addresses issue #36 but does not fix it totally; helix idxs can now b…

…e changed one at a time, and not with a recalculation of view order until #407 is addressed

lib/src/actions/actions.dart

@@ -141,7 +141,7 @@ abstract class BatchAction
 
   /************************ begin BuiltValue boilerplate ************************/
   factory BatchAction(Iterable<UndoableAction> actions) =>
-      BatchAction.from((b) => b..actions.replace(BuiltList<UndoableAction>(actions)));
+      BatchAction.from((b) => b..actions.replace(actions));
 
   factory BatchAction.from([void Function(BatchActionBuilder) updates]) = _$BatchAction;
 
@@ -1225,6 +1225,25 @@ abstract class HelixMajorTickPeriodicDistancesChangeAll
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // Helix change min/max offsets
 
+abstract class HelixIdxsChange
+    with BuiltJsonSerializable, UndoableAction
+    implements Built<HelixIdxsChange, HelixIdxsChangeBuilder> {
+  BuiltMap<int, int> get idx_replacements;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory HelixIdxsChange({Map<int,int> idx_replacements}) =>
+      HelixIdxsChange.from((b) => b..idx_replacements.replace(idx_replacements));
+
+  factory HelixIdxsChange.from([void Function(HelixIdxsChangeBuilder) updates]) = _$HelixIdxsChange;
+
+  HelixIdxsChange._();
+
+  static Serializer<HelixIdxsChange> get serializer => _$helixIdxsChangeSerializer;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Helix change min/max offsets
+
 abstract class HelixOffsetChange
     with BuiltJsonSerializable, UndoableAction
     implements HelixIndividualAction, Built<HelixOffsetChange, HelixOffsetChangeBuilder> {

lib/src/app.dart

@@ -37,8 +37,8 @@ import 'dna_sequence_constants.dart';
 // global variable for whole program
 App app = App();
 
-const USE_REDUX_DEV_TOOLS = false;
-//const USE_REDUX_DEV_TOOLS = true;
+//const USE_REDUX_DEV_TOOLS = false;
+const USE_REDUX_DEV_TOOLS = true;
 
 const RUN_TEST_CODE_INSTEAD_OF_APP = false;
 //const RUN_TEST_CODE_INSTEAD_OF_APP = true;

lib/src/middleware/all_middleware.dart

@@ -10,6 +10,7 @@ import 'export_dna_sequences.dart';
 import 'dna_ends_move_start.dart';
 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 'load_file.dart';
@@ -38,6 +39,7 @@ final all_middleware = List<Middleware<AppState>>.unmodifiable([
   strand_create_middleware,
   helix_remove_middleware,
   helix_change_offsets_middleware,
+  helix_idxs_change_middleware,
   helix_grid_offsets_middleware,
   helix_hide_all_middleware,
   helix_positions_set_based_on_crossovers_middleware,

lib/src/middleware/helix_idxs_change.dart

@@ -0,0 +1,24 @@
+import 'dart:html';
+
+import 'package:redux/redux.dart';
+import 'package:scadnano/src/state/design.dart';
+
+import '../actions/actions.dart' as actions;
+import '../state/app_state.dart';
+
+/// Check whether user wants to remove helix that has strands on it.
+helix_idxs_change_middleware(Store<AppState> store, dynamic action, NextDispatcher next) {
+  if (action is actions.HelixIdxsChange) {
+    Set<int> existing_idxs = store.state.design.helices.keys.toSet();
+    Set<int> old_idxs = action.idx_replacements.keys.toSet();
+    Set<int> remaining_idxs = existing_idxs.difference(old_idxs);
+    for (int new_idx in action.idx_replacements.values) {
+      if (remaining_idxs.contains(new_idx)) {
+        var msg = 'Index ${new_idx} is already taken.';
+        window.alert(msg);
+        return;
+      }
+    }
+  }
+  next(action);
+}

