closes #494; allow deletions/insertions to be added to all domains in…

… a HelixGroup occupying the clicked offset, which helps with implementing twist correcting-deletions for flat square-lattice origami, for instance

README.md

@@ -578,7 +578,11 @@ There are different edit modes available, shown on the right side of the screen.
   then adding/removing an insertion/deletion at that offset adds/removes on both bound domains.
   The Python scripting library lets one specify insertions/deletions on one bound domain but not the other, 
   but this is currently [unsupported](https://github.com/UC-Davis-molecular-computing/scadnano/issues/90) in the web interface to create such a solitary deletion/insertion directly. 
-  (If necessary, one hack is to move one domain out of the way, add the deletion/insertion to the other, and then move the first back.)
+  (If necessary, one hack is to move one domain out of the way, add the deletion/insertion to the other domain, and then move the first domain back.)
+
+  A useful shortcut is to press Ctrl while clicking a Domain in deletion (respectively, insertion) mode. 
+  If Ctrl is pressed while clicking on a domain, then deletions (respectively, insertions) will be added at *all* domains on all helices in the same HelixGroup that overlap the same offset (unless that offset is the start or end of the domain, which is disallowed from having a deletion/insertion).
+  This helps to implement, for example, twist correction in DNA origami (see https://doi.org/10.1038/nchem.1070 for a description), where vertical "columns" of deletions need to be added to every domain in every helix at a given offset.
 
   *Note for cadnano users:* From the user's perspective, cadnano associates each deletion/insertion to an "address", i.e., a helix and offset on that helix. For instance, it is possible to have a "deletion" where there is no DNA strand, and if DNA strand(s) are later placed there, they will have the deletion. By contrast, insertions and deletions in scadnano are associated to a bound domain. If the whole strand moves or is copied, the insertions/deletions move along with it.
 

lib/src/actions/actions.dart

@@ -235,15 +235,19 @@ abstract class LocalStorageDesignChoiceSet
 
 abstract class ClearHelixSelectionWhenLoadingNewDesignSet
     with BuiltJsonSerializable
-    implements Action, Built<ClearHelixSelectionWhenLoadingNewDesignSet, ClearHelixSelectionWhenLoadingNewDesignSetBuilder> {
+    implements
+        Action,
+        Built<ClearHelixSelectionWhenLoadingNewDesignSet, ClearHelixSelectionWhenLoadingNewDesignSetBuilder> {
   bool get clear;
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory ClearHelixSelectionWhenLoadingNewDesignSet({bool clear}) = _$ClearHelixSelectionWhenLoadingNewDesignSet._;
+  factory ClearHelixSelectionWhenLoadingNewDesignSet({bool clear}) =
+      _$ClearHelixSelectionWhenLoadingNewDesignSet._;
 
   ClearHelixSelectionWhenLoadingNewDesignSet._();
 
-  static Serializer<ClearHelixSelectionWhenLoadingNewDesignSet> get serializer => _$clearHelixSelectionWhenLoadingNewDesignSetSerializer;
+  static Serializer<ClearHelixSelectionWhenLoadingNewDesignSet> get serializer =>
+      _$clearHelixSelectionWhenLoadingNewDesignSetSerializer;
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -368,8 +372,7 @@ abstract class ShowDomainNamesSet
   factory ShowDomainNamesSet(bool show) => ShowDomainNamesSet.from((b) => b..show = show);
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory ShowDomainNamesSet.from([void Function(ShowDomainNamesSetBuilder) updates]) =
-      _$ShowDomainNamesSet;
+  factory ShowDomainNamesSet.from([void Function(ShowDomainNamesSetBuilder) updates]) = _$ShowDomainNamesSet;
 
   ShowDomainNamesSet._();
 
@@ -494,10 +497,12 @@ abstract class ShowDomainNameMismatchesSet
     implements Action, Built<ShowDomainNameMismatchesSet, ShowDomainNameMismatchesSetBuilder> {
   bool get show_domain_name_mismatches;
 
-  factory ShowDomainNameMismatchesSet(bool show_domain_name_mismatches) => ShowDomainNameMismatchesSet.from((b) => b..show_domain_name_mismatches = show_domain_name_mismatches);
+  factory ShowDomainNameMismatchesSet(bool show_domain_name_mismatches) =>
+      ShowDomainNameMismatchesSet.from((b) => b..show_domain_name_mismatches = show_domain_name_mismatches);
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory ShowDomainNameMismatchesSet.from([void Function(ShowDomainNameMismatchesSetBuilder) updates]) = _$ShowDomainNameMismatchesSet;
+  factory ShowDomainNameMismatchesSet.from([void Function(ShowDomainNameMismatchesSetBuilder) updates]) =
+      _$ShowDomainNameMismatchesSet;
 
   ShowDomainNameMismatchesSet._();
 
@@ -2093,9 +2098,11 @@ abstract class InsertionOrDeletionAction implements UndoableAction, StrandPartAc
 
   int get offset;
 
+  bool get all_helices;
+
   StrandPart get strand_part; // => substrand;
 
-  InsertionOrDeletionAction clone_for_adjacent_substrand(Domain other_domain);
+  InsertionOrDeletionAction clone_for_other_domain(Domain other_domain);
 }
 
 abstract class InsertionAdd
@@ -2105,12 +2112,14 @@ abstract class InsertionAdd
 
   int get offset;
 
+  bool get all_helices;
+
   StrandPart get strand_part => domain;
 
-  InsertionAdd clone_for_adjacent_substrand(Domain domain) => InsertionAdd(domain: domain, offset: offset);
+  InsertionAdd clone_for_other_domain(Domain domain) => rebuild((b) => b..domain.replace(domain));
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory InsertionAdd({Domain domain, int offset}) = _$InsertionAdd._;
+  factory InsertionAdd({Domain domain, int offset, bool all_helices}) = _$InsertionAdd._;
 
   InsertionAdd._();
 
@@ -2126,18 +2135,31 @@ abstract class InsertionLengthChange
 
   int get length;
 
+  bool get all_helices;
+
   int get offset => insertion.offset;
 
   StrandPart get strand_part => domain;
 
-  InsertionLengthChange clone_for_adjacent_substrand(Domain other_domain) => InsertionLengthChange(
+  InsertionLengthChange clone_for_other_domain(Domain other_domain) => InsertionLengthChange(
         domain: other_domain,
         insertion: other_domain.insertions.firstWhere((i) => i.offset == offset),
         length: length,
       );
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory InsertionLengthChange({Domain domain, Insertion insertion, int length}) = _$InsertionLengthChange._;
+  factory InsertionLengthChange({Domain domain, Insertion insertion, int length}) {
+    return InsertionLengthChange.from((b) => b
+      ..domain.replace(domain)
+      ..insertion.replace(insertion)
+      ..length = length
+      ..all_helices = false);
+  }
+
+  factory InsertionLengthChange.from([void Function(InsertionLengthChangeBuilder) updates]) =
+      _$InsertionLengthChange;
+
+  // factory InsertionLengthChange({Domain domain, Insertion insertion, int length}) = _$InsertionLengthChange._;
 
   InsertionLengthChange._();
 
@@ -2151,13 +2173,14 @@ abstract class DeletionAdd
 
   int get offset;
 
+  bool get all_helices;
+
   StrandPart get strand_part => domain;
 
-  DeletionAdd clone_for_adjacent_substrand(Domain other_domain) =>
-      DeletionAdd(domain: other_domain, offset: offset);
+  DeletionAdd clone_for_other_domain(Domain domain) => rebuild((b) => b..domain.replace(domain));
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory DeletionAdd({Domain domain, int offset}) = _$DeletionAdd._;
+  factory DeletionAdd({Domain domain, int offset, bool all_helices}) = _$DeletionAdd._;
 
   DeletionAdd._();
 
@@ -2171,17 +2194,26 @@ abstract class InsertionRemove
 
   Insertion get insertion;
 
+  bool get all_helices;
+
   int get offset => insertion.offset;
 
   StrandPart get strand_part => domain;
 
-  InsertionRemove clone_for_adjacent_substrand(Domain other_domain) => InsertionRemove(
+  InsertionRemove clone_for_other_domain(Domain other_domain) => InsertionRemove(
         domain: other_domain,
         insertion: other_domain.insertions.firstWhere((i) => i.offset == offset),
       );
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory InsertionRemove({Domain domain, Insertion insertion}) = _$InsertionRemove._;
+  factory InsertionRemove({Domain domain, Insertion insertion}) {
+    return InsertionRemove.from((b) => b
+      ..domain.replace(domain)
+      ..insertion.replace(insertion)
+      ..all_helices = false);
+  }
+
+  factory InsertionRemove.from([void Function(InsertionRemoveBuilder) updates]) = _$InsertionRemove;
 
   InsertionRemove._();
 
@@ -2195,13 +2227,24 @@ abstract class DeletionRemove
 
   int get offset;
 
+  bool get all_helices;
+
   StrandPart get strand_part => domain;
 
-  DeletionRemove clone_for_adjacent_substrand(Domain other_domain) =>
+  DeletionRemove clone_for_other_domain(Domain other_domain) =>
       DeletionRemove(domain: other_domain, offset: offset);
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory DeletionRemove({Domain domain, int offset}) = _$DeletionRemove._;
+  factory DeletionRemove({Domain domain, int offset}) {
+    return DeletionRemove.from((b) => b
+      ..domain.replace(domain)
+      ..offset = offset
+      ..all_helices = false);
+  }
+
+  factory DeletionRemove.from([void Function(DeletionRemoveBuilder) updates]) = _$DeletionRemove;
+
+  // factory DeletionRemove({Domain domain, int offset}) = _$DeletionRemove._;
 
   DeletionRemove._();
 
@@ -2403,7 +2446,9 @@ abstract class ContextMenuHide
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // strand color picker
 
-abstract class StrandColorPickerShow with BuiltJsonSerializable implements Action, Built<StrandColorPickerShow, StrandColorPickerShowBuilder> {
+abstract class StrandColorPickerShow
+    with BuiltJsonSerializable
+    implements Action, Built<StrandColorPickerShow, StrandColorPickerShowBuilder> {
   Strand get strand;
 
   /************************ begin BuiltValue boilerplate ************************/
@@ -2414,10 +2459,14 @@ abstract class StrandColorPickerShow with BuiltJsonSerializable implements Actio
   static Serializer<StrandColorPickerShow> get serializer => _$strandColorPickerShowSerializer;
 }
 
-abstract class StrandColorPickerHide with BuiltJsonSerializable implements Action, Built<StrandColorPickerHide, StrandColorPickerHideBuilder> {
+abstract class StrandColorPickerHide
+    with BuiltJsonSerializable
+    implements Action, Built<StrandColorPickerHide, StrandColorPickerHideBuilder> {
   /************************ begin BuiltValue boilerplate ************************/
   factory StrandColorPickerHide() => StrandColorPickerHide.from((b) => b);
-  factory StrandColorPickerHide.from([void Function(StrandColorPickerHideBuilder) updates]) = _$StrandColorPickerHide;
+
+  factory StrandColorPickerHide.from([void Function(StrandColorPickerHideBuilder) updates]) =
+      _$StrandColorPickerHide;
 
   StrandColorPickerHide._();
 

lib/src/middleware/all_middleware.dart

@@ -14,7 +14,7 @@ import 'helix_grid_change.dart';
 import 'helix_hide_all.dart';
 import 'helix_idxs_change.dart';
 import 'helix_offsets_change.dart';
-import 'insertion_deletion_pairing.dart';
+import 'insertion_deletion_batching.dart';
 import 'load_file.dart';
 import 'periodic_save_design_local_storage.dart';
 import 'reselect_moved_dna_ends.dart';
@@ -55,7 +55,7 @@ final all_middleware = List<Middleware<AppState>>.unmodifiable([
   reselect_moved_dna_ends_middleware,
   reselect_moved_strands_middleware,
   selections_intersect_box_compute_middleware,
-  insertion_deletion_pairing_middleware,
+  insertion_deletion_batching_middleware,
   adjust_grid_position_middleware,
   invalidate_png_middleware,
   check_reflect_strands_legal_middleware,

