closes #993 allow per-helix-group geometry

lib/src/middleware/dna_extensions_move_start.dart

@@ -34,12 +34,15 @@ dna_extensions_move_start_middleware(Store<AppState> store, action, NextDispatch
           helix,
           store.state.helix_idx_to_svg_position_map[extension.adjacent_domain.helix]!.y);
 
+      var group = design.groups[helix.group]!;
+      var geometry = group.geometry ?? design.geometry;
+
       // extension_start_point is in helix group coordinate space, so add it with helix group position
       // to get canvas coordinate space
-      extension_start_point += design.groups[helix.group]!.translation(design.geometry);
+      extension_start_point += group.translation(geometry);
 
       var extension_end_point = util.compute_extension_free_end_svg(
-          extension_start_point, extension, extension.adjacent_domain, design.geometry);
+          extension_start_point, extension, extension.adjacent_domain, geometry);
       var color = design.extension_end_to_strand(end).color;
       var move = DNAExtensionMove(
           dna_end: end,

lib/src/middleware/helices_positions_set_based_on_crossovers.dart

@@ -53,14 +53,15 @@ List<actions.UndoableAction> get_helix_position_and_roll_actions(AppState state)
   for (var group_name in state.design.groups.keys) {
     if (group_names_to_skip.contains(group_name)) continue;
     var group = state.design.groups[group_name]!;
+    var geometry = group.geometry ?? state.design.geometry;
     List<Helix> helices = _get_helices_to_process(state, group);
     List<Tuple2<Address, Address>>? addresses = _get_addresses_to_process(state, helices);
     if (addresses == null) {
       continue;
     }
     double first_roll = helices[0].roll;
     List<RollXY> rolls_and_positions =
-        _calculate_rolls_and_positions(state.design, helices, addresses, first_roll);
+        _calculate_rolls_and_positions(state.design, geometry, helices, addresses, first_roll);
     var all_actions_this_group = set_rolls_and_positions(helices, rolls_and_positions);
     all_actions.addAll(all_actions_this_group);
   }
@@ -277,12 +278,10 @@ class RollXY {
 /// Return list of rolls, same length as [helices], giving the roll that each should be to point
 /// each pair of helix backbones at each other through the given [addresses].
 /// The first roll is [first_roll].
-List<RollXY> _calculate_rolls_and_positions(
-    Design design, List<Helix> helices, List<Tuple2<Address, Address>> addresses, double first_roll) {
+List<RollXY> _calculate_rolls_and_positions(Design design, Geometry geometry, List<Helix> helices,
+    List<Tuple2<Address, Address>> addresses, double first_roll) {
   assert(helices.length == addresses.length + 1);
 
-  Geometry geometry = design.geometry;
-
   double x = helices[0].position3d.z;
   double y = helices[0].position3d.y;
   List<RollXY> rollxys = [RollXY(roll: first_roll, x: x, y: y)];

lib/src/middleware/helix_grid_change.dart

@@ -15,7 +15,8 @@ helix_grid_offsets_middleware(Store<AppState> store, dynamic action, NextDispatc
   if (action is actions.GridChange &&
       !action.grid.is_none &&
       store.state.design.groups[action.group_name]!.grid.is_none) {
-    Geometry geometry = store.state.design.geometry;
+    var group = store.state.design.groups[action.group_name]!;
+    Geometry geometry = group.geometry ?? store.state.design.geometry;
     Map<int, GridPosition> new_grid_positions_map = {
       for (var helix in store.state.design.helices_in_group(action.group_name).values)
         helix.idx: util.position3d_to_grid_position(helix.position, action.grid, geometry)

lib/src/middleware/oxdna_export.dart

@@ -425,7 +425,7 @@ Tuple3<OxdnaVector, OxdnaVector, OxdnaVector> oxdna_get_helix_vectors(Design des
   */
   var group = design.groups[helix.group]!;
   var grid = group.grid;
-  var geometry = design.geometry;
+  var geometry = group.geometry ?? design.geometry;
 
