Changeset 1584 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java

Timestamp:

06/27/14 15:25:25 (10 years ago)

Author:

rkrimmel

Message:

Some refactoring for storing the initial alignments so we don't need to do them again.

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java (modified) (4 diffs)

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

@@ -17 +17 @@
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.BinaryAlignmentStorage;
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.UPGMAMatrix;
 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier;
@@ -41 +42 @@
          * @param m distance matrix
          */
-        public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, UPGMAMatrix m)
-        {
-                if (m.size() < 2)
+        public UPGMAAligningTree(ArrayList<NumberSequence> numberseqs, BinaryAlignmentStorage alignments)
+        {
+                if (alignments.getDistanceMatrix().size() < 2)
                 {
                         new IllegalArgumentException("LESS THAN 2 TAXA IN DISTANCE MATRIX");
@@ -49 +50 @@
         
                 this.numberseqs = numberseqs;
-                init(m);
+                this.alignments = alignments;
+                init(alignments.getDistanceMatrix());
 
                 while (true)
@@ -73 +75 @@
         //
         private ArrayList<NumberSequence> numberseqs;
+        private BinaryAlignmentStorage alignments;
         private int numClusters;
         private int besti, abi;