- Timestamp:
- 06/23/14 00:05:33 (10 years ago)
- File:
-
- 1 edited
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branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java
r1570 r1572 15 15 package de.ugoe.cs.autoquest.tasktrees.temporalrelation; 16 16 17 import java.io.File; 18 import java.io.FileNotFoundException; 19 import java.io.PrintWriter; 17 20 import java.util.ArrayList; 18 21 import java.util.HashMap; … … 28 31 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; 29 32 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated; 30 import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.ObjectDistanceSubstitionMatrix; 31 import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.TriangleMatrix; 33 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix; 34 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.TriangleMatrix; 35 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix; 36 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree.UPGMATree; 32 37 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality; 33 38 import de.ugoe.cs.autoquest.tasktrees.treeifc.IIteration; … … 161 166 submat.generate(); 162 167 163 TriangleMatrix sequenceDistances = new TriangleMatrix(numberseqs.size());168 UPGMAMatrix sequenceDistances = new UPGMAMatrix(numberseqs.size()); 164 169 sequenceDistances.initialize(Double.POSITIVE_INFINITY); 165 170 … … 186 191 SmithWatermanRepeated randomSequence = new SmithWatermanRepeated( 187 192 ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold); 188 //randomSequence.printDPMatrix();189 //randomSequence.traceback();190 193 191 194 double score = twoSequences.getAlignmentScore(); … … 235 238 } 236 239 System.out.println(sequenceDistances.toString()); 240 UPGMATree guidetree = new UPGMATree(numberseqs, sequenceDistances); 241 System.out.println(guidetree.toString()); 237 242 238 243 do {
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