Merge branch 'dev' into 789-saved-dialog-for-future

.gitignore

@@ -21,3 +21,7 @@ doc/api/
 
 codenano.html
 *.log
+
+todo.txt
+
+todo extensions.txt

lib/src/actions/actions.dart

@@ -34,6 +34,7 @@ import '../state/grid.dart';
 import '../state/helix.dart';
 import '../state/local_storage_design_choice.dart';
 import '../state/loopout.dart';
+import '../state/extension.dart';
 import '../state/modification.dart';
 import '../state/position3d.dart';
 import '../state/potential_crossover.dart';
@@ -631,15 +632,18 @@ abstract class ShowUnpairedInsertionDeletionsSet
   bool get show_unpaired_insertion_deletions;
 
   factory ShowUnpairedInsertionDeletionsSet(bool show_unpaired_insertion_deletions) =>
-      ShowUnpairedInsertionDeletionsSet.from((b) => b..show_unpaired_insertion_deletions = show_unpaired_insertion_deletions);
+      ShowUnpairedInsertionDeletionsSet.from(
+          (b) => b..show_unpaired_insertion_deletions = show_unpaired_insertion_deletions);
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory ShowUnpairedInsertionDeletionsSet.from([void Function(ShowUnpairedInsertionDeletionsSetBuilder) updates]) =
-  _$ShowUnpairedInsertionDeletionsSet;
+  factory ShowUnpairedInsertionDeletionsSet.from(
+          [void Function(ShowUnpairedInsertionDeletionsSetBuilder) updates]) =
+      _$ShowUnpairedInsertionDeletionsSet;
 
   ShowUnpairedInsertionDeletionsSet._();
 
-  static Serializer<ShowUnpairedInsertionDeletionsSet> get serializer => _$showUnpairedInsertionDeletionsSetSerializer;
+  static Serializer<ShowUnpairedInsertionDeletionsSet> get serializer =>
+      _$showUnpairedInsertionDeletionsSetSerializer;
 }
 
 abstract class SetShowEditor
@@ -1939,22 +1943,131 @@ abstract class StrandPartAction extends Action {
   StrandPart get strand_part;
 }
 
+abstract class ExtensionDisplayLengthAngleSet
+    with BuiltJsonSerializable, UndoableAction
+    implements
+        StrandPartAction,
+        Built<ExtensionDisplayLengthAngleSet, ExtensionDisplayLengthAngleSetBuilder> {
+  Extension get ext;
+
+  num get display_length;
+
+  num get display_angle;
+
+  StrandPart get strand_part => ext;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExtensionDisplayLengthAngleSet({Extension ext, num display_length, num display_angle}) =>
+      ExtensionDisplayLengthAngleSet.from((b) => b
+        ..ext.replace(ext)
+        ..display_length = display_length
+        ..display_angle = display_angle);
+
+  factory ExtensionDisplayLengthAngleSet.from(
+      [void Function(ExtensionDisplayLengthAngleSetBuilder) updates]) = _$ExtensionDisplayLengthAngleSet;
+
+  ExtensionDisplayLengthAngleSet._();
+
+  static Serializer<ExtensionDisplayLengthAngleSet> get serializer =>
+      _$extensionDisplayLengthAngleSetSerializer;
+
+  @override
+  String short_description() => "change extension display length/angle";
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// add extension to strand
+
+abstract class ExtensionAdd
+    with BuiltJsonSerializable, UndoableAction
+    implements SingleStrandAction, Built<ExtensionAdd, ExtensionAddBuilder> {
+  Strand get strand;
+
+  bool get is_5p;
+
+  int get num_bases;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExtensionAdd({Strand strand, bool is_5p, int num_bases}) => ExtensionAdd.from((b) => b
+    ..strand.replace(strand)
+    ..is_5p = is_5p
+    ..num_bases = num_bases);
+
+  factory ExtensionAdd.from([void Function(ExtensionAddBuilder) updates]) = _$ExtensionAdd;
+
+  ExtensionAdd._();
+
+  static Serializer<ExtensionAdd> get serializer => _$extensionAddSerializer;
+
+  @override
+  String short_description() => "add extension to strand";
+}
+
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// loopout length change
+// loopout/extension length change
+
+abstract class ExtensionNumBasesChange
+    with BuiltJsonSerializable, UndoableAction
+    implements StrandPartAction, Built<ExtensionNumBasesChange, ExtensionNumBasesChangeBuilder> {
+  Extension get ext;
+
+  int get num_bases;
+
+  StrandPart get strand_part => ext;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExtensionNumBasesChange(Extension ext, int num_bases) => ExtensionNumBasesChange.from((b) => b
+    ..ext.replace(ext)
+    ..num_bases = num_bases);
+
+  factory ExtensionNumBasesChange.from([void Function(ExtensionNumBasesChangeBuilder) updates]) =
+      _$ExtensionNumBasesChange;
+
+  ExtensionNumBasesChange._();
+
+  static Serializer<ExtensionNumBasesChange> get serializer => _$extensionNumBasesChangeSerializer;
+
+  @override
+  String short_description() => "change extension number of bases";
+}
+
+abstract class ExtensionsNumBasesChange
+    with BuiltJsonSerializable, UndoableAction
+    implements Built<ExtensionsNumBasesChange, ExtensionsNumBasesChangeBuilder> {
+  BuiltList<Extension> get extensions;
+
+  int get num_bases;
+
+  /************************ begin BuiltValue boilerplate ************************/
+  factory ExtensionsNumBasesChange(Iterable<Extension> extensions, int num_bases) =>
+      ExtensionsNumBasesChange.from((b) => b
+        ..extensions.replace(extensions)
+        ..num_bases = num_bases);
+
+  factory ExtensionsNumBasesChange.from([void Function(ExtensionsNumBasesChangeBuilder) updates]) =
+      _$ExtensionsNumBasesChange;
+
+  ExtensionsNumBasesChange._();
+
+  static Serializer<ExtensionsNumBasesChange> get serializer => _$extensionsNumBasesChangeSerializer;
+
+  @override
+  String short_description() => "change extensions number of bases";
+}
 
