Changeset 1578 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

Timestamp:

06/25/14 19:21:42 (10 years ago)

Author:

rkrimmel

Message:

Added Constants for the gap and unmatched symbol

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (3 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -63 +63 @@
  * </p>
  * <p>
- * For determining the longest sequence occurring most often, the implementation
- * uses a {@link Trie}. The depth of the tree is initially 3. If the algorithm
- * has a longest sequence occurring most often whose length is equal to the
- * depth of the trie, it recalculates the trie with an increased depth.
- * </p>
+
  * 
  * @author Patrick Harms
@@ -183 +179 @@
                                                         ns2.getSequence(), ns2.getSequence(), submat,
                                                         smithWatermanThreshold);
-                                        
                                         SmithWatermanRepeated randomSequence = new SmithWatermanRepeated(
                                                         ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold);
                                         
+                                        // Score of the aligmnment
                                         double score = twoSequences.getAlignmentScore();
-                                        // Scores of the sequence being aligned to itself
+                                        // Scores of the sequence being aligned to itself (maximum score)
                                         double sSelf1 = sameSequence1.getAlignmentScore();
                                         double sSelf2 = sameSequence2.getAlignmentScore();
-
+                                        // Score of sequences shuffled before aligned  
                                         double sRand = randomSequence.getAlignmentScore();
 
@@ -210 +206 @@
                         }
                 }
+                //System.out.println(sequenceDistances.toString());
                 UPGMATree guidetree = new UPGMATree(numberseqs, sequenceDistances);
                 
+        
                 /*
                 do {
-                        System.out.println();
-                        //FengDoolittle fd = new FengDoolittle();
 
                         // appData.getStopWatch().start("whole loop");