Changeset 1583 for branches/ralph/src/main/java/de/ugoe/cs/autoquest

Timestamp:

06/26/14 23:34:58 (10 years ago)

Author:

rkrimmel

Message:

Small fixes and comments.

Location:

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees

Files:

• alignment/pal/tree/FengDoolittleNode.java (modified) (4 diffs)
• alignment/pal/tree/Node.java (modified) (1 diff)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (3 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/FengDoolittleNode.java

@@ -11 +11 @@
 
 import java.util.ArrayList;
+import java.util.logging.Level;
 
 import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence;
 import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier;
+import de.ugoe.cs.util.console.Console;
 
 
 /**
- * data structure for a node (includes branch) in a binary/non-binary
- * rooted/unrooted tree
  *
  * @version $Id: SimpleNode.java,v 1.20 2002/01/14 04:16:53 matt Exp $
@@ -377 +377 @@
                 
                 if(newNode instanceof FengDoolittleNode) {
-                        ((FengDoolittleNode) newNode).alignSequences();
+                        newNode.setSequences(((FengDoolittleNode) newNode).alignSequences());
                 }
                 
@@ -397 +397 @@
 
 
-        private void alignSequences() {
+        private ArrayList<NumberSequence> alignSequences() {
+                ArrayList<NumberSequence> alignment = new ArrayList<NumberSequence>();
                 if(this.getChildCount()<3) {
                         
@@ -406 +407 @@
                         int seqCount2 = node2.getSequences().size();
                         
+                        //Align 2 sequences
+                        if(seqCount1 == 1 && seqCount2 == 1) {
+                        }
+                        //Align a sequence to a group
+                        else if( seqCount1 > 1 && seqCount2 == 1) {
                         
-                        
+                        }
+                        //Align a sequence to a group
+                        else if(seqCount1 == 1 && seqCount2 > 1) {
+                                
+                        }
+                        //Align 2 groups
+                        else if((seqCount1 > 1) && (seqCount2 > 1)){
+                                        
+                        }
+                        else {
+                                Console.traceln(Level.INFO,"No sequences to align while merging two nodes.");
+                        }
                 }
                 else {
-                        System.out.println("This should never happen, it's a binary tree.");
-                }
-                
-        }
-
+                        Console.traceln(Level.WARNING,"More than 2 children! This should never happen, it's a binary tree.");
+                }
+                return alignment;
+        }
+
+        public void setSequences(ArrayList<NumberSequence> alignSequences) {
+                this.sequences = alignSequences;
+        }
         
 }

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/Node.java

@@ -138 +138 @@
         void addSequence(NumberSequence numberSequence);
 
+        void setSequences(ArrayList<NumberSequence> alignSequences);
+
+
+
+
 
         

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

@@ -160 +160 @@
                 UPGMAMatrix sequenceDistances = new UPGMAMatrix(numberseqs.size());
                 sequenceDistances.initialize(Double.POSITIVE_INFINITY);
+                
+                //Save the alignments so we do not need to recalculate those when aligning them again in feng doolittle algorithm
+                SmithWatermanRepeated[][] alignments = new SmithWatermanRepeated[numberseqs.size()][numberseqs.size()]; 
 
                 for (int i = 0; i < numberseqs.size(); i++) {
@@ -169 +172 @@
                                         int smithWatermanThreshold = 10;
 
-                                        SmithWatermanRepeated twoSequences = new SmithWatermanRepeated(
+                                        alignments[i][j] = new SmithWatermanRepeated(
                                                         ns1.getSequence(), ns2.getSequence(), submat,
                                                         smithWatermanThreshold);
@@ -182 +185 @@
                                         
                                         // Score of the aligmnment
-                                        double score = twoSequences.getAlignmentScore();
+                                        double score = alignments[i][j].getAlignmentScore();
                                         // Scores of the sequence being aligned to itself (maximum score)
                                         double sSelf1 = sameSequence1.getAlignmentScore();