/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
-*/\r
-package jalview.datamodel;\r
-\r
-public class BinaryNode {\r
- Object element;\r
- String name;\r
- BinaryNode left;\r
- BinaryNode right;\r
- BinaryNode parent;\r
- public int bootstrap;\r
-\r
- public BinaryNode() {\r
- left = right = parent = null;\r
- bootstrap = 0;\r
- }\r
-\r
- public BinaryNode(Object element, BinaryNode parent, String name) {\r
- this.element = element;\r
- this.parent = parent;\r
- this.name = name;\r
-\r
- left = right = null;\r
- }\r
-\r
- public Object element() {\r
- return element;\r
- }\r
-\r
- public Object setElement(Object v) {\r
- return element = v;\r
- }\r
-\r
- public BinaryNode left() {\r
- return left;\r
- }\r
-\r
- public BinaryNode setLeft(BinaryNode n) {\r
- return left = n;\r
- }\r
-\r
- public BinaryNode right() {\r
- return right;\r
- }\r
-\r
- public BinaryNode setRight(BinaryNode n) {\r
- return right = n;\r
- }\r
-\r
- public BinaryNode parent() {\r
- return parent;\r
- }\r
-\r
- public BinaryNode setParent(BinaryNode n) {\r
- return parent = n;\r
- }\r
-\r
- public boolean isLeaf() {\r
- return (left == null) && (right == null);\r
- }\r
-\r
- /**
- * 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.
- *
- */\r
- public void SetChildren(BinaryNode leftchild, BinaryNode rightchild) {\r
- if (leftchild != null) {\r
- this.setLeft(leftchild);\r
- leftchild.detach();\r
- leftchild.setParent(this);\r
- }\r
-\r
- if (rightchild != null) {\r
- this.setRight(rightchild);\r
- rightchild.detach();\r
- rightchild.setParent(this);\r
- }\r
- }\r
-\r
- /**
- * Detaches the node from the binary tree, along with all its child nodes.
- * @return BinaryNode The detached node.
- */\r
- public BinaryNode detach() {\r
- if (this.parent != null) {\r
- if (this.parent.left == this) {\r
- this.parent.left = null;\r
- } else {\r
- if (this.parent.right == this) {\r
- this.parent.right = null;\r
- }\r
- }\r
- }\r
-\r
- this.parent = null;\r
-\r
- return this;\r
- }\r
-\r
- /**
- * Traverses up through the tree until a node with a free leftchild is discovered.
- * @return BinaryNode
- */\r
- public BinaryNode ascendLeft() {\r
- BinaryNode c = this;\r
-\r
- do {\r
- c = c.parent();\r
- } while ((c != null) && (c.left() != null) && !c.left().isLeaf());\r
-\r
- return c;\r
- }\r
-\r
- /**
- * 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
- */\r
- public BinaryNode ascendRight() {\r
- BinaryNode c = this;\r
-\r
- do {\r
- c = c.parent();\r
- } while ((c != null) && (c.right() != null) && !c.right().isLeaf());\r
-\r
- return c;\r
- }\r
-\r
- public void setName(String name) {\r
- this.name = name;\r
- }\r
-\r
- public String getName() {\r
- return this.name;\r
- }\r
-\r
- public void setBootstrap(int boot) {\r
- this.bootstrap = boot;\r
- }\r
-\r
- public int getBootstrap() {\r
- return bootstrap;\r
- }\r
-}\r
+ * 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.
+ *
+ * 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;
+
+import java.awt.Color;
+
+/**
+ * Represent a node in a binary tree
+ *
+ * @author $mclamp (probably!)$
+ * @version $Revision$
+ */
+public class BinaryNode<T>
+{
+ T element;
+
+ String name;
+
+ BinaryNode<T> left;
+
+ BinaryNode<T> right;
+
+ BinaryNode<T> parent;
+
+ /** 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.
+ */
+ public BinaryNode()
+ {
+ left = right = parent = null;
+ bootstrap = 0;
+ dist = 0;
+ }
+
+ /**
+ * Creates a new BinaryNode object.
+ *
+ * @param element
+ * DOCUMENT ME!
+ * @param parent
+ * DOCUMENT ME!
+ * @param name
+ * DOCUMENT ME!
+ */
+ 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;
+ }
+
+ public BinaryNode(T val, BinaryNode<T> parent, String name, double dist,
+ int bootstrap, boolean dummy)
+ {
+ this(val, parent, name, dist, bootstrap);
+ this.dummy = dummy;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public T element()
+ {
+ return element;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param v
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public T setElement(T v)
+ {
+ return element = v;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BinaryNode<T> left()
+ {
+ return left;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BinaryNode<T> setLeft(BinaryNode<T> n)
+ {
+ return left = n;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BinaryNode<T> right()
+ {
+ return right;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BinaryNode<T> setRight(BinaryNode<T> n)
+ {
+ return right = n;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BinaryNode<T> parent()
+ {
+ return parent;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public BinaryNode<T> setParent(BinaryNode<T> 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<T> leftchild, BinaryNode<T> 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<T> 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<T> ascendLeft()
+ {
+ BinaryNode<T> 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<T> ascendRight()
+ {
+ BinaryNode<T> 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;
+ }
+
+ /**
+ * @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