Changeset 1449 for trunk/autoquest-plugin-alignment/src/main/java

Timestamp:

03/26/14 19:47:27 (11 years ago)

Author:

rkrimmel

Message:

 

Location:

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

Files:

• FengDoolittle.java (added)
• ProgressiveMultiAlignment.java (added)
• commands/CMDbinaryAlignment.java (modified) (3 diffs)
• commands/CMDgenerateNumberSequences.java (added)
• seqgen/NumberSequence.java (added)
• seqgen/RandomSequenceGenerator.java (modified) (2 diffs)
• seqgen/SequenceGenerator.java (moved) (moved from trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/ISequenceGenerator.java) (1 diff)
• seqgen/SimpleSequenceGenerator.java (modified) (5 diffs)
• substitution/ObjectDistanceSubstitionMatrix.java (modified) (2 diffs)

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

@@ -44 +44 @@
          * @see de.ugoe.cs.util.console.Command#run(java.util.List)
          */
+        @SuppressWarnings("unchecked")
         public void run(List<Object> parameters) {
                 String sequencesName = "sequences";
@@ -58 +59 @@
                 Collection<List<Event>> sequences = new LinkedList<List<Event>>();
                 Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
-                if(obj.getClass().equals(sequences.getClass())) {
-                        sequences = (Collection<List<Event>>) obj;
-                }
+                if(obj != null) {
+                        
+                        if(obj.getClass().equals(sequences.getClass())) {
+                                sequences = (Collection<List<Event>>) obj;
+                        }
                  
-        
-                
-                
-
-                                if(sequences != null) {
+                                
                                         Console.println("Number of sequences: " + sequences.size());
 
@@ -73 +72 @@
                                         int[] seq1 = gen.get(0).getSequence();
                                         int[] seq2 = gen.get(0).getSequence();
-                                        ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
-                                        submat.generate(sequences);
-                                        SmithWaterman sw = new SmithWaterman(seq1, seq2,
-                                                        new NearbySubstitutionMatrix(seq1, seq2, 10));
+                                        //ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
+                                        //submat.generate(sequences);
+                                        //SmithWaterman sw = new SmithWaterman(seq1, seq2,
+                                        //              new NearbySubstitutionMatrix(seq1, seq2, 10));
 
-                                sw.printDPMatrix();
-                                System.out.println();
-                                sw.printAlignments();
+                                //sw.printDPMatrix();
+                                //System.out.println();
+                                //sw.printAlignments();
                                 // sw.getMatches();
+                                        System.out.println("foo");
                                 }
                         }

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

@@ -5 +5 @@
 import java.util.List;
 
-public class RandomSequenceGenerator implements ISequenceGenerator{
+public class RandomSequenceGenerator implements SequenceGenerator{
 
         private int min;
@@ -33 +33 @@
 
         @Override
-        public int[] get(int index) {
+        public NumberSequence get(int index) {
                 // TODO Auto-generated method stub
                 return null;

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

@@ -6 +6 @@
 import de.ugoe.cs.autoquest.eventcore.Event;
 
-public interface ISequenceGenerator {
+public interface SequenceGenerator {
         
         public void generate(Collection<List<Event>> eventList);
-        public int[] get(int index);
+        public NumberSequence get(int index);
         
         

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

@@ -17 +17 @@
 import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder;
 import de.ugoe.cs.autoquest.usageprofiles.SymbolMap;
+import de.ugoe.cs.util.console.Console;
 
 
-public class SimpleSequenceGenerator implements ISequenceGenerator {
+public class SimpleSequenceGenerator implements SequenceGenerator {
 
-        private ArrayList<int[]> numberseqs;
+        private ArrayList<NumberSequence> numberseqs;
 
 
         public SimpleSequenceGenerator() {
-                this.numberseqs = new ArrayList<int[]>();
+                this.numberseqs = new ArrayList<NumberSequence>();
         
         }
         
+        public void print() {
+                for (NumberSequence sequence : numberseqs) {
+                                System.out.println(sequence.toString());
+                }
+                
+        }
         
         public void generate(Collection<List<Event>> sequences) {
@@ -35 +42 @@
                 if (sequences != null) {
                         TaskTreeManager ttm = new TaskTreeManager();
+                        Console.println("Creating the task model");
                         ttm.createTaskModel(sequences);
-                        
+                        Console.println("Finished creating the task model");
                         TaskHandlingStrategy preparationTaskHandlingStrategy  = new TaskHandlingStrategy(TaskEquality.SEMANTICALLY_EQUAL);
                         SymbolMap<ITaskInstance, ITask> uniqueTasks = preparationTaskHandlingStrategy
@@ -49 +57 @@
                         for (IUserSession session : sessions) {
                                 //Creating a new sequence that just consists of integers
-                                int[] templist = new int[session.size()];
+                                NumberSequence templist = new NumberSequence(session.size()) ;
                                 for (int i = 0; i < session.size(); i++) {
                                         ITaskInstance taskInstance = session.get(i); 
@@ -57 +65 @@
                                                 uniqueTasks.addSymbol(taskInstance,
                                                                 taskInstance.getTask());
-                                                                templist[i]=taskInstance.getTask().getId();
+                                                                templist.getSequence()[i]=taskInstance.getTask().getId();
                                                                 
                                         } else {
                                                 taskBuilder.setTask(taskInstance, task);
-                                                templist[i]=task.getId();
+                                                templist.getSequence()[i]=task.getId();
                                                 
                                         }
@@ -77 +85 @@
 
         @Override
-        public int[] get(int index) {
+        public NumberSequence get(int index) {
                 return numberseqs.get(index);
         }

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

@@ -37 +37 @@
                 return matrix.get(currentSequence)[pos1][pos2];
         }
+        
+        public double getDistance(int sequence, int pos1, int pos2) {
+                return  matrix.get(sequence)[pos1][pos2];
+                
+                
+        }
 
         @Override
@@ -46 +52 @@
         @Override
         public void generate(Collection<List<Event>> eventList) {
-                GUIModel guimodel = (GUIModel) GlobalDataContainer.getInstance().getData("sequences_targets");
-                guimodel.condenseModel();
                 
                 for(Iterator<List<Event>> seqs = eventList.iterator(); seqs.hasNext();) {