Fixed issues with skips at crossovers, but needs testing

cadnano_segments.py

@@ -247,7 +247,7 @@ class cadnano_part(SegmentModel):
                 rev_idxs, rev_colors  = rev_ss.dump(xover_list)
             
                 strand_list.append((fwd_idxs, rev_idxs))
-        
+
         ## Get lists of 5/3prime ends
         strands5 = [o.strand5p() for o in part.oligos()]
         strands3 = [o.strand3p() for o in part.oligos()]
@@ -401,7 +401,7 @@ class cadnano_part(SegmentModel):
                 nt += self.insertions[hid][i].length()
         return nt
 
-    def _get_segment_nucleotide(self, hid, zid):
+    def _get_segment_nucleotide(self, hid, zid, get_forward_location=False):
         """ returns segments and zero-based nucleotide index """
         seg = self._get_segment(hid,zid)
         sid = self.helices[hid].index(seg)
@@ -409,23 +409,36 @@ class cadnano_part(SegmentModel):
 
         zMid = int(0.5*(zmin+zmax))
         occ = self.strand_occupancies[hid]
+        ins = self.insertions[hid]
 
         ## TODO combine if/else when nested TODO is resolved
+        # if zid in self.insertions[hid]:
+        #     import pdb
+        #     pdb.set_trace()
+
         if (zMid not in occ[0]) and (zMid in occ[1]):
             ## reversed ssDNA strand
             nt = zmax-zid
             # TODO: for i in range(zmin,zid+1): ?
-            for i in range(zid,zmax):
+            for i in range(zid,zmax+1):
                 if i in self.insertions[hid]:
                     nt += self.insertions[hid][i].length()
         else:
             ## normal condition
+            if get_forward_location:
+                while zid in ins and ins[zid].length() < 0 and zid <= zmax:
+                    zid+=1
+            # else:
+            #     while zid in ins and ins[zid].length() > 0 and zid >= zmax:
+            #         zid-=1
             nt = zid-zmin
-            # TODO: for i in range(zmin,zid+1): ?
             for i in range(zmin,zid):
-                if i in self.insertions[hid]:
-                    nt += self.insertions[hid][i].length()
+                if i in ins:
+                    nt += ins[i].length()
 
+            if not get_forward_location and zid in ins:
+                nt += ins[zid].length()
+                
         ## Find insertions
         return seg, nt
 
@@ -464,12 +477,14 @@ class cadnano_part(SegmentModel):
     def _add_crossovers(self):
         for h1,f1,z1,h2,f2,z2 in self.xover_list:
             # if (h1 == 52 or h2 == 52) and z1 == 221:
-            #     import pdb
-            #     pdb.set_trace()
-            seg1, nt1 = self._get_segment_nucleotide(h1,z1)
-            seg2, nt2 = self._get_segment_nucleotide(h2,z2)
+            if (h1 == 15 and z1 == 230) or h2 == 15 and z2 == 231:
+                import pdb
+                pdb.set_trace()
+            seg1, nt1 = self._get_segment_nucleotide(h1,z1,not f1)
+            seg2, nt2 = self._get_segment_nucleotide(h2,z2,f2)
             ## TODO: use different types of crossovers
             ## fwd?
+            ## 5'-to-3' direction
             seg1.add_crossover(nt1,seg2,nt2,[f1,f2])
 
     def _add_prime_ends(self):

segmentmodel.py

@@ -1047,10 +1047,9 @@ class Strand(Group):
 
     ## TODO disambiguate names of functions
     def add_dna(self, segment, start, end, is_fwd):
-        # TODOTODO use nt pos ? 
-        """ start/end should be provided expressed as contour_length, is_fwd tuples """
-        if not (segment.contour_to_nt_pos(np.abs(start-end)) > 0.9):
-            print( "WARNING: segment constructed with a very small number of nts ({})".format(segment.contour_to_nt_pos(np.abs(start-end))) )
+        """ start/end are given as nt """
+        if np.abs(start-end) <= 0.9:
+            print( "WARNING: segment constructed with a very small number of nts ({})".format(np.abs(start-end)) )
             # import pdb
             # pdb.set_trace()
         for s in self.strand_segments: