fixes bug in checking for legal cadnano export

lib/src/middleware/all_middleware.dart

@@ -6,7 +6,7 @@ import 'dna_extensions_move_start.dart';
 import 'forbid_create_circular_strand_no_crossovers_middleware.dart';
 import 'helix_group_move_start.dart';
 import 'adjust_grid_position.dart';
-import 'export_cadnano_or_codenano_file.dart';
+import 'export_cadnano_file.dart';
 import 'assign_dna.dart';
 import 'check_mirror_strands_legal.dart';
 import 'edit_select_mode_change.dart';
@@ -48,7 +48,7 @@ final all_middleware = List<Middleware<AppState>>.unmodifiable([
   export_svg_middleware,
   save_file_middleware,
   load_file_middleware,
-  export_cadnano_or_codenano_file_middleware,
+  export_cadnano_file_middleware,
   example_design_selected_middleware,
   throttle_middleware,
   assign_dna_middleware,

lib/src/middleware/export_cadnano_or_codenano_file.dart → lib/src/middleware/export_cadnano_file.dart

@@ -22,14 +22,12 @@ import '../state/app_state.dart';
 import '../constants.dart' as constants;
 import '../util.dart' as util;
 
-export_cadnano_or_codenano_file_middleware(Store<AppState> store, dynamic action, NextDispatcher next) {
+export_cadnano_file_middleware(Store<AppState> store, dynamic action, NextDispatcher next) {
   next(action);
 
   AppState state = store.state;
   if (action is actions.ExportCadnanoFile) {
     _save_file_cadnano(state, action.whitespace);
-  } else if (action is actions.ExportCodenanoFile) {
-    _save_file_codenano(state);
   }
 }
 
@@ -48,73 +46,13 @@ _save_file_cadnano(AppState state, bool whitespace) async {
   }
 }
 
-_save_file_codenano(AppState state) async {
-  Design? design = state.maybe_design;
-  if (design == null) {
-    return;
-  }
-
-  var grids = design.groups.values.map((group) => group.grid).toSet();
-  if (!(grids.length == 1 && grids.first == Grid.none)) {
-    var msg = 'Grid must be set to none for all helix groups to export to codenano. '
-        'First convert all grids to none.';
-    window.alert(msg);
-    return;
-  }
-
-  Map design_json = state.design.to_json_serializable(suppress_indent: true);
-
-  // codenano parameters; taken from an example file
-  design_json['parameters'] = {
-    "z_step": 0.332,
-    "helix_radius": 1.0,
-    "bases_per_turn": 10.5,
-    "groove_angle": -2.2175948142986774,
-    "inter_helix_gap": 0.65,
-  };
-
-  // change version to version of codenano when I got the example file
-  design_json[constants.version_key] = '0.4.12';
-
-  List helices_json = design_json[constants.helices_key];
-  for (Map<String, dynamic> helix_json in helices_json) {
-    // add pitch, roll, and yaw defaults explicitly, and convert to radians
-    for (var angle_key in [constants.pitch_key, constants.roll_key, constants.yaw_key]) {
-      double? degrees = helix_json[angle_key];
-      helix_json[angle_key] = degrees == null ? 0.0 : util.to_radians(degrees);
-    }
-    // change "position" to "origin"
-    var pos = helix_json[constants.position_key];
-    helix_json.remove(constants.position_key);
-    helix_json['origin'] = pos;
-  }
-
-  List strands_json = design_json[constants.strands_key];
-  for (Map strand_json in strands_json) {
-    // change color to integer convention
-    if (strand_json.containsKey(constants.color_key)) {
-      var color = strand_json[constants.color_key];
-      var color_int = util.color_hex_to_decimal_int(color);
-      strand_json[constants.color_key] = color_int;
-    }
-    // change "forward" to "right"
-    for (NoIndent no_indent_json in strand_json[constants.substrands_key]) {
-      Map domain_json = no_indent_json.value;
-      if (!domain_json.containsKey(constants.forward_key)) {
-        window.alert('To export, strands cannot have any loopouts. '
-            'Please remove all loopouts before exporting.');
-        return;
-      }
-      bool forward = domain_json[constants.forward_key];
-      domain_json.remove(constants.forward_key);
-      domain_json['right'] = forward;
-    }
-  }
-
-  var encoder = SuppressableIndentEncoder(Replacer(), suppress: true);
-  var json_str = encoder.convert(design_json);
-  var default_filename = path.setExtension(state.ui_state.loaded_filename, '-codenano.json');
-  util.save_file(default_filename, json_str);
+/// Converts the design to the cadnano v2 format.
+/// Please see the spec [`misc/cadnano-format-specs/v2.txt`](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/main/misc/cadnano-format-specs/v2.txt)
+/// for more info on that format.
+String to_cadnano_v2_json(Design design, [String name = ""]) {
+  var encoder = SuppressableIndentEncoder(Replacer());
+  var content_serializable = to_cadnano_v2_serializable(design, name);
+  return encoder.convert(content_serializable);
 }
 
