Changeset 1554

Timestamp:

05/23/14 21:54:40 (10 years ago)

Author:

rkrimmel

Message:

Moved alignment plugin into core-tasktrees

Location:

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

Files:

• alignment/algorithms/SmithWaterman.java (modified) (1 diff)
• alignment/substitution/DifferenceSubstitutionMatrix.java (modified) (2 diffs)
• alignment/substitution/NearbySubstitutionMatrix.java (modified) (2 diffs)
• alignment/substitution/ObjectDistanceSubstitionMatrix.java (modified) (3 diffs)
• alignment/substitution/SubstitutionMatrix.java (modified) (1 diff)
• alignment/substitution/TriangleMatrix.java (added)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (6 diffs)

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

@@ -70 +70 @@
 
                 System.out.println("Starting SmithWaterman algorithm with a "
-                                + submat.getClass() + " Substitution Matrix: " + submat.info());
+                                + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName());
                 scoreThreshold = 20;
                 score = new double[length1 + 1][length2 + 1];

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/DifferenceSubstitutionMatrix.java

@@ -29 +29 @@
          * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
          */
-        public double getDistance(int pos1, int pos2) {
+        public float getDistance(int pos1, int pos2) {
                 return maxValue - (input1[pos1] - input2[pos2]);
         }
@@ -49 +49 @@
 
         @Override
-        public double getGapPenalty() {
+        public float getGapPenalty() {
                 return -maxValue;
-        }
-
-        @Override
-        public String info() {
-                return "Max Value: " + maxValue;
         }
 
 
         @Override
-        public void generate(List<IUserSession> sessions) {
+        public void generate() {
                 // TODO Auto-generated method stub
                 

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/NearbySubstitutionMatrix.java

@@ -29 +29 @@
          * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int)
          */
-        public double getDistance(int pos1, int pos2) {
+        public float getDistance(int pos1, int pos2) {
                 int difference = Math.abs(input1[pos1]-input2[pos2]); 
                 if(difference < range) {
@@ -41 +41 @@
 
         @Override
-        public double getGapPenalty() {
+        public float getGapPenalty() {
                 return -range-1;
         }
 
-        @Override
-        public String info() {
-                return "Range: " + range;
-        }
 
         @Override
-        public void generate(List<IUserSession> sessions) {
+        public void generate() {
                 // TODO Auto-generated method stub
                 

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/ObjectDistanceSubstitionMatrix.java

@@ -3 +3 @@
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.Iterator;
 
@@ -13 +14 @@
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentHelpers;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IEventTaskInstance;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession;
+import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
 import de.ugoe.cs.util.console.GlobalDataContainer;
 
 public class ObjectDistanceSubstitionMatrix implements SubstitutionMatrix {
 
-        private ArrayList<int[][]> matrix;
-        private int currentSequence;
-        
-        
-        public ObjectDistanceSubstitionMatrix() {
-                currentSequence = 0;
-                matrix = new ArrayList<int[][]>();
-        }
-        
-        @Override
-        public String info() {
-                // TODO Auto-generated method stub
-                return null;
+        // private ArrayList<int[][]> matrix;
+        HashMap<Integer, Integer> idmapping;
+        private TriangleMatrix matrix;
+        private SymbolMap<ITaskInstance, ITask> uniqueTasks;
+
+        public ObjectDistanceSubstitionMatrix(
+                        SymbolMap<ITaskInstance, ITask> uniqueTasks) {
+                this.uniqueTasks = uniqueTasks;
+                idmapping = new HashMap<Integer, Integer>();
+                matrix = new TriangleMatrix(uniqueTasks.size()+1);
         }
 
         @Override
-        public double getDistance(int pos1, int pos2) {
-                // TODO Auto-generated method stub
-                
-                return matrix.get(currentSequence)[pos1][pos2];
-        }
-        
-        public double getDistance(int sequence, int pos1, int pos2) {
-                return  matrix.get(sequence)[pos1][pos2];
-                
-                
-        }
-
-        @Override
-        public double getGapPenalty() {
+        public float getGapPenalty() {
                 // TODO Auto-generated method stub
                 return 0;
@@ -53 +41 @@
 
