Changeset 1620 for branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

Timestamp:

07/23/14 18:18:11 (10 years ago)

Author:

rkrimmel

Message:

More intelligent match finding and creation

File:

• branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (modified) (6 diffs)

branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

@@ -231 +231 @@
                 ns1.setSequence(reversed1);
                 ns2.setSequence(reversed2);
-
-                alignment.add(ns1);
-                alignment.add(ns2);
+                ns1.setId(alignment.get(0).getId());
+                ns2.setId(alignment.get(1).getId());
+                
+                alignment.set(0, ns1);
+                alignment.set(1, ns2);
         }
         
@@ -272 +274 @@
         }
         
-        public ArrayList<ArrayList<NumberSequence>> getMatches() {
-                ArrayList<ArrayList<NumberSequence>> result = new ArrayList<ArrayList<NumberSequence>>();
+        public ArrayList<Match> getMatches() {
+                ArrayList<Match> result = new ArrayList<Match>();
                 
                 //both alignment sequences should be equally long
@@ -288 +290 @@
                                         count++;
                                 }
-                                //I am really missing memcpy here 
+                                //I am really missing memcpy here? How does one do this better in java? 
                                 int[] tmp1 = new int[count];
                                 int[] tmp2 = new int[count];
@@ -299 +301 @@
                                 tmpns1.setSequence(tmp1);
                                 tmpns2.setSequence(tmp2);
-                                ArrayList<NumberSequence> tmpal = new ArrayList<NumberSequence>();
-                                tmpal.add(tmpns1);
-                                tmpal.add(tmpns2);
+                                Match tmpal = new Match();
+                                tmpal.setFirstSequence(tmpns1);
+                                tmpal.setSecondSequence(tmpns2);
+                                tmpal.addOccurence(new MatchOccurence(start,alignment.get(0).getId()));
+                                tmpal.addOccurence(new MatchOccurence(start,alignment.get(1).getId()));
                                 result.add(tmpal);
                         }
                         i++;
                 }
-                
-                
-                
-                
-                
-                
                 return result;
-                
         }
         
@@ -354 +351 @@
 
         @Override
-        public void align(int[] input1, int[] input2, SubstitutionMatrix submat,
+        public void align(NumberSequence input1, NumberSequence input2, SubstitutionMatrix submat,
                         float threshold) {
-                this.input1 = input1;
-                this.input2 = input2;
-                length1 = input1.length;
-                length2 = input2.length;
+                
+                alignment = new ArrayList<NumberSequence>();
+                alignment.add(input1);
+                alignment.add(input2);
+                
+                this.input1=input1.getSequence();
+                this.input2=input2.getSequence();
+                
+                length1 = input1.size();
+                length2 = input2.size();
                 this.submat = submat;
 
@@ -367 +370 @@
                 
                 matrix = new MatrixEntry[length1+2][length2+1];
-                alignment = new ArrayList<NumberSequence>();
+                
                 
                 for (int i = 0; i <= length1+1; i++) {