ignore thumbnails

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

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index cefbc22..da63613 100755 (executable)
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,40 +1,56 @@
 /*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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;
 
+/**
+ * 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;
@@ -44,46 +60,99 @@ 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);
@@ -102,8 +171,8 @@ public class BinaryNode
       this.setLeft(leftchild);
       leftchild.detach();
       leftchild.setParent(this);
-
     }
+
     if (rightchild != null)
     {
       this.setRight(rightchild);
@@ -118,7 +187,8 @@ public class BinaryNode
    */
   public BinaryNode detach()
   {
-    if (this.parent!=null) {
+    if (this.parent != null)
+    {
       if (this.parent.left == this)
       {
         this.parent.left = null;
@@ -131,49 +201,82 @@ public class BinaryNode
         }
       }
     }
+
     this.parent = null;
+
     return this;
   }
+
   /**
    * 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.
    * @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;
   }
 
-
+  /**
+   * 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;