Changeset 1307

Timestamp:

09/12/13 01:04:37 (11 years ago)

Author:

rkrimmel

Message:

Some tests for Smith Waterman Algorithm (temporary)

File:

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

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

@@ -18 +18 @@
 import java.io.FilenameFilter;
 import java.util.Collection;
+import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
@@ -24 +25 @@
 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.DifferenceSubstitutionMatrix;
+import de.ugoe.cs.autoquest.plugin.alignment.seqgen.RandomSequenceGenerator;
 import de.ugoe.cs.util.console.Command;
 import de.ugoe.cs.util.console.Console;
@@ -36 +40 @@
  * @version 1.0
  */
-public class CMDbinaryAligment implements Command {
+public class CMDbinaryAlignment implements Command {
 
         /*
@@ -56 +60 @@
                 }
 
-                
                 Collection<List<Event>> sequences = new LinkedList<List<Event>>();
-                
+                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 randgen = new RandomSequenceGenerator(1,
+                                        80, 10);
+                        int[] seq1 = randgen.generate(ev);
+                        int[] seq2 = randgen.generate(ev);
+                        SmithWaterman sw = new SmithWaterman(seq1, seq2,
+                                        new DifferenceSubstitutionMatrix(seq1, seq2));
+
+                        sw.printDPMatrix();
+                        Console.println("Number of events in sequence: " + ev.size());
+                        for (Iterator<Event> foo = ev.iterator(); foo.hasNext();) {
+                                Event blubb = foo.next();
+                                // Console.println(blubb.toString());
+                        }
+                }
 
         }