X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=ec6e3464b8804154b1bbb2f3e08383b710316473;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6fb3be2f65372e1663498170a2387f17c59588ac;hpb=f008025f6aa0c2df0e1fbf556a89393e7052db72;p=jalview.git

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 6fb3be2..ec6e346 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,21 +1,65 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
 public class BinaryNode
 {
-
   Object element;
+
   String name;
+
   BinaryNode left;
+
   BinaryNode right;
+
   BinaryNode parent;
+
+  /** DOCUMENT ME!! */
   public int bootstrap;
 
+  /**
+   * Creates a new BinaryNode object.
+   */
   public BinaryNode()
   {
     left = right = parent = null;
     bootstrap = 0;
   }
 
+  /**
+   * Creates a new BinaryNode object.
+   * 
+   * @param element
+   *          DOCUMENT ME!
+   * @param parent
+   *          DOCUMENT ME!
+   * @param name
+   *          DOCUMENT ME!
+   */
   public BinaryNode(Object element, BinaryNode parent, String name)
   {
     this.element = element;
@@ -25,56 +69,114 @@ public class BinaryNode
     left = right = null;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public Object element()
   {
     return element;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param v
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public Object setElement(Object v)
   {
     return element = v;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public BinaryNode left()
   {
     return left;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public BinaryNode setLeft(BinaryNode n)
   {
     return left = n;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public BinaryNode right()
   {
     return right;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public BinaryNode setRight(BinaryNode n)
   {
     return right = n;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public BinaryNode parent()
   {
     return parent;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param n
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public BinaryNode setParent(BinaryNode n)
   {
     return parent = n;
   }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
   public boolean isLeaf()
   {
     return (left == null) && (right == null);
   }
 
   /**
-   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)
-   * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to  NULL - you  should use
+   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of
+   * this node (removing any old references) a null parameter DOES NOT mean that
+   * the pointer to the corresponding child node is set to NULL - you should use
    * setChild(null), or detach() for this.
-   *
+   * 
    */
   public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
   {
@@ -83,8 +185,8 @@ public class BinaryNode
       this.setLeft(leftchild);
       leftchild.detach();
       leftchild.setParent(this);
-
     }
+
     if (rightchild != null)
     {
       this.setRight(rightchild);
@@ -95,11 +197,13 @@ public class BinaryNode
 
   /**
    * Detaches the node from the binary tree, along with all its child nodes.
+   * 
    * @return BinaryNode The detached node.
    */
   public BinaryNode detach()
   {
-    if (this.parent!=null) {
+    if (this.parent != null)
+    {
       if (this.parent.left == this)
       {
         this.parent.left = null;
@@ -112,49 +216,85 @@ public class BinaryNode
         }
       }
     }
+
     this.parent = null;
+
     return this;
   }
+
   /**
-   * Traverses up through the tree until a node with a free leftchild is discovered.
+   * Traverses up through the tree until a node with a free leftchild is
+   * discovered.
+   * 
    * @return BinaryNode
    */
-  public BinaryNode ascendLeft() {
+  public BinaryNode ascendLeft()
+  {
     BinaryNode c = this;
-    do {
+
+    do
+    {
       c = c.parent();
-    }  while (c!=null && c.left()!=null && !c.left().isLeaf());
+    } while ((c != null) && (c.left() != null) && !c.left().isLeaf());
+
     return c;
   }
+
   /**
-   * Traverses up through the tree until a node with a free rightchild is discovered.
-   * Jalview builds trees by descent on the left, so this may be unused.
+   * Traverses up through the tree until a node with a free rightchild is
+   * discovered. Jalview builds trees by descent on the left, so this may be
+   * unused.
+   * 
    * @return BinaryNode
    */
-  public BinaryNode ascendRight() {
+  public BinaryNode ascendRight()
+  {
     BinaryNode c = this;
-    do {
+
+    do
+    {
       c = c.parent();
-    }  while (c!=null && c.right()!=null && !c.right().isLeaf());
+    } while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+
     return c;
   }
 
-
+  /**
+   * 
+   * set the display name
+   * 
+   * @param new name
+   */
   public void setName(String name)
   {
     this.name = name;
   }
 
+  /**
+   * 
+   * 
+   * @return the display name for this node
+   */
   public String getName()
   {
     return this.name;
   }
 
+  /**
+   * set integer bootstrap value
+   * 
+   * @param boot
+   */
   public void setBootstrap(int boot)
   {
     this.bootstrap = boot;
   }
 
+  /**
+   * get bootstrap
+   * 
+   * @return integer value
+   */
   public int getBootstrap()
   {
     return bootstrap;