Merge branch 'dev' of https://github.com/UC-Davis-molecular-computing…

…/scadnano into dev

lib/src/actions/actions.dart

@@ -4348,6 +4348,25 @@ 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/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;
 
@@ -434,6 +437,7 @@ 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

@@ -348,6 +348,7 @@ part 'serializers.g.dart';
   SetDisplayMajorTickWidthsAllHelices,
   SliceBarOffsetSet,
   DisablePngCachingDnaSequencesSet,
+  RetainStrandColorOnSelectionSet,
   DisplayReverseDNARightSideUpSet,
   SliceBarMoveStart,
   SliceBarMoveStop,

lib/src/state/app_ui_state.dart

@@ -233,6 +233,8 @@ 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;
@@ -173,6 +175,7 @@ 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/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_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;
 }
 

lib/src/view/design_main_strand.dart

@@ -85,6 +85,7 @@ mixin DesignMainStrandPropsMixin on UiProps {
   num modification_font_size;
   bool invert_y;
   BuiltMap<int, Point<num>> helix_idx_to_svg_position_map;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainStrandProps = UiProps with DesignMainStrandPropsMixin, TransformByHelixGroupPropsMixin;
@@ -100,7 +101,11 @@ class DesignMainStrandComponent extends UiComponent2<DesignMainStrandProps>
 
     var classname = constants.css_selector_strand;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.strand.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;
@@ -149,7 +154,8 @@ class DesignMainStrandComponent extends UiComponent2<DesignMainStrandProps>
         ..moving_dna_ends = props.moving_dna_ends
         ..geometry = props.geometry
         ..helix_idx_to_svg_position_map = helix_idx_to_svg_position_y_map_on_strand
-        ..only_display_selected_helices = props.only_display_selected_helices)(),
+        ..only_display_selected_helices = props.only_display_selected_helices
+        ..retain_strand_color_on_selection = props.retain_strand_color_on_selection)(),
       _insertions(),
       _deletions(),
       if (props.show_domain_names ||
@@ -188,6 +194,7 @@ class DesignMainStrandComponent extends UiComponent2<DesignMainStrandProps>
           ..display_connector = props.modification_display_connector
           ..helix_idx_to_svg_position_y_map =
               props.helix_idx_to_svg_position_map.map((i, p) => MapEntry(i, p.y))
+          ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
           ..key = 'modifications')(),
     ]);
   }
@@ -301,6 +308,7 @@ class DesignMainStrandComponent extends UiComponent2<DesignMainStrandProps>
             ..transform = transform_of_helix(domain.helix)
             ..svg_position_y = props.helix_idx_to_svg_position_map[helix.idx].y
             ..display_reverse_DNA_right_side_up = props.display_reverse_DNA_right_side_up
+            ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
             ..key = util.id_insertion(domain, selectable_insertion.insertion.offset))());
         }
       }
@@ -335,6 +343,7 @@ class DesignMainStrandComponent extends UiComponent2<DesignMainStrandProps>
             ..selected = props.selected_deletions_in_strand.contains(selectable_deletion)
             ..transform = transform_of_helix(domain.helix)
             ..svg_position_y = props.helix_idx_to_svg_position_map[domain.helix].y
+            ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
             ..key = id)());
         }
       }
@@ -481,7 +490,7 @@ assigned, assign the complementary DNA sequence to this strand.
                       (strand) => actions.StrandNameSet(name: null, strand: strand),
                       props.strand,
                       app.state.ui_state.selectables_store.selected_strands,
-                      'remove strand label'))),
+                      'remove strand name'))),
             ContextMenuItem(
               title: 'set domain name',
               on_click: () => set_domain_names(get_selected_domains()),

lib/src/view/design_main_strand_crossover.dart

@@ -38,6 +38,7 @@ mixin DesignMainStrandCrossoverPropsMixin on UiProps {
   Geometry geometry;
   num prev_domain_helix_svg_position_y;
   num next_domain_helix_svg_position_y;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainStrandCrossoverProps = UiProps
@@ -63,7 +64,11 @@ class DesignMainStrandCrossoverComponent
 
     var classname = constants.css_selector_crossover;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.strand.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_deletion.dart

@@ -26,6 +26,7 @@ mixin DesignMainStrandDeletionPropsMixin on UiProps {
   Domain get domain => selectable_deletion.domain;
   int get deletion => selectable_deletion.offset;
   num svg_position_y;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainStrandDeletionProps = UiProps with DesignMainStrandDeletionPropsMixin;
@@ -55,7 +56,11 @@ class DesignMainStrandDeletionComponent extends UiComponent2<DesignMainStrandDel
 
     var classname = constants.css_selector_deletion_group;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.selectable_deletion.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_dna_end.dart

@@ -62,6 +62,7 @@ mixin DesignMainDNAEndPropsMixin on UiProps {
   bool drawing_potential_crossover;
   bool moving_this_dna_end;
   Point<num> helix_svg_position;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainDNAEndProps = UiProps with DesignMainDNAEndPropsMixin;
@@ -94,7 +95,11 @@ class DesignMainDNAEndComponent extends UiComponent2<DesignMainDNAEndProps> with
     }
 
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_domain.dart

@@ -51,6 +51,7 @@ mixin DesignMainDomainPropsMixin on UiProps {
   BuiltMap<int, Helix> helices;
   BuiltMap<String, HelixGroup> groups;
   Geometry geometry;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainDomainProps = UiProps with DesignMainDomainPropsMixin, TransformByHelixGroupPropsMixin;
@@ -70,7 +71,11 @@ class DesignMainDomainComponent extends UiComponent2<DesignMainDomainProps>
 
     var classname = constants.css_selector_domain;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.strand.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_extension.dart

@@ -53,6 +53,7 @@ mixin DesignMainExtensionPropsMixin on UiProps {
   BuiltMap<int, Helix> helices;
   BuiltMap<String, HelixGroup> groups;
   Geometry geometry;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainExtensionProps = UiProps with DesignMainExtensionPropsMixin, TransformByHelixGroupPropsMixin;
@@ -76,7 +77,11 @@ class DesignMainExtensionComponent extends UiComponent2<DesignMainExtensionProps
 
     var classname = constants.css_selector_extension;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.strand.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_insertion.dart

@@ -39,6 +39,8 @@ mixin DesignMainStrandInsertionPropsMixin on UiProps {
   Insertion get insertion => selectable_insertion.insertion;
 
   Domain get domain => selectable_insertion.domain;
+
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainStrandInsertionProps = UiProps with DesignMainStrandInsertionPropsMixin;
@@ -50,7 +52,11 @@ class DesignMainStrandInsertionComponent extends UiComponent2<DesignMainStrandIn
   render() {
     var classname = constants.css_selector_insertion_group;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.selectable_insertion.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_loopout.dart

@@ -49,6 +49,7 @@ mixin DesignMainLoopoutPropsMixin on UiProps {
   Geometry geometry;
   num prev_helix_svg_position_y;
   num next_helix_svg_position_y;
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainLoopoutProps = UiProps with DesignMainLoopoutPropsMixin, TransformByHelixGroupPropsMixin;
@@ -69,7 +70,11 @@ class DesignMainLoopoutComponent extends UiStatefulComponent2<DesignMainLoopoutP
   render() {
     var classname = constants.css_selector_loopout;
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.strand.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_modification.dart

@@ -49,6 +49,8 @@ mixin DesignMainStrandModificationProps on UiProps {
   num helix_svg_position_y;
 
   Extension ext; // optional; used if mod is on extension
+
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainStrandModificationComponent extends UiComponent2<DesignMainStrandModificationProps> {
@@ -87,7 +89,11 @@ class DesignMainStrandModificationComponent extends UiComponent2<DesignMainStran
     }
 
     if (props.selected) {
-      classname += ' ' + constants.css_selector_selected;
+      if (props.retain_strand_color_on_selection) {
+        classname += ' ' + constants.css_selector_selected;
+      } else {
+        classname += ' ' + constants.css_selector_selected_pink;
+      }
     }
     if (props.strand.is_scaffold) {
       classname += ' ' + constants.css_selector_scaffold;

lib/src/view/design_main_strand_modifications.dart

@@ -34,6 +34,8 @@ mixin DesignMainStrandModificationsPropsMixin on UiProps {
 
   BuiltSet<SelectableModification> selected_modifications_in_strand;
   BuiltMap<int, num> helix_idx_to_svg_position_y_map;
+
+  bool retain_strand_color_on_selection;
 }
 
 class DesignMainStrandModificationsProps = UiProps
@@ -65,6 +67,7 @@ class DesignMainStrandModificationsComponent extends UiComponent2<DesignMainStra
           ..helix_svg_position_y = props.helix_idx_to_svg_position_y_map[helix_5p.idx]
           ..ext = ext
           ..geometry = props.geometry
+          ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
           ..key = "5'")());
       }
     }
@@ -88,6 +91,7 @@ class DesignMainStrandModificationsComponent extends UiComponent2<DesignMainStra
           ..helix_svg_position_y = props.helix_idx_to_svg_position_y_map[helix_3p.idx]
           ..ext = ext
           ..geometry = props.geometry
+          ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
           ..key = "3'")());
       }
     }
@@ -125,6 +129,7 @@ class DesignMainStrandModificationsComponent extends UiComponent2<DesignMainStra
             ..dna_idx_mod = dna_idx_mod
             ..helix_svg_position_y = props.helix_idx_to_svg_position_y_map[helix.idx]
             ..geometry = props.geometry
+            ..retain_strand_color_on_selection = props.retain_strand_color_on_selection
             ..key = "internal-${dna_idx_mod}")());
         }
       } else if (ss_with_mod is Loopout) {