Changeset 1578 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

06/25/14 19:21:42 (10 years ago)

Author:

rkrimmel

Message:

Added Constants for the gap and unmatched symbol

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (9 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 java.util.logging.Level;
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants;
 import de.ugoe.cs.util.console.Console;
 
@@ -79 +78 @@
          */
         private double similarity(int i, int j) { 
-                return submat.getDistance(input1[i - 1], input2[j - 1]);
+                return submat.getScore(input1[i - 1], input2[j - 1]);
         }
 
@@ -129 +128 @@
 
                         }
-                        
                                         
                         tempMax -= scoreThreshold;
@@ -145 +143 @@
                         {
                                 matrix[i][0].setXvalue(input1[i-1]);
-                                matrix[i][0].setYvalue(-2);
+                                matrix[i][0].setYvalue(Constants.UNMATCHED_SYMBOL);
                         }
                         else { 
@@ -161 +159 @@
 
                                 // find the directions that give the maximum scores.
-                                // Multiple directions are ignored TODO
+                                // TODO: Multiple directions are ignored, we choose the first maximum score 
                                 //True if we had a match
                                 if (diagScore == matrix[i][j].getScore()) {
@@ -171 +169 @@
                                 if (leftScore == matrix[i][j].getScore()) {
                                         matrix[i][j].setXvalue(input1[i-1]);
-                                        matrix[i][j].setYvalue(-1);
+                                        matrix[i][j].setYvalue(Constants.GAP_SYMBOL);
                                         matrix[i][j].setPrevious(matrix[i-1][j]);
                                 }
                                 //true if we took an event from sequence y and not from x
                                 if (upScore == matrix[i][j].getScore()) {
-                                        matrix[i][j].setXvalue(-1);
+                                        matrix[i][j].setXvalue(Constants.GAP_SYMBOL);
                                         matrix[i][j].setYvalue(input2[j-1]);
                                         matrix[i][j].setPrevious(matrix[i][j-1]);
@@ -184 +182 @@
                                         matrix[i][j].setPrevious(matrix[i][0]);
                                         matrix[i][j].setXvalue(input1[i-1]);
-                                        matrix[i][j].setYvalue(-2);
+                                        matrix[i][j].setYvalue(Constants.UNMATCHED_SYMBOL);
                                 }
                         }
@@ -271 +269 @@
                         String append2="";
                                         
-                        if(tmp.getXvalue() == -1) {
+                        if(tmp.getXvalue() == Constants.GAP_SYMBOL) {
                                 append1 = "  ___";
                         }
-                        else if(tmp.getXvalue() == -2) {
+                        else if(tmp.getXvalue() == Constants.UNMATCHED_SYMBOL) {
                                 append1 = "  ...";
                         }
@@ -281 +279 @@
                         }
 
-                        if(tmp.getYvalue() == -1) {
+                        if(tmp.getYvalue() == Constants.GAP_SYMBOL) {
                                 append2 = "  ___";
                         }
-                        else if(tmp.getYvalue() == -2) {
+                        else if(tmp.getYvalue() == Constants.UNMATCHED_SYMBOL) {
                                 append2 = "  ...";
                         }