fixes #725: moved domains should be reselected after move

lib/src/actions/actions.dart

@@ -2172,8 +2172,12 @@ abstract class DomainsMoveStartSelectedDomains
     implements Action, Built<DomainsMoveStartSelectedDomains, DomainsMoveStartSelectedDomainsBuilder> {
   Address get address;
 
+  BuiltMap<int, int> get original_helices_view_order_inverse;
+
   /************************ begin BuiltValue boilerplate ************************/
-  factory DomainsMoveStartSelectedDomains({Address address}) = _$DomainsMoveStartSelectedDomains._;
+  factory DomainsMoveStartSelectedDomains(
+      {Address address,
+      BuiltMap<int, int> original_helices_view_order_inverse}) = _$DomainsMoveStartSelectedDomains._;
 
   DomainsMoveStartSelectedDomains._();
 

lib/src/middleware/all_middleware.dart

@@ -23,6 +23,7 @@ import 'oxdna_export.dart';
 import 'periodic_save_design_local_storage.dart';
 import 'reselect_moved_dna_ends.dart';
 import 'reselect_moved_copied_strands.dart';
+import 'reselect_moved_domains.dart';
 import 'save_file.dart';
 import 'export_svg.dart';
 import 'local_storage.dart';
@@ -60,6 +61,7 @@ final all_middleware = List<Middleware<AppState>>.unmodifiable([
   export_dna_sequences_middleware,
   reselect_moved_dna_ends_middleware,
   reselect_moved_copied_strands_middleware,
+  reselect_moved_domains_middleware,
   selections_intersect_box_compute_middleware,
   insertion_deletion_batching_middleware,
   adjust_grid_position_middleware,

lib/src/middleware/reselect_moved_domains.dart

@@ -0,0 +1,70 @@
+import 'package:redux/redux.dart';
+import 'package:built_collection/built_collection.dart';
+
+import '../reducers/domains_move_reducer.dart' as domains_move_reducer;
+import '../state/domains_move.dart';
+import '../state/design.dart';
+import '../state/address.dart';
+import '../state/domain.dart';
+import '../state/dna_end.dart';
+import '../state/strand.dart';
+import '../state/strands_move.dart';
+import '../actions/actions.dart' as actions;
+import '../state/app_state.dart';
+
+reselect_moved_domains_middleware(Store<AppState> store, action, NextDispatcher next) {
+  // only reselect if there is more than 1 selected
+  // otherwise, if the user repeatedly clicks and drags one at a time,
+  // this builds up many selected items as they click each new one, moving all of them
+  if ((action is actions.DomainsMoveCommit) && action.domains_move.domains_moving.length > 1) {
+    Design old_design = store.state.design;
+    DomainsMove domains_move = action.domains_move;
+
+    if (!(domains_move_reducer.in_bounds(old_design, domains_move) &&
+        domains_move_reducer.is_allowable(old_design, domains_move) &&
+        domains_move.is_nontrivial)) {
+      return;
+    }
+
+    List<Address> addresses = [];
+
+    var new_address_helix_idx = domains_move.current_address.helix_idx;
+    var new_helix = old_design.helices[new_address_helix_idx];
+    var new_group = old_design.groups[new_helix.group];
+
+    BuiltList<int> new_helices_view_order = new_group.helices_view_order;
+    BuiltMap<int, int> old_helices_view_order_inverse =
+        domains_move.original_helices_view_order_inverse;
+
+    // first collect old addresses while design.end_to_substrand is still valid, convert them to
+    // their new addresses so we can look them up
+    for (Domain old_domain in domains_move.domains_moving) {
+      // Domain old_domain = strand.first_domain;
+      DNAEnd old_5p_end = old_domain.dnaend_5p;
+      int old_helix_view_order = old_helices_view_order_inverse[old_domain.helix];
+      int new_helix_view_order = old_helix_view_order + domains_move.delta_view_order;
+      int new_helix_idx = new_helices_view_order[new_helix_view_order];
+      int new_offset = old_5p_end.offset_inclusive + domains_move.delta_offset;
+      var new_forward = domains_move.delta_forward != old_domain.forward;
+      var address = Address(helix_idx: new_helix_idx, offset: new_offset, forward: new_forward);
+      addresses.add(address);
+    }
+
+    // then apply action to commit the move
+    next(action);
+
+    // now find new ends at given addresses
+    List<Domain> new_domains = [];
+    Design new_design = store.state.design;
+    // if domain polarity switched, the 3' end of each domain will now be where the 5' end was
+    BuiltMap<Address, Domain> address_to_domain =
+          domains_move.delta_forward ? new_design.address_3p_to_domain : new_design.address_5p_to_domain;
+    for (var address in addresses) {
+      Domain new_domain = address_to_domain[address];
+      new_domains.add(new_domain);
+    }
+    store.dispatch(actions.SelectAll(selectables: new_domains.toBuiltList(), only: true));
+  } else {
+    next(action);
+  }
+}

lib/src/reducers/domains_move_reducer.dart

@@ -36,6 +36,7 @@ DomainsMove domains_move_start_selected_domains_reducer(
       domains_moving: selected_domains.toBuiltList(),
       all_domains: state.design.all_domains,
       strands_with_domains_moving: strands_of_selected_domains.toBuiltList(),
+      original_helices_view_order_inverse: action.original_helices_view_order_inverse,
       helices: state.design.helices,
       groups: state.design.groups,
       original_address: action.address);
@@ -47,6 +48,9 @@ DomainsMove domains_move_stop_reducer(DomainsMove domains_move, actions.DomainsM
 // other domains
 // - is_allowable checks whether the domain overlaps other domains
 
