[1573] | 1 | // Node.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 | /** |
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| 20 | * interface for a node (includes branch) in a binary/non-binary |
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| 21 | * rooted/unrooted tree |
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| 22 | * |
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| 23 | * @version $Id: Node.java,v 1.20 2001/11/20 07:35:44 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 | |
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| 30 | public interface Node { |
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| 31 | |
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| 32 | /** Returns the parent node of this node. */ |
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| 33 | Node getParent(); |
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| 34 | |
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| 35 | /** Set the parent node of this node. */ |
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| 36 | void setParent(Node node); |
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| 37 | |
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| 38 | /** Returns the sequence at this node */ |
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| 39 | NumberSequence getSequence(int index); |
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| 40 | |
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| 41 | /** Sets the sequence using an array of bytes. */ |
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| 42 | void setSequence(int index,NumberSequence seq); |
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| 43 | |
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| 44 | /** return the index of this node */ |
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| 45 | int getNumber(); |
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| 46 | |
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| 47 | /** set the index of this node */ |
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| 48 | void setNumber(int number); |
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| 49 | |
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| 50 | /** Get the length of the branch attaching this node to its parent. */ |
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| 51 | double getBranchLength(); |
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| 52 | |
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| 53 | /** Set the length of the branch attaching this node to its parent. */ |
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| 54 | void setBranchLength(double value); |
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| 55 | |
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| 56 | /** Get the length SE of the branch attaching this node to its parent. */ |
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| 57 | double getBranchLengthSE(); |
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| 58 | |
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| 59 | /** Set the length SE of the branch attaching this node to its parent. */ |
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| 60 | void setBranchLengthSE(double value); |
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| 61 | |
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| 62 | /** Get the height of this node relative to the most recent node. */ |
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| 63 | double getNodeHeight(); |
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| 64 | |
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| 65 | /** Set the height of this node relative to the most recent node. */ |
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| 66 | void setNodeHeight(double value); |
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| 67 | |
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| 68 | /** Returns the identifier for this node. */ |
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| 69 | Identifier getIdentifier(); |
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| 70 | |
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| 71 | /** Set identifier for this node. */ |
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| 72 | Identifier setIdentifier(Identifier id); |
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| 73 | |
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| 74 | /** |
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| 75 | * Returns the number of children this node has. |
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| 76 | */ |
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| 77 | int getChildCount(); |
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| 78 | |
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| 79 | /** |
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| 80 | * check whether this node is an external node |
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| 81 | * |
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| 82 | * @return result (true or false) |
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| 83 | */ |
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| 84 | boolean isLeaf(); |
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| 85 | |
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| 86 | /** |
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| 87 | * check whether this node is a root node |
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| 88 | * |
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| 89 | * @return result (true or false) |
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| 90 | */ |
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| 91 | boolean isRoot(); |
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| 92 | |
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| 93 | /** |
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| 94 | * get child node |
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| 95 | * |
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| 96 | * @param n number of child |
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| 97 | * |
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| 98 | * @return child node |
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| 99 | */ |
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| 100 | Node getChild(int n); |
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| 101 | |
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| 102 | /** |
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| 103 | * set child node |
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| 104 | * |
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| 105 | * @param n number |
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| 106 | * @node node new child node |
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| 107 | */ |
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| 108 | void setChild(int n, Node node); |
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| 109 | |
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| 110 | /** |
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| 111 | * add new child node |
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| 112 | * |
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| 113 | * @param c new child node |
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| 114 | */ |
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| 115 | void addChild(Node c); |
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| 116 | |
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| 117 | /** |
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| 118 | * add new child node (insertion at a specific position) |
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| 119 | * |
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| 120 | * @param c new child node |
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| 121 | + @param pos position |
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| 122 | */ |
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| 123 | void insertChild(Node c, int pos); |
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| 124 | |
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| 125 | |
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| 126 | /** |
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| 127 | * remove child |
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| 128 | * |
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| 129 | * @param n number of child to be removed |
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| 130 | */ |
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| 131 | Node removeChild(int n); |
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| 132 | |
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| 133 | |
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| 134 | ArrayList<NumberSequence> getSequences(); |
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| 135 | |
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[1585] | 136 | Node joinChildren( int n1, int n2); |
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[1573] | 137 | |
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[1577] | 138 | void addSequence(NumberSequence numberSequence); |
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[1573] | 139 | |
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[1583] | 140 | void setSequences(ArrayList<NumberSequence> alignSequences); |
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[1577] | 141 | |
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[1583] | 142 | |
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| 143 | |
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| 144 | |
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| 145 | |
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[1573] | 146 | |
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| 147 | } |
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