lib/src/reducers/design_reducer.dart

@@ -60,8 +60,12 @@ Design design_error_message_set_reducer(Design design, actions.ErrorMessageSet a
 // whole: operate on the whole DNADesign
 // global: need the whole AppState
 GlobalReducer<Design, AppState> design_whole_global_reducer = combineGlobalReducers([
+  TypedGlobalReducer<Design, AppState, actions.HelixIdxsChange>(helix_idx_change_reducer),
   TypedGlobalReducer<Design, AppState, actions.HelixAdd>(helix_add_design_reducer),
   TypedGlobalReducer<Design, AppState, actions.HelixRemove>(helix_remove_design_global_reducer),
   TypedGlobalReducer<Design, AppState, actions.HelixRemoveAllSelected>(
       helix_remove_all_selected_design_global_reducer),
 ]);
+
+
+

lib/src/reducers/helices_reducer.dart

@@ -78,6 +78,52 @@ Reducer<Helix> _helix_individual_reducers = combineReducers([
   TypedReducer<Helix, actions.HelixRollSet>(helix_roll_set_reducer),
 ]);
 
+///////////////////////////////////////////////////////////////////////////////////////////////////////////
+// change idx
+
+Design helix_idx_change_reducer(Design design, AppState state, actions.HelixIdxsChange action) {
+  var helices = design.helices.toMap();
+  var strands = design.strands.toList();
+
+  // change helices
+  for (int old_idx in action.idx_replacements.keys) {
+    int new_idx = action.idx_replacements[old_idx];
+    var helix = helices[old_idx].rebuild((b) => b..idx = new_idx);
+    helices.remove(old_idx);
+    helices[new_idx] = helix;
+  }
+
+
+  // change helix idx refs on domains
+  for (int s = 0; s < strands.length; s++) {
+    var strand = strands[s];
+    var substrands = strand.substrands.toList();
+    bool changed_strand = false;
+    for (int d = 0; d < strand.substrands.length; d++) {
+      var substrand = strand.substrands[d];
+      if (substrand is Domain) {
+        Domain domain = substrand as Domain;
+        int new_idx = action.idx_replacements[domain.helix];
+        if (new_idx != null) {
+          domain = domain.rebuild((b) => b..helix = new_idx);
+          substrands[d] = domain;
+          changed_strand = true;
+        }
+      }
+    }
+    if (changed_strand) {
+      strands[s] = strand.rebuild((b) => b..substrands.replace(substrands));
+    }
+  }
+
+  //TODO: recalculate view order; first figure out if it was non-default by looking at Helix.view_order
+
+
+  helices = util.helices_assign_svg(design.geometry, state.ui_state.invert_yz, helices, design.grid);
+  design = design.rebuild((b) => b..helices.replace(helices)..strands.replace(strands));
+  return design;
+}
+
 ///////////////////////////////////////////////////////////////////////////////////////////////////////////
 // change min/max offsets
 

lib/src/serializers.dart

@@ -117,6 +117,7 @@ part 'serializers.g.dart';
   HelixRemoveAllSelected,
   HelixOffsetChange,
   HelixOffsetChangeAll,
+  HelixIdxsChange,
   HelixMajorTickDistanceChange,
   HelixMajorTickDistanceChangeAll,
   HelixMajorTicksChange,

lib/src/state/design.dart

@@ -617,13 +617,6 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
         throw IllegalDNADesignError(
             'grid is not none, but Helix $idx has position = ${helix_json[constants.position_key]}');
       }
-      // don't want to do this while codenano has different version numbers
-//      if (position_x_z_should_swap && grid_is_none) {
-//        // prior to version 0.10.0, x and z had the opposite role
-//        num swap = helix_builder.position_.x;
-//        helix_builder.position_.x = helix_builder.position_.z;
-//        helix_builder.position_.z = swap;
-//      }
       helix_builders.add(helix_builder);
       idx++;
     }

lib/src/view/helix_context_menu.dart

@@ -14,8 +14,6 @@ import '../util.dart' as util;
 
