Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

07/14/14 23:27:01 (10 years ago)

Author:

rkrimmel

Message:

Removed parameters from alignmentalgorihm factory constructor and changed interface by adding a new align() method, which now gets all the data via parameter

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (4 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.util.ArrayList;
 import java.util.HashMap;
@@ -26 +25 @@
 import java.util.logging.Level;
 
-
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory;
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentGenerator;
@@ -62 +61 @@
  * </p>
  * <p>
-
+ * 
  * 
  * @author Patrick Harms
@@ -158 +157 @@
                 submat.generate();
 
+                ArrayList<NumberSequence> matchseqs = new ArrayList<NumberSequence>();
+                PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat);
                 
-                PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat);
-        
-                
+                for (int i=0; i< numberseqs.size();i++) {
+                        for(int j=0; j< numberseqs.size();j++) {
+                                if(i != j) {
+                                        ArrayList<ArrayList<NumberSequence>> tmp = alignments.get(i, j).getMatches();
+                                        for(Iterator<ArrayList<NumberSequence>> it = tmp.iterator();it.hasNext();) {
+                                                matchseqs.addAll(it.next());
+                                        }
+                                }
+                        }
+                }
+                AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch");
+                PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(numberseqs, submat);
+                UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat);
                 System.out.println(alignments.getDistanceMatrix());
                 //UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat);
                 
-                
+                for(Iterator<NumberSequence> it = guidetree.getRoot().getSequences().iterator();it.hasNext();) {
+                        NumberSequence tmp = (NumberSequence) it.next();
+                        tmp.printSequence();
+                }