Changeset 1323 for trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs

Timestamp:

12/17/13 10:02:04 (11 years ago)

Author:

rkrimmel

Message:

Added Substitution Package, Fixed Array access error in SimpleSequenceGenerator?

Location:

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment

Files:

• SmithWaterman.java (modified) (1 diff)
• commands/CMDbinaryAlignment.java (modified) (3 diffs)
• seqgen/ISequenceGenerator.java (moved) (moved from trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java) (1 diff)
• seqgen/RandomSequenceGenerator.java (modified) (2 diffs)
• seqgen/SimpleSequenceGenerator.java (modified) (1 diff)
• substitution (added)
• substitution/DifferenceSubstitutionMatrix.java (moved) (moved from trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/DifferenceSubstitutionMatrix.java) (1 diff)
• substitution/NearbySubstitutionMatrix.java (moved) (moved from trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/NearbySubstitutionMatrix.java) (1 diff)
• substitution/SubstitutionMatrix.java (moved) (moved from trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SubstitutionMatrix.java) (1 diff)

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java

@@ -3 +3 @@
 import java.util.ArrayList;
 import java.util.List;
+
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.SubstitutionMatrix;
 
 public class SmithWaterman implements Alignment {

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java

@@ -25 +25 @@
 import de.ugoe.cs.autoquest.CommandHelpers;
 import de.ugoe.cs.autoquest.eventcore.Event;
-import de.ugoe.cs.autoquest.plugin.alignment.NearbySubstitutionMatrix;
 import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
-import de.ugoe.cs.autoquest.plugin.alignment.DifferenceSubstitutionMatrix;
 import de.ugoe.cs.autoquest.plugin.alignment.seqgen.RandomSequenceGenerator;
+import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.DifferenceSubstitutionMatrix;
+import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix;
+import de.ugoe.cs.autoquest.tasktrees.manager.TaskTreeManager;
+import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality;
+import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskInstanceComparator;
+import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskHandlingStrategy;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskBuilder;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance;
+import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession;
+import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder;
+import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -48 +59 @@
          * @see de.ugoe.cs.util.console.Command#run(java.util.List)
          */
-        @Override
         public void run(List<Object> parameters) {
                 String sequencesName;
@@ -64 +74 @@
                 sequences = (Collection<List<Event>>) GlobalDataContainer.getInstance()
                                 .getData(sequencesName);
-                Console.println("Number of sequences: " + sequences.size());
-                for (Iterator<List<Event>> it = sequences.iterator(); it.hasNext();) {
-                        List<Event> ev = it.next();
-                        RandomSequenceGenerator randgen1 = new RandomSequenceGenerator(1,
-                                        80, 3000);
-                        RandomSequenceGenerator randgen2 = new RandomSequenceGenerator(1,
-                                        80, 3000);
-                        
-                        int[] seq1 = randgen1.generate(ev);
-                        int[] seq2 = randgen2.generate(ev);
-                        SmithWaterman sw = new SmithWaterman(seq1, seq2,
-                                        new NearbySubstitutionMatrix(seq1, seq2,10));
+                                if(sequences != null) {
+                                        Console.println("Number of sequences: " + sequences.size());
 
-                        //sw.printDPMatrix();
-                        System.out.println();
-                        //sw.printAlignments();
-                        sw.getMatches();
-                        Console.println("Number of events in sequence: " + ev.size());
-                }
+                                        SimpleSequenceGenerator gen = new SimpleSequenceGenerator();
+                                        gen.generate(sequences);
+                                        int[] seq1 = gen.get(0);
+                                        int[] seq2 = gen.get(0);
+                                        SmithWaterman sw = new SmithWaterman(seq1, seq2,
+                                                        new NearbySubstitutionMatrix(seq1, seq2, 10));
 
-        }
+                                //printDPMatrix();
+                                System.out.println();
+                                sw.printAlignments();
+                                // sw.getMatches();
+                                }
+                        }
+
 
         /*

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/ISequenceGenerator.java

@@ -1 +1 @@
 package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
 
+import java.util.Collection;
 import java.util.List;
+
 import de.ugoe.cs.autoquest.eventcore.Event;
 
-public interface SequenceGenerator {
-        public int[] generate(List<Event> eventList);
+public interface ISequenceGenerator {
+        
+        public void generate(Collection<List<Event>> eventList);
+        public int[] get(int index);
+        
+        
+        
+        
 }

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java

@@ -1 +1 @@
 package de.ugoe.cs.autoquest.plugin.alignment.seqgen;
 import de.ugoe.cs.autoquest.eventcore.Event;
+
+import java.util.Collection;
 import java.util.List;
 
-public class RandomSequenceGenerator implements SequenceGenerator {
+public class RandomSequenceGenerator implements ISequenceGenerator{
 
         private int min;
@@ -23 +25 @@
                 return result;
         }
+
+        @Override
+        public void generate(Collection<List<Event>> eventList) {
+                // TODO Auto-generated method stub
+                
+        }
+
+        @Override
+        public int[] get(int index) {
+                // TODO Auto-generated method stub
+                return null;
+        }
 }

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java

@@ -57 +57 @@
                                                 uniqueTasks.addSymbol(taskInstance,
                                                                 taskInstance.getTask());
+                                                                templist[i]=taskInstance.getTask().getId();
                                         } else {
                                                 taskBuilder.setTask(taskInstance, task);
                                                 unifiedTasks++;
+                                                templist[i]=task.getId();
+                                                
                                         }
-                                        templist[i]=task.getId();
+                                        
                                 }
 

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java

@@ -2 +2 @@
  * 
  */
-package de.ugoe.cs.autoquest.plugin.alignment;
+package de.ugoe.cs.autoquest.plugin.alignment.substitution;
 
 /**

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java

@@ -2 +2 @@
  * 
  */
-package de.ugoe.cs.autoquest.plugin.alignment;
+package de.ugoe.cs.autoquest.plugin.alignment.substitution;
 
 /**

trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java

@@ -1 @@
-package de.ugoe.cs.autoquest.plugin.alignment;
+package de.ugoe.cs.autoquest.plugin.alignment.substitution;
 
 public interface SubstitutionMatrix {