Enabled automatic creation of terminal 5prime and 3prime ends

segmentmodel.py

@@ -2061,41 +2061,33 @@ class SegmentModel(ArbdModel):
         """ Ensure unconnected ends have 5prime Location objects """
         for seg in self.segments:
             ## TODO move into Segment calls
-            import pdb
-            if False: # TODO: Make this happen conditionally
-                if seg.start5.connection is None:
-                    add_end = True
-                    for l in seg.get_locations("5prime"):
-                        if l.address == 0 and l.on_fwd_strand:
-                            add_end = False
-                            break
-                    if add_end:
-                        seg.add_5prime(0) 
-                if 'end5' in seg.__dict__ and seg.end5.connection is None:
-                    add_end = True
-                    for l in seg.get_locations("5prime"):
-                        if l.address == 1 and (l.on_fwd_strand is False):
-                            add_end = False
-                            break
-                    if add_end:
-                        seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
-
-                if 'start3' in seg.__dict__ and seg.start3.connection is None:
-                    add_end = True
-                    for l in seg.get_locations("3prime"):
-                        if l.address == 0 and (l.on_fwd_strand is False):
-                            add_end = False
-                            break
-                    if add_end:
-                        seg.add_3prime(0,on_fwd_strand=False)
-                if seg.end3.connection is None:
-                    add_end = True
-                    for l in seg.get_locations("3prime"):
-                        if l.address == 1 and l.on_fwd_strand:
-                            add_end = False
-                            break
-                    if add_end:
-                        seg.add_3prime(seg.num_nt-1)
+            five_prime_locs = seg.get_locations("5prime")
+            three_prime_locs = seg.get_locations("3prime")
+
+            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
+            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
+
+            if seg.start5.connection is None:
+                if len(list(filter( is_start_5prime, five_prime_locs ))) == 0:
+                    seg.add_5prime(0) # TODO ensure this is the same place
+
+            if 'end5' in seg.__dict__ and seg.end5.connection is None:
+                if len(list(filter( is_end_5prime, five_prime_locs ))) == 0:
+                    seg.add_5prime(seg.num_nt-1,on_fwd_strand=False)
+
+            if 'start3' in seg.__dict__ and seg.start3.connection is None:
+                if len(list(filter( is_start_3prime, three_prime_locs ))) == 0:
+                    seg.add_3prime(0,on_fwd_strand=False)
+
+            if seg.end3.connection is None:
+                if len(list(filter( is_end_3prime, three_prime_locs ))) == 0:
+                    seg.add_3prime(seg.num_nt-1)
 
             # print( [(l,l.get_connected_location()) for l in seg.locations] )
             # addresses = np.array([l.address for l in seg.get_locations("5prime")])