From 122445cddf0a67b0d6b44a08074d914fcc22bf8f Mon Sep 17 00:00:00 2001
From: Benjamin Lee <bnllee@ucdavis.edu>
Date: Thu, 12 May 2022 16:41:49 -0700
Subject: [PATCH] In to, check for 3' extension; fixed some tests

---
 scadnano/scadnano.py    |  9 +++++++++
 tests/scadnano_tests.py | 10 ++++++----
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py
index 6b086c8a..ea31a71f 100644
--- a/scadnano/scadnano.py
+++ b/scadnano/scadnano.py
@@ -2351,6 +2351,9 @@ def to(self, offset: int) -> 'StrandBuilder[StrandLabel, DomainLabel]':
                                      '(strictly increasing or strictly decreasing) '
                                      'when calling to() twice in a row')
 
+        if self._contains_extension_3p():
+            raise IllegalDesignError('cannot make a new domain once 3\' extension has been added')
+
         if offset > self.current_offset:
             forward = True
             start = self.current_offset
@@ -2374,6 +2377,12 @@ def to(self, offset: int) -> 'StrandBuilder[StrandLabel, DomainLabel]':
 
         return self
 
+    def _contains_extension_3p(self) -> bool:
+        if self._strand is None:
+            return False
+        domains = self._strand.domains
+        return len(domains) > 1 and isinstance(domains[-1], Extension)
+
     # remove quotes when Py3.6 support dropped
     def update_to(self, offset: int) -> 'StrandBuilder[StrandLabel, DomainLabel]':
         """
diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py
index bf0ca38c..b7ce7d33 100644
--- a/tests/scadnano_tests.py
+++ b/tests/scadnano_tests.py
@@ -121,13 +121,14 @@ def test_strand__5p_extension(self) -> None:
 
     def test_strand__update_to_after_5p_extension_ok(self) -> None:
         design = self.design_6helix
-        sb = design.draw_strand(0, 0, extension_5p_length=5)
+        sb = design.draw_strand(0, 0)
+        sb.extension_5p(5)
 
         sb.to(10)
         sb.update_to(15)
 
         expected_strand: sc.Strand = sc.Strand([
-            sc.Extension(5, (-1, -1)),
+            sc.Extension(5),
             sc.Domain(0, True, 0, 15),
         ])
 
@@ -136,12 +137,13 @@ def test_strand__update_to_after_5p_extension_ok(self) -> None:
 
     def test_strand__move_after_5p_extension_ok(self) -> None:
         design = self.design_6helix
-        sb = design.draw_strand(0, 0, extension_5p_length=5)
+        sb = design.draw_strand(0, 0)
+        sb.extension_5p(5)
 
         sb.move(15)
 
         expected_strand: sc.Strand = sc.Strand([
-            sc.Extension(5, (-1, -1)),
+            sc.Extension(5),
             sc.Domain(0, True, 0, 15),
         ])