From 2b485beecad86d0167eba2a532bfa61888221ca9 Mon Sep 17 00:00:00 2001
From: Benjamin Lee <bnllee@ucdavis.edu>
Date: Sun, 22 May 2022 21:29:45 -0700
Subject: [PATCH] Add ligate and half crossover error cases

---
 scadnano/scadnano.py    |  2 +-
 tests/scadnano_tests.py | 35 +++++++++++++++++++++++++++++++++--
 2 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py
index 8fa1aa71..8f5b1db4 100644
--- a/scadnano/scadnano.py
+++ b/scadnano/scadnano.py
@@ -7823,7 +7823,7 @@ def _convert_design_to_oxdna_system(design: Design) -> _OxdnaSystem:
             else:
                 # we place the loopout nucleotides at temporary nonsense positions and orientations
                 # these will be updated later, for now we just need the base
-                for i in range(domain.num_bases):
+                for i in range(domain.length):
                     base = seq[i]
                     nuc = _OxdnaNucleotide(_OxdnaVector(), _OxdnaVector(0, -1, 0), _OxdnaVector(0, 0, 1),
                                            base)
diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py
index 231468c6..03e85c82 100644
--- a/tests/scadnano_tests.py
+++ b/tests/scadnano_tests.py
@@ -3268,14 +3268,27 @@ def test_add_nick_then_add_crossovers__6_helix_rectangle(self) -> None:
         ])
         self.assertIn(scaf, self.origami.strands)
 
+    def test_ligate_on_middle_domain_should_error(self) -> None:
+        """
+        [-----+[----->
+              |
+        <-----+
+        """
+        design: sc.Design = sc.Design(helices=[sc.Helix(max_offset=100), sc.Helix(max_offset=100)])
+        design.draw_strand(0, 0).to(10).cross(1).to(0)
+        design.draw_strand(0, 10).to(20)
+
+        with self.assertRaises(sc.IllegalDesignError):
+            design.ligate(0, 10, True)
+
     def test_ligate_on_extension_side_should_error(self) -> None:
         """
                       ↗
                      /
                     /
             [-------[----->
-                   ^
-                   |
+                    ^
+                    |
           error to ligate here
         """
         design: sc.Design = sc.Design(helices=[sc.Helix(max_offset=100)])
@@ -3454,6 +3467,24 @@ def test_add_half_crossover_on_extension_error(self) -> None:
         with self.assertRaises(sc.IllegalDesignError):
             design.add_half_crossover(0, 1, 0, True)
 
+    def test_add_half_crossover_on_existing_crossover_should_error(self) -> None:
+        """
+        0  +------]
+           |
+        1  +------>
+
+        2  <------]
+        """
+        # Setup
+        design: sc.Design = sc.Design(
+            helices=[sc.Helix(max_offset=100), sc.Helix(max_offset=100), sc.Helix(max_offset=100)]
+        )
+        design.draw_strand(0, 10).to(0).cross(1).to(10)
+        design.draw_strand(2, 10).to(0)
+
+        with self.assertRaises(sc.IllegalDesignError):
+            design.add_half_crossover(1, 2, 0, True)
+
     def test_nick_on_extension(self) -> None:
         """
         Before: