/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
+import java.awt.Color;
+
/**
- * DOCUMENT ME!
+ * Represent a node in a binary tree
*
- * @author $author$
+ * @author $mclamp (probably!)$
* @version $Revision$
*/
-public class BinaryNode
+public class BinaryNode<T>
{
- Object element;
+ T element;
String name;
- BinaryNode left;
+ BinaryNode<T> left;
- BinaryNode right;
+ BinaryNode<T> right;
- BinaryNode parent;
+ BinaryNode<T> parent;
- /** DOCUMENT ME!! */
+ /** Bootstrap value */
public int bootstrap;
+ /** DOCUMENT ME!! */
+ public double dist;
+
+ /** DOCUMENT ME!! */
+ public int count;
+
+ /** DOCUMENT ME!! */
+ public double height;
+
+ /** DOCUMENT ME!! */
+ public float ycount;
+
+ /** DOCUMENT ME!! */
+ public Color color = Color.black;
+
+ /**
+ * if true, node is created to simulate polytomy between parent and its 3 or
+ * more children
+ */
+ public boolean dummy = false;
+
/**
* Creates a new BinaryNode object.
*/
{
left = right = parent = null;
bootstrap = 0;
+ dist = 0;
}
/**
* Creates a new BinaryNode object.
*
* @param element
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param parent
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public BinaryNode(Object element, BinaryNode parent, String name)
+ public BinaryNode(T element, BinaryNode<T> parent, String name,
+ double dist)
{
+ this();
this.element = element;
this.parent = parent;
this.name = name;
+ this.dist = dist;
+ }
- left = right = null;
+ public BinaryNode(T element, BinaryNode<T> parent, String name,
+ double dist, int bootstrap)
+ {
+ this(element, parent, name, dist);
+ this.bootstrap = bootstrap;
+ }
+
+ public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
+ int bootstrap, boolean dummy)
+ {
+ this(val, parent, name, dist, bootstrap);
+ this.dummy = dummy;
}
/**
*
* @return DOCUMENT ME!
*/
- public Object element()
+ public T element()
{
return element;
}
* DOCUMENT ME!
*
* @param v
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public Object setElement(Object v)
+ public T setElement(T v)
{
return element = v;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode left()
+ public BinaryNode<T> left()
{
return left;
}
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public BinaryNode setLeft(BinaryNode n)
+ public BinaryNode<T> setLeft(BinaryNode<T> n)
{
return left = n;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode right()
+ public BinaryNode<T> right()
{
return right;
}
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public BinaryNode setRight(BinaryNode n)
+ public BinaryNode<T> setRight(BinaryNode<T> n)
{
return right = n;
}
*
* @return DOCUMENT ME!
*/
- public BinaryNode parent()
+ public BinaryNode<T> parent()
{
return parent;
}
* DOCUMENT ME!
*
* @param n
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public BinaryNode setParent(BinaryNode n)
+ public BinaryNode<T> setParent(BinaryNode<T> n)
{
return parent = n;
}
* setChild(null), or detach() for this.
*
*/
- public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+ public void SetChildren(BinaryNode<T> leftchild, BinaryNode<T> rightchild)
{
if (leftchild != null)
{
*
* @return BinaryNode The detached node.
*/
- public BinaryNode detach()
+ public BinaryNode<T> detach()
{
if (this.parent != null)
{
*
* @return BinaryNode
*/
- public BinaryNode ascendLeft()
+ public BinaryNode<T> ascendLeft()
{
- BinaryNode c = this;
+ BinaryNode<T> c = this;
do
{
*
* @return BinaryNode
*/
- public BinaryNode ascendRight()
+ public BinaryNode<T> ascendRight()
{
- BinaryNode c = this;
+ BinaryNode<T> c = this;
do
{
}
/**
- * DOCUMENT ME!
*
- * @param name
- * DOCUMENT ME!
+ * set the display name
+ *
+ * @param new
+ * name
*/
public void setName(String name)
{
}
/**
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ *
+ * @return the display name for this node
*/
public String getName()
{
}
/**
- * DOCUMENT ME!
+ * set integer bootstrap value
*
* @param boot
- * DOCUMENT ME!
*/
public void setBootstrap(int boot)
{
}
/**
- * DOCUMENT ME!
+ * get bootstrap
*
- * @return DOCUMENT ME!
+ * @return integer value
*/
public int getBootstrap()
{
return bootstrap;
}
+
+ /**
+ * @param dummy
+ * true if node is created for the representation of polytomous trees
+ */
+ public boolean isDummy()
+ {
+ return dummy;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newstate
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setDummy(boolean newstate)
+ {
+ boolean oldstate = dummy;
+ dummy = newstate;
+
+ return oldstate;
+ }
+
+ /**
+ * ascends the tree but doesn't stop until a non-dummy node is discovered.
+ *
+ */
+ public BinaryNode<T> AscendTree()
+ {
+ BinaryNode<T> c = this;
+
+ do
+ {
+ c = c.parent();
+ } while ((c != null) && c.dummy);
+
+ return c;
+ }
}
git://source.jalview.org / jalview.git / blobdiff