closes #501; make deletions/insertions selectable/deletable; this mak…

…es it easier to select large groups of deletions or insertions and delete them, instead of clicking one at a time

lib/src/constants.dart

@@ -346,6 +346,8 @@ const css_selector_helix__mouseover_invisible_rectangle = 'helix-mouseover';
 
 const css_selector_insertion = 'insertion-curve';
 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';
 
 

lib/src/middleware/selections_intersect_box_compute.dart

@@ -30,7 +30,8 @@ selections_intersect_box_compute_middleware(Store<AppState> store, action, NextD
 
     //XXX: Firefox does not have getIntersectionList or getEnclosureList
     // (no progress for 10 years on that: https://bugzilla.mozilla.org/show_bug.cgi?id=501421)
-    // Besides, it didn't work well in Chrome and I basically had to implement it myself based on bounding boxes.
+    // Besides, it didn't work well in Chrome and I
+    // basically had to implement it myself based on bounding boxes.
 
     bool is_origami = state.design.is_origami;
     var select_modes = state.ui_state.select_mode_state.modes;

lib/src/reducers/delete_reducer.dart

@@ -35,6 +35,14 @@ BuiltList<Strand> delete_all_reducer(
   } else if (select_mode_state.domains_selectable()) {
     var domains = List<Domain>.from(items.where((item) => item is Domain));
     strands = remove_domains(strands, state, domains);
+  } else if (select_mode_state.deletions_selectable() || select_mode_state.insertions_selectable()) {
+    var deletions = select_mode_state.deletions_selectable()
+        ? List<SelectableDeletion>.from(items.where((item) => item is SelectableDeletion))
+        : [];
+    var insertions = select_mode_state.insertions_selectable()
+        ? List<SelectableInsertion>.from(items.where((item) => item is SelectableInsertion))
+        : [];
+    strands = remove_deletions_and_insertions(strands, state, deletions, insertions);
   }
 
   return strands;
@@ -210,7 +218,7 @@ BuiltList<Strand> remove_domains(BuiltList<Strand> strands, AppState state, Iter
     strand_to_substrands[strand].add(substrand);
   }
 
-  // remove crossovers one strand at a time
+  // remove domains one strand at a time
   for (var strand in strand_to_substrands.keys) {
     strands_to_remove.add(strand);
     var split_strands = _remove_domains_from_strand(strand, strand_to_substrands[strand]);
@@ -259,3 +267,60 @@ List<Strand> _remove_domains_from_strand(Strand strand, Set<Domain> substrands_t
 
   return create_new_strands_from_substrand_lists(substrands_list, strand);
 }
+
+BuiltList<Strand> remove_deletions_and_insertions(BuiltList<Strand> strands, AppState state,
+    List<SelectableDeletion> deletions, List<SelectableInsertion> insertions) {
+  // collect all deletions/insertions for each strand
+
+  Map<Strand, Map<Domain, Set<SelectableDeletion>>> strand_to_deletions = {};
+  Map<Strand, Map<Domain, Set<SelectableInsertion>>> strand_to_insertions = {};
+  for (var strand in strands) {
+    strand_to_deletions[strand] = {};
+    strand_to_insertions[strand] = {};
+    for (var domain in strand.domains()) {
+      strand_to_deletions[strand][domain] = {};
+      strand_to_insertions[strand][domain] = {};
+    }
+  }
+  for (var deletion in deletions) {
+    var strand = state.design.substrand_to_strand[deletion.domain];
+    strand_to_deletions[strand][deletion.domain].add(deletion);
+  }
+  for (var insertion in insertions) {
+    var strand = state.design.substrand_to_strand[insertion.domain];
+    strand_to_insertions[strand][insertion.domain].add(insertion);
+  }
+
+  // remove deletions/insertions one strand at a time
+  // need to do deletions and insertions at the same time because Domain built object will be invalidated
+  // after removing one of them.
+  var new_strands = strands.toList();
+  for (int i = 0; i < strands.length; i++) {
+    Strand strand = strands[i];
+    var substrands = strand.substrands.toList();
+    for (int j = 0; j < substrands.length; j++) {
+      if (substrands[j] is Domain) {
+        var domain = substrands[j] as Domain;
+        var deletions = strand_to_deletions[strand][domain];
+        var insertions = strand_to_insertions[strand][domain];
+        var deletions_offsets_to_remove = {for (var deletion in deletions) deletion.offset};
+        var insertions_offsets_to_remove = {for (var insertion in insertions) insertion.insertion.offset};
+        if (deletions_offsets_to_remove.isNotEmpty || insertions_offsets_to_remove.isNotEmpty) {
+          var deletions_existing = domain.deletions.toList();
+          var insertions_existing = domain.insertions.toList();
+          deletions_existing.removeWhere((offset) => deletions_offsets_to_remove.contains(offset));
+          insertions_existing
+              .removeWhere((insertion) => insertions_offsets_to_remove.contains(insertion.offset));
+          domain = domain.rebuild(
+              (b) => b..deletions.replace(deletions_existing)..insertions.replace(insertions_existing));
+          substrands[j] = domain;
+        }
+      }
+    }
+    strand = strand.rebuild((b) => b..substrands.replace(substrands));
+    strand = strand.initialize();
+    new_strands[i] = strand;
+  }
+
+  return new_strands.build();
+}

lib/src/reducers/select_mode_state_reducer.dart

@@ -25,13 +25,31 @@ SelectModeState toggle_select_mode_reducer(SelectModeState state, actions.Select
     } else if (SelectModeChoice.strand_parts.contains(mode)) {
       new_state = new_state.remove_mode(SelectModeChoice.strand);
       if (mode == SelectModeChoice.crossover || mode == SelectModeChoice.loopout) {
-        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() + [SelectModeChoice.domain]);
+        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() +
+            [SelectModeChoice.domain, SelectModeChoice.deletion, SelectModeChoice.insertion]);
       } else if (SelectModeChoice.ends.contains(mode)) {
-        new_state = new_state
-            .remove_modes([SelectModeChoice.crossover, SelectModeChoice.loopout, SelectModeChoice.domain]);
+        new_state = new_state.remove_modes([
+          SelectModeChoice.crossover,
+          SelectModeChoice.loopout,
+          SelectModeChoice.domain,
+          SelectModeChoice.deletion,
+          SelectModeChoice.insertion,
+        ]);
       } else if (mode == SelectModeChoice.domain) {
-        new_state = new_state.remove_modes(
-            SelectModeChoice.ends.toList() + [SelectModeChoice.crossover, SelectModeChoice.loopout]);
+        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() +
+            [
+              SelectModeChoice.crossover,
+              SelectModeChoice.loopout,
+              SelectModeChoice.deletion,
+              SelectModeChoice.insertion,
+            ]);
+      } else if (mode == SelectModeChoice.deletion || mode == SelectModeChoice.insertion) {
+        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() +
+            [
+              SelectModeChoice.crossover,
+              SelectModeChoice.loopout,
+              SelectModeChoice.domain,
+            ]);
       }
     }
   }
@@ -49,13 +67,35 @@ SelectModeState add_select_modes_reducer(SelectModeState state, actions.SelectMo
     } else if (SelectModeChoice.strand_parts.contains(mode)) {
       new_state = new_state.remove_mode(SelectModeChoice.strand);
       if (mode == SelectModeChoice.crossover || mode == SelectModeChoice.loopout) {
-        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() + [SelectModeChoice.domain]);
+        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() +
+            [
+              SelectModeChoice.domain,
+              SelectModeChoice.deletion,
+              SelectModeChoice.insertion,
+            ]);
       } else if (SelectModeChoice.ends.contains(mode)) {
-        new_state = new_state
-            .remove_modes([SelectModeChoice.crossover, SelectModeChoice.loopout, SelectModeChoice.domain]);
+        new_state = new_state.remove_modes([
+          SelectModeChoice.crossover,
+          SelectModeChoice.loopout,
+          SelectModeChoice.domain,
+          SelectModeChoice.deletion,
+          SelectModeChoice.insertion,
+        ]);
       } else if (mode == SelectModeChoice.domain) {
-        new_state = new_state.remove_modes(
-            SelectModeChoice.ends.toList() + [SelectModeChoice.crossover, SelectModeChoice.loopout]);
+        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() +
+            [
+              SelectModeChoice.crossover,
+              SelectModeChoice.loopout,
+              SelectModeChoice.deletion,
+              SelectModeChoice.insertion,
+            ]);
+      }else if (mode == SelectModeChoice.deletion || mode == SelectModeChoice.insertion) {
+        new_state = new_state.remove_modes(SelectModeChoice.ends.toList() +
+            [
+              SelectModeChoice.crossover,
+              SelectModeChoice.loopout,
+              SelectModeChoice.domain,
+            ]);
       }
     }
   }

lib/src/serializers.dart

@@ -175,6 +175,9 @@ part 'serializers.g.dart';
   ExportDNA,
   ExportDNAFormat,
   ErrorMessageSet,
+  Insertion,
+  SelectableInsertion,
+  SelectableDeletion,
   InsertionAdd,
   DeletionAdd,
   InsertionRemove,

lib/src/state/design.dart

@@ -294,6 +294,32 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
     return builder.build();
   }
 
