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

Timestamp:

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

Author:

rkrimmel

Message:

Added Substitution Package, Fixed Array access error in SimpleSequenceGenerator?

File:

• trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java (modified) (3 diffs)

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();
+                                }
+                        }
+
 
         /*