Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / datamodel / BinaryNode.java

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 5b55594..624c2b9 100755 (executable)
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -23,22 +23,22 @@ package jalview.datamodel;
 import java.awt.Color;
 
 /**
- * DOCUMENT ME!
+ * Represent a node in a binary tree
  * 
- * @author $author$
+ * @author $mclamp (probably!)$
  * @version $Revision$
  */
-public class BinaryNode
+public class BinaryNode<T>
 {
-  Object element;
+  T element;
 
   String name;
 
-  BinaryNode left;
+  BinaryNode<T> left;
 
-  BinaryNode right;
+  BinaryNode<T> right;
 
-  BinaryNode parent;
+  BinaryNode<T> parent;
 
   /** Bootstrap value */
   public int bootstrap;
@@ -58,7 +58,10 @@ public class BinaryNode
   /** DOCUMENT ME!! */
   public Color color = Color.black;
 
-  /** DOCUMENT ME!! */
+  /**
+   * if true, node is created to simulate polytomy between parent and its 3 or
+   * more children
+   */
   public boolean dummy = false;
 
   /**
@@ -81,7 +84,7 @@ public class BinaryNode
    * @param name
    *          DOCUMENT ME!
    */
-  public BinaryNode(Object element, BinaryNode parent, String name,
+  public BinaryNode(T element, BinaryNode<T> parent, String name,
           double dist)
   {
     this();
@@ -91,14 +94,14 @@ public class BinaryNode
     this.dist = dist;
   }
 
-  public BinaryNode(Object element, BinaryNode parent, String name,
+  public BinaryNode(T element, BinaryNode<T> parent, String name,
           double dist, int bootstrap)
   {
     this(element, parent, name, dist);
     this.bootstrap = bootstrap;
   }
 
-  public BinaryNode(Object val, BinaryNode parent, String name, double dist,
+  public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
           int bootstrap, boolean dummy)
   {
     this(val, parent, name, dist, bootstrap);
@@ -110,7 +113,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public Object element()
+  public T element()
   {
     return element;
   }
@@ -123,7 +126,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public Object setElement(Object v)
+  public T setElement(T v)
   {
     return element = v;
   }
@@ -133,7 +136,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode left()
+  public BinaryNode<T> left()
   {
     return left;
   }
@@ -146,7 +149,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setLeft(BinaryNode n)
+  public BinaryNode<T> setLeft(BinaryNode<T> n)
   {
     return left = n;
   }
@@ -156,7 +159,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode right()
+  public BinaryNode<T> right()
   {
     return right;
   }
@@ -169,7 +172,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setRight(BinaryNode n)
+  public BinaryNode<T> setRight(BinaryNode<T> n)
   {
     return right = n;
   }
@@ -179,7 +182,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode parent()
+  public BinaryNode<T> parent()
   {
     return parent;
   }
@@ -192,7 +195,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setParent(BinaryNode n)
+  public BinaryNode<T> setParent(BinaryNode<T> n)
   {
     return parent = n;
   }
@@ -214,7 +217,7 @@ public class BinaryNode
    * setChild(null), or detach() for this.
    * 
    */
-  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+  public void SetChildren(BinaryNode<T> leftchild, BinaryNode<T> rightchild)
   {
     if (leftchild != null)
     {
@@ -236,7 +239,7 @@ public class BinaryNode
    * 
    * @return BinaryNode The detached node.
    */
-  public BinaryNode detach()
+  public BinaryNode<T> detach()
   {
     if (this.parent != null)
     {
@@ -264,9 +267,9 @@ public class BinaryNode
    * 
    * @return BinaryNode
    */
-  public BinaryNode ascendLeft()
+  public BinaryNode<T> ascendLeft()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
@@ -283,9 +286,9 @@ public class BinaryNode
    * 
    * @return BinaryNode
    */
-  public BinaryNode ascendRight()
+  public BinaryNode<T> ascendRight()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
@@ -366,9 +369,9 @@ public class BinaryNode
    * ascends the tree but doesn't stop until a non-dummy node is discovered.
    * 
    */
-  public BinaryNode AscendTree()
+  public BinaryNode<T> AscendTree()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {