Merge pull request #976 from UC-Davis-molecular-computing/dev

Dev

Author: dave-doty

lib/src/.DS_Store

@@ -883,6 +883,25 @@ abstract class InvertYSet
   static Serializer<InvertYSet> get serializer => _$invertYSetSerializer;
 }
 
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// dynamically update helices
+
+abstract class DynamicHelixUpdateSet
+    with BuiltJsonSerializable
+    implements
+        Action,
+        SvgPngCacheInvalidatingAction,
+        Built<DynamicHelixUpdateSet, DynamicHelixUpdateSetBuilder> {
+  bool get dynamically_update_helices;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory DynamicHelixUpdateSet({bool dynamically_update_helices}) = _$DynamicHelixUpdateSet._;
+
+  DynamicHelixUpdateSet._();
+
+  static Serializer<DynamicHelixUpdateSet> get serializer => _$dynamicHelixUpdateSetSerializer;
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // warn on exit if unsaved
 

lib/src/actions/actions.dart

@@ -8,11 +8,12 @@ import 'state/grid.dart';
 
 // WARNING: Do not modify line below, except for the version string
 //          (and also add new version string to scadnano_versions_to_link).
-const String CURRENT_VERSION = "0.19.2";
+const String CURRENT_VERSION = "0.19.3";
 const String INITIAL_VERSION = "0.1.0";
 
 // scadnano versions that we deploy so that older versions can be used.
 final scadnano_older_versions_to_link = [
+  "0.19.2",
   "0.19.1",
   "0.18.10",
   "0.17.14",
@@ -473,3 +474,13 @@ const css_selector_context_menu_item_disabled = 'context_menu_item_disabled';
 
 const default_vendor_scale = "25nm";
 const default_vendor_purification = "STD";
+
+enum strand_bounds_status {
+  helix_not_in_design,
+  helix_out_of_bounds,
+  min_offset_out_of_bounds,
+  max_offset_out_of_bounds,
+  in_bounds_with_min_offset_changes,
+  in_bounds_with_max_offset_changes,
+  in_bounds
+}

lib/src/constants.dart

@@ -186,7 +186,7 @@ Map point_to_map(svg.Point point) {
 }
 
 // creates a new separate text svg for the jth character on a svg text element
-TextElement create_portable_element(TextContentElement text_ele, int j) {
+TextElement create_portable_text(TextContentElement text_ele, int j) {
   TextElement char_ele = document.createElementNS("http://www.w3.org/2000/svg", "text");
   char_ele.text = text_ele.text[j];
   char_ele.setAttribute("style", text_ele.style.cssText);
@@ -223,19 +223,46 @@ TextElement create_portable_element(TextContentElement text_ele, int j) {
   return char_ele;
 }
 
+// fix the 5' extension rectangle missing
+RectElement create_portable_rect(RectElement ele) {
+  RectElement portableEle = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+
+  portableEle.style.cssText = ele.style.cssText;
+  if (portableEle.style.transformOrigin != "") {
+    portableEle.style.transformOrigin = "";
+  }
+  // remove transform box attribute. dart doesn't support the normal way
+  portableEle.style.cssText = portableEle.style.cssText.replaceAll(RegExp(r'transform-box:[^;]+;'), '');
+  Rect pos = ele.getBBox();
+  portableEle.setAttribute("x", pos.x.toString());
+  portableEle.setAttribute("y", pos.y.toString());
+  portableEle.setAttribute("rx", ele.rx.baseVal.value.toString());
+  portableEle.setAttribute("ry", ele.ry.baseVal.value.toString());
+  portableEle.setAttribute("width", pos.width.toString());
+  portableEle.setAttribute("height", pos.height.toString());
+  for (int i = 0; i < ele.transform.baseVal.numberOfItems; ++i) {
+    Transform item = ele.transform.baseVal.getItem(i);
+    if (item.angle != 0) {
+      portableEle.setAttribute(
+          "transform", "rotate(${item.angle} ${pos.x + pos.width / 2} ${pos.y + pos.height / 2})");
+    }
+  }
+  return portableEle;
+}
+
 // makes a svg compatible for PowerPoint
 Element make_portable(Element src) {
   var src_children = src.querySelectorAll("*");
   document.body.append(src);
   for (int i = 0; i < src_children.length; ++i) {
-    if (src_children[i] is svg.TextContentElement) {
+    if (src_children[i] is TextContentElement) {
       TextContentElement text_ele = src_children[i] as TextContentElement;
       if (text_ele.children.length == 1 && text_ele.children[0].tagName == "textPath") {
         continue;
       }
       List<TextContentElement> portable_eles = [];
       for (int j = 0; j < text_ele.getNumberOfChars(); ++j) {
-        var char_ele = create_portable_element(text_ele, j);
+        var char_ele = create_portable_text(text_ele, j);
         portable_eles.add(char_ele);
       }
       if (text_ele is TextPathElement) {
@@ -248,6 +275,10 @@ Element make_portable(Element src) {
       }
       portable_eles.forEach((v) => text_ele.parentNode.append(v));
       text_ele.remove();
+    } else if (src_children[i] is RectElement) {
+      RectElement portableEle = create_portable_rect(src_children[i] as RectElement);
+      src_children[i].parentNode.append(portableEle);
+      src_children[i].remove();
     }
   }
   src.remove();
@@ -337,6 +368,8 @@ const List<String> path_styles = [
   'stroke-linecap',
   'stroke-opacity',
   'visibility',
+  'transform-box',
+  'transform-origin',
 ];
 
