fixup: Enabled automatic creation of terminal...

segmentmodel.py

@@ -2059,17 +2059,17 @@ class SegmentModel(ArbdModel):
         """ Ensure unconnected ends have 5prime Location objects """
         for seg in self.segments:
             ## TODO move into Segment calls
-            five_prime_locs = seg.get_locations("5prime")
-            three_prime_locs = seg.get_locations("3prime")
+            five_prime_locs = sum([seg.get_locations(s) for s in ("5prime","crossover","terminal_crossover")],[])
+            three_prime_locs = sum([seg.get_locations(s) for s in ("3prime","crossover","terminal_crossover")],[])
 
             def is_start_5prime(l):
                 return l.get_nt_pos() < 1 and l.on_fwd_strand
             def is_end_5prime(l):
-                return l.get_nt_pos() > seg.num_nt-1 and not l.on_fwd_strand
+                return l.get_nt_pos() > seg.num_nt-2 and not l.on_fwd_strand
             def is_start_3prime(l):
                 return l.get_nt_pos() < 1 and not l.on_fwd_strand
             def is_end_3prime(l):
-                return l.get_nt_pos() > seg.num_nt-1 and l.on_fwd_strand
+                return l.get_nt_pos() > seg.num_nt-2 and l.on_fwd_strand
 
             if seg.start5.connection is None:
                 if len(list(filter( is_start_5prime, five_prime_locs ))) == 0: