Changeset 1612 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms

Timestamp:

07/14/14 23:27:01 (10 years ago)

Author:

rkrimmel

Message:

Removed parameters from alignmentalgorihm factory constructor and changed interface by adding a new align() method, which now gets all the data via parameter

Location:

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

Files:

• AlignmentAlgorithm.java (modified) (1 diff)
• AlignmentAlgorithmFactory.java (modified) (2 diffs)
• NeedlemanWunsch.java (modified) (2 diffs)
• SmithWaterman.java (modified) (2 diffs)
• SmithWatermanRepeated.java (modified) (2 diffs)

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

@@ -3 +3 @@
 import java.util.ArrayList;
 
+import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix;
+
 public interface AlignmentAlgorithm {
 
+        public abstract void align(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold);
+        
         /**
          * Get the alignment score between the two input strings.

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;
@@ -5 +8 @@
 public class AlignmentAlgorithmFactory {
         
+        public static void setDefaultAlgorithm(String algorithmname) {
+                //TODO: check for valid algorihm class names here
+                algorithmclass = algorithmname;
+        }
         
-        public static AlignmentAlgorithm create(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold) {
-                
+        private static String algorithmclass = "de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated";
+        
+        
+        
+        public static AlignmentAlgorithm create() {
+                Class<?> newclass;
+                Object object = null;
+                try {
+                         newclass = Class.forName(algorithmclass);
+                         object = newclass.newInstance();
+                        
+                } catch (ClassNotFoundException | SecurityException | InstantiationException | IllegalAccessException | IllegalArgumentException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                }
                 //return new SmithWaterman(input1,input2,submat,threshold);
                 //return new NeedlemanWunsch(input1,input2,submat,threshold);
-                return new SmithWatermanRepeated(input1,input2,submat,threshold);
+                //return new SmithWatermanRepeated(input1,input2,submat,threshold);
+                return (AlignmentAlgorithm) object;
         }
 }

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

@@ -39 +39 @@
         private SubstitutionMatrix submat;
 
-        public NeedlemanWunsch(int[] input1, int[] input2, SubstitutionMatrix submat,
-                        float threshold) {
-                this.input1 = input1;
-                this.input2 = input2;
-                length1 = input1.length;
-                length2 = input2.length;
-                this.submat = submat;
-
-                // System.out.println("Starting SmithWaterman algorithm with a "
-                // + submat.getClass() + " Substitution Matrix: " +
-                // submat.getClass().getCanonicalName());
-
-                matrix = new MatrixEntry[length1 + 1][length2 + 1];
-                alignment = new ArrayList<NumberSequence>();
-
-                for (int i = 0; i < length1+1; i++) {
-                        for (int j = 0; j < length2+1; j++) {
-                                matrix[i][j] = new MatrixEntry();
-                        }
-                }
-
-                buildMatrix();
-                traceback();
-        }
 
         /**
@@ -289 +265 @@
         }
 
+        @Override
+        public void align(int[] input1, int[] input2, SubstitutionMatrix submat,
+                        float threshold) {
+                this.input1 = input1;
+                this.input2 = input2;
+                length1 = input1.length;
+                length2 = input2.length;
+                this.submat = submat;
+
+                // System.out.println("Starting SmithWaterman algorithm with a "
+                // + submat.getClass() + " Substitution Matrix: " +
+                // submat.getClass().getCanonicalName());
+
+                matrix = new MatrixEntry[length1 + 1][length2 + 1];
+                alignment = new ArrayList<NumberSequence>();
+
+                for (int i = 0; i < length1+1; i++) {
+                        for (int j = 0; j < length2+1; j++) {
+                                matrix[i][j] = new MatrixEntry();
+                        }
+                }
+
+                buildMatrix();
+                traceback();
+                
+        }
+
 
 

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

@@ -38 +38 @@
         private SubstitutionMatrix submat;
 
-        public SmithWaterman(int[] input1, int[] input2, SubstitutionMatrix submat,
-                        float threshold) {
-                this.input1 = input1;
-                this.input2 = input2;
-                length1 = input1.length;
-                length2 = input2.length;
-                this.submat = submat;
-
-                // System.out.println("Starting SmithWaterman algorithm with a "
-                // + submat.getClass() + " Substitution Matrix: " +
-                // submat.getClass().getCanonicalName());
-
-                matrix = new MatrixEntry[length1 + 1][length2 + 1];
-                alignment = new ArrayList<NumberSequence>();
-
-                for (int i = 0; i < length1+1; i++) {
-                        for (int j = 0; j < length2+1; j++) {
-                                matrix[i][j] = new MatrixEntry();
-                        }
-                }
-
-                buildMatrix();
-                traceback();
-        }
 
         /**
@@ -294 +270 @@
         }
 
+        @Override
+        public void align(int[] input1, int[] input2, SubstitutionMatrix submat,
+                        float threshold) {
+                this.input1 = input1;
+                this.input2 = input2;
+                length1 = input1.length;
+                length2 = input2.length;
+                this.submat = submat;
+
+                // System.out.println("Starting SmithWaterman algorithm with a "
+                // + submat.getClass() + " Substitution Matrix: " +
+                // submat.getClass().getCanonicalName());
+
+                matrix = new MatrixEntry[length1 + 1][length2 + 1];
+                alignment = new ArrayList<NumberSequence>();
+
+                for (int i = 0; i < length1+1; i++) {
+                        for (int j = 0; j < length2+1; j++) {
+                                matrix[i][j] = new MatrixEntry();
+                        }
+                }
+
+                buildMatrix();
+                traceback();
+                
+        }
+
 }

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

@@ -43 +43 @@
         private SubstitutionMatrix submat;
 
-        public SmithWatermanRepeated(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold) {
-                this.input1 = input1;
-                this.input2 = input2;
-                length1 = input1.length;
-                length2 = input2.length;
-                this.submat = submat;
-
-                //System.out.println("Starting SmithWaterman algorithm with a "
-                //              + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
-                this.scoreThreshold = threshold;
-                
-                matrix = new MatrixEntry[length1+2][length2+1];
-                alignment = new ArrayList<NumberSequence>();
-                
-                for (int i = 0; i <= length1+1; i++) {
-                        for(int j = 0; j< length2; j++) {
-                                matrix[i][j] = new MatrixEntry();
-                        }
-                }
-        
-
-                buildMatrix();
-                traceback();
+        public SmithWatermanRepeated() {
+        
         }
 
@@ -374 +353 @@
         }
 
+        @Override
+        public void align(int[] input1, int[] input2, SubstitutionMatrix submat,
+                        float threshold) {
+                this.input1 = input1;
+                this.input2 = input2;
+                length1 = input1.length;
+                length2 = input2.length;
+                this.submat = submat;
+
+                //System.out.println("Starting SmithWaterman algorithm with a "
+                //              + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
+                this.scoreThreshold = threshold;
+                
+                matrix = new MatrixEntry[length1+2][length2+1];
+                alignment = new ArrayList<NumberSequence>();
+                
+                for (int i = 0; i <= length1+1; i++) {
+                        for(int j = 0; j< length2; j++) {
+                                matrix[i][j] = new MatrixEntry();
+                        }
+                }
+        
+
+                buildMatrix();
+                traceback();
+        }
+
 }