X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=624c2b9af0bd01e32df0ff8b8a94e00ae49a2f5f;hb=a0bd24f90375fc1d4be619bf65746a912dfcfc89;hp=cae018586137b64fede2a087393b14a87c484490;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index cae0185..624c2b9 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,43 +1,69 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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
{
- Object element;
+ T element;
String name;
- BinaryNode left;
+ BinaryNode left;
- BinaryNode right;
+ BinaryNode right;
- BinaryNode parent;
+ BinaryNode 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.
*/
@@ -45,6 +71,7 @@ public class BinaryNode
{
left = right = parent = null;
bootstrap = 0;
+ dist = 0;
}
/**
@@ -57,13 +84,28 @@ public class BinaryNode
* @param name
* DOCUMENT ME!
*/
- public BinaryNode(Object element, BinaryNode parent, String name)
+ public BinaryNode(T element, BinaryNode parent, String name,
+ double dist)
{
+ this();
this.element = element;
this.parent = parent;
this.name = name;
+ this.dist = dist;
+ }
+
+ public BinaryNode(T element, BinaryNode parent, String name,
+ double dist, int bootstrap)
+ {
+ this(element, parent, name, dist);
+ this.bootstrap = bootstrap;
+ }
- left = right = null;
+ public BinaryNode(T val, BinaryNode parent, String name, double dist,
+ int bootstrap, boolean dummy)
+ {
+ this(val, parent, name, dist, bootstrap);
+ this.dummy = dummy;
}
/**
@@ -71,7 +113,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public Object element()
+ public T element()
{
return element;
}
@@ -84,7 +126,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public Object setElement(Object v)
+ public T setElement(T v)
{
return element = v;
}
@@ -94,7 +136,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public BinaryNode left()
+ public BinaryNode left()
{
return left;
}
@@ -107,7 +149,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public BinaryNode setLeft(BinaryNode n)
+ public BinaryNode setLeft(BinaryNode n)
{
return left = n;
}
@@ -117,7 +159,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public BinaryNode right()
+ public BinaryNode right()
{
return right;
}
@@ -130,7 +172,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public BinaryNode setRight(BinaryNode n)
+ public BinaryNode setRight(BinaryNode n)
{
return right = n;
}
@@ -140,7 +182,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public BinaryNode parent()
+ public BinaryNode parent()
{
return parent;
}
@@ -153,7 +195,7 @@ public class BinaryNode
*
* @return DOCUMENT ME!
*/
- public BinaryNode setParent(BinaryNode n)
+ public BinaryNode setParent(BinaryNode n)
{
return parent = n;
}
@@ -175,7 +217,7 @@ public class BinaryNode
* setChild(null), or detach() for this.
*
*/
- public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
+ public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)
{
if (leftchild != null)
{
@@ -197,7 +239,7 @@ public class BinaryNode
*
* @return BinaryNode The detached node.
*/
- public BinaryNode detach()
+ public BinaryNode detach()
{
if (this.parent != null)
{
@@ -225,9 +267,9 @@ public class BinaryNode
*
* @return BinaryNode
*/
- public BinaryNode ascendLeft()
+ public BinaryNode ascendLeft()
{
- BinaryNode c = this;
+ BinaryNode c = this;
do
{
@@ -244,9 +286,9 @@ public class BinaryNode
*
* @return BinaryNode
*/
- public BinaryNode ascendRight()
+ public BinaryNode ascendRight()
{
- BinaryNode c = this;
+ BinaryNode c = this;
do
{
@@ -260,7 +302,8 @@ public class BinaryNode
*
* set the display name
*
- * @param new name
+ * @param new
+ * name
*/
public void setName(String name)
{
@@ -296,4 +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 AscendTree()
+ {
+ BinaryNode c = this;
+
+ do
+ {
+ c = c.parent();
+ } while ((c != null) && c.dummy);
+
+ return c;
+ }
}