Changeset 3194 for trunk/yat/utility/Aligner.cc

Timestamp:

Apr 22, 2014, 11:24:56 AM (9 years ago)

Author:

Peter

Message:

add missing file. see r3173

File:

• trunk/yat/utility/Aligner.cc (modified) (2 diffs)

trunk/yat/utility/Aligner.cc

@@ -84 +84 @@
         if (x(i-1, j-1) + score(i-1, j-1) > x(i,j)) {
           x(i,j) = x(i-1, j-1) + score(i-1, j-1);
-          cigar(i, j) = diagonal;
+          directions(i, j) = diagonal;
         }
 
-        if (cigar(i, j-1) == right) {
+        if (directions(i, j-1) == right) {
           if (x(i, j-1)-horizon_gap_ > x(i,j)) {
             x(i,j) = x(i,j-1) - horizon_gap_;
-            cigar(i,j) = right;
+            directions(i,j) = right;
           }
         }
         else if(x(i,j-1)-horizon_gap_-open_horizon_gap_ > x(i,j)) {
           x(i,j) = x(i,j-1) - horizon_gap_ - open_horizon_gap_;
-          cigar(i,j) = right;
+          directions(i,j) = right;
         }
 
-        if (cigar(i-1,j) == down) {
+        if (directions(i-1,j) == down) {
           if (x(i-1,j) - vertical_gap_ > x(i,j)) {
             x(i,j) = x(i-1,j) - vertical_gap_;
-            cigar(i,j) = down;
+            directions(i,j) = down;
           }
         }
         else if (x(i-1,j) - vertical_gap_ - open_vertical_gap_ > x(i,j)) {
           x(i,j) = x(i-1,j) - vertical_gap_ - open_vertical_gap_;
-          cigar(i,j) = down;
+          directions(i,j) = down;
         }
       }
@@ -118 +118 @@
 
 
-  Aligner::direction& Aligner::cigar(size_t i, size_t j)
+  Aligner::direction& Aligner::directions(size_t i, size_t j)
   {
     return alignment_[i*columns_ + j];