[1573] | 1 | // SimpleNode.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 | |
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| 12 | import java.util.ArrayList; |
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| 13 | |
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| 14 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; |
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| 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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| 19 | * data structure for a node (includes branch) in a binary/non-binary |
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| 20 | * rooted/unrooted tree |
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| 21 | * |
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| 22 | * @version $Id: SimpleNode.java,v 1.20 2002/01/14 04:16:53 matt Exp $ |
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| 23 | * |
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| 24 | * @author Korbinian Strimmer |
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| 25 | * @author Alexei Drummond |
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| 26 | */ |
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| 27 | public class FengDoolittleNode implements Node { |
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| 28 | |
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| 29 | /** parent node */ |
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| 30 | private Node parent; |
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| 31 | |
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| 32 | /** number of node as displayed */ |
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| 33 | private int number; |
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| 34 | |
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| 35 | /** sequences associated with node */ |
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| 36 | private ArrayList<NumberSequence> sequences; |
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| 37 | |
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| 38 | /** length of branch to parent node */ |
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| 39 | private double length; |
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| 40 | |
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| 41 | /** standard error of length of branch to parent node */ |
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| 42 | private double lengthSE; |
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| 43 | |
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| 44 | /** height of this node */ |
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| 45 | private double height; |
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| 46 | |
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| 47 | /** identifier of node/associated branch */ |
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| 48 | private Identifier identifier; |
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| 49 | |
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| 50 | private Node[] child; |
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| 51 | |
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| 52 | // the following constructors should eventually become |
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| 53 | // "friendly" to prevent anyone calling them directly. |
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| 54 | // Instead, the NodeFactory should be used! |
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| 55 | |
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| 56 | /** constructor default node */ |
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| 57 | public FengDoolittleNode() |
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| 58 | { |
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| 59 | parent = null; |
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| 60 | child = null; |
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| 61 | length = 0.0; |
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| 62 | lengthSE = 0.0; |
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| 63 | height = 0.0; |
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| 64 | identifier = Identifier.ANONYMOUS; |
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| 65 | |
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| 66 | number = 0; |
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| 67 | sequences = new ArrayList<NumberSequence>(); |
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| 68 | } |
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| 69 | |
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| 70 | public FengDoolittleNode(String name, double branchLength) { |
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| 71 | this(); |
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| 72 | identifier = new Identifier(name); |
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| 73 | length = branchLength; |
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| 74 | } |
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| 75 | |
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| 76 | |
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| 77 | public void reset() |
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| 78 | { |
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| 79 | parent = null; |
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| 80 | child = null; |
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| 81 | length = 0.0; |
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| 82 | lengthSE = 0.0; |
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| 83 | height = 0.0; |
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| 84 | identifier = Identifier.ANONYMOUS; |
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| 85 | |
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| 86 | number = 0; |
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| 87 | sequences = null; |
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| 88 | } |
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| 89 | |
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| 90 | |
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| 91 | /** |
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| 92 | * Returns the parent node of this node. |
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| 93 | */ |
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| 94 | public final Node getParent() { |
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| 95 | return parent; |
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| 96 | } |
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| 97 | |
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| 98 | /** Set the parent node of this node. */ |
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| 99 | public void setParent(Node node) |
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| 100 | { |
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| 101 | parent = node; |
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| 102 | } |
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| 103 | |
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| 104 | /** |
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| 105 | * removes parent. |
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| 106 | */ |
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| 107 | public final void removeParent() { |
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| 108 | parent = null; |
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| 109 | } |
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| 110 | |
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[1577] | 111 | public void addSequence(NumberSequence s) { |
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| 112 | sequences.add(s); |
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| 113 | } |
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| 114 | |
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| 115 | |
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[1573] | 116 | /** |
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| 117 | * Returns the sequence at this node, in the form of a String. |
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| 118 | */ |
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| 119 | public String getSequenceString(int index) { |
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| 120 | return sequences.get(index).getSequence().toString(); |
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| 121 | } |
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| 122 | |
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| 123 | /** |
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| 124 | * Returns the sequence at this node, in the form of an array of bytes. |
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| 125 | */ |
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| 126 | public NumberSequence getSequence(int index) { |
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| 127 | return sequences.get(index); |
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| 128 | } |
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| 129 | |
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| 130 | /** |
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| 131 | * Sets the sequence at this node, in the form of an array of bytes. |
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| 132 | */ |
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| 133 | public void setSequence(int index,NumberSequence s) { |
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| 134 | sequences.set(index, s); |
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| 135 | } |
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| 136 | |
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| 137 | /** |
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| 138 | * Get the length of the branch attaching this node to its parent. |
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| 139 | */ |
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| 140 | public final double getBranchLength() { |
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| 141 | return length; |
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| 142 | } |
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| 143 | |
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| 144 | /** |
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| 145 | * Set the length of the branch attaching this node to its parent. |
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| 146 | */ |
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| 147 | public final void setBranchLength(double value) { |
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| 148 | length = value; |
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| 149 | } |
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| 150 | |
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| 151 | /** |
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| 152 | * Get the length SE of the branch attaching this node to its parent. |
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| 153 | */ |
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| 154 | public final double getBranchLengthSE() { |
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| 155 | return lengthSE; |
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| 156 | } |
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| 157 | |
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| 158 | /** |
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| 159 | * Set the length SE of the branch attaching this node to its parent. |
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| 160 | */ |
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| 161 | public final void setBranchLengthSE(double value) { |
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| 162 | lengthSE = value; |
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| 163 | } |
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| 164 | |
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| 165 | |
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| 166 | /** |
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| 167 | * Get the height of this node relative to the most recent node. |
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| 168 | */ |
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| 169 | public final double getNodeHeight() { |
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| 170 | return height; |
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| 171 | } |
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| 172 | |
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| 173 | /** |
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| 174 | * Set the height of this node relative to the most recent node. |
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| 175 | */ |
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| 176 | public final void setNodeHeight(double value) { |
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| 177 | height = Math.abs(value); |
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| 178 | } |
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| 179 | |
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| 180 | /** |
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| 181 | * Returns the identifier for this node. |
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| 182 | */ |
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| 183 | public final Identifier getIdentifier() { |
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| 184 | return identifier; |
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| 185 | } |
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| 186 | |
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| 187 | /** |
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| 188 | * Set identifier for this node. |
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| 189 | */ |
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| 190 | public final Identifier setIdentifier(Identifier id) { |
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| 191 | identifier = id; |
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| 192 | return identifier; |
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| 193 | } |
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| 194 | |
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| 195 | public void setNumber(int n) { |
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| 196 | number = n; |
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| 197 | } |
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| 198 | |
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| 199 | public int getNumber() { |
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| 200 | return number; |
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| 201 | } |
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| 202 | |
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| 203 | /** |
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| 204 | * get child node |
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| 205 | * |
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| 206 | * @param n number of child |
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| 207 | * |
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| 208 | * @return child node |
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| 209 | */ |
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| 210 | public Node getChild(int n) |
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| 211 | { |
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| 212 | return child[n]; |
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| 213 | } |
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| 214 | |
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| 215 | /** |
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| 216 | * set child node |
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| 217 | * |
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| 218 | * @param n number |
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| 219 | * @node node new child node |
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| 220 | */ |
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| 221 | public void setChild(int n, Node node) |
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| 222 | { |
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| 223 | child[n] = node; |
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| 224 | child[n].setParent(this); |
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| 225 | } |
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| 226 | |
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| 227 | /** |
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| 228 | * check whether this node is an internal node |
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| 229 | * |
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| 230 | * @return result (true or false) |
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| 231 | */ |
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| 232 | public boolean hasChildren() |
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| 233 | { |
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| 234 | return !isLeaf(); |
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| 235 | } |
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| 236 | |
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| 237 | /** |
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| 238 | * check whether this node is an external node |
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| 239 | * |
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| 240 | * @return result (true or false) |
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| 241 | */ |
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| 242 | public boolean isLeaf() { |
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| 243 | return (getChildCount() == 0); |
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| 244 | } |
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| 245 | |
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| 246 | /** |
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| 247 | * check whether this node is a root node |
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| 248 | * |
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| 249 | * @return result (true or false) |
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| 250 | */ |
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| 251 | public boolean isRoot() |
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| 252 | { |
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| 253 | if (parent == null) |
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| 254 | { |
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| 255 | return true; |
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| 256 | } |
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| 257 | else |
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| 258 | { |
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| 259 | return false; |
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| 260 | } |
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| 261 | } |
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| 262 | |
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| 263 | |
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| 264 | /** |
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| 265 | * add new child node |
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| 266 | * |
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| 267 | * @param n new child node |
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| 268 | */ |
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| 269 | public void addChild(Node n) |
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| 270 | { |
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| 271 | insertChild(n, getChildCount()); |
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| 272 | } |
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| 273 | |
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| 274 | /** |
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| 275 | * add new child node (insertion at a specific position) |
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| 276 | * |
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| 277 | * @param n new child node |
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| 278 | + @param pos position |
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| 279 | */ |
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| 280 | public void insertChild(Node n, int pos) |
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| 281 | { |
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| 282 | int numChildren = getChildCount(); |
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| 283 | |
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| 284 | Node[] newChild = new Node[numChildren + 1]; |
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| 285 | |
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| 286 | for (int i = 0; i < pos; i++) |
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| 287 | { |
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| 288 | newChild[i] = child[i]; |
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| 289 | } |
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| 290 | newChild[pos] = n; |
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| 291 | for (int i = pos; i < numChildren; i++) |
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| 292 | { |
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| 293 | newChild[i+1] = child[i]; |
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| 294 | } |
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| 295 | |
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| 296 | child = newChild; |
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| 297 | |
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| 298 | n.setParent(this); |
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| 299 | } |
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| 300 | |
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| 301 | |
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| 302 | /** |
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| 303 | * remove child |
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| 304 | * |
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| 305 | * @param n number of child to be removed |
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| 306 | */ |
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| 307 | public Node removeChild(int n) |
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| 308 | { |
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| 309 | int numChildren = getChildCount(); |
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| 310 | |
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| 311 | if (n >= numChildren) |
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| 312 | { |
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| 313 | throw new IllegalArgumentException("Nonexistent child"); |
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| 314 | } |
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| 315 | Node[] newChild = new Node[numChildren-1]; |
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| 316 | |
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| 317 | for (int i = 0; i < n; i++) |
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| 318 | { |
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| 319 | newChild[i] = child[i]; |
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| 320 | } |
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| 321 | |
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| 322 | for (int i = n; i < numChildren-1; i++) |
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| 323 | { |
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| 324 | newChild[i] = child[i+1]; |
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| 325 | } |
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| 326 | |
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| 327 | Node removed = child[n]; |
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| 328 | |
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| 329 | //remove parent link from removed child! |
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| 330 | removed.setParent(null); |
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| 331 | |
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| 332 | child = newChild; |
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| 333 | |
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| 334 | return removed; |
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| 335 | } |
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| 336 | |
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| 337 | |
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| 338 | |
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| 339 | /** |
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| 340 | * join two children, introducing a new node/branch in the tree |
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| 341 | * that replaces the first child |
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| 342 | * |
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| 343 | * @param n1 number of first child |
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| 344 | * @param n2 number of second child |
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| 345 | */ |
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| 346 | public void joinChildren( int n1, int n2) { |
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| 347 | |
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| 348 | if (n1 == n2) { |
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| 349 | throw new IllegalArgumentException("CHILDREN MUST BE DIFFERENT"); |
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| 350 | } |
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| 351 | |
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| 352 | int c1, c2; |
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| 353 | if (n2 < n1) |
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| 354 | { |
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| 355 | c1 = n2; |
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| 356 | c2 = n1; |
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| 357 | } |
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| 358 | else |
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| 359 | { |
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| 360 | c1 = n1; |
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| 361 | c2 = n2; |
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| 362 | } |
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| 363 | |
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| 364 | Node newNode = NodeFactory.createNode(); |
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| 365 | |
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| 366 | Node child1 = this.getChild(c1); |
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| 367 | Node child2 = this.getChild(c2); |
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| 368 | |
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| 369 | setChild(c1, newNode); |
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| 370 | newNode.setParent(this); |
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| 371 | this.removeChild(c2); // now parent of child2 = null |
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| 372 | |
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| 373 | newNode.addChild(child1); |
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| 374 | newNode.addChild(child2); |
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[1577] | 375 | newNode.setIdentifier(new Identifier(child1.getIdentifier().getName() + " " + child2.getIdentifier().getName())); |
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[1580] | 376 | //System.out.println("Merging " + child1.getIdentifier() + " with " + child2.getIdentifier()); |
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[1573] | 377 | |
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| 378 | if(newNode instanceof FengDoolittleNode) { |
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| 379 | ((FengDoolittleNode) newNode).alignSequences(); |
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| 380 | } |
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| 381 | |
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| 382 | } |
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| 383 | |
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| 384 | |
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| 385 | /** |
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| 386 | * Returns the number of children this node has. |
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| 387 | */ |
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| 388 | public final int getChildCount() { |
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| 389 | if (child == null) return 0; |
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| 390 | return child.length; |
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| 391 | } |
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| 392 | |
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| 393 | |
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| 394 | public ArrayList<NumberSequence> getSequences() { |
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| 395 | return sequences; |
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| 396 | } |
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| 397 | |
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| 398 | |
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| 399 | private void alignSequences() { |
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| 400 | if(this.getChildCount()<3) { |
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| 401 | |
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| 402 | Node node1 = getChild(0); |
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| 403 | Node node2 = getChild(1); |
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| 404 | |
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| 405 | int seqCount1 = node1.getSequences().size(); |
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| 406 | int seqCount2 = node2.getSequences().size(); |
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| 407 | |
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| 408 | |
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| 409 | |
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| 410 | } |
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| 411 | else { |
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[1580] | 412 | System.out.println("This should never happen, it's a binary tree."); |
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[1573] | 413 | } |
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| 414 | |
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| 415 | } |
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| 416 | |
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| 417 | |
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| 418 | } |
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