added with_deletions and with_insertions methods to `StrandBuilde…

…r` and used them in unit tests

scadnano/scadnano.py

@@ -2529,10 +2529,11 @@ def with_domain_name(self, name: str) -> 'StrandBuilder[StrandLabel, DomainLabel
         Assigns `name` as of the most recently created :any:`Domain` or :any:`Loopout` in
         the :any:`Strand` being built. This should be called immediately after a :any:`Domain` is created
         via a call to
-        :py:meth:`StrandBuilder.to`,
-        :py:meth:`StrandBuilder.update_to`,
+        :meth:`StrandBuilder.to`,
+        :meth:`StrandBuilder.move`,
+        :meth:`StrandBuilder.update_to`,
         or
-        :py:meth:`StrandBuilder.loopout`, e.g.,
+        :meth:`StrandBuilder.loopout`, e.g.,
 
         .. code-block:: Python
 
@@ -2551,17 +2552,20 @@ def with_domain_name(self, name: str) -> 'StrandBuilder[StrandLabel, DomainLabel
     def with_domain_label(self, label: DomainLabel) -> 'StrandBuilder[StrandLabel, DomainLabel]':
         """
         Assigns `label` as label of the most recently created :any:`Domain` or :any:`Loopout` in
-        the :any:`Strand` being built. This should be called immediately after a :any:`Domain` is created
-        via a call to
-        :py:meth:`StrandBuilder.to`,
-        :py:meth:`StrandBuilder.update_to`,
+        the :any:`Strand` being built. This should be called immediately after
+        a :any:`Domain` or :any:`Loopout` is created via a call to
+        :meth:`StrandBuilder.to`,
+        :meth:`StrandBuilder.move`,
+        :meth:`StrandBuilder.update_to`,
         or
-        :py:meth:`StrandBuilder.loopout`, e.g.,
+        :meth:`StrandBuilder.loopout`, e.g.,
 
         .. code-block:: Python
 
-            design.draw_strand(0, 5).to(8).with_domain_label('domain 1')\\
-                .cross(1).to(5).with_domain_label('domain 2')\\
+            design.draw_strand(0, 5)\\
+                .to(8).with_domain_label('domain 1')\\
+                .cross(1)\\
+                .to(5).with_domain_label('domain 2')\\
                 .loopout(2, 4).with_domain_label('domain 3')\\
                 .to(10).with_domain_label('domain 4')
 
@@ -2574,6 +2578,90 @@ def with_domain_label(self, label: DomainLabel) -> 'StrandBuilder[StrandLabel, D
         last_domain.set_label(label)
         return self
 