lib/src/middleware/insertion_deletion_batching.dart

@@ -0,0 +1,72 @@
+import 'package:redux/redux.dart';
+import 'package:scadnano/src/state/group.dart';
+import '../state/domain.dart';
+import '../state/design.dart';
+
+import '../actions/actions.dart' as actions;
+import '../state/app_state.dart';
+
+/// Ensures that actions on insertions and deletions happen in pairs on adjacent domains.
+/// Alternately, if Ctrl is pressed when the deletion/insertion is added, then it is added to every
+/// domain in that HelixGroup at that offset.
+insertion_deletion_batching_middleware(Store<AppState> store, dynamic action, NextDispatcher next) {
+  if (action is actions.InsertionOrDeletionAction) {
+    if (action.all_helices) {
+      // add deletion/insertion to all domains at this offset on all helices in same helix group
+      List<Domain> other_domains = find_other_domains(store.state.design, action.domain, action.offset);
+      if (other_domains.isEmpty) {
+        next(action);
+      } else {
+        var other_actions = [
+          for (var other_domain in other_domains) action.clone_for_other_domain(other_domain)
+        ];
+        var batch_action = actions.BatchAction([action] + other_actions);
+        store.dispatch(batch_action);
+      }
+    } else {
+      // add deletion/insertion to other domain at this offset on this helix, if it exists
+      Domain paired_domain = find_paired_domain(store.state.design, action.domain, action.offset);
+      if (paired_domain == null) {
+        next(action);
+      } else {
+        var other_action = action.clone_for_other_domain(paired_domain);
+        var batch_action = actions.BatchAction([action, other_action]);
+        store.dispatch(batch_action);
+      }
+    }
+  } else {
+    next(action);
+  }
+}
+
+/// find all domains on other helices (including other direction on this helix)
+/// in same HelixGroup as [domain].
+List<Domain> find_other_domains(Design design, Domain domain, int offset) {
+  String group_name = design.group_name_of_domain(domain);
+  var helix_idxs_in_group = design.helix_idxs_in_group[group_name];
+  List<Domain> other_domains = [];
+  for (var helix_idx in helix_idxs_in_group) {
+    if (helix_idx == domain.helix) {
+      var paired_domain = find_paired_domain(design, domain, offset);
+      if (paired_domain != null) {
+        other_domains.add(paired_domain);
+      }
+    } else {
+      // only add to domains that don't have this offset as start or end
+      var other_domains_on_helix = design.domains_on_helix_at_offset_internal(helix_idx, offset);
+      other_domains.addAll(other_domains_on_helix);
+    }
+  }
+  return other_domains;
+}
+
+Domain find_paired_domain(Design design, Domain domain, int offset) {
+  var other_domains = design.domains_on_helix_at_offset_internal(domain.helix, offset);
+  for (var other_domain in other_domains) {
+    if (other_domain != domain) {
+      assert(other_domain.forward != domain.forward);
+      return other_domain;
+    }
+  }
+  return null;
+}

lib/src/reducers/app_state_reducer.dart

@@ -50,9 +50,11 @@ AppState app_state_reducer(AppState state, action) {
     ..ui_state.replace(ui_state_global_reducer(state.ui_state, original_state, action)));
 
   // Batch actions are grouped together but should just have one entry on the undo stack.
-  // So we set a variable telling the Undo reducer not to put anything on the stack for any of these atomic actions.
+  // So we set a variable telling the Undo reducer not to put anything on the stack
+  // for any of these atomic actions.
   // However, it has already put something on the stack above for the BatchAction itself.
-  // This seems like it belongs in undo_redo_reducer, but the logic was tricky to handle, so we make a special case.
+  // This seems like it belongs in undo_redo_reducer, but the logic was tricky to handle,
+  // so we make a special case.
   if (action is actions.BatchAction) {
     for (actions.UndoableAction atomic_action in action.actions) {
       state = app_state_reducer(state, actions.SkipUndo(atomic_action));