Merge branch 'dev' into 941-dna-sequences-justified

README.md

@@ -1,8 +1,7 @@
 # scadnano
 
 [scadnano](http://scadnano.org)
-("
-scriptable-cadnano", [source code repository here](https://github.com/UC-Davis-molecular-computing/scadnano))
+("scriptable-cadnano", [source code repository here](https://github.com/UC-Davis-molecular-computing/scadnano))
 is a program for designing synthetic DNA structures such as DNA origami.
 The scadnano project is developed and maintained by the UC Davis Molecular Computing group.
 Note that [cadnano](https://cadnano.org) is a separate project, developed and maintained by

lib/src/actions/actions.dart

@@ -4369,6 +4369,25 @@ abstract class DisablePngCachingDnaSequencesSet
       _$disablePngCachingDnaSequencesSetSerializer;
 }
 
+abstract class RetainStrandColorOnSelectionSet
+    with BuiltJsonSerializable
+    implements Action, Built<RetainStrandColorOnSelectionSet, RetainStrandColorOnSelectionSetBuilder> {
+  bool get retain_strand_color_on_selection;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory RetainStrandColorOnSelectionSet(bool retain_strand_color_on_selection) =>
+      RetainStrandColorOnSelectionSet.from(
+          (b) => b..retain_strand_color_on_selection = retain_strand_color_on_selection);
+
+  factory RetainStrandColorOnSelectionSet.from(
+      [void Function(RetainStrandColorOnSelectionSetBuilder) updates]) = _$RetainStrandColorOnSelectionSet;
+
+  RetainStrandColorOnSelectionSet._();
+
+  static Serializer<RetainStrandColorOnSelectionSet> get serializer =>
+      _$retainStrandColorOnSelectionSetSerializer;
+}
+
 abstract class DisplayReverseDNARightSideUpSet
     with BuiltJsonSerializable
     implements Action, Built<DisplayReverseDNARightSideUpSet, DisplayReverseDNARightSideUpSetBuilder> {

lib/src/constants.dart

@@ -466,6 +466,7 @@ const css_selector_deletion = 'deletion-cross';
 const css_selector_insertion_group = 'insertion-group';
 const css_selector_deletion_group = 'deletion-group';
 const css_selector_selected = 'selected';
+const css_selector_selected_pink = 'selected-pink';
 
 const css_selector_context_menu_item_disabled = 'context_menu_item_disabled';
 

lib/src/middleware/export_svg.dart

@@ -43,7 +43,7 @@ export_svg_middleware(Store<AppState> store, dynamic action, NextDispatcher next
             action.type == actions.ExportSvgType.selected) {
           var elt = document.getElementById("main-view-svg");
           if (action.type == actions.ExportSvgType.selected) {
-            List<Element> selected_elts = get_selected_strands(store);
+            List<Element> selected_elts = get_selected_svg_elements(store.state);
             if (selected_elts.length == 0) {
               window.alert("No strands are selected, so there is nothing to export.\n"
                   "Please select some strands before choosing this option.");
@@ -64,7 +64,7 @@ export_svg_middleware(Store<AppState> store, dynamic action, NextDispatcher next
           _export_from_element(elt, 'side');
         }
       } else if (action is actions.CopySelectedStandsToClipboardImage) {
-        List<Element> selected_elts = get_selected_strands(store);
+        List<Element> selected_elts = get_selected_svg_elements(store.state);
         if (selected_elts.length != 0) {
           _copy_from_elements(selected_elts);
         }
@@ -75,18 +75,38 @@ export_svg_middleware(Store<AppState> store, dynamic action, NextDispatcher next
   }
 }
 
-List<Element> get_selected_strands(Store<AppState> store) {
-  var selected_strands = store.state.ui_state.selectables_store.selected_strands;
+List<Element> get_selected_svg_elements(AppState state) {
+  BuiltSet<Strand> selected_strands = state.ui_state.selectables_store.selected_strands;
   List<Element> selected_elts = [];
-  if (selected_strands.length != 0) {
-    for (var strand in selected_strands) {
+  if (app.state.ui_state.show_base_pair_lines) {
+    var base_pairs = state.ui_state.show_base_pair_lines_with_mismatches
+        ? state.design.selected_base_pairs_with_mismatches(selected_strands)
+        : state.design.selected_base_pairs(selected_strands);
+    selected_elts.addAll(get_svg_elements_of_base_pairs(base_pairs));
+  }
+  selected_elts.addAll(get_svg_elements_of_strands(selected_strands));
+  return selected_elts;
+}
+
+List<Element> get_svg_elements_of_strands(BuiltSet<Strand> strands) {
+  List<Element> elts = [];
+  if (strands.length != 0) {
+    for (var strand in strands) {
       var strand_elt = document.getElementById(strand.id);
       var dna_seq_elt = document.getElementById('dna-sequence-${strand.id}');
       var mismatch_elts = document.getElementsByClassName('mismatch-${strand.id}');
-      selected_elts.addAll([strand_elt, if (dna_seq_elt != null) dna_seq_elt, ...mismatch_elts]);
+      elts.addAll([strand_elt, if (dna_seq_elt != null) dna_seq_elt, ...mismatch_elts]);
     }
   }
-  return selected_elts;
+  return elts;
+}
+
+List<Element> get_svg_elements_of_base_pairs(BuiltMap<int, BuiltList<int>> base_pairs) {
+  List<Element> elts = [];
+  for (int helix in base_pairs.keys) {
+    elts.addAll(base_pairs[helix].map((offset) => document.getElementById('base_pair-${helix}-${offset}')));
+  }
+  return elts;
 }
 
 List<double> rotate_vector(List<double> vec, double ang) {
@@ -284,10 +304,11 @@ _copy_from_elements(List<Element> svg_elements) {
 
 _export_from_element(Element svg_element, String filename_append) {
   var cloned_svg_element_with_style;
-  if (filename_append != "selected")
+  if (filename_append != "selected") {
     cloned_svg_element_with_style = clone_and_apply_style(svg_element);
-  else
+  } else {
     cloned_svg_element_with_style = svg_element;
+  }
   // if element is not an svg element (it can be a child element of svg e.g. groups, lines, text, etc), wrap in svg tag
   if (!(svg_element is svg.SvgSvgElement))
     cloned_svg_element_with_style = SvgSvgElement()..children = [cloned_svg_element_with_style];

lib/src/reducers/app_ui_state_reducer.dart

@@ -213,6 +213,9 @@ int slice_bar_offset_set_reducer(int _, actions.SliceBarOffsetSet action) => act
 bool disable_png_caching_dna_sequences_reducer(bool _, actions.DisablePngCachingDnaSequencesSet action) =>
     action.disable_png_caching_dna_sequences;
 
+bool retain_strand_color_on_selection_reducer(bool _, actions.RetainStrandColorOnSelectionSet action) =>
+    action.retain_strand_color_on_selection;
+
 bool display_reverse_DNA_right_side_up_reducer(bool _, actions.DisplayReverseDNARightSideUpSet action) =>
     action.display_reverse_DNA_right_side_up;
 
@@ -437,6 +440,7 @@ AppUIStateStorables app_ui_state_storable_local_reducer(AppUIStateStorables stor
     ..show_slice_bar = TypedReducer<bool, actions.ShowSliceBarSet>(show_slice_bar_reducer)(storables.show_slice_bar, action)
     ..slice_bar_offset = TypedReducer<int, actions.SliceBarOffsetSet>(slice_bar_offset_set_reducer)(storables.slice_bar_offset, action)
     ..disable_png_caching_dna_sequences = TypedReducer<bool, actions.DisablePngCachingDnaSequencesSet>(disable_png_caching_dna_sequences_reducer)(storables.disable_png_caching_dna_sequences, action)
+    ..retain_strand_color_on_selection = TypedReducer<bool, actions.RetainStrandColorOnSelectionSet>(retain_strand_color_on_selection_reducer)(storables.retain_strand_color_on_selection, action)
     ..display_reverse_DNA_right_side_up = TypedReducer<bool, actions.DisplayReverseDNARightSideUpSet>(display_reverse_DNA_right_side_up_reducer)(storables.display_reverse_DNA_right_side_up, action)
     ..local_storage_design_choice = TypedReducer<LocalStorageDesignChoice, actions.LocalStorageDesignChoiceSet>(local_storage_design_choice_reducer)(storables.local_storage_design_choice, action).toBuilder()
     ..clear_helix_selection_when_loading_new_design = TypedReducer<bool, actions.ClearHelixSelectionWhenLoadingNewDesignSet>(clear_helix_selection_when_loading_new_design_set_reducer)(storables.clear_helix_selection_when_loading_new_design, action)

lib/src/serializers.dart

@@ -349,6 +349,7 @@ part 'serializers.g.dart';
   SetDisplayMajorTickWidthsAllHelices,
   SliceBarOffsetSet,
   DisablePngCachingDnaSequencesSet,
+  RetainStrandColorOnSelectionSet,
   DisplayReverseDNARightSideUpSet,
   SliceBarMoveStart,
   SliceBarMoveStop,

lib/src/state/app_ui_state.dart

@@ -235,6 +235,8 @@ abstract class AppUIState with BuiltJsonSerializable implements Built<AppUIState
 
   bool get disable_png_caching_dna_sequences => storables.disable_png_caching_dna_sequences;
 
