Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 47cd108..624c2b9 100755 (executable)
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,44 +1,69 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
 
+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.
    */
@@ -46,6 +71,7 @@ public class BinaryNode
   {
     left = right = parent = null;
     bootstrap = 0;
+    dist = 0;
   }
 
   /**
@@ -58,13 +84,28 @@ public class BinaryNode
    * @param name
    *          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;
+  }
+
+  public BinaryNode(T element, BinaryNode<T> parent, String name,
+          double dist, int bootstrap)
+  {
+    this(element, parent, name, dist);
+    this.bootstrap = bootstrap;
+  }
 
-    left = right = null;
+  public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
+          int bootstrap, boolean dummy)
+  {
+    this(val, parent, name, dist, bootstrap);
+    this.dummy = dummy;
   }
 
   /**
@@ -72,7 +113,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public Object element()
+  public T element()
   {
     return element;
   }
@@ -85,7 +126,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public Object setElement(Object v)
+  public T setElement(T v)
   {
     return element = v;
   }
@@ -95,7 +136,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode left()
+  public BinaryNode<T> left()
   {
     return left;
   }
@@ -108,7 +149,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setLeft(BinaryNode n)
+  public BinaryNode<T> setLeft(BinaryNode<T> n)
   {
     return left = n;
   }
@@ -118,7 +159,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode right()
+  public BinaryNode<T> right()
   {
     return right;
   }
@@ -131,7 +172,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setRight(BinaryNode n)
+  public BinaryNode<T> setRight(BinaryNode<T> n)
   {
     return right = n;
   }
@@ -141,7 +182,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode parent()
+  public BinaryNode<T> parent()
   {
     return parent;
   }
@@ -154,7 +195,7 @@ public class BinaryNode
    * 
    * @return DOCUMENT ME!
    */
-  public BinaryNode setParent(BinaryNode n)
+  public BinaryNode<T> setParent(BinaryNode<T> n)
   {
     return parent = n;
   }
@@ -176,7 +217,7 @@ public class BinaryNode
    * 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)
     {
@@ -198,7 +239,7 @@ public class BinaryNode
    * 
    * @return BinaryNode The detached node.
    */
-  public BinaryNode detach()
+  public BinaryNode<T> detach()
   {
     if (this.parent != null)
     {
@@ -226,9 +267,9 @@ public class BinaryNode
    * 
    * @return BinaryNode
    */
-  public BinaryNode ascendLeft()
+  public BinaryNode<T> ascendLeft()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
@@ -245,9 +286,9 @@ public class BinaryNode
    * 
    * @return BinaryNode
    */
-  public BinaryNode ascendRight()
+  public BinaryNode<T> ascendRight()
   {
-    BinaryNode c = this;
+    BinaryNode<T> c = this;
 
     do
     {
@@ -261,7 +302,8 @@ public class BinaryNode
    * 
    * set the display name
    * 
-   * @param new name
+   * @param new
+   *          name
    */
   public void setName(String name)
   {
@@ -297,4 +339,45 @@ public class BinaryNode
   {
     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;
+  }
 }