Changeset 1577 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees

Timestamp:

06/25/14 16:31:25 (10 years ago)

Author:

rkrimmel

Message:

Finished UPGMA implementation

Location:

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

Files:

• FengDoolittleNode.java (modified) (2 diffs)
• Node.java (modified) (1 diff)
• UPGMATree.java (modified) (3 diffs)

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

@@ -165 +165 @@
         }
 
+        public void addSequence(NumberSequence s) {
+                sequences.add(s);
+        }
+        
+        
         /**
          * Returns the sequence at this node, in the form of a String.
@@ -424 +429 @@
                 newNode.addChild(child1);
                 newNode.addChild(child2);
+                newNode.setIdentifier(new Identifier(child1.getIdentifier().getName() + " " + child2.getIdentifier().getName()));
+                System.out.println("Merging " + child1.getIdentifier() + " with " + child2.getIdentifier());
                 
                 if(newNode instanceof FengDoolittleNode) {

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

@@ -137 +137 @@
         void joinChildren( int n1, int n2);
 
+        void addSequence(NumberSequence numberSequence);
+
 
         

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

@@ -48 +48 @@
                 }
         
-                
+                this.numberseqs = numberseqs;
                 init(m);
 
@@ -104 +104 @@
                         Node tmp = NodeFactory.createNode();
                         tmp.setIdentifier(new Identifier(Integer.toString(i)));
-                        tmp.setSequence(0, numberseqs.get(i));
+                        tmp.addSequence(numberseqs.get(i));
                         getRoot().addChild(tmp);
                 }
@@ -147 +147 @@
                 abi = alias[besti];
                 abj = alias[bestj];
-                System.out.println("Found best pair: " + abi + "/" +abj + " - "+ besti+ "/"+bestj +" with distance " + dmin);
+                //System.out.println("Found best pair: " + abi + "/" +abj + " - "+ besti+ "/"+bestj +" with distance " + dmin);
                 
         }