X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=ec6e3464b8804154b1bbb2f3e08383b710316473;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=77b5971105b1070f560528054bb79be7da443f5e;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 77b5971..ec6e346 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,73 +1,302 @@
-package jalview.datamodel;
-
-public class BinaryNode {
-
-  Object element;
-  String name;
-  BinaryNode left;
-  BinaryNode right;
-  BinaryNode parent;
-  public int bootstrap;
-
-  public BinaryNode() {
-    left = right = parent = null;
-  }
-
-  public BinaryNode(Object element, BinaryNode parent,String name) {
-    this.element = element;
-    this.parent  = parent;
-    this.name    = name;
-
-    left=right=null;
-  }
-
-  public Object element() {
-    return element;
-  }
-
-  public Object setElement(Object v) {
-    return element=v;
-  }
-
-  public BinaryNode left() {
-    return left;
-  }
-
-  public BinaryNode setLeft(BinaryNode n) {
-    return left=n;
-  }
-
-  public BinaryNode right() {
-    return right;
-  }
-
-  public BinaryNode setRight(BinaryNode n) {
-    return right=n;
-  }
-
-  public BinaryNode parent() {
-    return parent;
-  }
-
-  public BinaryNode setParent(BinaryNode n) {
-    return parent=n;
-  }
-
-  public boolean isLeaf() {
-    return (left == null) && (right == null);
-  }
-
-    public void setName(String name) {
-	  this.name = name;
-    }
-    public String getName() {
-	return this.name;
-    }
-  public void setBootstrap(int boot) {
-    this.bootstrap = boot;
-	}
-  public int getBootstrap() {
-    return bootstrap;
-  }
-}
-
+/*
+ * 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;
+    this.parent = parent;
+    this.name = name;
+
+    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
+   * 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)
+    {
+      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)
+      {
+        this.parent.left = null;
+      }
+      else
+      {
+        if (this.parent.right == this)
+        {
+          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;
+
+    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;
+  }
+
+  /**
+   * 
+   * 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;
+  }
+}