+    def with_deletions(self,
+                       deletions: Union[int, Iterable[int]]) -> 'StrandBuilder[StrandLabel, DomainLabel]':
+        """
+        Assigns `deletions` as the deletion(s) of the most recently created
+        :any:`Domain` the :any:`Strand` being built. This should be called immediately after
+        a :any:`Domain` is created via a call to
+        :meth:`StrandBuilder.to`,
+        :meth:`StrandBuilder.move`,
+        :meth:`StrandBuilder.update_to`, e.g.,
+
+        .. code-block:: Python
+
+            design.draw_strand(0, 0)\\
+                .move(8).with_deletions(4)\\
+                .cross(1)\\
+                .move(-8).with_deletions([2, 3])
+
+        :param deletions:
+            a single int, or an Iterable of ints, indicating the offset at which to put the deletion(s)
+        :return: self
+        """
+        if self._strand is None:
+            raise ValueError('no Strand created yet; make at least one domain first')
+        last_domain = self._strand.domains[-1]
+
+        if not isinstance(last_domain, Domain):
+            raise ValueError(f'can only create a deletion on a bound Domain, not a {type(last_domain)};\n'
+                             f'be sure only to call with_deletions immediately after a call to '
+                             f'to, move, or update_to')
+        if not isinstance(deletions, int) and not hasattr(deletions, '__iter__'):
+            raise ValueError(f'deletions must be a single int or an iterable of ints, '
+                             f'but it is {type(deletions)}')
+        if isinstance(deletions, int):
+            last_domain.deletions = [deletions]
+        else:
+            last_domain.deletions = list(deletions)
+
+        return self
+
+    def with_insertions(self, insertions: Union[Tuple[int, int], Iterable[Tuple[int, int]]]) \
+            -> 'StrandBuilder[StrandLabel, DomainLabel]':
+        """
+        Assigns `insertions` as the insertion(s) of the most recently created
+        :any:`Domain` the :any:`Strand` being built. This should be called immediately after
+        a :any:`Domain` is created via a call to
+        :meth:`StrandBuilder.to`,
+        :meth:`StrandBuilder.move`,
+        :meth:`StrandBuilder.update_to`, e.g.,
+
+        .. code-block:: Python
+
+            design.draw_strand(0, 0)\\
+                .move(8).with_insertions((4, 2))\\
+                .cross(1)\\
+                .move(-8).with_insertions([(2, 3), (3, 3)])
+
+        :param insertions:
+            a single pair of ints (tuple), or an Iterable of pairs of ints (tuples)
+            indicating the offset at which to put the insertion(s)
+        :return: self
+        """
+        if self._strand is None:
+            raise ValueError('no Strand created yet; make at least one domain first')
+        last_domain = self._strand.domains[-1]
+        if not isinstance(last_domain, Domain):
+            raise ValueError(f'can only create an insertion on a bound Domain, not a {type(last_domain)};\n'
+                             f'be sure only to call with_insertions immediately after a call to '
+                             f'to, move, or update_to')
+
+        type_msg = (f'insertions must be a single pair of ints or an iterable of pairs of ints, '
+                    f'but it is {type(insertions)}')
+
+        if not hasattr(insertions, '__iter__'):
+            raise ValueError(type_msg)
+        if isinstance(insertions, tuple) and len(insertions) > 0 and isinstance(insertions[0], int):
+            last_domain.insertions = [insertions]
+        else:
+            for ins in insertions:
+                if not (isinstance(ins, tuple) and len(ins) > 0 and isinstance(ins[0], int)):
+                    raise ValueError(type_msg)
+            last_domain.insertions = list(insertions)
+
+        return self
+
 
 @dataclass
 class Strand(_JSONSerializable, Generic[StrandLabel, DomainLabel]):

tests/scadnano_tests.py

@@ -1710,6 +1710,26 @@ class TestInlineInsDel(unittest.TestCase):
     Tests inlining of insertions/deletions.
     """
 
+    def setUp(self) -> None:
+        self.design = sc.Design(
+            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
+            strands=[],
+            grid=sc.square)
+
+
+    def test_no_deletion_after_loopout(self) -> None:
+        # not really a test of inlining, but I added the with_deletions and with_insertions to help these
+        # tests, so easier just to test this behavior here
+        with self.assertRaises(ValueError):
+            self.design.draw_strand(0, 0).move(8).loopout(0, 5, 10).with_deletions(4)
+
+    def test_no_insertion_after_loopout(self) -> None:
+        # not really a test of inlining, but I added the with_deletions and with_insertions to help these
+        # tests, so easier just to test this behavior here
+        with self.assertRaises(ValueError):
+            self.design.draw_strand(0, 0).move(8).loopout(0, 5, 10).with_insertions((4, 2))
+
+
     def test_inline_deletions_insertions__one_deletion(self) -> None:
         """
         before
@@ -1722,10 +1742,8 @@ def test_inline_deletions_insertions__one_deletion(self) -> None:
         |      |       |       |
     0   [----->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 8, deletions=[4])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(8).with_deletions(4)
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=23, major_ticks=[0, 7, 15, 23], start=0, end=7)
 
@@ -1753,10 +1771,8 @@ def test_inline_deletions_insertions__two_deletions(self) -> None:
         |     |       |       |
     0   [---->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 8, deletions=[2, 4])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(8).with_deletions([2, 4])
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=22, major_ticks=[0, 6, 14, 22], start=0, end=6)
 
@@ -1772,10 +1788,8 @@ def test_inline_deletions_insertions__one_insertion(self) -> None:
         |        |       |       |
     0   [------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 8, insertions=[(4, 1)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(8).with_insertions((4, 1))
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=25, major_ticks=[0, 9, 17, 25], start=0, end=9)
 
