Changeset 1616

Timestamp:

07/15/14 20:54:58 (10 years ago)

Author:

rkrimmel

Message:

Small fixes

Location:

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

Files:

• AlignmentAlgorithmFactory.java (modified) (2 diffs)
• NeedlemanWunsch.java (modified) (2 diffs)

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

@@ -1 +1 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
 
-import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
-
-import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
 
 public class AlignmentAlgorithmFactory {
@@ -25 +21 @@
                         
                 } catch (ClassNotFoundException | SecurityException | InstantiationException | IllegalAccessException | IllegalArgumentException e) {
-                        // TODO Auto-generated catch block
                         e.printStackTrace();
                 }

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

@@ -187 +187 @@
         }
 
-        public void printAlignment() {
-                MatrixEntry tmp = matrix[length1][length2];
-                String aligned1 = "";
-                String aligned2 = "";
-                int count = 0;
-                do {
-                        System.out.println(tmp);
-                        String append1 = "";
-                        String append2 = "";
-
-                        if (tmp.getXvalue() == Constants.GAP_SYMBOL) {
-                                append1 = "  ___";
-                        } else {
-                                append1 = String.format("%5d", tmp.getXvalue());
-                        }
-
-                        if (tmp.getYvalue() == Constants.GAP_SYMBOL) {
-                                append2 = "  ___";
-                        } else {
-                                append2 = String.format("%5d", tmp.getYvalue());
-                        }
-                        if (count != 0) {
-                                aligned1 = append1 + aligned1;
-                                aligned2 = append2 + aligned2;
-                        }
-
-                        tmp = tmp.getPrevious();
-                        count++;
-
-                } while (tmp != null);
-                System.out.println(aligned1);
-                System.out.println(aligned2);
-        }
-
+        
         /**
          * print the dynmaic programming matrix
@@ -241 +208 @@
                 }
         }
+        
+        public void printAlignment() {
+                int[] tmp1 = alignment.get(0).getSequence();
+                int[] tmp2 = alignment.get(1).getSequence();
+                for (int i=0; i< tmp1.length;i++) {
+                        if(tmp1[i] == Constants.GAP_SYMBOL) {
+                                System.out.print("  ___");
+                        }
+                        else if(tmp1[i] == Constants.UNMATCHED_SYMBOL) {
+                                System.out.print("  ...");
+                        }
+                        else {
+                                System.out.format("%5d", tmp1[i]);
+                        }
+                        
+                }
+                System.out.println();
+                for (int i=0; i< tmp2.length;i++) {
+                        if(tmp2[i] == Constants.GAP_SYMBOL) {
+                                System.out.print("  ___");
+                        }
+                        else if(tmp2[i] == Constants.UNMATCHED_SYMBOL) {
+                                System.out.print("  ...");
+                        }
+                        else {
+                                System.out.format("%5d", tmp2[i]);
+                        }
+                        
+                }
+                System.out.println();
+                
+                
+        
+        }
 
         /*