 final relevant_styles = {

lib/src/middleware/export_svg.dart

@@ -8,6 +8,7 @@ import 'package:scadnano/src/state/clipboard.dart';
 import 'package:scadnano/src/state/group.dart';
 import 'package:scadnano/src/state/modification.dart';
 import 'package:scadnano/src/state/strand.dart';
+import 'package:scadnano/src/reducers/strands_move_reducer.dart';
 
 import '../reducers/strands_move_reducer.dart' as strands_move_reducer;
 import '../actions/actions.dart' as actions;
@@ -78,9 +79,35 @@ void handle_autopaste_initiate(Store<AppState> store, actions.AutoPasteInitiate
     strands_move = copy_info.create_strands_move(store.state, start_at_copied: false);
   }
 
-  var paste_commit_action = actions.StrandsMoveCommit(strands_move: strands_move, autopaste: true);
-
-  store.dispatch(paste_commit_action);
+  List<actions.UndoableAction> batch_actions_list = [];
+  Map new_strand_moving_details = get_strand_bounds_details(store.state.design, strands_move);
+  if (store.state.ui_state.dynamically_update_helices) {
+    if (new_strand_moving_details['status'] == constants.strand_bounds_status.min_offset_out_of_bounds ||
+        new_strand_moving_details['status'] == constants.strand_bounds_status.max_offset_out_of_bounds) {
+      var helices_offset_change_action;
+      for (int helix_idx in new_strand_moving_details['offsets'].keys) {
+        if (new_strand_moving_details['status'] == constants.strand_bounds_status.min_offset_out_of_bounds)
+          helices_offset_change_action = actions.HelixOffsetChange(
+              helix_idx: helix_idx, min_offset: new_strand_moving_details['offsets'][helix_idx]);
+        else
+          helices_offset_change_action = actions.HelixOffsetChange(
+              helix_idx: helix_idx, max_offset: new_strand_moving_details['offsets'][helix_idx]);
+
+        batch_actions_list.add(helices_offset_change_action);
+      }
+    }
+  }
+  if (new_strand_moving_details['status'] == constants.strand_bounds_status.in_bounds ||
+      new_strand_moving_details['status'] ==
+          constants.strand_bounds_status.in_bounds_with_min_offset_changes ||
+      new_strand_moving_details['status'] ==
+          constants.strand_bounds_status.in_bounds_with_max_offset_changes) {
+    var paste_commit_action = actions.StrandsMoveCommit(strands_move: strands_move, autopaste: true);
+    batch_actions_list.add(paste_commit_action);
+    var batch_action =
+        actions.BatchAction(batch_actions_list, 'Changing helix offsets and then executing autopaste');
+    store.dispatch(batch_action);
+  }
 }
 
 // either

lib/src/middleware/system_clipboard.dart

@@ -4,13 +4,15 @@ import 'package:built_collection/built_collection.dart';
 import 'package:redux/redux.dart';
 import 'package:scadnano/src/reducers/design_reducer.dart';
 import 'package:scadnano/src/reducers/strands_copy_info_reducer.dart';
+import 'package:scadnano/src/state/design.dart';
 import 'package:scadnano/src/state/base_pair_display_type.dart';
 import 'package:scadnano/src/state/dna_assign_options.dart';
 import 'package:scadnano/src/state/modification.dart';
 import 'package:scadnano/src/state/strand.dart';
 import 'package:scadnano/src/state/copy_info.dart';
 import 'package:scadnano/src/state/substrand.dart';
 import 'package:scadnano/src/util.dart';
+import 'package:tuple/tuple.dart';
 import '../reducers/context_menu_reducer.dart';
 import '../state/example_designs.dart';
 import '../state/grid_position.dart';
@@ -188,6 +190,9 @@ bool show_unpaired_insertion_deletions_reducer(bool _, actions.ShowUnpairedInser
 
 bool invert_y_reducer(bool _, actions.InvertYSet action) => action.invert_y;
 
+bool dynamic_helix_update_reducer(bool _, actions.DynamicHelixUpdateSet action) =>
+    action.dynamically_update_helices;
+
 bool warn_on_exit_if_unsaved_reducer(bool _, actions.WarnOnExitIfUnsavedSet action) => action.warn;
 
 bool show_helix_circles_main_view_reducer(bool _, actions.ShowHelixCirclesMainViewSet action) =>
@@ -438,6 +443,7 @@ AppUIStateStorables app_ui_state_storable_local_reducer(AppUIStateStorables stor
     ..show_domain_name_mismatches = TypedReducer<bool, actions.ShowDomainNameMismatchesSet>(show_domain_name_mismatches_reducer)(storables.show_domain_name_mismatches, action)
     ..show_unpaired_insertion_deletions = TypedReducer<bool, actions.ShowUnpairedInsertionDeletionsSet>(show_unpaired_insertion_deletions_reducer)(storables.show_unpaired_insertion_deletions, action)
     ..invert_y = TypedReducer<bool, actions.InvertYSet>(invert_y_reducer)(storables.invert_y, action)
+    ..dynamically_update_helices = TypedReducer<bool, actions.DynamicHelixUpdateSet>(dynamic_helix_update_reducer)(storables.dynamically_update_helices, action)
     ..warn_on_exit_if_unsaved = TypedReducer<bool, actions.WarnOnExitIfUnsavedSet>(warn_on_exit_if_unsaved_reducer)(storables.warn_on_exit_if_unsaved, action)
     ..show_helix_circles_main_view = TypedReducer<bool, actions.ShowHelixCirclesMainViewSet>(show_helix_circles_main_view_reducer)(storables.show_helix_circles_main_view, action)
     ..show_helix_components_main_view = TypedReducer<bool, actions.ShowHelixComponentsMainViewSet>(show_helix_components_main_view_reducer)(storables.show_helix_components_main_view, action)
@@ -601,7 +607,22 @@ AppUIState ui_state_global_reducer(AppUIState ui_state, AppState state, action)
   ..strands_move = strands_move_global_reducer(ui_state.strands_move, state, action)?.toBuilder()
   ..domains_move = domains_move_global_reducer(ui_state.domains_move, state, action)?.toBuilder()
   ..strand_creation = strand_creation_global_reducer(ui_state.strand_creation, state, action)?.toBuilder()
-  ..copy_info = copy_info_global_reducer(ui_state.copy_info, state, action)?.toBuilder());
+  ..copy_info = copy_info_global_reducer(ui_state.copy_info, state, action)?.toBuilder()
+  ..original_helix_offsets =
+      original_helix_offsets_reducer(ui_state.original_helix_offsets, state, action).toBuilder());
+
+BuiltMap<int, Tuple2> original_helix_offsets_reducer(
+    BuiltMap<int, Tuple2> original_helix_offsets, AppState state, action) {
+  if (action is actions.StrandsMoveStartSelectedStrands || action is actions.StrandCreateStart) {
+    var helix_offsets = original_helix_offsets.toMap();
+    for (int key in state.design.helices.keys) {
+      var helix = state.design.helices[key];
+      helix_offsets[state.design.helices[key].idx] = Tuple2.fromList([helix.min_offset, helix.max_offset]);
+    }
+    return helix_offsets.build();
+  }
+  return original_helix_offsets;
+}
 