 abstract class LoopoutLengthChange
     with BuiltJsonSerializable, UndoableAction
     implements StrandPartAction, Built<LoopoutLengthChange, LoopoutLengthChangeBuilder> {
   Loopout get loopout;
 
-  int get length;
+  int get num_bases;
 
   StrandPart get strand_part => loopout;
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory LoopoutLengthChange(Loopout loopout, int length) => LoopoutLengthChange.from((b) => b
+  factory LoopoutLengthChange(Loopout loopout, int num_bases) => LoopoutLengthChange.from((b) => b
     ..loopout.replace(loopout)
-    ..length = length);
+    ..num_bases = num_bases);
 
   factory LoopoutLengthChange.from([void Function(LoopoutLengthChangeBuilder) updates]) =
       _$LoopoutLengthChange;
@@ -3474,12 +3587,15 @@ abstract class StrandColorPickerHide
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// scaffold set/unset
+// abstract supertype of actions that operate on a single strand
 
 abstract class SingleStrandAction implements Action {
   Strand get strand;
 }
 
+/////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// scaffold set/unset
+
 abstract class ScaffoldSet
     with BuiltJsonSerializable, UndoableAction
     implements SingleStrandAction, Built<ScaffoldSet, ScaffoldSetBuilder> {
@@ -3743,19 +3859,20 @@ abstract class ShowAxisArrowsSet
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////
-// show or hide grid coordinates in side view
+// show or hide loopout and extension lengths displayed next to the substrand
 
-abstract class ShowLoopoutLengthSet
+abstract class ShowLoopoutExtensionLengthSet
     with BuiltJsonSerializable
-    implements Built<ShowLoopoutLengthSet, ShowLoopoutLengthSetBuilder> {
-  bool get show_loopout_length;
+    implements Built<ShowLoopoutExtensionLengthSet, ShowLoopoutExtensionLengthSetBuilder> {
+  bool get show_length;
 
   /************************ begin BuiltValue boilerplate ************************/
-  factory ShowLoopoutLengthSet({bool show_loopout_length}) = _$ShowLoopoutLengthSet._;
+  factory ShowLoopoutExtensionLengthSet({bool show_length}) = _$ShowLoopoutExtensionLengthSet._;
 
