -810,12 +808,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      Vector leaves = new Vector();
-      tree.findLeaves(highlightNode, leaves);
+      Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
 
       for (int i = 0; i < leaves.size(); i++)
       {
-        SequenceI seq = (SequenceI) ((SequenceNode) leaves.elementAt(i))
+        SequenceI seq = (SequenceI) leaves.elementAt(i)
                 .element();
         treeSelectionChanged(seq);
       }
@@ -876,10 +873,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   }
 
   /**
-   * DOCUMENT ME!
+   * Handles a mouse press on a sequence name or the tree background canvas
+   * (click on a node is handled in mouseClicked). The action is to create
+   * groups by partitioning the tree at the mouse position. Colours for the
+   * groups (and sequence names) are generated randomly.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void mousePressed(MouseEvent e)
@@ -901,8 +900,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     /*
      * defer right-click handling on Windows to
-     * mouseClicked; this also matches Cmd-click on Mac
-     * which should do nothing here
+     * mouseClicked; note isRightMouseButton
+     * also matches Cmd-click on Mac which should do
+     * nothing here
      */
     if (SwingUtilities.isRightMouseButton(e))
     {
@@ -969,14 +969,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
               (int) (Math.random() * 255), (int) (Math.random() * 255));
       setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves(
-              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+      Vector<SequenceNode> l = tree.findLeaves((SequenceNode) tree
+              .getGroups().elementAt(i));
 
-      Vector sequences = new Vector();
+      Vector<SequenceI> sequences = new Vector<SequenceI>();
 
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) ((SequenceNode) l.elementAt(j))
+        SequenceI s1 = (SequenceI) l.elementAt(j)
                 .element();
 
         if (!sequences.contains(s1))