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

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (6 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

@@ -2 +2 @@
 
 import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.List;
 
-import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.SubstitutionMatrix;
-
-public class SmithWatermanRepeated implements Alignment {
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
+
+public class SmithWatermanRepeated {
 
         /**
@@ -29 +31 @@
         private MatrixEntry[][] matrix;
 
-        
+
+        private List<NumberSequence> alignment;
         
         private float scoreThreshold;
@@ -50 +53 @@
                 
                 matrix = new MatrixEntry[length1+2][length2+1];
+                alignment = new ArrayList<NumberSequence>();
                 
                 for (int i = 0; i <= length1+1; i++) {
@@ -218 +222 @@
         }
         
-        public List<Match> traceback() {
+        
+        public void traceback() {
+                MatrixEntry tmp = matrix[length1+1][0];
+                
+                int aligned1[] = new int[length1+length2];
+                int aligned2[] = new int[length1+length2];
+                int count = 0;
+                do
+                {       
+                        if(count != 0)
+                        {
+                                aligned1[count] = tmp.getXvalue();
+                                aligned2[count] = tmp.getYvalue();
+                        }
+                        
+                        tmp = tmp.getPrevious();
+                        count++;
+                        
+                } while(tmp != null);
+
+                //reverse order
+                int reversed1[] = new int[count];
+                int reversed2[] = new int[count];
+                
+                for(int i = count; count > 0; count ++) {
+                        
+                }
+                
+                NumberSequence ns1 = new NumberSequence(reversed1.length);
+                NumberSequence ns2 = new NumberSequence(reversed2.length);
+                ns1.setSequence(reversed1);
+                ns2.setSequence(reversed2);
+                
+                alignment.add(ns1);
+                alignment.add(ns2);
+        }
+        
+        public void printAlignment() {
                 MatrixEntry tmp = matrix[length1+1][0];
                 String aligned1 = "";
@@ -259 +300 @@
                 System.out.println(aligned1);
                 System.out.println(aligned2);
-                return null;
         }
         
@@ -321 +361 @@
                 return matchList;
         }
+        
+
+        public List<NumberSequence> getAlignment() {
+                return alignment;
+        }
+
+        public void setAlignment(List<NumberSequence> alignment) {
+                this.alignment = alignment;
+        }
 
 }