X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=a7e8254d05140f1a7e074750518a06b5c492484c;hb=ccc0d91abe38690088a6050faba8ef66cde1f271;hp=215ea6d961ca9018619e59bb09aee61dd6245bce;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 215ea6d..a7e8254 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -26,259 +26,259 @@ package jalview.datamodel;
  */
 public class BinaryNode
 {
-    Object element;
-    String name;
-    BinaryNode left;
-    BinaryNode right;
-    BinaryNode parent;
+  Object element;
+  String name;
+  BinaryNode left;
+  BinaryNode right;
+  BinaryNode parent;
 
-    /** DOCUMENT ME!! */
-    public int bootstrap;
+  /** DOCUMENT ME!! */
+  public int bootstrap;
 
-    /**
-     * Creates a new BinaryNode object.
-     */
-    public BinaryNode()
-    {
-        left = right = parent = null;
-        bootstrap = 0;
-    }
+  /**
+   * 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;
-        this.parent = parent;
-        this.name = name;
+  /**
+   * 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;
+    this.parent = parent;
+    this.name = name;
 
-        left = right = null;
-    }
+    left = right = null;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Object element()
-    {
-        return element;
-    }
+  /**
+   * 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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @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!
+   *
+   * @param n DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public BinaryNode setParent(BinaryNode n)
+  {
+    return parent = n;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isLeaf()
+  /**
+   * 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
+   * setChild(null), or detach() for this.
+   *
+   */
+  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+  {
+    if (leftchild != null)
     {
-        return (left == null) && (right == null);
+      this.setLeft(leftchild);
+      leftchild.detach();
+      leftchild.setParent(this);
     }
 
-    /**
-     * 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)
+    if (rightchild != null)
     {
-        if (leftchild != null)
-        {
-            this.setLeft(leftchild);
-            leftchild.detach();
-            leftchild.setParent(this);
-        }
-
-        if (rightchild != null)
-        {
-            this.setRight(rightchild);
-            rightchild.detach();
-            rightchild.setParent(this);
-        }
+      this.setRight(rightchild);
+      rightchild.detach();
+      rightchild.setParent(this);
     }
+  }
 
-    /**
-     * Detaches the node from the binary tree, along with all its child nodes.
-     * @return BinaryNode The detached node.
-     */
-    public BinaryNode detach()
+  /**
+   * 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;
+      }
+      else
+      {
+        if (this.parent.right == this)
         {
-            if (this.parent.left == this)
-            {
-                this.parent.left = null;
-            }
-            else
-            {
-                if (this.parent.right == this)
-                {
-                    this.parent.right = null;
-                }
-            }
+          this.parent.right = null;
         }
-
-        this.parent = null;
-
-        return this;
+      }
     }
 
-    /**
-     * Traverses up through the tree until a node with a free leftchild is discovered.
-     * @return BinaryNode
-     */
-    public BinaryNode ascendLeft()
-    {
-        BinaryNode c = this;
+    this.parent = null;
 
-        do
-        {
-            c = c.parent();
-        }
-        while ((c != null) && (c.left() != null) && !c.left().isLeaf());
+    return this;
+  }
 
-        return c;
-    }
+  /**
+   * Traverses up through the tree until a node with a free leftchild is discovered.
+   * @return BinaryNode
+   */
+  public BinaryNode ascendLeft()
+  {
+    BinaryNode c = this;
 
-    /**
-     * 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()
+    do
     {
-        BinaryNode c = this;
+      c = c.parent();
+    }
+    while ( (c != null) && (c.left() != null) && !c.left().isLeaf());
 
-        do
-        {
-            c = c.parent();
-        }
-        while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+    return c;
+  }
 
-        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.
+   * @return BinaryNode
+   */
+  public BinaryNode ascendRight()
+  {
+    BinaryNode c = this;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
+    do
     {
-        this.name = name;
+      c = c.parent();
     }
+    while ( (c != null) && (c.right() != null) && !c.right().isLeaf());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return this.name;
-    }
+    return c;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param boot DOCUMENT ME!
-     */
-    public void setBootstrap(int boot)
-    {
-        this.bootstrap = boot;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getBootstrap()
-    {
-        return bootstrap;
-    }
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return this.name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param boot DOCUMENT ME!
+   */
+  public void setBootstrap(int boot)
+  {
+    this.bootstrap = boot;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getBootstrap()
+  {
+    return bootstrap;
+  }
 }