X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=cbec833d327774e37af932b1fc47fbe17ad41fdd;hb=8c2ee75d86492f03e4c01404855f9ad2dd305719;hp=850730b3f24e6adb4d0eebeb79bff34b8a552000;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 850730b..cbec833 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,37 +1,58 @@
-/*
-* 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
+ * 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;
+
+    /** DOCUMENT ME!! */
     public int bootstrap;
 
-    public BinaryNode() {
+    /**
+     * Creates a new BinaryNode object.
+     */
+    public BinaryNode()
+    {
         left = right = parent = null;
         bootstrap = 0;
     }
 
-    public BinaryNode(Object element, BinaryNode parent, String 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;
@@ -39,72 +60,143 @@ public class BinaryNode {
         left = right = null;
     }
 
-    public Object element() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object element()
+    {
         return element;
     }
 
-    public Object setElement(Object v) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param v DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Object setElement(Object v)
+    {
         return element = v;
     }
 
-    public BinaryNode left() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode left()
+    {
         return left;
     }
 
-    public BinaryNode setLeft(BinaryNode n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setLeft(BinaryNode n)
+    {
         return left = n;
     }
 
-    public BinaryNode right() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode right()
+    {
         return right;
     }
 
-    public BinaryNode setRight(BinaryNode n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setRight(BinaryNode n)
+    {
         return right = n;
     }
 
-    public BinaryNode parent() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode parent()
+    {
         return parent;
     }
 
-    public BinaryNode setParent(BinaryNode n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public BinaryNode setParent(BinaryNode n)
+    {
         return parent = n;
     }
 
-    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) {
+    /**
+     * 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);
         }
 
-        if (rightchild != null) {
+        if (rightchild != null)
+        {
             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() {
-        if (this.parent != null) {
-            if (this.parent.left == this) {
+    /**
+     * 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) {
+            }
+            else
+            {
+                if (this.parent.right == this)
+                {
                     this.parent.right = null;
                 }
             }
@@ -115,48 +207,78 @@ public class BinaryNode {
         return this;
     }
 
-    /**
- * Traverses up through the tree until a node with a free leftchild is discovered.
- * @return BinaryNode
- */
-    public BinaryNode ascendLeft() {
+    /**
+     * Traverses up through the tree until a node with a free leftchild is discovered.
+     * @return BinaryNode
+     */
+    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() {
+    /**
+     * 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 {
+        do
+        {
             c = c.parent();
-        } while ((c != null) && (c.right() != null) && !c.right().isLeaf());
+        }
+        while ((c != null) && (c.right() != null) && !c.right().isLeaf());
 
         return c;
     }
 
-    public void setName(String name) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
         this.name = name;
     }
 
-    public String getName() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
         return this.name;
     }
 
-    public void setBootstrap(int boot) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param boot DOCUMENT ME!
+     */
+    public void setBootstrap(int boot)
+    {
         this.bootstrap = boot;
     }
 
-    public int getBootstrap() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getBootstrap()
+    {
         return bootstrap;
     }
 }