+  bool get retain_strand_color_on_selection => storables.retain_strand_color_on_selection;
+
   bool get display_reverse_DNA_right_side_up => storables.display_reverse_DNA_right_side_up;
 
   bool get show_mouseover_data => storables.show_mouseover_data;

lib/src/state/app_ui_state_storables.dart

@@ -119,6 +119,8 @@ abstract class AppUIStateStorables
 
   bool get disable_png_caching_dna_sequences;
 
+  bool get retain_strand_color_on_selection;
+
   bool get display_reverse_DNA_right_side_up;
 
   bool get selection_box_intersection;
@@ -175,6 +177,7 @@ abstract class AppUIStateStorables
     b.show_slice_bar = false;
     b.slice_bar_offset = null;
     b.disable_png_caching_dna_sequences = false;
+    b.retain_strand_color_on_selection = false;
     b.display_reverse_DNA_right_side_up = false;
     b.local_storage_design_choice = LocalStorageDesignChoice().toBuilder();
     b.clear_helix_selection_when_loading_new_design = false;

lib/src/state/design.dart

@@ -2101,21 +2101,39 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
 
   /// maps each helix_idx to a list of offsets where there is a complementary base pair on each strand
   @memoized
-  BuiltMap<int, BuiltList<int>> get base_pairs => this._base_pairs(false);
+  BuiltMap<int, BuiltList<int>> get base_pairs => this._base_pairs(false, strands.toBuiltSet());
 
   /// maps each helix_idx to a list of offsets where there is a base on each strand,
   /// NOT necessarily complementary
   @memoized
-  BuiltMap<int, BuiltList<int>> get base_pairs_with_mismatches => this._base_pairs(true);
+  BuiltMap<int, BuiltList<int>> get base_pairs_with_mismatches =>
+      this._base_pairs(true, strands.toBuiltSet());
 
-  BuiltMap<int, BuiltList<int>> _base_pairs(bool allow_mismatches) {
+  // returns a subset of base_pairs that is connected to selected_strands
+  BuiltMap<int, BuiltList<int>> selected_base_pairs(BuiltSet<Strand> selected_strands) =>
+      this._base_pairs(false, selected_strands);
+
+  // returns a subset of base_pairs_with_mismatches that is connected to selected_strands
+  BuiltMap<int, BuiltList<int>> selected_base_pairs_with_mismatches(BuiltSet<Strand> selected_strands) =>
+      this._base_pairs(true, selected_strands);
+
+  BuiltMap<int, BuiltList<int>> _base_pairs(bool allow_mismatches, BuiltSet<Strand> selected_strands) {
     var base_pairs = Map<int, BuiltList<int>>();
+    BuiltSet<Domain> selected_domains = selected_strands
+        .map((s) => s.substrands)
+        .expand((x) => x)
+        .where((x) => x is Domain)
+        .map((x) => x as Domain)
+        .toBuiltSet();
     for (int idx in this.helices.keys) {
       List<int> offsets = [];
       List<Tuple2<Domain, Domain>> overlapping_domains = find_overlapping_domains_on_helix(idx);
       for (var domain_pair in overlapping_domains) {
         Domain dom1 = domain_pair.item1;
         Domain dom2 = domain_pair.item2;
+        if (!selected_domains.contains(dom1) || !selected_domains.contains(dom2)) {
+          continue;
+        }
         var start_and_end = dom1.compute_overlap(dom2);
         int start = start_and_end.item1;
         int end = start_and_end.item2;

