Changeset 1589 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

Timestamp:

07/09/14 12:13:13 (10 years ago)

Author:

rkrimmel

Message:

Refactoring and code cleanup

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java (modified) (8 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

@@ -15 +15 @@
 
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.logging.Level;
 
-import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm;
 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.algorithms.SmithWatermanRepeated;
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.PairwiseAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
@@ -48 +47 @@
          * @param m distance matrix
          */
-        public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, BinaryAlignmentStorage alignments, ObjectDistanceSubstitionMatrix submat)
+        public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, PairwiseAlignmentStorage alignments, ObjectDistanceSubstitionMatrix submat)
         {
                 if (alignments.getDistanceMatrix().size() < 2)
@@ -82 +81 @@
         //
         private ArrayList<NumberSequence> numberseqs;
-        private BinaryAlignmentStorage alignments;
+        private PairwiseAlignmentStorage alignments;
         private ObjectDistanceSubstitionMatrix submat;
         private int numClusters;
@@ -216 +215 @@
                         int seqCount1 = node1.getSequences().size();
                         int seqCount2 = node2.getSequences().size();
-                        
-                        /*
-                        for(int i = 0; i < seqCount1; i++) {
-                                for(int j = 0; j < seqCount2; j++) {
-                                        node1.getSequence(i).printSequence();
-                                        node2.getSequence(j).printSequence();
-                                }
-                        }
-                        */
+
                         
                         Console.traceln(Level.INFO,"Merging node " + node1.getIdentifier() + " with " + node2.getIdentifier());
@@ -237 +228 @@
                                 alignment.addAll(node1.getSequences());
                                 
-                                BinaryAlignmentStorage tempStorage = new BinaryAlignmentStorage(seqCount1,seqCount2);
+                                PairwiseAlignmentStorage tempStorage = new PairwiseAlignmentStorage(seqCount1,seqCount2);
                                 double maxScore = 0.0;
                                 int maxIndex = 0;
@@ -254 +245 @@
                         else if(seqCount1 == 1 && seqCount2 > 1) {
                                 alignment.addAll(node2.getSequences());
-                                BinaryAlignmentStorage tempStorage = new BinaryAlignmentStorage(seqCount1,seqCount2);
+                                PairwiseAlignmentStorage tempStorage = new PairwiseAlignmentStorage(seqCount1,seqCount2);
                                 double maxScore = 0.0;
                                 int maxIndex = 0;
@@ -270 +261 @@
                         //Align 2 groups
                         else if((seqCount1 > 1) && (seqCount2 > 1)){
-                                        BinaryAlignmentStorage tempStorage1 = new BinaryAlignmentStorage(seqCount2,1);
-                                        BinaryAlignmentStorage tempStorage2 = new BinaryAlignmentStorage(seqCount1,1);
+                                        PairwiseAlignmentStorage tempStorage1 = new PairwiseAlignmentStorage(seqCount2,1);
+                                        PairwiseAlignmentStorage tempStorage2 = new PairwiseAlignmentStorage(seqCount1,1);
                                         double maxScore1 = 0.0;
                                         double maxScore2 = 0.0;
@@ -334 +325 @@
                         (oc[aj]/ocsum)*jdist;
         }
+
+
+        public void printMultipleAlignment() {
+                for (Iterator<NumberSequence> it =  getRoot().getSequences().iterator(); it.hasNext();) {
+                        NumberSequence tmp  = it.next();
+                        tmp.printSequence();
+                }
+        }
 }