[1573] | 1 | // SimpleTree.java |
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| 2 | // |
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| 3 | // (c) 1999-2001 PAL Development Core Team |
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| 4 | // |
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| 5 | // This package may be distributed under the |
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| 6 | // terms of the Lesser GNU General Public License (LGPL) |
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| 7 | |
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| 8 | |
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| 9 | package de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree; |
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| 10 | |
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| 11 | import java.io.PrintWriter; |
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| 12 | import java.io.Serializable; |
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| 13 | import java.io.StringWriter; |
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| 14 | import java.util.Hashtable; |
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| 15 | |
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| 16 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; |
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| 17 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.LabelMapping; |
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| 18 | |
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| 19 | |
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| 20 | |
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| 21 | /** |
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| 22 | * data structure for a binary/non-binary rooted/unrooted trees |
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| 23 | * |
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| 24 | * @version $Id: SimpleTree.java,v 1.19 2002/01/13 23:13:24 matt Exp $ |
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| 25 | * |
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| 26 | * @author Alexei Drummond |
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| 27 | * @author Korbinian Strimmer |
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| 28 | * |
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| 29 | */ |
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| 30 | public class SimpleTree implements Tree |
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| 31 | { |
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| 32 | // |
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| 33 | // This class has explicit serialization code so if you alter any fields please alter |
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| 34 | // the serialization code too (make sure you use a new version number - see readObject/writeObject |
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| 35 | // Thanks, Matthew |
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| 36 | |
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| 37 | // |
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| 38 | // Public stuff |
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| 39 | // |
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| 40 | |
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| 41 | // |
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| 42 | // Private stuff |
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| 43 | /** root node */ |
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| 44 | private Node root; |
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| 45 | |
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| 46 | /** list of internal nodes (including root) */ |
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| 47 | private Node[] internalNode = null; |
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| 48 | |
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| 49 | /** number of internal nodes (including root) */ |
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| 50 | private int numInternalNodes; |
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| 51 | |
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| 52 | /** list of external nodes */ |
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| 53 | private Node[] externalNode = null; |
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| 54 | |
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| 55 | /** number of external nodes */ |
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| 56 | private int numExternalNodes; |
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| 57 | |
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| 58 | /** attributes attached to this tree. */ |
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| 59 | private Hashtable[] attributes = null; |
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| 60 | |
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| 61 | |
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| 62 | |
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| 63 | /** constructor tree consisting solely of root node */ |
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| 64 | public SimpleTree() { |
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| 65 | |
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| 66 | // Default configuration |
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| 67 | root = new FengDoolittleNode(); |
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| 68 | root.setIdentifier(new Identifier("ROOT")); |
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| 69 | root.setBranchLength(0.0); |
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| 70 | root.setBranchLengthSE(0.0); |
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| 71 | } |
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| 72 | |
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| 73 | /** constructor taking a root node */ |
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| 74 | public SimpleTree(Node r) { |
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| 75 | |
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| 76 | root = r; |
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| 77 | createNodeList(); |
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| 78 | } |
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| 79 | |
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| 80 | /** clone constructor */ |
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| 81 | public SimpleTree(Tree tree) |
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| 82 | { |
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| 83 | root = new FengDoolittleNode(tree.getRoot()); |
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| 84 | createNodeList(); |
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| 85 | } |
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| 86 | |
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| 87 | /** clone constructor */ |
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| 88 | public SimpleTree(Tree tree, boolean keepIdentifiers) |
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| 89 | { |
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| 90 | root = new FengDoolittleNode(tree.getRoot(), keepIdentifiers); |
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| 91 | createNodeList(); |
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| 92 | } |
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| 93 | /** |
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| 94 | * clone constructor |
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| 95 | * @param lm - a label mapping use for translating the original label names into something else |
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| 96 | */ |
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| 97 | public SimpleTree(Tree tree, LabelMapping lm) |
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| 98 | { |
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| 99 | root = new FengDoolittleNode(tree.getRoot(), lm); |
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| 100 | createNodeList(); |
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| 101 | } |
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| 102 | |
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| 103 | |
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| 104 | |
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| 105 | /** |
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| 106 | * Returns the number of external nodes. |
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| 107 | */ |
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| 108 | public final int getExternalNodeCount() { |
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| 109 | if(externalNode==null) { |
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| 110 | createNodeList(); |
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| 111 | } |
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| 112 | return numExternalNodes; |
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| 113 | } |
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| 114 | |
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| 115 | /** |
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| 116 | * Returns the ith external node. |
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| 117 | */ |
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| 118 | public final Node getExternalNode(int i) { |
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| 119 | if(externalNode==null) { |
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| 120 | createNodeList(); |
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| 121 | } |
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| 122 | return externalNode[i]; |
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| 123 | } |
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| 124 | |
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| 125 | /** |
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| 126 | * Returns the number of internal nodes. |
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| 127 | */ |
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| 128 | public final int getInternalNodeCount() { |
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| 129 | if(internalNode==null) { |
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| 130 | createNodeList(); |
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| 131 | } |
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| 132 | return numInternalNodes; |
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| 133 | } |
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| 134 | |
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| 135 | /** |
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| 136 | * Returns the ith internal node. |
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| 137 | */ |
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| 138 | public final Node getInternalNode(int i) { |
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| 139 | if(internalNode==null) { |
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| 140 | createNodeList(); |
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| 141 | } |