+bool in_bounds_and_allowable(Design design, DomainsMove domains_move) =>
+    in_bounds(design, domains_move) && is_allowable(design, domains_move);
+
 DomainsMove domains_adjust_address_reducer(
     DomainsMove domains_move, AppState state, actions.DomainsMoveAdjustAddress action) {
   DomainsMove new_domains_move = domains_move.rebuild((b) => b..current_address.replace(action.address));

lib/src/state/design.dart

@@ -72,16 +72,15 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     if (helices != null) {
       helix_builders = helices.map((e) => e.toBuilder());
     } else if (num_helices != null) {
-
       helix_builders = [
-          for (int idx in Iterable<int>.generate(num_helices))
-            HelixBuilder()
-              ..idx = idx
-              ..grid = grid
-              ..geometry = geometry.toBuilder()
-              ..grid_position = (grid == Grid.none ? null : default_grid_position(idx).toBuilder())
-              ..position_ = grid != Grid.none ? null : default_position(geometry, idx).toBuilder()
-        ];
+        for (int idx in Iterable<int>.generate(num_helices))
+          HelixBuilder()
+            ..idx = idx
+            ..grid = grid
+            ..geometry = geometry.toBuilder()
+            ..grid_position = (grid == Grid.none ? null : default_grid_position(idx).toBuilder())
+            ..position_ = grid != Grid.none ? null : default_position(geometry, idx).toBuilder()
+      ];
     } else if (helix_builders != null) {
       // We will use the parameter directly
     } else {
@@ -95,7 +94,6 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
 
     set_helices_min_max_offsets(helix_builders_map, strands);
 
-
     if (groups == null) {
       groups = _calculate_groups_from_helix_builder(helix_builders, grid);
     }
@@ -106,9 +104,7 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     var 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)
-      );
+      helices_map[key] = helices_map[key].rebuild((b) => b..geometry.replace(geometry));
     }
 
     var design = Design.from((b) => b
@@ -631,6 +627,32 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     return map.build();
   }
 
+  /// Gets Domain with 5p end at given address (helix,offset,forward)
+  /// Offset is inclusive, i.e., dna_end.offset_inclusive
+  @memoized
+  BuiltMap<Address, Domain> get address_5p_to_domain {
+    var map = Map<Address, Domain>();
+    for (Domain domain in domains_by_id.values) {
+      var key = Address(
+          helix_idx: domain.helix, offset: domain.dnaend_5p.offset_inclusive, forward: domain.forward);
+      map[key] = domain;
+    }
+    return map.build();
+  }
+
+  /// Gets Domain with 3p end at given address (helix,offset,forward)
+  /// Offset is inclusive, i.e., dna_end.offset_inclusive
+  @memoized
+  BuiltMap<Address, Domain> get address_3p_to_domain {
+    var map = Map<Address, Domain>();
+    for (Domain domain in domains_by_id.values) {
+      var key = Address(
+          helix_idx: domain.helix, offset: domain.dnaend_3p.offset_inclusive, forward: domain.forward);
+      map[key] = domain;
+    }
+    return map.build();
+  }
+
   /// Maps Addresses to PotentialVerticalCrossovers.
   /// The end on TOP (i.e., lower helix idx) has the address with the key in the map.
   @memoized
@@ -1188,7 +1210,6 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
       strands.add(strand);
     }
 
-
     // build groups
     Map<String, HelixGroup> groups_map =
         group_builders_map.map((key, value) => MapEntry<String, HelixGroup>(key, value.build()));
@@ -1887,7 +1908,8 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
       }
     }
 
-    return Design(helix_builders: helix_builders.values, strands: strands, grid: grid_type, invert_y: invert_y);
+    return Design(
+        helix_builders: helix_builders.values, strands: strands, grid: grid_type, invert_y: invert_y);
   }
 
   /// Routine that will follow a cadnano v2 strand accross helices and create
@@ -2072,7 +2094,8 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
   }
 }
 
