/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
*/\r
public class BinaryNode\r
{\r
- Object element;\r
- String name;\r
- BinaryNode left;\r
- BinaryNode right;\r
- BinaryNode parent;\r
+ Object element;\r
+ String name;\r
+ BinaryNode left;\r
+ BinaryNode right;\r
+ BinaryNode parent;\r
\r
- /** DOCUMENT ME!! */\r
- public int bootstrap;\r
+ /** DOCUMENT ME!! */\r
+ public int bootstrap;\r
\r
- /**\r
- * Creates a new BinaryNode object.\r
- */\r
- public BinaryNode()\r
- {\r
- left = right = parent = null;\r
- bootstrap = 0;\r
- }\r
+ /**\r
+ * Creates a new BinaryNode object.\r
+ */\r
+ public BinaryNode()\r
+ {\r
+ left = right = parent = null;\r
+ bootstrap = 0;\r
+ }\r
\r
- /**\r
- * Creates a new BinaryNode object.\r
- *\r
- * @param element DOCUMENT ME!\r
- * @param parent DOCUMENT ME!\r
- * @param name DOCUMENT ME!\r
- */\r
- public BinaryNode(Object element, BinaryNode parent, String name)\r
- {\r
- this.element = element;\r
- this.parent = parent;\r
- this.name = name;\r
+ /**\r
+ * Creates a new BinaryNode object.\r
+ *\r
+ * @param element DOCUMENT ME!\r
+ * @param parent DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public BinaryNode(Object element, BinaryNode parent, String name)\r
+ {\r
+ this.element = element;\r
+ this.parent = parent;\r
+ this.name = name;\r
\r
- left = right = null;\r
- }\r
+ left = right = null;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Object element()\r
- {\r
- return element;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Object element()\r
+ {\r
+ return element;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param v DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Object setElement(Object v)\r
- {\r
- return element = v;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Object setElement(Object v)\r
+ {\r
+ return element = v;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public BinaryNode left()\r
- {\r
- return left;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode left()\r
+ {\r
+ return left;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public BinaryNode setLeft(BinaryNode n)\r
- {\r
- return left = n;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param n DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode setLeft(BinaryNode n)\r
+ {\r
+ return left = n;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public BinaryNode right()\r
- {\r
- return right;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode right()\r
+ {\r
+ return right;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public BinaryNode setRight(BinaryNode n)\r
- {\r
- return right = n;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param n DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode setRight(BinaryNode n)\r
+ {\r
+ return right = n;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public BinaryNode parent()\r
- {\r
- return parent;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode parent()\r
+ {\r
+ return parent;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public BinaryNode setParent(BinaryNode n)\r
- {\r
- return parent = n;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param n DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode setParent(BinaryNode n)\r
+ {\r
+ return parent = n;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean isLeaf()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean isLeaf()\r
+ {\r
+ return (left == null) && (right == null);\r
+ }\r
+\r
+ /**\r
+ * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)\r
+ * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to NULL - you should use\r
+ * setChild(null), or detach() for this.\r
+ *\r
+ */\r
+ public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)\r
+ {\r
+ if (leftchild != null)\r
{\r
- return (left == null) && (right == null);\r
+ this.setLeft(leftchild);\r
+ leftchild.detach();\r
+ leftchild.setParent(this);\r
}\r
\r
- /**\r
- * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references)\r
- * a null parameter DOES NOT mean that the pointer to the corresponding child node is set to NULL - you should use\r
- * setChild(null), or detach() for this.\r
- *\r
- */\r
- public void SetChildren(BinaryNode leftchild, BinaryNode rightchild)\r
+ if (rightchild != null)\r
{\r
- if (leftchild != null)\r
- {\r
- this.setLeft(leftchild);\r
- leftchild.detach();\r
- leftchild.setParent(this);\r
- }\r
-\r
- if (rightchild != null)\r
- {\r
- this.setRight(rightchild);\r
- rightchild.detach();\r
- rightchild.setParent(this);\r
- }\r
+ this.setRight(rightchild);\r
+ rightchild.detach();\r
+ rightchild.setParent(this);\r
}\r
+ }\r
\r
- /**\r
- * Detaches the node from the binary tree, along with all its child nodes.\r
- * @return BinaryNode The detached node.\r
- */\r
- public BinaryNode detach()\r
+ /**\r
+ * Detaches the node from the binary tree, along with all its child nodes.\r
+ * @return BinaryNode The detached node.\r
+ */\r
+ public BinaryNode detach()\r
+ {\r
+ if (this.parent != null)\r
{\r
- if (this.parent != null)\r
+ if (this.parent.left == this)\r
+ {\r
+ this.parent.left = null;\r
+ }\r
+ else\r
+ {\r
+ if (this.parent.right == this)\r
{\r
- if (this.parent.left == this)\r
- {\r
- this.parent.left = null;\r
- }\r
- else\r
- {\r
- if (this.parent.right == this)\r
- {\r
- this.parent.right = null;\r
- }\r
- }\r
+ this.parent.right = null;\r
}\r
-\r
- this.parent = null;\r
-\r
- return this;\r
+ }\r
}\r
\r
- /**\r
- * Traverses up through the tree until a node with a free leftchild is discovered.\r
- * @return BinaryNode\r
- */\r
- public BinaryNode ascendLeft()\r
- {\r
- BinaryNode c = this;\r
+ this.parent = null;\r
\r
- do\r
- {\r
- c = c.parent();\r
- }\r
- while ((c != null) && (c.left() != null) && !c.left().isLeaf());\r
+ return this;\r
+ }\r
\r
- return c;\r
- }\r
+ /**\r
+ * Traverses up through the tree until a node with a free leftchild is discovered.\r
+ * @return BinaryNode\r
+ */\r
+ public BinaryNode ascendLeft()\r
+ {\r
+ BinaryNode c = this;\r
\r
- /**\r
- * Traverses up through the tree until a node with a free rightchild is discovered.\r
- * Jalview builds trees by descent on the left, so this may be unused.\r
- * @return BinaryNode\r
- */\r
- public BinaryNode ascendRight()\r
+ do\r
{\r
- BinaryNode c = this;\r
+ c = c.parent();\r
+ }\r
+ while ( (c != null) && (c.left() != null) && !c.left().isLeaf());\r
\r
- do\r
- {\r
- c = c.parent();\r
- }\r
- while ((c != null) && (c.right() != null) && !c.right().isLeaf());\r
+ return c;\r
+ }\r
\r
- return c;\r
- }\r
+ /**\r
+ * Traverses up through the tree until a node with a free rightchild is discovered.\r
+ * Jalview builds trees by descent on the left, so this may be unused.\r
+ * @return BinaryNode\r
+ */\r
+ public BinaryNode ascendRight()\r
+ {\r
+ BinaryNode c = this;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param name DOCUMENT ME!\r
- */\r
- public void setName(String name)\r
+ do\r
{\r
- this.name = name;\r
+ c = c.parent();\r
}\r
+ while ( (c != null) && (c.right() != null) && !c.right().isLeaf());\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String getName()\r
- {\r
- return this.name;\r
- }\r
+ return c;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param boot DOCUMENT ME!\r
- */\r
- public void setBootstrap(int boot)\r
- {\r
- this.bootstrap = boot;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public void setName(String name)\r
+ {\r
+ this.name = name;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getBootstrap()\r
- {\r
- return bootstrap;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return this.name;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param boot DOCUMENT ME!\r
+ */\r
+ public void setBootstrap(int boot)\r
+ {\r
+ this.bootstrap = boot;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getBootstrap()\r
+ {\r
+ return bootstrap;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff