+/*
+ * 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;
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
+ * 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)
{
this.setLeft(leftchild);
leftchild.detach();
leftchild.setParent(this);
-
}
+
if (rightchild != null)
{
this.setRight(rightchild);
/**
* 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;
}
}
}
+
this.parent = null;
+
return this;
}
+
/**
- * Traverses up through the tree until a node with a free leftchild is discovered.
+ * 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.
+ * 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;
}
-
+ /**
+ *
+ * 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;
git://source.jalview.org / jalview.git / blobdiff