added ability to control whether base pair lines are exported for a s…

…elected strand when the other strand to which it is bound is not selected

lib/src/actions/actions.dart

@@ -4398,6 +4398,29 @@ abstract class ShowBasePairLinesSet
   int get hashCode;
 }
 
+abstract class ExportBasePairLinesIfOtherStrandNotSelectedSet
+    with
+        BuiltJsonSerializable
+    implements
+        Action,
+        Built<ExportBasePairLinesIfOtherStrandNotSelectedSet,
+            ExportBasePairLinesIfOtherStrandNotSelectedSetBuilder> {
+  bool get export_base_pair_lines_if_other_strand_not_selected;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExportBasePairLinesIfOtherStrandNotSelectedSet(
+          {required bool export_base_pair_lines_if_other_strand_not_selected}) =
+      _$ExportBasePairLinesIfOtherStrandNotSelectedSet._;
+
+  ExportBasePairLinesIfOtherStrandNotSelectedSet._();
+
+  static Serializer<ExportBasePairLinesIfOtherStrandNotSelectedSet> get serializer =>
+      _$exportBasePairLinesIfOtherStrandNotSelectedSetSerializer;
+
+  @memoized
+  int get hashCode;
+}
+
 abstract class ShowBasePairLinesWithMismatchesSet
     with BuiltJsonSerializable
     implements Action, Built<ShowBasePairLinesWithMismatchesSet, ShowBasePairLinesWithMismatchesSetBuilder> {

lib/src/middleware/export_svg.dart

@@ -84,9 +84,11 @@ List<Element> get_selected_svg_elements(AppState state) {
   BuiltSet<Strand> selected_strands = state.ui_state.selectables_store.selected_strands;
   List<Element> selected_elts = [];
   if (app.state.ui_state.base_pair_display_type != BasePairDisplayType.none) {
+    bool export_bp_if_other_not_selected =
+        app.state.ui_state.export_base_pair_lines_if_other_strand_not_selected;
     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);
+        ? state.design.selected_base_pairs_with_mismatches(selected_strands, export_bp_if_other_not_selected)
+        : state.design.selected_base_pairs(selected_strands, export_bp_if_other_not_selected);
     selected_elts.addAll(get_svg_elements_of_base_pairs(base_pairs));
   }
   selected_elts.addAll(get_svg_elements_of_strands(selected_strands));

lib/src/middleware/oxdna_export.dart

@@ -143,7 +143,8 @@ String to_oxview_format(Design design, List<Strand> strands_to_export) {
   }
 
   //TODO: this hasn't been tested well
-  var base_pairs_map = design.base_pairs_with_domain_strand(false, true, strands_to_export.toSet().build());
+  var base_pairs_map =
+      design.base_pairs_with_domain_strand(false, true, strands_to_export.toSet().build(), true);
   for (int helix in base_pairs_map.keys) {
     for (var offset_dom_strands in base_pairs_map[helix]!) {
       int offset = offset_dom_strands.item1;

lib/src/reducers/app_ui_state_reducer.dart

@@ -251,6 +251,10 @@ BasePairDisplayType base_pair_type_idx_reducer(
 
 bool show_base_pair_lines_reducer(bool _, actions.ShowBasePairLinesSet action) => action.show_base_pair_lines;
 
+bool export_base_pair_lines_if_other_strand_not_selected_reducer(
+        bool _, actions.ExportBasePairLinesIfOtherStrandNotSelectedSet action) =>
+    action.export_base_pair_lines_if_other_strand_not_selected;
+
 bool show_base_pair_lines_with_mismatches_reducer(
         bool _, actions.ShowBasePairLinesWithMismatchesSet action) =>
     action.show_base_pair_lines_with_mismatches;
@@ -531,6 +535,10 @@ AppUIStateStorables app_ui_state_storable_local_reducer(AppUIStateStorables stor
             storables.base_pair_display_type, action)
     ..show_base_pair_lines = TypedReducer<bool, actions.ShowBasePairLinesSet>(show_base_pair_lines_reducer)(
         storables.show_base_pair_lines, action)
+    ..export_base_pair_lines_if_other_strand_not_selected =
+        TypedReducer<bool, actions.ExportBasePairLinesIfOtherStrandNotSelectedSet>(
+                export_base_pair_lines_if_other_strand_not_selected_reducer)(
+            storables.export_base_pair_lines_if_other_strand_not_selected, action)
     ..show_base_pair_lines_with_mismatches = TypedReducer<bool, actions.ShowBasePairLinesWithMismatchesSet>(
         show_base_pair_lines_with_mismatches_reducer)(storables.show_base_pair_lines_with_mismatches, action)
     ..export_svg_text_separately =

lib/src/serializers.dart

@@ -82,6 +82,7 @@ part 'serializers.g.dart';
   SubstrandLabelSet,
   DomainNameMismatch,
   ShowBasePairLinesSet,
+  ExportBasePairLinesIfOtherStrandNotSelectedSet,
   ShowBasePairLinesWithMismatchesSet,
   ShowDomainNameMismatchesSet,
   ShowUnpairedInsertionDeletionsSet,

lib/src/state/app_ui_state.dart

@@ -156,6 +156,9 @@ abstract class AppUIState with BuiltJsonSerializable implements Built<AppUIState
 
   bool get show_base_pair_lines => storables.show_base_pair_lines;
 
