Changeset 1330 for trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java

Timestamp:

01/22/14 15:45:55 (10 years ago)

Author:

rkrimmel

Message:

Removing unused code

File:

• trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java (modified) (4 diffs)

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

@@ -15 +15 @@
 package de.ugoe.cs.autoquest.plugin.alignment.commands;
 
-import java.io.File;
-import java.io.FilenameFilter;
+
 import java.util.Collection;
-import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
-import java.util.logging.Level;
 
-import de.ugoe.cs.autoquest.CommandHelpers;
 import de.ugoe.cs.autoquest.eventcore.Event;
 import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman;
-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.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -49 +34 @@
  * </p>
  * 
- * @author Steffen Herbold
+ * @author Ralph Krimmel
  * @version 1.0
  */
@@ -72 +57 @@
 
                 Collection<List<Event>> sequences = new LinkedList<List<Event>>();
-                sequences = (Collection<List<Event>>) GlobalDataContainer.getInstance()
-                                .getData(sequencesName);
+                Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
+                if(obj.getClass().equals(sequences.getClass())) {
+                        sequences = (Collection<List<Event>>) obj;
+                }
+                 
+        
+                
+                
+
                                 if(sequences != null) {
                                         Console.println("Number of sequences: " + sequences.size());
@@ -81 +73 @@
                                         int[] seq1 = gen.get(0);
                                         int[] seq2 = gen.get(0);
+                                        ObjectDistanceSubstitionMatrix submat = new ObjectDistanceSubstitionMatrix();
+                                        submat.generate(sequences);
                                         SmithWaterman sw = new SmithWaterman(seq1, seq2,
                                                         new NearbySubstitutionMatrix(seq1, seq2, 10));
 
-                                //printDPMatrix();
+                                sw.printDPMatrix();
                                 System.out.println();
-                                sw.printAlignments();
+                                //sw.printAlignments();
                                 // sw.getMatches();
                                 }