Changeset 1572 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.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

Location:

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

Files:

• . (moved) (moved from branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution)
• UPGMAMatrix.java (copied) (copied from branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/FitchMargoliashMatrix.java) (1 diff)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java

@@ -1 @@
-package de.ugoe.cs.autoquest.tasktrees.alignment.substitution;
+package de.ugoe.cs.autoquest.tasktrees.alignment.matrix;
 
-public class FitchMargoliashMatrix extends TriangleMatrix {
+import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier;
 
-        public FitchMargoliashMatrix(int size) {
+
+public class UPGMAMatrix extends TriangleMatrix {
+
+        public UPGMAMatrix(int size) {
                 super(size);
         }
-        
-        
+
+        public int size() {
+                return size;
+        }
+
+        public String toString() {
+                String result = "";
+                for (int i = 0; i < size; i++) {
+                        result = result + String.format("%8d", i);
+                }
+                result += "\n";
+                
+                for (int i = 0; i < size; i++) {
+                        for(int j = 0; j< size; j++) {
+                                if(i<j) {
+                                        if(Double.isInfinite(this.get(i,j))) {
+                                                result = result + " -------";
+                                        }
+                                        else {
+                                                result = result + String.format("%+8.2f",this.get(i,j));
+                                        }
+                                }
+                                else {
+                                        result = result + ("        ");
+                                }
+                        }
+                        result = result + "   " + i + "\n";
+                }
+                return result;
+        }
+