[1573] | 1 | // UPGMATree.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 | // Known bugs and limitations: |
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| 9 | // - computational complexity O(numSeqs^3) |
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| 10 | // (this could be brought down to O(numSeqs^2) |
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| 11 | // but this needs more clever programming ...) |
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| 12 | |
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| 13 | |
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| 14 | package de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree; |
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| 15 | |
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| 16 | import java.util.ArrayList; |
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[1585] | 17 | import java.util.logging.Level; |
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[1573] | 18 | |
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[1586] | 19 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm; |
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| 20 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory; |
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[1573] | 21 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; |
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[1585] | 22 | import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated; |
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[1584] | 23 | import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage; |
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[1585] | 24 | import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix; |
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[1573] | 25 | import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix; |
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| 26 | import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; |
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[1585] | 27 | import de.ugoe.cs.util.console.Console; |
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[1573] | 28 | |
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| 29 | |
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| 30 | /** |
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| 31 | * constructs a UPGMA tree from pairwise distances |
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| 32 | * |
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| 33 | * @version $Id: UPGMATree.java,v 1.9 2001/07/13 14:39:13 korbinian Exp $ |
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| 34 | * |
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| 35 | * @author Korbinian Strimmer |
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| 36 | * @author Alexei Drummond |
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| 37 | */ |
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[1579] | 38 | public class UPGMAAligningTree extends SimpleTree |
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[1573] | 39 | { |
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| 40 | // |
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| 41 | // Public stuff |
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| 42 | // |
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| 43 | |
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| 44 | /** |
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| 45 | * constructor UPGMA tree |
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| 46 | * @param numberseqs |
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| 47 | * |
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| 48 | * @param m distance matrix |
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| 49 | */ |
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[1585] | 50 | public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, BinaryAlignmentStorage alignments, ObjectDistanceSubstitionMatrix submat) |
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[1573] | 51 | { |
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[1584] | 52 | if (alignments.getDistanceMatrix().size() < 2) |
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[1573] | 53 | { |
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| 54 | new IllegalArgumentException("LESS THAN 2 TAXA IN DISTANCE MATRIX"); |
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| 55 | } |
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| 56 | |
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[1577] | 57 | this.numberseqs = numberseqs; |
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[1584] | 58 | this.alignments = alignments; |
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[1585] | 59 | this.submat = submat; |
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[1584] | 60 | init(alignments.getDistanceMatrix()); |
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[1573] | 61 | |
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| 62 | while (true) |
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| 63 | { |
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| 64 | findNextPair(); |
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| 65 | newBranchLengths(); |
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| 66 | |
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| 67 | if (numClusters == 2) |
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| 68 | { |
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| 69 | break; |
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| 70 | } |
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| 71 | |
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| 72 | newCluster(); |
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| 73 | } |
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| 74 | |
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| 75 | finish(); |
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| 76 | createNodeList(); |
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| 77 | } |
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| 78 | |
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| 79 | |
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| 80 | // |
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| 81 | // Private stuff |
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| 82 | // |
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| 83 | private ArrayList<NumberSequence> numberseqs; |
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[1584] | 84 | private BinaryAlignmentStorage alignments; |
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[1585] | 85 | private ObjectDistanceSubstitionMatrix submat; |
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[1573] | 86 | private int numClusters; |
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| 87 | private int besti, abi; |
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| 88 | private int bestj, abj; |
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| 89 | private int[] alias; |
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| 90 | private double[][] distance; |
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| 91 | |
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| 92 | private double[] height; |
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| 93 | private int[] oc; |
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| 94 | |
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| 95 | private double getDist(int a, int b) |
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| 96 | { |
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| 97 | return distance[alias[a]][alias[b]]; |
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| 98 | } |
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| 99 | |
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| 100 | private void init(UPGMAMatrix m) |
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| 101 | { |
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| 102 | numClusters = m.size(); |
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| 103 | |
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| 104 | distance = new double[numClusters][numClusters]; |
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| 105 | for (int i = 0; i < numClusters; i++) |
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| 106 | { |
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| 107 | for (int j = 0; j < numClusters; j++) |
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| 108 | { |
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| 109 | distance[i][j] = m.get(i,j); |
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| 110 | } |
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| 111 | } |
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| 112 | |
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| 113 | for (int i = 0; i < numClusters; i++) |
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| 114 | { |
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| 115 | Node tmp = NodeFactory.createNode(); |
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| 116 | tmp.setIdentifier(new Identifier(Integer.toString(i))); |
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[1585] | 117 | tmp.setNumber(i); |
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[1577] | 118 | tmp.addSequence(numberseqs.get(i)); |
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[1573] | 119 | getRoot().addChild(tmp); |
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| 120 | } |
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| 121 | |
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| 122 | alias = new int[numClusters]; |
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| 123 | for (int i = 0; i < numClusters; i++) |
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| 124 | { |
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| 125 | alias[i] = i; |
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| 126 | } |
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| 127 | |
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| 128 | height = new double[numClusters]; |
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| 129 | oc = new int[numClusters]; |
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| 130 | for (int i = 0; i < numClusters; i++) |
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| 131 | { |
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| 132 | height[i] = 0.0; |
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| 133 | oc[i] = 1; |
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| 134 | } |
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| 135 | } |
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| 136 | |
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| 137 | private void finish() |
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| 138 | { |
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[1587] | 139 | this.getRoot().setSequences(alignSequences(this.getRoot())); |
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[1573] | 140 | distance = null; |
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| 141 | } |
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| 142 | |
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| 143 | private void findNextPair() |
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| 144 | { |
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| 145 | besti = 0; |
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| 146 | bestj = 1; |
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| 147 | double dmin = getDist(0, 1); |
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| 148 | for (int i = 0; i < numClusters-1; i++) |
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| 149 | { |
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| 150 | for (int j = i+1; j < numClusters; j++) |
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| 151 | { |
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| 152 | if (getDist(i, j) < dmin) |
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| 153 | { |
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| 154 | dmin = getDist(i, j); |
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| 155 | besti = i; |
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| 156 | bestj = j; |
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| 157 | } |
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| 158 | } |
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| 159 | } |
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| 160 | abi = alias[besti]; |
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| 161 | abj = alias[bestj]; |
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[1577] | 162 | //System.out.println("Found best pair: " + abi + "/" +abj + " - "+ besti+ "/"+bestj +" with distance " + dmin); |
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[1573] | 163 | |
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| 164 | } |
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| 165 | |
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| 166 | private void newBranchLengths() |
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| 167 | { |
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| 168 | double dij = getDist(besti, bestj); |
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| 169 | |
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| 170 | getRoot().getChild(besti).setBranchLength(dij/2.0-height[abi]); |
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| 171 | getRoot().getChild(bestj).setBranchLength(dij/2.0-height[abj]); |
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| 172 | } |
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| 173 | |
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| 174 | private void newCluster() |
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| 175 | { |
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| 176 | // Update distances |
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| 177 | for (int k = 0; k < numClusters; k++) |
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| 178 | { |
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| 179 | if (k != besti && k != bestj) |
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| 180 | { |
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| 181 | int ak = alias[k]; |
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| 182 | double updated = updatedDistance(besti,bestj,k); |
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| 183 | distance[ak][abi] = distance[abi][ak] = updated; |
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| 184 | } |
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| 185 | } |
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| 186 | distance[abi][abi] = 0.0; |
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| 187 | |
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| 188 | // Update UPGMA variables |
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| 189 | height[abi] = getDist(besti, bestj)/2.0; |
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| 190 | oc[abi] += oc[abj]; |
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| 191 | |
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| 192 | // Index besti now represent the new cluster |
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[1585] | 193 | Node newNode = getRoot().joinChildren(besti, bestj); |
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[1573] | 194 | |
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[1585] | 195 | if(newNode instanceof FengDoolittleNode) { |
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| 196 | newNode.setSequences(alignSequences(newNode)); |
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| 197 | } |
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| 198 | |
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[1573] | 199 | // Update alias |
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| 200 | for (int i = bestj; i < numClusters-1; i++) |
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| 201 | { |
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| 202 | alias[i] = alias[i+1]; |
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| 203 | } |
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| 204 | |
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| 205 | numClusters--; |
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| 206 | } |
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[1585] | 207 | |
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| 208 | |
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| 209 | public ArrayList<NumberSequence> alignSequences(Node parent) { |
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| 210 | ArrayList<NumberSequence> alignment = new ArrayList<NumberSequence>(); |
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| 211 | if(parent.getChildCount()<3) { |
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| 212 | |
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| 213 | Node node1 = parent.getChild(0); |
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| 214 | Node node2 = parent.getChild(1); |
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| 215 | |
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| 216 | int seqCount1 = node1.getSequences().size(); |
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| 217 | int seqCount2 = node2.getSequences().size(); |
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[1587] | 218 | |
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| 219 | for(int i = 0; i < seqCount1; i++) { |
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| 220 | for(int j = 0; j < seqCount2; j++) { |
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| 221 | node1.getSequence(i).printSequence(); |
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| 222 | node2.getSequence(j).printSequence(); |
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| 223 | } |
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| 224 | } |
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| 225 | |
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[1585] | 226 | Console.traceln(Level.INFO,"Merging node " + node1.getIdentifier() + " with " + node2.getIdentifier()); |
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| 227 | //Console.println("SeqCount1: " + seqCount1 + " seqCount2 " + seqCount2); |
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| 228 | //Align 2 sequences |
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| 229 | if(seqCount1 == 1 && seqCount2 == 1) { |
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| 230 | alignment = (alignments.get(node1.getNumber(), node2.getNumber())).getAlignment(); |
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[1587] | 231 | |
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[1585] | 232 | } |
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| 233 | //Align a sequence to a group |
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| 234 | else if( seqCount1 > 1 && seqCount2 == 1) { |
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| 235 | alignment.addAll(node1.getSequences()); |
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| 236 | |
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| 237 | BinaryAlignmentStorage tempStorage = new BinaryAlignmentStorage(seqCount1,seqCount2); |
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| 238 | double maxScore = 0.0; |
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| 239 | int maxIndex = 0; |
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| 240 | for(int i=0;i<seqCount1;i++) { |
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[1586] | 241 | tempStorage.set(i, 1, AlignmentAlgorithmFactory.create(node1.getSequence(i).getSequence(), node2.getSequence(0).getSequence() , submat, 5)); |
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[1585] | 242 | if(maxScore < tempStorage.get(i, 1).getAlignmentScore()) { |
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| 243 | maxScore = tempStorage.get(i, 1).getAlignmentScore(); |
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| 244 | maxIndex = i; |
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| 245 | } |
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| 246 | } |
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[1586] | 247 | //if(maxScore > 0) |
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[1587] | 248 | |
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[1585] | 249 | alignment.add(tempStorage.get(maxIndex, 1).getAlignment().get(1)); |
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| 250 | } |
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| 251 | //Align a sequence to a group |
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| 252 | else if(seqCount1 == 1 && seqCount2 > 1) { |
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| 253 | alignment.addAll(node2.getSequences()); |
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| 254 | BinaryAlignmentStorage tempStorage = new BinaryAlignmentStorage(seqCount1,seqCount2); |
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| 255 | double maxScore = 0.0; |
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| 256 | int maxIndex = 0; |
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| 257 | for(int i=0;i<seqCount2;i++) { |
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[1586] | 258 | tempStorage.set(1, i, AlignmentAlgorithmFactory.create(node2.getSequence(i).getSequence(), node1.getSequence(0).getSequence() , submat, 5)); |
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[1585] | 259 | if(maxScore < tempStorage.get(1, i).getAlignmentScore()) { |
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| 260 | maxScore = tempStorage.get(1, i).getAlignmentScore(); |
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| 261 | maxIndex = i; |
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| 262 | } |
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| 263 | } |
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[1586] | 264 | //if(maxScore > 0) |
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[1587] | 265 | |
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[1585] | 266 | alignment.add(tempStorage.get(1,maxIndex).getAlignment().get(1)); |
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| 267 | } |
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| 268 | //Align 2 groups |
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| 269 | else if((seqCount1 > 1) && (seqCount2 > 1)){ |
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| 270 | BinaryAlignmentStorage tempStorage1 = new BinaryAlignmentStorage(seqCount2,1); |
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| 271 | BinaryAlignmentStorage tempStorage2 = new BinaryAlignmentStorage(seqCount1,1); |
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| 272 | double maxScore1 = 0.0; |
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| 273 | double maxScore2 = 0.0; |
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| 274 | int maxIndex1 = 0; |
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| 275 | int maxIndex2 = 0; |
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| 276 | for(int i=0;i<seqCount1;i++) { |
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| 277 | for(int j=0;j<seqCount2;j++) { |
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[1586] | 278 | tempStorage1.set(j, 0, AlignmentAlgorithmFactory.create(node1.getSequence(i).getSequence(), node2.getSequence(j).getSequence() , submat, 5)); |
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[1585] | 279 | if(maxScore1 < tempStorage1.get(j, 0).getAlignmentScore()) { |
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| 280 | maxScore1 = tempStorage1.get(j, 0).getAlignmentScore(); |
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| 281 | maxIndex1 = j; |
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| 282 | } |
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| 283 | } |
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[1586] | 284 | //if(maxScore1 > 0) |
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[1585] | 285 | alignment.add(tempStorage1.get(maxIndex1,0).getAlignment().get(0)); |
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| 286 | } |
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| 287 | for(int i=0; i<seqCount2;i++) { |
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| 288 | for (int j=0;j<seqCount1;j++) { |
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[1586] | 289 | tempStorage2.set(j, 0, AlignmentAlgorithmFactory.create(node2.getSequence(i).getSequence(),node1.getSequence(j).getSequence(),submat,5)); |
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[1585] | 290 | if(maxScore2 < tempStorage2.get(j, 0).getAlignmentScore()) { |
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| 291 | maxScore2 = tempStorage2.get(j, 0).getAlignmentScore(); |
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| 292 | maxIndex2 = j; |
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| 293 | } |
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| 294 | } |
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[1586] | 295 | //if(maxScore2 > 0) |
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[1585] | 296 | alignment.add(tempStorage2.get(maxIndex2,0).getAlignment().get(0)); |
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| 297 | } |
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| 298 | |
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| 299 | } |
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| 300 | else { |
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| 301 | Console.traceln(Level.WARNING,"No sequences to align while merging " + node1.getIdentifier() + " with " + node2.getIdentifier()); |
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| 302 | } |
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| 303 | } |
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| 304 | else { |
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| 305 | Console.traceln(Level.WARNING,"More than 2 children! This should never happen, it's a binary tree."); |
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| 306 | } |
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| 307 | return alignment; |
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| 308 | } |
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[1573] | 309 | |
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| 310 | |
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| 311 | /** |
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| 312 | * compute updated distance between the new cluster (i,j) |
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| 313 | * to any other cluster k |
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| 314 | */ |
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| 315 | private double updatedDistance(int i, int j, int k) |
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| 316 | { |
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| 317 | int ai = alias[i]; |
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| 318 | int aj = alias[j]; |
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| 319 | |
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| 320 | double ocsum = (double) (oc[ai]+oc[aj]); |
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| 321 | double idist = getDist(k,i); |
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| 322 | double jdist = getDist(k,j); |
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| 323 | //TODO: Dirty hack to deal with infinity, insert proper solution here |
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| 324 | if(Double.isInfinite(idist)) { |
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| 325 | idist = 100; |
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| 326 | } |
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| 327 | if(Double.isInfinite(jdist)) { |
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| 328 | jdist = 100; |
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| 329 | } |
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| 330 | |
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| 331 | return (oc[ai]/ocsum)*idist+ |
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| 332 | (oc[aj]/ocsum)*jdist; |
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| 333 | } |
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| 334 | } |
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[1585] | 335 | |
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| 336 | |
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