         @Override
-        public void generate(List<IUserSession> sessions) {
-                
-                for(Iterator it = sessions.iterator(); it.hasNext();) {
-                        IUserSession session = (IUserSession) it.next();
-                        matrix.add(new int[sessions.size()][sessions.size()]);
-                
-                        
-                        for (int i=0; i < session.size(); i++) {
-                                for (int j=0; j < session.size(); j++) {
-                                        //TODO Check if ITaskInstance is of type IEventTaskInstance 
-                                        IEventTaskInstance eti1 = (IEventTaskInstance) session.get(i);
-                                        IEventTaskInstance eti2 = (IEventTaskInstance) session.get(j);
-                                        IGUIElement first = (IGUIElement) eti1.getEvent().getTarget();
-                                        IGUIElement second =(IGUIElement) eti2.getEvent().getTarget();
-                                        matrix.get(currentSequence)[i][j] = AlignmentHelpers.distanceBetween(first, second);
+        public void generate() {
+                int i = 0;
+                for (Iterator<ITaskInstance> it = uniqueTasks.getSymbols().iterator(); it
+                                .hasNext();) {
+                        Object obj1 = it.next();
+                        IEventTaskInstance eti1 = null;
+                        if (obj1 instanceof IEventTaskInstance) {
+                                eti1 = (IEventTaskInstance) obj1;
+                        }
+                        int j = 0;
+                        for (Iterator<ITaskInstance> jt = uniqueTasks.getSymbols()
+                                        .iterator(); jt.hasNext();) {
+                                IEventTaskInstance eti2 = null;
+                                Object obj2 = jt.next();
+                                if (obj2 instanceof IEventTaskInstance) {
+                                        eti2 = (IEventTaskInstance) obj2;
                                 }
-                        }                       
+                                IGUIElement first = (IGUIElement) eti1.getEvent().getTarget();
+                                IGUIElement second = (IGUIElement) eti2.getEvent().getTarget();
+                                idmapping.put(eti1.getTask().getId(), i);
+                                idmapping.put(eti2.getTask().getId(), j);
+                                matrix.set(i, j, AlignmentHelpers.distanceBetween(first, second));
+                                j++;
+                        }
+                        i++;
                 }
         }
+
+        @Override
+        public float getDistance(int taskId1, int taskId2) {
+                return matrix.get(idmapping.get(taskId1),idmapping.get(taskId2));
+        }
+
 }
+

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/substitution/SubstitutionMatrix.java

@@ -9 +9 @@
 
 public interface SubstitutionMatrix {
+        
 
-        public String info();
-        
-        public double getDistance(int pos1, int pos2);
+        public float getDistance(int pos1, int pos2);
 
-        public double getGapPenalty();
+        public float getGapPenalty();
 
-        public void generate(List<IUserSession> sessions);
+        public void generate();
 
         

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -26 +26 @@
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
+import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWaterman;
+import de.ugoe.cs.autoquest.tasktrees.alignment.substitution.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IIteration;
@@ -140 +142 @@
         numberseqs = new ArrayList<NumberSequence>();
         
+        
+        
         // this is the real rule application. Loop while something is replaced.
-        harmonizeEventTaskInstancesModel(appData);
+        SymbolMap<ITaskInstance, ITask> uniqueTasks = harmonizeEventTaskInstancesModel(appData,numberseqs);
+        ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix(uniqueTasks);  
+        submat.generate();
+        
+        
+        SmithWaterman sm = new SmithWaterman(numberseqs.get(0).getSequence(), numberseqs.get(0).getSequence(), submat);
+        sm.printDPMatrix();
+      
         
         
@@ -188 +199 @@
      *
      * @param appData the rule application data combining all data used for applying this rule
-     */
-    private void harmonizeEventTaskInstancesModel(RuleApplicationData appData) {
+     * @return Returns the unique tasks symbol map
+     */
+    private SymbolMap<ITaskInstance, ITask> harmonizeEventTaskInstancesModel(RuleApplicationData appData, ArrayList<NumberSequence> numberseqs) {
         Console.traceln(Level.INFO, "harmonizing task model of event task instances");
         appData.getStopWatch().start("harmonizing event tasks");
@@ -201 +213 @@
         List<IUserSession> sessions = appData.getSessions();
         int sessionNo = 0;
+        numberseqs = new ArrayList<NumberSequence>();
         for (IUserSession session : sessions) {
             Console.traceln(Level.FINE, "handling " + (++sessionNo) + ". " + session);
@@ -219 +232 @@
                 }
             }
-            
+            numberseqs.add(templist);
             comparator.clearBuffers();
         }
@@ -229 +242 @@
         appData.getStopWatch().dumpStatistics(System.out);
         appData.getStopWatch().reset();
+                return uniqueTasks;
     }