-Map<String, HelixGroup> _calculate_groups_from_helix_builder(Iterable<HelixBuilder> helix_builders, Grid grid) {
+Map<String, HelixGroup> _calculate_groups_from_helix_builder(
+    Iterable<HelixBuilder> helix_builders, Grid grid) {
   if (helix_builders.isEmpty) {
     return {constants.default_group_name: HelixGroup(grid: grid, helices_view_order: [])};
   }
@@ -2336,6 +2359,7 @@ class StrandError extends IllegalDesignError {
 class HelixPitchYaw {
   double pitch;
   double yaw;
+
   // Helix idx of the first helix found with this pitch and yaw value
   int helix_idx;
 

lib/src/state/domains_move.dart

@@ -26,20 +26,26 @@ abstract class DomainsMove with BuiltJsonSerializable implements Built<DomainsMo
   factory DomainsMove(
       {BuiltList<Domain> domains_moving,
       BuiltList<Domain> all_domains,
-        BuiltList<Strand> strands_with_domains_moving,
+      BuiltList<Strand> strands_with_domains_moving,
       BuiltMap<int, Helix> helices,
       BuiltMap<String, HelixGroup> groups,
+      BuiltMap<int, int> original_helices_view_order_inverse,
       Address original_address,
       bool copy = false,
       bool keep_color = true}) {
-    var domains_fixed =
-        copy ? all_domains : [for (var domain in all_domains) if (!domains_moving.contains(domain)) domain];
+    var domains_fixed = copy
+        ? all_domains
+        : [
+            for (var domain in all_domains)
+              if (!domains_moving.contains(domain)) domain
+          ];
     return DomainsMove.from((b) => b
       ..domains_moving.replace(domains_moving)
       ..domains_fixed.replace(domains_fixed)
       ..strands_with_domains_moving.replace(strands_with_domains_moving)
       ..helices.replace(helices)
       ..groups.replace(groups)
+      ..original_helices_view_order_inverse.replace(original_helices_view_order_inverse)
       ..original_address.replace(original_address)
       ..current_address.replace(original_address)
       ..copy = copy
@@ -57,6 +63,10 @@ abstract class DomainsMove with BuiltJsonSerializable implements Built<DomainsMo
 
   BuiltList<Strand> get strands_with_domains_moving;
 
+  // Since copied Domains may come from a different Design with different groups, we need to
+  // store this to know how to position them in new HelixGroups.
+  BuiltMap<int, int> get original_helices_view_order_inverse;
+
   Address get original_address;
 
   Address get current_address;

lib/src/view/design_main_strand_domain.dart

@@ -42,7 +42,9 @@ mixin DesignMainDomainPropsMixin on UiProps {
   Point<num> helix_svg_position;
 
   List<ContextMenuItem> Function(Strand strand,
-      {@required Domain domain, @required Address address, @required ModificationType type}) context_menu_strand;
+      {@required Domain domain,
+      @required Address address,
+      @required ModificationType type}) context_menu_strand;
 
   bool selected;
 
@@ -61,8 +63,10 @@ class DesignMainDomainComponent extends UiComponent2<DesignMainDomainProps>
     Domain domain = props.domain;
     String id = domain.id;
 
-    Point<num> start_svg = props.helix.svg_base_pos(domain.offset_5p, domain.forward, props.helix_svg_position.y);
-    Point<num> end_svg = props.helix.svg_base_pos(domain.offset_3p, domain.forward, props.helix_svg_position.y);
+    Point<num> start_svg =
+        props.helix.svg_base_pos(domain.offset_5p, domain.forward, props.helix_svg_position.y);
+    Point<num> end_svg =
+        props.helix.svg_base_pos(domain.offset_3p, domain.forward, props.helix_svg_position.y);
 
     var classname = constants.css_selector_domain;
     if (props.selected) {
@@ -131,9 +135,13 @@ class DesignMainDomainComponent extends UiComponent2<DesignMainDomainProps>
       if (domain_selectable(props.domain)) {
         // select/deselect
         props.domain.handle_selection_mouse_down(event);
-        // set up drag detection for moving DNA ends
-        var address = util.find_closest_address(event, [props.helix], props.groups, props.geometry, {props.helix.idx: props.helix_svg_position}.build());
-        app.dispatch(actions.DomainsMoveStartSelectedDomains(address: address));
+        // set up drag detection for moving domains
+        var address = util.find_closest_address(event, [props.helix], props.groups, props.geometry,
+            {props.helix.idx: props.helix_svg_position}.build());
+        HelixGroup group = app.state.design.group_of_domain(props.domain);
+        var view_order_inverse = group.helices_view_order_inverse;
+        app.dispatch(actions.DomainsMoveStartSelectedDomains(
+            address: address, original_helices_view_order_inverse: view_order_inverse));
       }
     }
   }
@@ -173,8 +181,8 @@ class DesignMainDomainComponent extends UiComponent2<DesignMainDomainProps>
     if (!event.shiftKey) {
       event.preventDefault();
       event.stopPropagation();
-      Address address =
-          util.get_address_on_helix(event, props.helix, props.groups[props.helix.group], props.geometry, props.helix_svg_position);
+      Address address = util.get_address_on_helix(
+          event, props.helix, props.groups[props.helix.group], props.geometry, props.helix_svg_position);
       app.dispatch(actions.ContextMenuShow(
           context_menu: ContextMenu(
               items: props.context_menu_strand(props.strand, domain: props.domain, address: address).build(),