Changeset 1572 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

06/23/14 00:05:33 (10 years ago)

Author:

rkrimmel

Message:

Added parts of the PAL library, implemented UPGMA Algoritm for Feng Doolittle guide tree

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (5 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -15 +15 @@
 package de.ugoe.cs.autoquest.tasktrees.temporalrelation;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -28 +31 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated;
-import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.ObjectDistanceSubstitionMatrix;
-import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.TriangleMatrix;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.TriangleMatrix;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
+import de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree.UPGMATree;
 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IIteration;
@@ -161 +166 @@
                 submat.generate();
 
-                TriangleMatrix sequenceDistances = new TriangleMatrix(numberseqs.size());
+                UPGMAMatrix sequenceDistances = new UPGMAMatrix(numberseqs.size());
                 sequenceDistances.initialize(Double.POSITIVE_INFINITY);
 
@@ -186 +191 @@
                                         SmithWatermanRepeated randomSequence = new SmithWatermanRepeated(
                                                         ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold);
-                                        //randomSequence.printDPMatrix();
-                                        //randomSequence.traceback();
                                         
                                         double score = twoSequences.getAlignmentScore();
@@ -235 +238 @@
                 }
                 System.out.println(sequenceDistances.toString());
+                UPGMATree guidetree = new UPGMATree(numberseqs, sequenceDistances);
+                System.out.println(guidetree.toString());
                 
                 do {