 GlobalReducer<BuiltList<MouseoverData>, AppState> mouseover_datas_global_reducer = combineGlobalReducers([
   TypedGlobalReducer<BuiltList<MouseoverData>, AppState, actions.HelixRollSetAtOther>(

lib/src/reducers/app_ui_state_reducer.dart

@@ -4,7 +4,11 @@ import 'package:collection/collection.dart';
 import 'package:redux/redux.dart';
 import 'package:built_collection/built_collection.dart';
 import 'package:scadnano/src/reducers/groups_reducer.dart';
+import 'package:scadnano/src/reducers/strands_move_reducer.dart';
 import 'package:scadnano/src/state/group.dart';
+import 'package:scadnano/src/state/strand_creation.dart';
+import 'package:scadnano/src/state/strands_move.dart';
+import 'package:scadnano/src/state/substrand.dart';
 import '../reducers/util_reducer.dart';
 import '../state/app_state.dart';
 
@@ -51,6 +55,13 @@ GlobalReducer<BuiltMap<int, Helix>, AppState> helices_global_reducer = combineGl
   TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.HelixMaxOffsetSetByDomainsAllSameMax>(
     helix_max_offset_set_by_domains_all_same_max_reducer,
   ),
+  TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.StrandsMoveAdjustAddress>(
+      helix_offset_change_all_with_moving_strands_reducer),
+  TypedGlobalReducer<BuiltMap<int, Helix>, AppState, actions.StrandCreateAdjustOffset>(
+      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)
 ]);
 
 BuiltMap<int, Helix> helix_individual_reducer(
@@ -186,6 +197,136 @@ Helix _change_offset_one_helix(Helix helix, int min_offset, int max_offset) => h
   ..min_offset = min_offset ?? helix.min_offset
   ..max_offset = max_offset ?? helix.max_offset);
 