   // var forward = OxdnaVector(0, 0, 1);
   // var normal = OxdnaVector(0, -1, 0);
@@ -482,8 +482,6 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
   }
 
   var system = OxdnaSystem();
-  var geometry = design.geometry;
-  var step_rot = -360 / geometry.bases_per_turn;
 
   // each entry is the number of insertions - deletions since the start of a given helix
   Map<int, List<int>> mod_map = {};
@@ -533,6 +531,9 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
       // handle normal domains
       if (domain is Domain) {
         var helix = design.helices[domain.helix]!;
+        var group = design.groups[helix.group]!;
+        var geometry = group.geometry ?? design.geometry;
+        var step_rot = -360 / geometry.bases_per_turn;
         var origin_forward_normal = helix_vectors[helix.idx]!;
         var origin = origin_forward_normal.item1;
         var forward = origin_forward_normal.item2;
@@ -554,7 +555,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
           insertions[insertion.offset] = insertion.length;
         }
 
-        // use Design.geometry field to figure out various distances
+        // use Design.geometry or HelixGroup.geometry field to figure out various distances
         // https://github.com/UC-Davis-molecular-computing/scadnano/blob/master/lib/src/state/geometry.dart
 
         // index is used for finding the base in our sequence
@@ -608,8 +609,16 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
         strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, true));
       } else if (domain is Extension) {
         bool is_5p = ss_idx == 0;
+        var helix = design.helices[domain.adjacent_domain.helix]!;
+        var group = design.groups[helix.group]!;
+        var geometry = group.geometry ?? design.geometry;
         var nucleotides = _compute_extension_nucleotides(
-            design: design, strand: strand, is_5p: is_5p, helix_vectors: helix_vectors, mod_map: mod_map);
+            design: design,
+            geometry: geometry,
+            strand: strand,
+            is_5p: is_5p,
+            helix_vectors: helix_vectors,
+            mod_map: mod_map);
         ox_strand.nucleotides.addAll(nucleotides);
         strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, false));
       } else {
@@ -651,11 +660,11 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
 
 List<OxdnaNucleotide> _compute_extension_nucleotides(
     {required Design design,
+    required Geometry geometry,
     required Strand strand,
     required bool is_5p,
     required Map<int, Tuple3<OxdnaVector, OxdnaVector, OxdnaVector>> helix_vectors,
     required Map<int, List<int>> mod_map}) {
-  var geometry = design.geometry;
   var step_rot = -360 / geometry.bases_per_turn;
 
   var adj_dom = is_5p ? strand.domains.first : strand.domains.last;

lib/src/reducers/groups_reducer.dart

@@ -13,6 +13,7 @@ Reducer<BuiltMap<String, HelixGroup>> groups_local_reducer = combineReducers([
   TypedReducer<BuiltMap<String, HelixGroup>, actions.GroupRemove>(group_remove_reducer),
   TypedReducer<BuiltMap<String, HelixGroup>, actions.GroupChange>(group_change_reducer),
   TypedReducer<BuiltMap<String, HelixGroup>, actions.GridChange>(grid_change_reducer),
+  TypedReducer<BuiltMap<String, HelixGroup>, actions.GeometryHelixGroupSet>(geometry_helix_group_set_reducer),
 ]);
 
 GlobalReducer<BuiltMap<String, HelixGroup>, AppState> groups_global_reducer = combineGlobalReducers([
@@ -29,6 +30,15 @@ BuiltMap<String, HelixGroup> grid_change_reducer(
       return group;
     });
 