 /// Converts the design to the cadnano v2 format.
@@ -210,15 +148,6 @@ Map<String, dynamic> to_cadnano_v2_serializable(Design design, [String name = ""
   return dct;
 }
 
-/// Converts the design to the cadnano v2 format.
-/// Please see the spec [`misc/cadnano-format-specs/v2.txt`](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/blob/main/misc/cadnano-format-specs/v2.txt)
-/// for more info on that format.
-String to_cadnano_v2_json(Design design, [String name = ""]) {
-  var encoder = SuppressableIndentEncoder(Replacer());
-  var content_serializable = to_cadnano_v2_serializable(design, name);
-  return encoder.convert(content_serializable);
-}
-
 int _get_multiple_of_x_sup_closest_to_y(int x, int y) {
   return y % x == 0 ? y : y + (x - y % x);
 }
@@ -419,9 +348,21 @@ void _cadnano_v2_place_crossover(Map<String, dynamic> helix_from_dct, Map<String
     helix_from_dct[strand_type][end_from - 1]
         .setRange(2, helix_from_dct[strand_type][end_from - 1].length, [helix_to, start_to]);
     helix_to_dct[strand_type][end_to - 1].setRange(0, 2, [helix_from, start_from]);
+    if (helix_from_dct['row'] % 2 != helix_to_dct['row'] % 2) {
+      throw new IllegalCadnanoDesignError('''\
+Paranemic crossovers are only allowed between helices that have the same parity of 
+row number, here helix num ${helix_from_dct['num']} and helix num ${helix_to_dct['num']} 
+have different parity of row number: respectively ${helix_from_dct['row']} and ${helix_to_dct['row']}''');
+    }
   } else if (!forward_from && !forward_to) {
     helix_from_dct[strand_type][start_from]
         .setRange(2, helix_from_dct[strand_type][start_from].length, [helix_to, end_to - 1]);
     helix_to_dct[strand_type][start_to].setRange(0, 2, [helix_from, end_from - 1]);
+    if (helix_from_dct['row'] % 2 != helix_to_dct['row'] % 2) {
+      throw new IllegalCadnanoDesignError('''\
+Paranemic crossovers are only allowed between helices that have the same parity of 
+row number, here helix num ${helix_from_dct['num']} and helix num ${helix_to_dct['num']} 
+have different parity of row number: respectively ${helix_from_dct['row']} and ${helix_to_dct['row']}''');
+    }
   }
 }

lib/src/middleware/oxdna_export.dart

@@ -20,7 +20,7 @@ import '../state/app_state.dart';
 import '../actions/actions.dart' as actions;
 import '../state/helix.dart';
 import '../util.dart' as util;
-import 'export_cadnano_or_codenano_file.dart' as export_cadnano;
+import 'export_cadnano_file.dart' as export_cadnano;
 import '../constants.dart' as constants;
 
 oxdna_export_middleware(Store<AppState> store, dynamic action, NextDispatcher next) {

lib/src/middleware/oxview_update_view.dart

@@ -23,7 +23,7 @@ import '../actions/actions.dart' as actions;
 import '../state/helix.dart';
 import '../util.dart' as util;
 import '../util.dart';
-import 'export_cadnano_or_codenano_file.dart' as export_cadnano;
+import 'export_cadnano_file.dart' as export_cadnano;
 import '../constants.dart' as constants;
 import 'oxdna_export.dart';
 import '../app.dart';

test/export_cadnano_v2_test.dart

@@ -1,7 +1,7 @@
 import 'package:built_collection/built_collection.dart';
 import 'package:scadnano/src/actions/actions.dart';
 import 'package:scadnano/src/json_serializable.dart';
-import 'package:scadnano/src/middleware/export_cadnano_or_codenano_file.dart';
+import 'package:scadnano/src/middleware/export_cadnano_file.dart';
 import 'package:scadnano/src/state/design.dart';
 import 'package:scadnano/src/state/domain.dart';
 import 'package:scadnano/src/state/grid.dart';
@@ -296,6 +296,22 @@ main() {
       expect(output_design.helices.length, 4);
     });
 
+    test('test_paranemic_crossover_other_direction', () async {
+      var helices = [
+        Helix(idx: 1, max_offset: 64, grid_position: GridPosition(19, 14), grid: Grid.square),
+        Helix(idx: 0, max_offset: 64, grid_position: GridPosition(19, 15), grid: Grid.square),
+        Helix(idx: 3, max_offset: 64, grid_position: GridPosition(19, 16), grid: Grid.square),
+        Helix(idx: 2, max_offset: 64, grid_position: GridPosition(19, 17), grid: Grid.square),
+      ];
+      var design = Design(helices: helices);
+      design = design.draw_strand(3, 24).to(8).cross(1, 24).to(8).commit();
+      design = design.draw_strand(2, 50).to(24).cross(0, 50).to(24).commit();
+
+      String output_json = to_cadnano_v2_json(design);
+      Design output_design = Design.from_cadnano_v2_json_str(output_json);
+      expect(output_design.helices.length, 4);
+    });
+
     // We do not handle Loopouts and design where the parity of the helix
     // does not correspond to the direction.
     test('test_parity_issue', () {