 List<ContextMenuItem> context_menu_helix(Helix helix, bool helix_change_apply_to_all) {
   Future<void> dialog_helix_adjust_length() async {
-    int helix_idx = helix.idx;
-
     var dialog = Dialog(title: 'adjust helix length', items: [
       DialogNumber(label: 'minimum', value: helix.min_offset),
       DialogNumber(label: 'maximum', value: helix.max_offset),
@@ -38,10 +36,22 @@ List<ContextMenuItem> context_menu_helix(Helix helix, bool helix_change_apply_to
       app.dispatch(actions.HelixOffsetChangeAll(min_offset: min_offset, max_offset: max_offset));
     } else {
       app.dispatch(
-          actions.HelixOffsetChange(helix_idx: helix_idx, min_offset: min_offset, max_offset: max_offset));
+          actions.HelixOffsetChange(helix_idx: helix.idx, min_offset: min_offset, max_offset: max_offset));
     }
   }
 
+  Future<void> dialog_helix_adjust_idx() async {
+    var dialog = Dialog(title: 'adjust helix index', items: [
+      DialogNumber(label: 'new index', value: helix.idx),
+    ]);
+    List<DialogItem> results = await util.dialog(dialog);
+    if (results == null) return;
+
+    int new_idx = (results[0] as DialogNumber).value;
+
+    app.dispatch(actions.HelixIdxsChange(idx_replacements: {helix.idx: new_idx}));
+  }
+
   Future<void> dialog_helix_adjust_roll() async {
     int helix_idx = helix.idx;
 
@@ -277,6 +287,10 @@ minimum offset ${helix.min_offset} of helix ${helix.min_offset}.''');
     app.disable_keyboard_shortcuts_while(dialog_helix_adjust_length);
   }
 
+  helix_adjust_idx() {
+    app.disable_keyboard_shortcuts_while(dialog_helix_adjust_idx);
+  }
+
   helix_adjust_major_tick_marks() {
     app.disable_keyboard_shortcuts_while(dialog_helix_adjust_major_tick_marks);
   }
@@ -308,6 +322,10 @@ minimum offset ${helix.min_offset} of helix ${helix.min_offset}.''');
       title: 'adjust length',
       on_click: helix_adjust_length,
     ),
+    ContextMenuItem(
+      title: 'adjust index',
+      on_click: helix_adjust_idx,
+    ),
     ContextMenuItem(
       title: 'adjust tick marks',
       on_click: helix_adjust_major_tick_marks,

test/reducer_test.dart

@@ -3519,7 +3519,6 @@ main() {
           app_state_reducer(state, MouseoverDataUpdate(mouseover_params: [mouseoverParams].toBuiltList()));
 
       Helix helix = two_helices_design.helices[1];
-      int offset = 12;
       Domain domain = two_helices_design.strands[2].domains()[0];
 
       mouseoverParams = MouseoverParams(1, 13, true);
@@ -3586,10 +3585,6 @@ main() {
       state =
           app_state_reducer(state, MouseoverDataUpdate(mouseover_params: [mouseoverParams].toBuiltList()));
 
-      Helix helix = two_helices_design.helices[1];
-      int offset = 12;
-      Domain domain = two_helices_design.strands[2].domains()[0];
-
       state = app_state_reducer(state, MouseoverDataClear());
 
       expect(state.ui_state.mouseover_datas, BuiltList<MouseoverData>());

web/scadnano-styles.css

@@ -7,15 +7,6 @@ html, body {
     font-family: sans-serif;
 }
 
-/* https://stackoverflow.com/questions/15904416/placing-a-link-inside-of-a-tooltip */
-.parent .tooltip {
-    display: none;
-}
-
-.parent:hover .tooltip {
-    display: block;
-}
-
 /************************************************
 ** BEGIN layout
 ************************************************/