Allow penalized in global alignment (fix)

ChangeLog

@@ -1,6 +1,10 @@
 <<<<<<< HEAD
 === 2018
 
+
+2.0.0RC5 (2018-05-08)
+	Allow penalized in global alignment
+
 2.0.0RC4 (2018-05-04)
 	Bugfixes:
 	---------
@@ -18,7 +22,6 @@
 	------------------------
         Add stopwatch (for consensus computation)
 	Introduce parameter --consensus-gamma for mea consensus 'gamma'
-	Allow penalized in global alignment
 
 	API:
 	------------------------

configure.ac

@@ -2,7 +2,7 @@ dnl                                               -*- Autoconf -*-
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([LocARNA], [2.0.0RC4], [will@informatik.uni-freiburg.de], [locarna],
+AC_INIT([LocARNA], [2.0.0RC5], [will@informatik.uni-freiburg.de], [locarna],
         [http://www.bioinf.uni-freiburg.de/Software/LocARNA/])
 
 dnl special dir for aux config files

src/LocARNA/aligner.cc

@@ -733,14 +733,15 @@ namespace LocARNA {
 
     // align the top level in case of free end gaps
     //
+    template <class ScoringView>
     infty_score_t
-    AlignerImpl::align_top_level_free_endgaps() {
+    AlignerImpl::align_top_level_free_endgaps(const ScoringView *sv) {
 
         M_matrix_t &M = Ms_[E_NO_NO];
 
         init_state(E_NO_NO, r_.startA() - 1, r_.endA() + 1, r_.startB() - 1,
                    r_.endB() + 1, !params_->free_endgaps_.allow_left_2(), false,
-                   !params_->free_endgaps_.allow_left_1(), false, &def_scoring_view_);
+                   !params_->free_endgaps_.allow_left_1(), false, sv);
 
         // need to handle anchor constraints:
         // search maximum to the right of (or at) rightmost anchor constraint
@@ -761,7 +762,7 @@ namespace LocARNA {
 
             for (pos_type j = min_col; j <= max_col; j++) {
                 M(i, j) = align_noex(E_NO_NO, r_.startA() - 1, r_.startB() - 1,
-                                     i, j, &def_scoring_view_);
+                                     i, j, sv);
             }
         }
 
@@ -936,7 +937,7 @@ namespace LocARNA {
 
             // align toplevel globally with potentially free endgaps (as given
             // by description params_->free_endgaps)
-            return align_top_level_free_endgaps();
+            return align_top_level_free_endgaps(&def_scoring_view_);
 
             // Without free end gaps, we could call (much simpler):
             // (we just call the more general method
@@ -1608,8 +1609,12 @@ namespace LocARNA {
 
         mod_scoring_view->set_lambda(position_penalty);
 
-        infty_score_t score =
-            align_top_level_locally(mod_scoring_view.get());
+        infty_score_t score;
+        if (params_->sequ_local_) {
+            score = align_top_level_locally(mod_scoring_view.get());
+        } else {
+            score = align_top_level_free_endgaps(mod_scoring_view.get());
+        }
 
         trace(mod_scoring_view.get());
 

src/LocARNA/aligner_impl.hh

@@ -395,8 +395,9 @@ namespace LocARNA {
          * align the top-level with potential free end gaps
          * and return the maximal score
          */
+        template <class ScoringView>
         infty_score_t
-        align_top_level_free_endgaps();
+        align_top_level_free_endgaps(const ScoringView *s);
 
         /**
          * align the top-level in a sequence local alignment

src/locarna.cc

@@ -422,6 +422,7 @@ run_and_report() {
             clp.sequ_local = true;
         }
     }
+
     //
     // important: in the Aligner class, we rely on sequ_local==true in
     // normalized alignment mode