[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.StringWriter; |
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| 13 | |
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[1579] | 14 | |
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[1573] | 15 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; |
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| 16 | |
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| 17 | |
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| 18 | |
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[1579] | 19 | |
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[1573] | 20 | /** |
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| 21 | * data structure for a binary/non-binary rooted/unrooted trees |
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| 22 | * |
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| 23 | * @version $Id: SimpleTree.java,v 1.19 2002/01/13 23:13:24 matt Exp $ |
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| 24 | * |
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| 25 | * @author Alexei Drummond |
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| 26 | * @author Korbinian Strimmer |
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| 27 | * |
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| 28 | */ |
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| 29 | public class SimpleTree implements Tree |
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| 30 | { |
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| 31 | // |
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| 32 | // This class has explicit serialization code so if you alter any fields please alter |
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| 33 | // the serialization code too (make sure you use a new version number - see readObject/writeObject |
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| 34 | // Thanks, Matthew |
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| 35 | |
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| 36 | // |
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| 37 | // Public stuff |
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| 38 | // |
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| 39 | |
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| 40 | // |
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| 41 | // Private stuff |
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| 42 | /** root node */ |
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| 43 | private Node root; |
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| 44 | |
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| 45 | /** list of internal nodes (including root) */ |
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| 46 | private Node[] internalNode = null; |
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| 47 | |
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| 48 | /** number of internal nodes (including root) */ |
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| 49 | private int numInternalNodes; |
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| 50 | |
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| 51 | /** list of external nodes */ |
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| 52 | private Node[] externalNode = null; |
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| 53 | |
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| 54 | /** number of external nodes */ |
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| 55 | private int numExternalNodes; |
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| 56 | |
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| 57 | /** constructor tree consisting solely of root node */ |
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| 58 | public SimpleTree() { |
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| 59 | |
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| 60 | // Default configuration |
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| 61 | root = new FengDoolittleNode(); |
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| 62 | root.setIdentifier(new Identifier("ROOT")); |
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| 63 | root.setBranchLength(0.0); |
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| 64 | root.setBranchLengthSE(0.0); |
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| 65 | } |
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| 66 | |
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| 67 | /** constructor taking a root node */ |
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| 68 | public SimpleTree(Node r) { |
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| 69 | |
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| 70 | root = r; |
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| 71 | createNodeList(); |
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| 72 | } |
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| 73 | |
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| 74 | |
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| 75 | /** |
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| 76 | * Returns the number of external nodes. |
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| 77 | */ |
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| 78 | public final int getExternalNodeCount() { |
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| 79 | if(externalNode==null) { |
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| 80 | createNodeList(); |
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| 81 | } |
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| 82 | return numExternalNodes; |
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| 83 | } |
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| 84 | |
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| 85 | /** |
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| 86 | * Returns the ith external node. |
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| 87 | */ |
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| 88 | public final Node getExternalNode(int i) { |
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| 89 | if(externalNode==null) { |
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| 90 | createNodeList(); |
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| 91 | } |
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| 92 | return externalNode[i]; |
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| 93 | } |
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| 94 | |
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| 95 | /** |
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| 96 | * Returns the number of internal nodes. |
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| 97 | */ |
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| 98 | public final int getInternalNodeCount() { |
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| 99 | if(internalNode==null) { |
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| 100 | createNodeList(); |
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| 101 | } |
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| 102 | return numInternalNodes; |
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| 103 | } |
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| 104 | |
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| 105 | /** |
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| 106 | * Returns the ith internal node. |
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| 107 | */ |
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| 108 | public final Node getInternalNode(int i) { |
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| 109 | if(internalNode==null) { |
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| 110 | createNodeList(); |
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| 111 | } |
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| 112 | return internalNode[i]; |
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| 113 | } |
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| 114 | |
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| 115 | /** |
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| 116 | * Returns the root node of this tree. |
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| 117 | */ |
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| 118 | public final Node getRoot() { |
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| 119 | return root; |
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| 120 | } |
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| 121 | |
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| 122 | /** |
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| 123 | * Set a new node as root node. |
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| 124 | */ |
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| 125 | public final void setRoot(Node r) { |
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| 126 | root = r; |
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| 127 | createNodeList(); |
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| 128 | } |
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| 129 | |
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| 130 | /** count and list external and internal nodes and |
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| 131 | compute heights of each node */ |
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| 132 | public void createNodeList() |
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| 133 | { |
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| 134 | numInternalNodes = 0; |
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| 135 | numExternalNodes = 0; |
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| 136 | Node node = root; |
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| 137 | do |
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| 138 | { |
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| 139 | node = NodeUtils.postorderSuccessor(node); |
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| 140 | if (node.isLeaf()) |
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| 141 | { |
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| 142 | node.setNumber(numExternalNodes); |
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| 143 | numExternalNodes++; |
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| 144 | } |
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| 145 | else |
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| 146 | { |
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| 147 | node.setNumber(numInternalNodes); |
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| 148 | numInternalNodes++; |
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| 149 | } |
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| 150 | } |
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| 151 | while(node != root); |
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| 152 | |
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| 153 | internalNode = new Node[numInternalNodes]; |
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| 154 | externalNode = new Node[numExternalNodes]; |
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| 155 | node = root; |
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| 156 | do |
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| 157 | { |
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| 158 | node = NodeUtils.postorderSuccessor(node); |
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| 159 | if (node.isLeaf()) |
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| 160 | { |
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| 161 | externalNode[node.getNumber()] = node; |
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| 162 | } |
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| 163 | else |
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| 164 | { |
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| 165 | internalNode[node.getNumber()] = node; |
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| 166 | } |
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| 167 | } |
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| 168 | while(node != root); |
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| 169 | |
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| 170 | // compute heights if it seems necessary |
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| 171 | if (root.getNodeHeight() == 0.0) { |
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| 172 | NodeUtils.lengths2Heights(root); |
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| 173 | } |
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| 174 | } |
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| 175 | |
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| 176 | /** |
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| 177 | * return node with number num (as displayed in ASCII tree) |
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| 178 | * |
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| 179 | * @param num number of node |
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| 180 | * |
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| 181 | * @return node |
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| 182 | */ |
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| 183 | public Node findNode(int num) |
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| 184 | { |
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| 185 | createNodeList(); |
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| 186 | |
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| 187 | if (num <= numExternalNodes) |
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| 188 | { |
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| 189 | return externalNode[num-1]; |
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| 190 | } |
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| 191 | else |
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| 192 | { |
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| 193 | return internalNode[num-1-numExternalNodes]; |
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| 194 | } |
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| 195 | } |
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| 196 | |
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| 197 | |
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| 198 | |
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[1579] | 199 | |
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[1573] | 200 | public String toString() { |
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| 201 | StringWriter sw = new StringWriter(); |
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| 202 | NodeUtils.printNH(new PrintWriter(sw), getRoot(), false, true, 0, true); |
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| 203 | sw.write(";"); |
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| 204 | return sw.toString(); |
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| 205 | } |
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| 206 | |
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| 207 | |
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| 208 | |
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| 209 | |
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| 210 | |
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| 211 | |
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| 212 | } |
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