+BuiltMap<String, HelixGroup> geometry_helix_group_set_reducer(
+        BuiltMap<String, HelixGroup> groups, actions.GeometryHelixGroupSet action) =>
+    groups.map_values((name, group) {
+      if (name == action.group_name) {
+        group = group.rebuild((b) => b..geometry.replace(action.geometry));
+      }
+      return group;
+    });
+
 BuiltMap<String, HelixGroup> group_add_reducer(
         BuiltMap<String, HelixGroup> groups, actions.GroupAdd action) =>
     groups.rebuild((b) {

lib/src/reducers/helices_reducer.dart

@@ -63,7 +63,9 @@ GlobalReducer<BuiltMap<int, Helix>, AppState> helices_global_reducer = combineGl
       helix_offset_change_all_while_creating_strand_reducer),
   TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.ReplaceStrands>(first_replace_strands_reducer),
   TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.SelectionsClear>(
-      reset_helices_offsets_after_selections_clear)
+      reset_helices_offsets_after_selections_clear),
+  TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.GeometryHelixGroupSet>(
+      helix_geometry_helix_group_set_reducer),
 ]);
 
 BuiltMap<int, Helix> helix_individual_reducer(
@@ -79,6 +81,18 @@ BuiltMap<int, Helix> helix_individual_reducer(
   }
 }
 
+BuiltMap<int, Helix> helix_geometry_helix_group_set_reducer(
+    BuiltMap<int, Helix> helices, AppState state, actions.GeometryHelixGroupSet action) {
+  var helices_new = helices.toMap();
+  for (int helix_idx in helices.keys) {
+    var helix = helices[helix_idx]!;
+    var group = state.design.groups[helix.group]!;
+    var geometry = group.geometry ?? state.design.geometry;
+    helices_new[helix_idx] = helix.rebuild((b) => b..geometry.replace(geometry));
+  }
+  return helices_new.build();
+}
+
 GlobalReducer<Helix, AppState> _helix_individual_reducers = combineGlobalReducers([
   TypedGlobalReducer<Helix, AppState, actions.HelixOffsetChange>(helix_offset_change_reducer),
   TypedGlobalReducer<Helix, AppState, actions.HelixMinOffsetSetByDomains>(
@@ -473,8 +487,9 @@ BuiltMap<int, Helix> helix_roll_set_at_other_reducer(
     BuiltMap<int, Helix> helices, AppState state, actions.HelixRollSetAtOther action) {
   Helix helix = helices[action.helix_idx]!;
   Helix helix_other = helices[action.helix_other_idx]!;
+  var group = state.design.groups[helix.group]!;
 
-  var geometry = state.design.geometry;
+  var geometry = group.geometry ?? state.design.geometry;
   num rotation = util.rotation_between_helices(helix, helix_other, action.forward, geometry);
   double old_rotation_at_anchor = state.design.helix_rotation_forward(helix.idx, action.anchor);
   double delta_roll = rotation - old_rotation_at_anchor;
@@ -521,12 +536,13 @@ Design? helix_add_design_reducer(Design? design, AppState state, actions.HelixAd
   var new_group = group.rebuild((b) => b..helices_view_order.replace(new_helices_view_order));
   var new_groups = design.groups.toMap();
   new_groups[state.ui_state.displayed_group_name] = new_group;
+  var geometry = new_group.geometry ?? design.geometry;
 
   Helix helix = Helix(
     idx: new_idx,
     grid: group.grid,
     group: state.ui_state.displayed_group_name,
-    geometry: design.geometry,
+    geometry: geometry,
     grid_position: action.grid_position,
     position: action.position,
     min_offset: min_offset,
@@ -631,7 +647,8 @@ BuiltMap<int, Helix> helix_grid_change_reducer(
     BuiltMap<int, Helix> helices, AppState state, actions.GridChange action) {
   // make builder of all helices
   Map<int, Helix> new_helices = helices.toMap();
-  Geometry geometry = state.design.geometry;
+  var group = state.design.groups[action.group_name]!;
+  Geometry geometry = group.geometry ?? state.design.geometry;
 
   // process only those in this group
   var helix_idxs_in_group = state.design.helix_idxs_in_group[action.group_name]!;
@@ -676,8 +693,13 @@ BuiltMap<int, Helix> relax_helix_rolls_reducer(
 