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| 142 | return internalNode[i]; |
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| 143 | } |
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| 144 | |
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| 145 | /** |
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| 146 | * Returns the root node of this tree. |
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| 147 | */ |
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| 148 | public final Node getRoot() { |
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| 149 | return root; |
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| 150 | } |
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| 151 | |
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| 152 | /** |
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| 153 | * Set a new node as root node. |
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| 154 | */ |
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| 155 | public final void setRoot(Node r) { |
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| 156 | root = r; |
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| 157 | createNodeList(); |
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| 158 | } |
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| 159 | |
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| 160 | /** count and list external and internal nodes and |
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| 161 | compute heights of each node */ |
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| 162 | public void createNodeList() |
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| 163 | { |
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| 164 | numInternalNodes = 0; |
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| 165 | numExternalNodes = 0; |
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| 166 | Node node = root; |
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| 167 | do |
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| 168 | { |
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| 169 | node = NodeUtils.postorderSuccessor(node); |
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| 170 | if (node.isLeaf()) |
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| 171 | { |
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| 172 | node.setNumber(numExternalNodes); |
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| 173 | numExternalNodes++; |
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| 174 | } |
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| 175 | else |
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| 176 | { |
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| 177 | node.setNumber(numInternalNodes); |
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| 178 | numInternalNodes++; |
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| 179 | } |
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| 180 | } |
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| 181 | while(node != root); |
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| 182 | |
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| 183 | internalNode = new Node[numInternalNodes]; |
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| 184 | externalNode = new Node[numExternalNodes]; |
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| 185 | node = root; |
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| 186 | do |
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| 187 | { |
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| 188 | node = NodeUtils.postorderSuccessor(node); |
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| 189 | if (node.isLeaf()) |
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| 190 | { |
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| 191 | externalNode[node.getNumber()] = node; |
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| 192 | } |
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| 193 | else |
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| 194 | { |
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| 195 | internalNode[node.getNumber()] = node; |
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| 196 | } |
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| 197 | } |
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| 198 | while(node != root); |
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| 199 | |
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| 200 | // compute heights if it seems necessary |
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| 201 | if (root.getNodeHeight() == 0.0) { |
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| 202 | NodeUtils.lengths2Heights(root); |
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| 203 | } |
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| 204 | } |
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| 205 | |
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| 206 | /** |
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| 207 | * return node with number num (as displayed in ASCII tree) |
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| 208 | * |
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| 209 | * @param num number of node |
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| 210 | * |
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| 211 | * @return node |
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| 212 | */ |
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| 213 | public Node findNode(int num) |
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| 214 | { |
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| 215 | createNodeList(); |
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| 216 | |
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| 217 | if (num <= numExternalNodes) |
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| 218 | { |
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| 219 | return externalNode[num-1]; |
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| 220 | } |
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| 221 | else |
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| 222 | { |
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| 223 | return internalNode[num-1-numExternalNodes]; |
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| 224 | } |
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| 225 | } |
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| 226 | |
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| 227 | private int getIndex(Node node) { |
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| 228 | if (node.isLeaf()) return node.getNumber(); |
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| 229 | return getExternalNodeCount() + node.getNumber(); |
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| 230 | } |
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| 231 | |
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| 232 | /** |
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| 233 | * Sets an named attribute for a given node. |
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| 234 | * @param node the node whose attribute is being set. |
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| 235 | * @param name the name of the attribute. |
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| 236 | * @param value the new value of the attribute. |
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| 237 | */ |
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| 238 | public void setAttribute(Node node, String name, Object value) { |
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| 239 | if (node instanceof AttributeNode) { |
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| 240 | ((AttributeNode)node).setAttribute(name, value); |
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| 241 | } else { |
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| 242 | int index = getIndex(node); |
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| 243 | if (attributes == null) { |
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| 244 | attributes = new Hashtable[getExternalNodeCount() + getInternalNodeCount()]; |
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| 245 | } |
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| 246 | if (attributes[index] == null) { |
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| 247 | attributes[index] = new Hashtable(); |
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| 248 | } |
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| 249 | attributes[index].put(name, value); |
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| 250 | } |
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| 251 | } |
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| 252 | |
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| 253 | public String toString() { |
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| 254 | StringWriter sw = new StringWriter(); |
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| 255 | NodeUtils.printNH(new PrintWriter(sw), getRoot(), false, true, 0, true); |
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| 256 | sw.write(";"); |
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| 257 | return sw.toString(); |
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| 258 | } |
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| 259 | |
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| 260 | /** |
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| 261 | * @return an object representing the named attributed for the numbered node. |
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| 262 | * @param node the node being interrogated. |
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| 263 | * @param name the name of the attribute of interest. |
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| 264 | */ |
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| 265 | public Object getAttribute(Node node, String name) { |
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| 266 | if (node instanceof AttributeNode) { |
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| 267 | return ((AttributeNode)node).getAttribute(name); |
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| 268 | } else { |
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| 269 | int index = getIndex(node); |
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| 270 | if (attributes == null || attributes[index] == null) { |
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| 271 | return null; |
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| 272 | } |
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| 273 | return attributes[index].get(name); |
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| 274 | } |
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| 275 | } |
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| 276 | |
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| 277 | |
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| 278 | |
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| 279 | |
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| 280 | |
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| 281 | } |
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