+  bool get export_base_pair_lines_if_other_strand_not_selected =>
+      storables.export_base_pair_lines_if_other_strand_not_selected;
+
   bool get show_base_pair_lines_with_mismatches => storables.show_base_pair_lines_with_mismatches;
 
   double get strand_name_font_size => storables.strand_name_font_size;

lib/src/state/app_ui_state_storables.dart

@@ -39,6 +39,8 @@ abstract class AppUIStateStorables
 
   bool get show_base_pair_lines;
 
+  bool get export_base_pair_lines_if_other_strand_not_selected;
+
   bool get show_base_pair_lines_with_mismatches;
 
   double get strand_name_font_size;
@@ -147,6 +149,7 @@ abstract class AppUIStateStorables
     b.show_domain_labels = false;
     b.base_pair_display_type = BasePairDisplayType.none;
     b.show_base_pair_lines = false;
+    b.export_base_pair_lines_if_other_strand_not_selected = false;
     b.show_base_pair_lines_with_mismatches = false;
     b.strand_name_font_size = constants.default_strand_name_font_size;
     b.strand_label_font_size = constants.default_strand_label_font_size;

lib/src/state/design.dart

@@ -2152,21 +2152,23 @@ 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,
   /// or when at least one of the strands lacks DNA (is null or is `?` wildcard)
   @memoized
-  BuiltMap<int, BuiltList<int>> get base_pairs => this._base_pairs(false, strands.toBuiltSet());
+  BuiltMap<int, BuiltList<int>> get base_pairs => this._base_pairs(false, strands.toBuiltSet(), true);
 
   /// 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, strands.toBuiltSet());
+      this._base_pairs(true, strands.toBuiltSet(), true);
 
   // 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);
+  BuiltMap<int, BuiltList<int>> selected_base_pairs(
+          BuiltSet<Strand> selected_strands, bool include_base_pair_lines_if_other_strand_not_selected) =>
+      this._base_pairs(false, selected_strands, include_base_pair_lines_if_other_strand_not_selected);
 
   // 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>> selected_base_pairs_with_mismatches(
+          BuiltSet<Strand> selected_strands, bool include_base_pair_lines_if_other_strand_not_selected) =>
+      this._base_pairs(true, selected_strands, include_base_pair_lines_if_other_strand_not_selected);
 
   /// Teturns a list of tuples (offset, d1, d2, s1, s2), where offset is the offset on the helix
   /// of a base pair, and d1/d2/s1/s2 are the domains/strands in the base pair.
@@ -2175,7 +2177,10 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
   /// Otherwise we only consider them paired if they both have DNA; [allow_mismatches] then determines
   /// whether they need to be complementary to be considered a base pair.
   BuiltMap<int, BuiltList<Tuple5<int, Domain, Domain, Strand, Strand>>> base_pairs_with_domain_strand(
-      bool allow_mismatches, bool allow_unassigned_dna, BuiltSet<Strand> selected_strands) {
+      bool allow_mismatches,
+      bool allow_unassigned_dna,
+      BuiltSet<Strand> selected_strands,
+      bool include_base_pair_lines_if_other_strand_not_selected) {
     var base_pairs_with_domain_strand = Map<int, BuiltList<Tuple5<int, Domain, Domain, Strand, Strand>>>();
     BuiltSet<Domain> selected_domains = selected_strands
         .map((s) => s.substrands)
@@ -2193,8 +2198,18 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
           // If not allowing unassigned DNA, then skip if either has no DNA sequence
           continue;
         }
-        if (!selected_domains.contains(dom1) || !selected_domains.contains(dom2)) {
-          continue;
+        if (include_base_pair_lines_if_other_strand_not_selected) {
+          // If we include base pair lines when one strand is not selected, we still need to check
+          // that the OTHER strand is selected.
+          if (!selected_domains.contains(dom1) && !selected_domains.contains(dom2)) {
+            continue;
+          }
+        } else {
+          // If we only include base pair lines when both strands are selected, then skip if either
+          // strand is not selected.
+          if (!selected_domains.contains(dom1) || !selected_domains.contains(dom2)) {
+            continue;
+          }
         }
         // We already checked that these domains are overlapping by calling
         // `find_overlapping_domains_on_helix`, so the next call should not return null.
@@ -2234,9 +2249,10 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     return base_pairs_with_domain_strand.build();
   }
 
-  BuiltMap<int, BuiltList<int>> _base_pairs(bool allow_mismatches, BuiltSet<Strand> selected_strands) {
-    var base_pairs_with_domain_strand =
-        this.base_pairs_with_domain_strand(allow_mismatches, true, selected_strands);
+  BuiltMap<int, BuiltList<int>> _base_pairs(bool allow_mismatches, BuiltSet<Strand> selected_strands,
+      bool include_base_pair_lines_if_other_strand_not_selected) {
+    var base_pairs_with_domain_strand = this.base_pairs_with_domain_strand(
+        allow_mismatches, true, selected_strands, include_base_pair_lines_if_other_strand_not_selected);
     var base_pairs = Map<int, BuiltList<int>>();
     for (int idx in base_pairs_with_domain_strand.keys) {
       base_pairs[idx] = base_pairs_with_domain_strand[idx]!.map((x) => x.item1).toList().build();

lib/src/view/design_main_base_pair_lines.dart

@@ -37,8 +37,8 @@ class DesignMainBasePairLinesComponent extends UiComponent2<DesignMainBasePairLi
   List<ReactElement> create_base_pair_lines_components(BuiltSet<Strand> strands) {
     List<ReactElement> base_pair_lines_components = [];
     BuiltMap<int, BuiltList<int>> base_pairs = props.with_mismatches
-        ? props.design.selected_base_pairs_with_mismatches(strands)
-        : props.design.selected_base_pairs(strands);
+        ? props.design.selected_base_pairs_with_mismatches(strands, true)
+        : props.design.selected_base_pairs(strands, true);
 
     for (int helix_idx in base_pairs.keys) {
       if (!props.only_display_selected_helices || props.side_selected_helix_idxs.contains(helix_idx)) {

lib/src/view/design_main_base_pair_rectangle.dart

@@ -38,8 +38,8 @@ class DesignMainBasePairRectangleComponent extends UiComponent2<DesignMainBasePa
   List<ReactElement> create_base_pair_lines_components(BuiltSet<Strand> strands) {
     List<ReactElement> base_pair_lines_components = [];
     BuiltMap<int, BuiltList<int>> base_pairs = props.with_mismatches
-        ? props.design.selected_base_pairs_with_mismatches(strands)
-        : props.design.selected_base_pairs(strands);
+        ? props.design.selected_base_pairs_with_mismatches(strands, true)
+        : props.design.selected_base_pairs(strands, true);
 
     for (int helix_idx in base_pairs.keys) {
       if (!props.only_display_selected_helices || props.side_selected_helix_idxs.contains(helix_idx)) {

lib/src/view/menu.dart

@@ -909,7 +909,7 @@ or real coordinates in nanometers, depending on whether a grid is selected).'''
       ..key = 'view_menu_base_pairs-dropdown'
       ..className = 'submenu_item')([
       (MenuBoolean()
-        ..value = props.state.ui_state.base_pair_display_type.toIndex() == 1
+        ..value = props.state.ui_state.base_pair_display_type == BasePairDisplayType.lines
         ..display = 'Display as ${BasePairDisplayType.lines.display_name()}'
         ..key = 'base-pair-display-lines'
         ..on_change = (_) {
@@ -919,6 +919,20 @@ or real coordinates in nanometers, depending on whether a grid is selected).'''
             app.dispatch(actions.BasePairTypeSet(selected_idx: BasePairDisplayType.lines.toIndex()));
           }
         })(),
+      (MenuBoolean()
+        ..value = props.state.ui_state.export_base_pair_lines_if_other_strand_not_selected
+        ..hide = props.state.ui_state.base_pair_display_type != BasePairDisplayType.lines
+        ..display = 'Export base pair lines if other strand not selected'
+        ..tooltip = '''\
+When exporting an image of strands while base pair lines are displayed, either through 
+Edit-->Copy/Paste/Select-->Copy image (Ctrl+I), or through 
+Export-->SVG of selected strands, where it is possible that some strands are not selected,
+but are bound to strands that are selected, this determines whether to export the base pair 
+lines connecting the exported strand to the other (non-exported) strand.'''
+        ..on_change = ((_) => app.dispatch(actions.ExportBasePairLinesIfOtherStrandNotSelectedSet(
+            export_base_pair_lines_if_other_strand_not_selected:
+                !props.state.ui_state.export_base_pair_lines_if_other_strand_not_selected)))
+        ..key = 'display-major-tick-offsets-on-all-helices')(),
       (MenuBoolean()
         ..value = props.state.ui_state.base_pair_display_type.toIndex() == 2
         ..display = 'Display as ${BasePairDisplayType.rectangle.display_name()}'