lib/src/view/design_main.dart

@@ -88,6 +88,7 @@ UiFactory<DesignMainProps> ConnectedDesignMain = connect<AppState, DesignMainPro
         ..invert_y = state.ui_state.invert_y
         ..selection_rope = state.ui_state.selection_rope
         ..disable_png_caching_dna_sequences = state.ui_state.disable_png_caching_dna_sequences
+        ..retain_strand_color_on_selection = state.ui_state.retain_strand_color_on_selection
         ..display_reverse_DNA_right_side_up = state.ui_state.display_reverse_DNA_right_side_up);
     }
   },
@@ -137,6 +138,7 @@ mixin DesignMainPropsMixin on UiProps {
   String displayed_group_name;
   SelectionRope selection_rope;
   bool disable_png_caching_dna_sequences;
+  bool retain_strand_color_on_selection;
   bool display_reverse_DNA_right_side_up;
   BuiltMap<int, Point<num>> helix_idx_to_svg_position_map;
   bool invert_y;
@@ -263,6 +265,7 @@ class DesignMainComponent extends UiComponent2<DesignMainProps> {
           ..only_display_selected_helices = props.only_display_selected_helices
           ..helix_idx_to_svg_position_map = props.helix_idx_to_svg_position_map
           ..disable_png_caching_dna_sequences = props.disable_png_caching_dna_sequences
+          ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
           ..display_reverse_DNA_right_side_up = props.display_reverse_DNA_right_side_up
           ..key = 'dna-sequences')(),
 

lib/src/view/design_main_base_pair_lines.dart

@@ -2,6 +2,7 @@ import 'dart:html';
 
 import 'package:over_react/over_react.dart';
 import 'package:built_collection/built_collection.dart';
+import 'package:scadnano/scadnano.dart';
 import 'package:scadnano/src/state/group.dart';
 import 'package:scadnano/src/state/helix.dart';
 
@@ -28,14 +29,16 @@ mixin DesignMainBasePairLinesProps on UiProps {
 class DesignMainBasePairLinesComponent extends UiComponent2<DesignMainBasePairLinesProps> with PureComponent {
   @override
   render() {
-    List<ReactElement> base_pair_lines_components = this._create_base_pair_lines_components();
+    List<ReactElement> base_pair_lines_components =
+        this.create_base_pair_lines_components(app.state.design.strands.toBuiltSet());
     return (Dom.g()..className = 'base-pair-lines-main-view')(base_pair_lines_components);
   }
 
-  List<ReactElement> _create_base_pair_lines_components() {
+  List<ReactElement> create_base_pair_lines_components(BuiltSet<Strand> strands) {
     List<ReactElement> base_pair_lines_components = [];
-    var base_pairs =
-        props.with_mismatches ? props.design.base_pairs_with_mismatches : props.design.base_pairs;
+    BuiltMap<int, BuiltList<int>> base_pairs = props.with_mismatches
+        ? props.design.selected_base_pairs_with_mismatches(strands)
+        : props.design.selected_base_pairs(strands);
 
     for (int helix_idx in base_pairs.keys) {
       if (!props.only_display_selected_helices || props.side_selected_helix_idxs.contains(helix_idx)) {
@@ -52,6 +55,7 @@ class DesignMainBasePairLinesComponent extends UiComponent2<DesignMainBasePairLi
           var base_svg_forward_pos = helix.svg_base_pos(offset, true, svg_position_y);
           var base_svg_reverse_pos = helix.svg_base_pos(offset, false, svg_position_y);
           var base_pair_line = (Dom.line()
+            ..id = 'base_pair-${helix_idx}-${offset}'
             ..x1 = base_svg_forward_pos.x
             ..y1 = base_svg_forward_pos.y
             ..x2 = base_svg_reverse_pos.x

lib/src/view/design_main_dna_sequence.dart

@@ -247,7 +247,7 @@ class DesignMainDNASequenceComponent extends UiComponent2<DesignMainDNASequenceP
       ..startOffset = start_offset
       ..style = style_map);
     return (Dom.text()
-      ..key = 'extension-dna-'
+      ..key = 'extension-dna-${ext.is_5p ? "5'" : "3'"}'
           'H${ext.adjacent_domain.helix},${ext.adjacent_domain.start}-${ext.adjacent_domain.end}'
       ..dy = dy)(text_path_props(subseq));
   }

lib/src/view/design_main_dna_sequences.dart

@@ -33,6 +33,7 @@ mixin DesignMainDNASequencesProps on UiProps {
   bool only_display_selected_helices;
   BuiltMap<int, Point<num>> helix_idx_to_svg_position_map;
   bool disable_png_caching_dna_sequences;
+  bool retain_strand_color_on_selection;
   bool display_reverse_DNA_right_side_up;
 }