-  ShowLoopoutLengthSet._();
+  ShowLoopoutExtensionLengthSet._();
 
-  static Serializer<ShowLoopoutLengthSet> get serializer => _$showLoopoutLengthSetSerializer;
+  static Serializer<ShowLoopoutExtensionLengthSet> get serializer =>
+      _$showLoopoutExtensionLengthSetSerializer;
 }
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////

lib/src/constants.dart

@@ -78,7 +78,7 @@ const default_max_offset = 64;
 final default_geometry = Geometry();
 
 const scadnano_css_stylesheet_name_no_ext = r'scadnano-styles';
-const scadnano_css_stylesheet_name = r'scadnano-styles.css';
+const scadnano_css_stylesheet_name = '${scadnano_css_stylesheet_name_no_ext}.css';
 
 const NUM_DIGITS_PRECISION_POSITION_DISPLAYED = 2;
 
@@ -165,6 +165,10 @@ const default_pitch = 0.0;
 const default_yaw = 0.0;
 //const default_helix_rotation_anchor = 0;
 
+// for extensions
+const default_display_angle = 35.0;
+const default_display_length = 1.5;
+
 const default_side_pane_width = '8%';
 
 const default_group_name = 'default_group';
@@ -352,6 +356,19 @@ const loopout_keys = [
   name_key,
 ];
 
+// Extension keys
+const extension_key = 'extension_num_bases';
+const is_5p_key = 'is_5p';
+const display_length_key = 'display_length';
+const display_angle_key = 'display_angle';
+const extension_keys = [
+  extension_key,
+  is_5p_key,
+  display_length_key,
+  display_angle_key,
+  label_key,
+  name_key,
+];
 ////////////////////////////////////////////////////
 /// svg-png-caching constants
 
@@ -367,7 +384,7 @@ const int DNA_SEQUENCE_VERTICAL_OFFSET = 50;
 const int DNA_SEQUENCE_HORIZONTAL_OFFSET = 50;
 
 // Zoom threshold used for caching the svg as png.
-const num ZOOM_THRESHOLD = 1;
+const num ZOOM_THRESHOLD = 0.5;
 
 /////////////////////////////////////////////////////////////
 // Backend
@@ -384,21 +401,24 @@ const css_selector_strand = 'strand';
 const css_selector_scaffold = 'scaffold';
 const css_selector_staple = 'staple';
 const css_selector_domain = 'domain-line';
+const css_selector_extension = 'extension-line';
 const css_selector_crossover = 'crossover-curve';
 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';
 const css_selector_end_5p_domain = 'five-prime-end';
 const css_selector_end_3p_domain = 'three-prime-end';
 const css_selector_end_parent_group = 'dna-ends';
-const css_selector_loopout_length = 'loopout-length';
+const css_selector_loopout_extension_length = 'loopout-extension-length';
 
 const css_selector_domain_name = 'domain-name';
 const css_selector_strand_name = 'strand-name';
 const css_selector_domain_name_text = 'domain-name-text';
 const css_selector_strand_name_text = 'strand-name-text';
 const css_selector_loopout_name = 'loopout-name';
 const css_selector_loopout_name_text = 'loopout-name-text';
+const css_selector_extension_name = 'extension-name';
+const css_selector_extension_name_text = 'extension-name-text';
 
 const css_selector_domain_moving = 'domain-line-moving';
 const css_selector_disallowed = 'disallowed';

lib/src/middleware/dna_ends_move_start.dart

@@ -19,7 +19,7 @@ import '../state/app_state.dart';
 // it triggers a new action to be dispatched.
 dna_ends_move_start_middleware(Store<AppState> store, action, NextDispatcher next) {
   if (action is actions.DNAEndsMoveStart) {
-    BuiltSet<DNAEnd> selected_ends = store.state.ui_state.selectables_store.selected_dna_ends;
+    BuiltSet<DNAEnd> selected_ends = store.state.ui_state.selectables_store.selected_dna_ends_on_domains;
     List<DNAEndMove> moves = [];
     for (var end in selected_ends) {
       int lowest_offset = find_allowable_offset(store.state.design, end, selected_ends, false);