Merge pull request #972 from UC-Davis-molecular-computing/dev

Dev

Author: dave-doty

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

@@ -1571,9 +1571,13 @@ abstract class SelectAllWithSameAsSelected
 
   BuiltList<SelectableTrait> get traits;
 
+  bool get exclude_scaffolds;
+
   /************************ begin BuiltValue boilerplate ************************/
-  factory SelectAllWithSameAsSelected({BuiltList<Selectable> templates, BuiltList<SelectableTrait> traits}) =
-      _$SelectAllWithSameAsSelected._;
+  factory SelectAllWithSameAsSelected(
+      {BuiltList<Selectable> templates,
+      BuiltList<SelectableTrait> traits,
+      bool exclude_scaffolds}) = _$SelectAllWithSameAsSelected._;
 
   SelectAllWithSameAsSelected._();
 
@@ -2076,6 +2080,8 @@ abstract class ExportDNA with BuiltJsonSerializable implements Action, Built<Exp
 
   bool get include_only_selected_strands;
 
+  bool get exclude_selected_strands;
+
   ExportDNAFormat get export_dna_format;
 
   @nullable
@@ -2093,16 +2099,19 @@ abstract class ExportDNA with BuiltJsonSerializable implements Action, Built<Exp
   factory ExportDNA({
     bool include_scaffold,
     bool include_only_selected_strands,
+    bool exclude_selected_strands,
     ExportDNAFormat export_dna_format,
     String delimiter,
     String domain_delimiter,
     StrandOrder strand_order = null,
     bool column_major_strand = true,
     bool column_major_plate = true,
   }) {
+    assert(!(include_only_selected_strands && exclude_selected_strands));
     return ExportDNA.from((b) => b
       ..include_scaffold = include_scaffold
       ..include_only_selected_strands = include_only_selected_strands
+      ..exclude_selected_strands = exclude_selected_strands
       ..export_dna_format = export_dna_format
       ..delimiter = delimiter
       ..domain_delimiter = domain_delimiter
@@ -2153,6 +2162,27 @@ abstract class ExportSvg with BuiltJsonSerializable implements Action, Built<Exp
   ExportSvgType get type;
 }
 
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Export every text in a DNA sequence separately
+
+abstract class ExportSvgTextSeparatelySet
+    with BuiltJsonSerializable
+    implements Action, Built<ExportSvgTextSeparatelySet, ExportSvgTextSeparatelySetBuilder> {
+  bool get export_svg_text_separately;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExportSvgTextSeparatelySet(bool export_svg_text_separately) =>
+      ExportSvgTextSeparatelySet.from((b) => b..export_svg_text_separately = export_svg_text_separately);
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExportSvgTextSeparatelySet.from([void Function(ExportSvgTextSeparatelySetBuilder) updates]) =
+      _$ExportSvgTextSeparatelySet;
+
+  ExportSvgTextSeparatelySet._();
+
+  static Serializer<ExportSvgTextSeparatelySet> get serializer => _$exportSvgTextSeparatelySetSerializer;
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // Strand part action
 
@@ -3981,6 +4011,22 @@ abstract class ExampleDesignsLoad
   static Serializer<ExampleDesignsLoad> get serializer => _$exampleDesignsLoadSerializer;
 }
 
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// pair lines display
+
+abstract class BasePairTypeSet
+    with BuiltJsonSerializable
+    implements Action, Built<BasePairTypeSet, BasePairTypeSetBuilder> {
+  int get selected_idx;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory BasePairTypeSet({int selected_idx}) = _$BasePairTypeSet._;
+
+  BasePairTypeSet._();
+
+  static Serializer<BasePairTypeSet> get serializer => _$basePairTypeSetSerializer;
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // change helix position
 
@@ -4348,6 +4394,25 @@ 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> {
@@ -4458,3 +4523,40 @@ abstract class OxdnaExport
   @memoized
   int get hashCode;
 }
+
+abstract class OxviewExport
+    with BuiltJsonSerializable
+    implements Action, Built<OxviewExport, OxviewExportBuilder> {
+  bool get selected_strands_only;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory OxviewExport({bool selected_strands_only = false}) {
+    return OxviewExport.from((b) => b..selected_strands_only = selected_strands_only);
+  }
+
+  OxviewExport._();
+
+  factory OxviewExport.from([void Function(OxviewExportBuilder) updates]) = _$OxviewExport;
+
+  static Serializer<OxviewExport> get serializer => _$oxviewExportSerializer;
+
+  @memoized
+  int get hashCode;
+}
+
+abstract class OxExportOnlySelectedStrandsSet
+    with BuiltJsonSerializable
+    implements Action, Built<OxExportOnlySelectedStrandsSet, OxExportOnlySelectedStrandsSetBuilder> {
+  bool get only_selected;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory OxExportOnlySelectedStrandsSet({bool only_selected}) = _$OxExportOnlySelectedStrandsSet._;
+
+  OxExportOnlySelectedStrandsSet._();
+
+  static Serializer<OxExportOnlySelectedStrandsSet> get serializer =>
+      _$oxExportOnlySelectedStrandsSetSerializer;
+
+  @memoized
+  int get hashCode;
+}

lib/src/constants.dart

@@ -8,12 +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 = "0.19.1";
+const String CURRENT_VERSION = "0.19.2";
 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 = [
-  "0.19.0",
+  "0.19.1",
   "0.18.10",
   "0.17.14",
   // "0.17.13",
@@ -428,8 +428,10 @@ const css_selector_scaffold = 'scaffold';
 const css_selector_staple = 'staple';
 const css_selector_domain = 'domain-line';
 const css_selector_base_pair_line = 'base-pair-line';
+const css_selector_base_pair_rect = 'base-pair-rect';
 const css_selector_extension = 'extension-line';
 const css_selector_crossover = 'crossover-curve';
+const css_selector_crossover_same_helix = 'crossover-curve-same-helix';
 const css_selector_loopout = 'loopout-curve';
 const css_selector_end_5p_strand = 'five-prime-end-first-substrand';
 const css_selector_end_3p_strand = 'three-prime-end-last-substrand';
@@ -465,6 +467,7 @@ 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_dna_sequences.dart

@@ -45,6 +45,11 @@ export_dna_sequences_middleware(Store<AppState> store, action, NextDispatcher ne
     List<Strand> strands;
     if (action.include_only_selected_strands) {
       strands = state.ui_state.selectables_store.selected_strands.toList();
+    } else if (action.exclude_selected_strands) {
+      strands = state.design.strands.toList();
+      for (var strand in state.ui_state.selectables_store.selected_strands) {
+        strands.remove(strand);
+      }
     } else {
       strands = state.design.strands.toList();
     }
@@ -107,15 +112,16 @@ Future<void> export_dna() async {
 
   int idx_include_scaffold = 0;
   int idx_include_only_selected_strands = 1;
-  int idx_format_str = 2;
-  int idx_delimiter = 3;
-  int idx_domain_delimiter = 4;
-  int idx_column_major_plate = 5;
-  int idx_sort = 6;
-  int idx_column_major_strand = 7;
-  int idx_strand_order_str = 8;
+  int idx_exclude_selected_strands = 2;
+  int idx_format_str = 3;
+  int idx_delimiter = 4;
+  int idx_domain_delimiter = 5;
+  int idx_column_major_plate = 6;
+  int idx_sort = 7;
+  int idx_column_major_strand = 8;
+  int idx_strand_order_str = 9;
 
-  List<DialogItem> items = List<DialogItem>.filled(9, null);
+  List<DialogItem> items = List<DialogItem>.filled(idx_strand_order_str + 1, null);
 
   items[idx_delimiter] = DialogText(label: 'delimiter between IDT fields', value: ',', tooltip: '''\
 Delimiter to separate IDT fields in a "bulk input" text file, for instance if set to ";", then a line 
@@ -132,6 +138,7 @@ if it had three domains each of length 5.''');
   items[idx_include_scaffold] = DialogCheckbox(label: 'include scaffold', value: false);
   items[idx_include_only_selected_strands] =
       DialogCheckbox(label: 'include only selected strands', value: false);
+  items[idx_exclude_selected_strands] = DialogCheckbox(label: 'exclude selected strands', value: false);
   items[idx_format_str] = DialogRadio(
     label: 'export format',
     options: export_options,
@@ -178,6 +185,10 @@ which part of the strand to use as the address.
       title: 'export DNA sequences',
       type: DialogType.export_dna_sequences,
       items: items,
+      disable_when_any_checkboxes_on: {
+        idx_include_only_selected_strands: [idx_exclude_selected_strands],
+        idx_exclude_selected_strands: [idx_include_only_selected_strands],
+      },
       disable_when_any_checkboxes_off: {
         idx_column_major_strand: [idx_sort],
         idx_strand_order_str: [idx_sort],
@@ -199,6 +210,7 @@ which part of the strand to use as the address.
 
   bool include_scaffold = (results[idx_include_scaffold] as DialogCheckbox).value;
   bool include_only_selected_strands = (results[idx_include_only_selected_strands] as DialogCheckbox).value;
+  bool exclude_selected_strands = (results[idx_exclude_selected_strands] as DialogCheckbox).value;
   String format_str = (results[idx_format_str] as DialogRadio).value;
   bool sort = (results[idx_sort] as DialogCheckbox).value;
   StrandOrder strand_order = null;
@@ -213,9 +225,12 @@ which part of the strand to use as the address.
   String delimiter = (results[idx_delimiter] as DialogText).value;
   String domain_delimiter = (results[idx_domain_delimiter] as DialogText).value;
 
+  assert(!(include_only_selected_strands && exclude_selected_strands));
+
   app.dispatch(actions.ExportDNA(
     include_scaffold: include_scaffold,
     include_only_selected_strands: include_only_selected_strands,
+    exclude_selected_strands: exclude_selected_strands,
     export_dna_format: format,
     delimiter: delimiter,
     domain_delimiter: domain_delimiter,