 BuiltMap<int, Helix> helix_group_change_reducer(
     BuiltMap<int, Helix> helices, AppState state, actions.GroupChange action) {
-  return helices.map_values((idx, helix) =>
-      helix.group == action.old_name ? helix.rebuild((b) => b..group = action.new_name) : helix);
+  var new_group = state.design.groups[action.new_name]!;
+  Geometry new_geometry = new_group.geometry ?? state.design.geometry;
+  return helices.map_values((idx, helix) => helix.group == action.old_name
+      ? helix.rebuild((b) => b
+        ..group = action.new_name
+        ..geometry.replace(new_geometry))
+      : helix);
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -726,6 +748,7 @@ BuiltMap<int, Helix> helix_position_set_reducer(
 // groups_reducer.dart file, which processes this same Action on the groups map.
 BuiltMap<int, Helix> move_helices_to_group_helices_reducer(
     BuiltMap<int, Helix> helices, actions.MoveHelicesToGroup action) {
+  //TODO: make this global and set helix.geometry if new group geometry is not null
   var helices_map = helices.toMap();
   for (int idx in action.helix_idxs) {
     assert(helices_map.keys.contains(idx));

lib/src/reducers/mouseover_datas_reducer.dart

@@ -47,7 +47,8 @@ BuiltList<MouseoverData> helix_rotation_set_at_other_mouseover_reducer(
     BuiltList<MouseoverData> mouseover_datas, AppState state, actions.HelixRollSetAtOther action) {
   Helix helix = state.design.helices[action.helix_idx]!;
   Helix helix_other = state.design.helices[action.helix_other_idx]!;
-  var geometry = state.design.geometry;
+  var group = state.design.groups[helix.group]!;
+  var geometry = group.geometry ?? state.design.geometry;
   double rotation = util.rotation_between_helices(helix, helix_other, action.forward, geometry);
   return _update_mouseover_datas_with_helix_rotation(
     model: state,

lib/src/reducers/strands_reducer.dart

@@ -405,13 +405,17 @@ BuiltList<Strand> strands_dna_extensions_move_commit_reducer(
     int substrand_idx = strand.substrands.indexOf(extension);
     var substrands_builder = strand.substrands.toBuilder();
     var extension_start_point = move.attached_end_position;
+    var adjacent_domain = extension.adjacent_domain;
+    var helix = state.design.helices[adjacent_domain.helix]!;
+    var group = state.design.groups[helix.group]!;
+    var geometry = group.geometry ?? state.design.geometry;
 
     var length_and_angle = util.compute_extension_length_and_angle_from_point(
         action.dna_extensions_move.current_point_of(move.dna_end)!,
         extension_start_point,
         extension,
         extension.adjacent_domain,
-        state.design.geometry);
+        geometry);
 
     Extension ext_new = extension.rebuild((b) => b
       ..display_length = length_and_angle.item1

lib/src/serializers.dart

@@ -203,6 +203,7 @@ part 'serializers.g.dart';
   EditModeToggle,
   EditModesSet,
   GeometrySet,
+  GeometryHelixGroupSet,
   HelixAdd,
   HelixRemove,
   HelixRemoveAllSelected,

lib/src/state/app_state.dart

@@ -76,8 +76,8 @@ in the app. Thank you!""");
     }
 
     BuiltMap<int, Point<double>> ret = util
-        .helices_assign_svg(design.geometry, ui_state.invert_y, design.helices, design.groups,
-            helix_idxs_to_calculate: helix_idxs_to_calculate)
+        .helices_assign_svg(design, ui_state.invert_y, design.helices, design.groups,
+        helix_idxs_to_calculate: helix_idxs_to_calculate)
         .build();
 
