-/*
-* 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
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\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
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class BinaryNode\r
+{\r
+ Object element;\r
+ String name;\r
+ BinaryNode left;\r
+ BinaryNode right;\r
+ BinaryNode parent;\r
\r
- public BinaryNode(Object element, BinaryNode parent, String name) {\r
- this.element = element;\r
- this.parent = parent;\r
- this.name = name;\r
+ /** DOCUMENT ME!! */\r
+ public int bootstrap;\r
\r
- left = right = null;\r
- }\r
+ /**\r
+ * Creates a new BinaryNode object.\r
+ */\r
+ public BinaryNode()\r
+ {\r
+ left = right = parent = null;\r
+ bootstrap = 0;\r
+ }\r
\r
- public Object element() {\r
- return element;\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
- public Object setElement(Object v) {\r
- return element = v;\r
- }\r
+ left = right = null;\r
+ }\r
\r
- public BinaryNode left() {\r
- return left;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Object element()\r
+ {\r
+ return element;\r
+ }\r
\r
- public BinaryNode setLeft(BinaryNode n) {\r
- return left = n;\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
- public BinaryNode right() {\r
- return right;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode left()\r
+ {\r
+ return left;\r
+ }\r
\r
- public BinaryNode setRight(BinaryNode n) {\r
- return right = 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
- public BinaryNode parent() {\r
- return parent;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode right()\r
+ {\r
+ return right;\r
+ }\r
\r
- public BinaryNode setParent(BinaryNode n) {\r
- return parent = 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
- public boolean isLeaf() {\r
- return (left == null) && (right == null);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public BinaryNode parent()\r
+ {\r
+ return parent;\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
+ * 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
- if (rightchild != null) {\r
- this.setRight(rightchild);\r
- rightchild.detach();\r
- rightchild.setParent(this);\r
- }\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean isLeaf()\r
+ {\r
+ return (left == null) && (right == null);\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
+ * 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
+ this.setLeft(leftchild);\r
+ leftchild.detach();\r
+ leftchild.setParent(this);\r
+ }\r
\r
- this.parent = null;\r
+ if (rightchild != null)\r
+ {\r
+ this.setRight(rightchild);\r
+ rightchild.detach();\r
+ rightchild.setParent(this);\r
+ }\r
+ }\r
\r
- return this;\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.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
}\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
+ this.parent = null;\r
\r
- do {\r
- c = c.parent();\r
- } while ((c != null) && (c.left() != null) && !c.left().isLeaf());\r
+ return this;\r
+ }\r
\r
- return c;\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
+ do\r
+ {\r
+ c = c.parent();\r
}\r
+ while ( (c != null) && (c.left() != null) && !c.left().isLeaf());\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
+ return c;\r
+ }\r
\r
- do {\r
- c = c.parent();\r
- } while ((c != null) && (c.right() != null) && !c.right().isLeaf());\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
- return c;\r
+ do\r
+ {\r
+ c = c.parent();\r
}\r
+ while ( (c != null) && (c.right() != null) && !c.right().isLeaf());\r
\r
- public void setName(String name) {\r
- this.name = name;\r
- }\r
+ return c;\r
+ }\r
\r
- public String getName() {\r
- return this.name;\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
- public void setBootstrap(int boot) {\r
- this.bootstrap = boot;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return this.name;\r
+ }\r
\r
- public int getBootstrap() {\r
- return bootstrap;\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