X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=cbec833d327774e37af932b1fc47fbe17ad41fdd;hb=eb7824b3ecfdef2aa8c83e4a8520cb866f364d88;hp=77b5971105b1070f560528054bb79be7da443f5e;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 77b5971..cbec833 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,73 +1,284 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
-public class BinaryNode {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinaryNode
+{
+    Object element;
+    String name;
+    BinaryNode left;
+    BinaryNode right;
+    BinaryNode parent;
 
-  Object element;
-  String name;
-  BinaryNode left;
-  BinaryNode right;
-  BinaryNode parent;
-  public int bootstrap;
+    /** DOCUMENT ME!! */
+    public int bootstrap;
 
-  public BinaryNode() {
-    left = right = parent = null;
-  }
+    /**
+     * 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;
 
-  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;
+    }
 
-  public Object element() {
-    return element;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object setElement(Object v)
+    {
+        return element = v;
+    }
 
-  public Object setElement(Object v) {
-    return element=v;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode left()
+    {
+        return left;
+    }
 
-  public BinaryNode left() {
-    return left;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setLeft(BinaryNode n)
+    {
+        return left = n;
+    }
 
-  public BinaryNode setLeft(BinaryNode n) {
-    return left=n;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode right()
+    {
+        return right;
+    }
 
-  public BinaryNode right() {
-    return right;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setRight(BinaryNode n)
+    {
+        return right = n;
+    }
 
-  public BinaryNode setRight(BinaryNode n) {
-    return right=n;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode parent()
+    {
+        return parent;
+    }
 
-  public BinaryNode parent() {
-    return parent;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setParent(BinaryNode n)
+    {
+        return parent = n;
+    }
 
-  public BinaryNode setParent(BinaryNode n) {
-    return parent=n;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isLeaf()
+    {
+        return (left == null) && (right == null);
+    }
 
-  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)
+        {
+            this.setLeft(leftchild);
+            leftchild.detach();
+            leftchild.setParent(this);
+        }
 
-    public void setName(String name) {
-	  this.name = name;
+        if (rightchild != null)
+        {
+            this.setRight(rightchild);
+            rightchild.detach();
+            rightchild.setParent(this);
+        }
     }
-    public String getName() {
-	return this.name;
+
+    /**
+     * 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.left == this)
+            {
+                this.parent.left = null;
+            }
+            else
+            {
+                if (this.parent.right == this)
+                {
+                    this.parent.right = null;
+                }
+            }
+        }
+
+        this.parent = null;
+
+        return this;
     }
-  public void setBootstrap(int boot) {
-    this.bootstrap = boot;
-	}
-  public int getBootstrap() {
-    return bootstrap;
-  }
-}
 
+    /**
+     * Traverses up through the tree until a node with a free leftchild is discovered.
+     * @return BinaryNode
+     */
+    public BinaryNode ascendLeft()
+    {
+        BinaryNode c = this;
+
+        do
+        {
+            c = c.parent();
+        }
+        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.
+     * @return BinaryNode
+     */
+    public BinaryNode ascendRight()
+    {
+        BinaryNode c = this;
+
+        do
+        {
+            c = c.parent();
+        }
+        while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+
+        return c;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
+        this.name = name;
+    }
+
+    /**
+     * 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;
+    }
+}