added direction serialization to the software

cadnano/fileio/v3decode.py

@@ -18,7 +18,8 @@
 )
 from cadnano.objectinstance import ObjectInstance
 from cadnano.cntypes import (
-    DocT
+    DocT,
+    Vec3T
 )
 
 def decode(document: DocT, obj: dict, emit_signals: bool = True):
@@ -134,6 +135,7 @@ def decodePart( document: DocT,
     vh_id_list = part_dict.get('vh_list')
     vh_props = part_dict.get('virtual_helices')
     origins = part_dict.get('origins', [])
+    directions = part_dict.get('directions', [])
     keys = list(vh_props.keys())
 
     if len(origins) == 0:
@@ -142,10 +144,12 @@ def decodePart( document: DocT,
     if not is_lattice or len(origins[0]) == 3:
         for id_num, size in vh_id_list:
             x, y, z = origins[id_num]
+            direction = directions[id_num]
             vh_props['eulerZ'][id_num] = 0.5*(360./10.5)
             vals = [vh_props[k][id_num] for k in keys]
             part.createVirtualHelix(x, y, z, size,
                                     id_num=id_num,
+                                    direction=direction,
                                     properties=(keys, vals),
                                     safe=False,
                                     use_undostack=False)
@@ -272,6 +276,7 @@ def importToPart(   part_instance : ObjectInstance,
         id_num_offset += 1
     vh_id_list = copy_dict['vh_list']
     origins = copy_dict['origins']
+    directions = copy_dict['directions']
     vh_props = copy_dict['virtual_helices']
     name_suffix = ".%d"
 
@@ -289,7 +294,11 @@ def importToPart(   part_instance : ObjectInstance,
 
     for i, pair in enumerate(vh_id_list):
         id_num, size = pair
+
+        ''' using `i` because we could be using a subset of all virtual
+        helices in a part'''
         x, y, z = origins[i]
+        the_dir: Vec3T = directions[i]
 
         if offset is not None:
             x += offx
@@ -318,6 +327,7 @@ def importToPart(   part_instance : ObjectInstance,
 
         did_create = part.createVirtualHelix(x, y, z, size,
                                 id_num=new_id_num,
+                                direction=the_dir,
                                 properties=(fixed_keys, fixed_vals),
                                 safe=use_undostack,
                                 use_undostack=use_undostack)

cadnano/fileio/v3encode.py

@@ -47,13 +47,20 @@ def encodePart(part: PartT) -> dict:
     group_props = part.getModelProperties().copy()
 
     if not group_props.get('is_lattice', True):
-        vh_props, origins = part.helixPropertiesAndOrigins()
+        vh_props, origins, directions = part.helixProperties()
         group_props['virtual_helices'] = vh_props
         group_props['origins'] = origins
+        group_props['directions'] = directions
     else:
-        vh_props, origins = part.helixPropertiesAndOrigins()
+        vh_props, origins, directions = part.helixProperties()
         group_props['virtual_helices'] = vh_props
         group_props['origins'] = origins
+        group_props['directions'] = directions
+
+    # print("ORIGINS")
+    # print(group_props['origins'])
+    # print("DIRECTIONS")
+    # print(group_props['directions'])
 
     xover_list = []
     strand_list = []
@@ -98,13 +105,15 @@ def reEmitPart(part: PartT):
     group_props = part.getModelProperties().copy()
 
     if not group_props.get('is_lattice', True):
-        vh_props, origins = part.helixPropertiesAndOrigins()
+        vh_props, origins, directions = part.helixProperties()
         group_props['virtual_helices'] = vh_props
         group_props['origins'] = origins
+        group_props['directions'] = directions
     else:
-        vh_props, origins = part.helixPropertiesAndOrigins()
+        vh_props, origins, directions = part.helixProperties()
         group_props['virtual_helices'] = vh_props
         group_props['origins'] = origins
+        group_props['directions'] = directions
 
     xover_list = []
     threshold = 2.1*part.radius()
@@ -152,7 +161,8 @@ def reEmitPart(part: PartT):
 # end def
 
 
-def encodePartList(part_instance: ObjectInstance, vh_group_list: List[int]) -> dict:
+def encodePartList( part_instance: ObjectInstance,
+                    vh_group_list: List[int]) -> dict:
     """ Used for copying and pasting
     TODO: unify encodePart and encodePartList
 
@@ -178,13 +188,15 @@ def encodePartList(part_instance: ObjectInstance, vh_group_list: List[int]) -> d
     assert('grid_type' in group_props)
 
     if not group_props.get('is_lattice', True):
-        vh_props, origins = part.helixPropertiesAndOrigins()
+        vh_props, origins, directions = part.helixProperties()
         group_props['virtual_helices'] = vh_props
         group_props['origins'] = origins
+        group_props['directions'] = directions
     else:
-        vh_props, origins = part.helixPropertiesAndOrigins(vh_group_list)
+        vh_props, origins, directions = part.helixProperties(vh_group_list)
         group_props['virtual_helices'] = vh_props
         group_props['origins'] = origins
+        group_props['directions'] = directions
 
     xover_list = []
     strand_list = []

cadnano/part/nucleicacidpart.py

@@ -1307,8 +1307,8 @@ def getVirtualHelixProperties(self, id_num: int,
             return props.item() if isinstance(props, (np.float64, np.int64, np.bool_)) else props
     # end
 
-    def helixPropertiesAndOrigins(self,
-                id_num_list: List[int] = None) -> Tuple[dict, np.ndarray]:
+    def helixProperties(self,
+                id_num_list: List[int] = None) -> Tuple[dict, np.ndarray, np.ndarray]:
         """
         Args:
             id_num_list (list): optional, of :obj:`int` list of virtual
@@ -1324,18 +1324,20 @@ def helixPropertiesAndOrigins(self,
             ValueError:
         """
         if id_num_list is None:
-            lim = max(self._highest_even_id_num_used + 2,
-                      self._highest_odd_id_num_used + 2)
+            lim = max(self._highest_even_id_num_used + 1,
+                      self._highest_odd_id_num_used + 1)
             props = self.vh_properties.iloc[:lim]
             props = props.to_dict(orient='list')
             origins = self._origin_pts[:lim]
-            return props, origins
+            directions = self.directions[:lim]
+            return props, origins, directions
         elif isinstance(id_num_list, list):
             # select by list of indices
             props = self.vh_properties.iloc[id_num_list].reset_index(drop=True)
             props = props.to_dict(orient='list')
             origins = self._origin_pts[id_num_list]
-            return props, origins
+            directions = self.getDirections(id_num_list)
+            return props, origins, directions
         else:
             raise ValueError("id_num_list bad type: {}".format(type(id_num_list)))
     # end def