     // print('${sw.elapsedMicroseconds} microseconds to calculate helix_idx_to_svg_position_map');
@@ -95,7 +95,7 @@ in the app. Thank you!""");
   Map<String, dynamic> toJson() {
     Map<String, dynamic> map = {};
     var design_to_store =
-        this.maybe_design != null ? design.to_json_serializable(suppress_indent: false) : null;
+    this.maybe_design != null ? design.to_json_serializable(suppress_indent: false) : null;
     map['design'] = design_to_store;
     map['ui_state'] = ui_state.toJson();
     map['error_message'] = error_message;

lib/src/state/design.dart

@@ -110,7 +110,10 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     Map<int, Helix> helices_map = {for (var helix in helices) helix.idx: helix};
 
     for (var key in helices_map.keys) {
-      helices_map[key] = helices_map[key]!.rebuild((b) => b..geometry.replace(geometry!));
+      var helix = helices_map[key]!;
+      var group = groups[helix.group]!;
+      Geometry helix_geometry = group.geometry ?? geometry;
+      helices_map[key] = helix.rebuild((b) => b..geometry.replace(helix_geometry));
     }
 
     var design = Design.from((b) => b

lib/src/state/design_side_rotation_data.dart

@@ -77,7 +77,9 @@ abstract class DesignSideRotationData
           break;
         }
       }
-      double minor_groove_angle = design.geometry.minor_groove_angle;
+      var group = design.groups[helix.group]!;
+      var geometry = group.geometry ?? design.geometry;
+      double minor_groove_angle = geometry.minor_groove_angle;
       design_side_rotation_datas_builder.add(DesignSideRotationData(
           helix, offset, color_forward, color_reverse, roll_forward, minor_groove_angle));
     }

lib/src/state/group.dart

@@ -31,13 +31,16 @@ abstract class HelixGroup with BuiltJsonSerializable implements Built<HelixGroup
 
   double get roll;
 
+  Geometry? get geometry;
+
   static void _initializeBuilder(HelixGroupBuilder b) {
     b.grid = Grid.none;
     b.position = Position3D.origin.toBuilder();
     b.pitch = 0;
     b.yaw = 0;
     b.roll = 0;
     b.helices_view_order = ListBuilder<int>();
+    b.geometry = null;
   }
 
   factory HelixGroup({
@@ -47,6 +50,7 @@ abstract class HelixGroup with BuiltJsonSerializable implements Built<HelixGroup
     double pitch = 0,
     double yaw = 0,
     double roll = 0,
+    Geometry? geometry = null,
   }) {
     if (position == null) {
       position = Position3D.origin;
@@ -57,7 +61,8 @@ abstract class HelixGroup with BuiltJsonSerializable implements Built<HelixGroup
       ..position.replace(position!)
       ..pitch = pitch
       ..yaw = yaw
-      ..roll = roll);
+      ..roll = roll
+      ..geometry = geometry?.toBuilder());
   }
 
   Map<String, dynamic> to_json_serializable({
@@ -88,6 +93,11 @@ abstract class HelixGroup with BuiltJsonSerializable implements Built<HelixGroup
           suppress_indent ? NoIndent(helices_view_order_to_write) : helices_view_order_to_write;
     }
 
+    if (this.geometry != null) {
+      json_map[constants.geometry_key] =
+          this.geometry!.to_json_serializable(suppress_indent: suppress_indent);
+    }
+
     return json_map;
   }
 
@@ -123,13 +133,22 @@ abstract class HelixGroup with BuiltJsonSerializable implements Built<HelixGroup
     double roll = util.optional_field(json_map, constants.roll_key, constants.default_roll);
     double yaw = util.optional_field(json_map, constants.yaw_key, constants.default_yaw);
 
+    Map<String, dynamic>? geometry_map =
+        util.optional_field_with_null_default(json_map, constants.geometry_key);
+    Geometry? geometry = null;
+    if (geometry_map != null) {
+      geometry = Geometry.from_json(geometry_map);
+    }
+
     return HelixGroup(
-        position: position,
-        pitch: pitch,
-        yaw: yaw,
-        roll: roll,
-        helices_view_order: helices_view_order,
-        grid: grid);
+      position: position,
+      pitch: pitch,
+      yaw: yaw,
+      roll: roll,
+      helices_view_order: helices_view_order,
+      grid: grid,
+      geometry: geometry,
+    );
   }
 
   /// Returns a map mapping helix indices to their view order.