@@ -1791,10 +1805,8 @@ def test_inline_deletions_insertions__two_insertions(self) -> None:
         |           |       |       |
     0   [---------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 8, insertions=[(2, 3), (4, 1)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(8).with_insertions([(2, 3), (4, 1)])
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=28, major_ticks=[0, 12, 20, 28], start=0, end=12)
 
@@ -1810,10 +1822,8 @@ def test_inline_deletions_insertions__one_deletion_one_insertion(self) -> None:
         |         |       |       |
     0   [-------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 8, deletions=[4], insertions=[(2, 3)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(8).with_deletions(4).with_insertions((2, 3))
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=26, major_ticks=[0, 10, 18, 26], start=0, end=10)
 
@@ -1829,10 +1839,8 @@ def test_inline_deletions_insertions__one_deletion_right_of_major_tick(self) ->
         |       |      |       |
     0   [--------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 12, deletions=[9])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(12).with_deletions(9)
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=23, major_ticks=[0, 8, 15, 23], start=0, end=11)
 
@@ -1849,10 +1857,8 @@ def test_inline_deletions_insertions__one_deletion_on_major_tick(self) -> None:
         | . . . . . . . | . . . . . . | . . . . . . . |
          [ - - - - - - - - - >
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 12, deletions=[8])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(12).with_deletions(8)
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=23, major_ticks=[0, 8, 15, 23], start=0, end=11)
 
@@ -1868,10 +1874,8 @@ def test_inline_deletions_insertions__one_deletion_left_of_major_tick(self) -> N
         |       |      |       |
     0   [--------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 12, deletions=[7])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(12).with_deletions(7)
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=23, major_ticks=[0, 7, 15, 23], start=0, end=11)
 
@@ -1887,10 +1891,8 @@ def test_inline_deletions_insertions__one_insertion_right_of_major_tick(self) ->
         |       |        |       |
     0   [----------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 12, insertions=[(9, 1)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(12).with_insertions((9, 1))
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=25, major_ticks=[0, 8, 17, 25], start=0, end=13)
 
@@ -1906,10 +1908,8 @@ def test_inline_deletions_insertions__one_insertion_on_major_tick(self) -> None:
         |       |        |       |
     0   [----------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 12, insertions=[(8, 1)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(12).with_insertions((8, 1))
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=25, major_ticks=[0, 8, 17, 25], start=0, end=13)
 
@@ -1925,10 +1925,8 @@ def test_inline_deletions_insertions__one_insertion_left_of_major_tick(self) ->
         |        |       |       |
     0   [----------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 12, insertions=[(7, 1)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(12).with_insertions((7, 1))
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=25, major_ticks=[0, 9, 17, 25], start=0, end=13)
 
@@ -1944,10 +1942,8 @@ def test_inline_deletions_insertions__deletions_insertions_in_multiple_domains(s
         |         |       |       |
     0   [------------------------->
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[sc.Strand([sc.Domain(0, True, 0, 24, deletions=[19], insertions=[(5, 2), (11, 1)])])],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(24).with_deletions(19).with_insertions([(5, 2), (11, 1)])
         design.inline_deletions_insertions()
         self.helix0_strand0_inlined_test(design, max_offset=26, major_ticks=[0, 10, 19, 26], start=0, end=26)
 
@@ -1964,13 +1960,9 @@ def test_inline_deletions_insertions__deletions_insertions_in_multiple_domains_t
         | . . . . . . . . | . . . . . . . . | . . . . . . |
          [ - - - - - - - - - - - - - - > [ - - - - - - - >
         """
-        design = sc.Design(
-            helices=[sc.Helix(max_offset=24, major_tick_distance=8)],
-            strands=[
-                sc.Strand([sc.Domain(0, True, 0, 14, deletions=[2], insertions=[(5, 2), (10, 1)])]),
-                sc.Strand([sc.Domain(0, True, 14, 24, deletions=[19])]),
-            ],
-            grid=sc.square)
+        design = self.design
+        design.draw_strand(0, 0).move(14).with_deletions(2).with_insertions([(5, 2), (10, 1)])
+        design.draw_strand(0, 14).to(24).with_deletions(19)
         design.inline_deletions_insertions()
         self.assertEqual(1, len(design.helices))
         self.assertEqual(2, len(design.strands))