Changeset 1449 for trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java

Timestamp:

03/26/14 19:47:27 (10 years ago)

Author:

rkrimmel

Message:

 

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

@@ -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");
                                 }
                         }