+BuiltMap<int, Helix> helix_offset_change_all_with_moving_strands_reducer(
+    BuiltMap<int, Helix> helices, AppState state, actions.StrandsMoveAdjustAddress action) {
+  if (state.ui_state.dynamically_update_helices) {
+    StrandsMove new_strands_move =
+        state.ui_state.strands_move.rebuild((b) => b..current_address.replace(action.address));
+    Map strand_bounds_details = get_strand_bounds_details(state.design, new_strands_move);
+    constants.strand_bounds_status status = strand_bounds_details['status'];
+
+    var offsets = strand_bounds_details['offsets'];
+    if (status == constants.strand_bounds_status.min_offset_out_of_bounds ||
+        status == constants.strand_bounds_status.in_bounds_with_min_offset_changes) {
+      Helix map_func(int idx, Helix helix) => _change_offset_one_helix(helix, offsets[idx], null);
+      helices = helices.map_values(map_func);
+    } else if (status == constants.strand_bounds_status.max_offset_out_of_bounds ||
+        status == constants.strand_bounds_status.in_bounds_with_max_offset_changes) {
+      Helix map_func(int idx, Helix helix) => _change_offset_one_helix(helix, null, offsets[idx]);
+      helices = helices.map_values(map_func);
+    }
+  }
+  return helices;
+}
+
+BuiltMap<int, Helix> helix_offset_change_all_while_creating_strand_reducer(
+    BuiltMap<int, Helix> helices, AppState state, actions.StrandCreateAdjustOffset action) {
+  if (state.ui_state.dynamically_update_helices) {
+    StrandCreation strand_creation = state.ui_state.strand_creation;
+    if (strand_creation != null) {
+      var helices_map = helices.toMap();
+      var original_helix_offsets = state.ui_state.original_helix_offsets;
+
+      // Increase helix size according to strand movement
+      if (helices_map[strand_creation.helix.idx].min_offset > action.offset) {
+        helices_map[strand_creation.helix.idx] =
+            helices_map[strand_creation.helix.idx].rebuild((b) => b..min_offset = action.offset);
+        return helices_map.build();
+      }
+      if (helices_map[strand_creation.helix.idx].max_offset <= action.offset) {
+        helices_map[strand_creation.helix.idx] =
+            helices_map[strand_creation.helix.idx].rebuild((b) => b..max_offset = action.offset + 1);
+        return helices_map.build();
+      }
+
+      // Decrease helix size according to strand movement
+      if (action.offset > helices_map[strand_creation.helix.idx].min_offset &&
+          helices_map[strand_creation.helix.idx].min_offset <
+              original_helix_offsets[strand_creation.helix.idx].item1) {
+        helices_map[strand_creation.helix.idx] =
+            helices_map[strand_creation.helix.idx].rebuild((b) => b..min_offset = action.offset);
+        return helices_map.build();
+      }
+      if (action.offset < helices_map[strand_creation.helix.idx].max_offset + 1 &&
+          helices_map[strand_creation.helix.idx].max_offset >
+              original_helix_offsets[strand_creation.helix.idx].item2) {
+        helices_map[strand_creation.helix.idx] =
+            helices_map[strand_creation.helix.idx].rebuild((b) => b.max_offset = action.offset + 1);
+        return helices_map.build();
+      }
+    }
+  }
+  return helices;
+}
+
+BuiltMap<int, Helix> first_replace_strands_reducer(
+    BuiltMap<int, Helix> helices, AppState state, actions.ReplaceStrands action) {
+  Map changed_strands = action.new_strands.toMap();
+  Map<int, int> min_offsets = {};
+  Map<int, int> max_offsets = {};
+  for (int key in changed_strands.keys) {
+    Strand strand = changed_strands[key];
+    List<Substrand> substrands = strand.substrands.toList();
+    for (var domain in substrands) {
+      if (domain is Domain) {
+        int helix_idx = domain.helix;
+        if (domain.start < helices[helix_idx].min_offset) {
+          if (min_offsets.containsKey(helix_idx))
+            min_offsets[helix_idx] = [min_offsets[helix_idx], domain.start].min;
+          else
+            min_offsets[helix_idx] = domain.start;
+        }
+        if (domain.end > helices[helix_idx].max_offset) {
+          if (max_offsets.containsKey(helix_idx))
+            max_offsets[helix_idx] = [max_offsets[helix_idx], domain.end].max;
+          else
+            max_offsets[helix_idx] = domain.end;
+        }
+      }
+    }
+  }
+  var helices_map = helices.toMap();
+  if (min_offsets.length > 0) {
+    for (int helix_idx in min_offsets.keys) {
+      helices_map[helix_idx] = helices_map[helix_idx].rebuild((b) => b..min_offset = min_offsets[helix_idx]);
+    }
+  }
+  if (max_offsets.length > 0) {
+    for (int helix_idx in max_offsets.keys) {
+      helices_map[helix_idx] = helices_map[helix_idx].rebuild((b) => b..max_offset = max_offsets[helix_idx]);
+    }
+  }
+  return helices_map.build();
+}
+
+BuiltMap<int, Helix> reset_helices_offsets(BuiltMap<int, Helix> helices, AppState state) {
+  var helices_updated = helices.toMap();
+  var original_helix_offsets = state.ui_state.original_helix_offsets;
+  for (int idx in original_helix_offsets.keys) {
+    int current_helix_min_offset = state.design.min_offset_of_strands_at(idx);
+    if (current_helix_min_offset >= original_helix_offsets[idx].item1) {
+      helices_updated[idx] =
+          helices_updated[idx].rebuild((b) => b.min_offset = original_helix_offsets[idx].item1);
+    }
+    int current_helix_max_offset = state.design.max_offset_of_strands_at(idx);
+    if (current_helix_max_offset <= original_helix_offsets[idx].item2) {
+      helices_updated[idx] =
+          helices_updated[idx].rebuild((b) => b.max_offset = original_helix_offsets[idx].item2);
+    }
+  }
+  return helices_updated.build();
+}
+
+BuiltMap<int, Helix> reset_helices_offsets_after_selections_clear(
+    BuiltMap<int, Helix> helices, AppState state, actions.SelectionsClear action) {
+  return reset_helices_offsets(helices, state);
+}
+
+// BuiltMap<int, Helix> reset_helices_offsets_after_creation(
+//     BuiltMap<int, Helix> helices, AppState state, actions.StrandCreateStop action) {
+//   return reset_helices_offsets(helices, state);
+// }
+
 BuiltMap<int, Helix> helix_offset_change_all_reducer(
     BuiltMap<int, Helix> helices, AppState state, actions.HelixOffsetChangeAll action) {
   Helix map_func(_, Helix helix) => _change_offset_one_helix(helix, action.min_offset, action.max_offset);