+  @memoized
+  BuiltMap<String, SelectableDeletion> get deletions_by_id {
+    var builder = MapBuilder<String, SelectableDeletion>();
+    for (var strand in strands) {
+      for (var domain in strand.domains()) {
+        for (var deletion in domain.selectable_deletions) {
+          builder[deletion.id()] = deletion;
+        }
+      }
+    }
+    return builder.build();
+  }
+
+  @memoized
+  BuiltMap<String, SelectableInsertion> get insertions_by_id {
+    var builder = MapBuilder<String, SelectableInsertion>();
+    for (var strand in strands) {
+      for (var domain in strand.domains()) {
+        for (var insertion in domain.selectable_insertions) {
+          builder[insertion.id()] = insertion;
+        }
+      }
+    }
+    return builder.build();
+  }
+
   @memoized
   BuiltMap<String, DNAEnd> get ends_by_id {
     var builder = MapBuilder<String, DNAEnd>();
@@ -357,7 +383,15 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
   @memoized
   BuiltMap<String, Selectable> get selectable_by_id {
     Map<String, Selectable> map = {};
-    for (var map_small in [strands_by_id, loopouts_by_id, crossovers_by_id, ends_by_id, domains_by_id]) {
+    for (var map_small in [
+      strands_by_id,
+      loopouts_by_id,
+      crossovers_by_id,
+      ends_by_id,
+      domains_by_id,
+      deletions_by_id,
+      insertions_by_id,
+    ]) {
       for (var key in map_small.keys) {
         var obj = map_small[key];
         map[key] = obj;

lib/src/state/domain.dart

@@ -160,6 +160,19 @@ abstract class Domain
       substrand_is_last: is_last,
       substrand_id: id());
 
+  @memoized
+  BuiltList<SelectableDeletion> get selectable_deletions => [
+        for (int deletion in deletions)
+          SelectableDeletion(offset: deletion, domain: this, is_scaffold: is_scaffold)
+      ].build();
+
+
+  @memoized
+  BuiltList<SelectableInsertion> get selectable_insertions => [
+        for (var insertion in insertions)
+          SelectableInsertion(insertion: insertion, domain: this, is_scaffold: is_scaffold)
+      ].build();
+
   Domain set_start(int start_new) => rebuild((ss) => ss..start = start_new);
 
   Domain set_end(int end_new) => rebuild((ss) => ss..end = end_new);
@@ -221,16 +234,16 @@ abstract class Domain
 
     deletions = util.remove_duplicates(deletions);
     insertions = util.remove_duplicates(insertions);
-    for (int i=0; i<insertions.length; i++) {
-      for (int j=i+1; j<insertions.length; j++) {
+    for (int i = 0; i < insertions.length; i++) {
+      for (int j = i + 1; j < insertions.length; j++) {
         var ins1 = insertions[i];
         var ins2 = insertions[j];
         if (ins1.offset == ins2.offset) {
           assert(ins1.length != ins2.length);
           throw IllegalDesignError('two insertions on a domain have the same offset but different lengths:'
               '\n${ins1}'
               '\n${ins2}'
-          '\n${pre_domain_description(helix, forward, start, end)}');
+              '\n${pre_domain_description(helix, forward, start, end)}');
         }
       }
     }
@@ -277,10 +290,10 @@ abstract class Domain
   }
 
   static String pre_domain_description(int helix, bool forward, int start, int end) =>
-      'This occurred on a ${forward? "forward": "reverse"} Domain with'
-          '\n  helix = ${helix}'
-          '\n  start = ${start}'
-          '\n  end   = ${end}.';
+      'This occurred on a ${forward ? "forward" : "reverse"} Domain with'
+      '\n  helix = ${helix}'
+      '\n  start = ${start}'
+      '\n  end   = ${end}.';
 
   static List<Insertion> parse_json_insertions(json_encoded_insertions) {
     // need to use List.from because List.map returns Iterable, not List

lib/src/state/select_mode.dart

@@ -19,6 +19,8 @@ class SelectModeChoice extends EnumClass {
   static const SelectModeChoice crossover = _$crossover;
   static const SelectModeChoice loopout = _$loopout;
   static const SelectModeChoice strand = _$strand;
+  static const SelectModeChoice deletion = _$deletion;
+  static const SelectModeChoice insertion = _$insertion;
   static const SelectModeChoice scaffold = _$scaffold;
   static const SelectModeChoice staple = _$staple;
 
@@ -61,6 +63,10 @@ class SelectModeChoice extends EnumClass {
         return constants.css_selector_crossover;
       case loopout:
         return constants.css_selector_loopout;
+      case deletion:
+        return constants.css_selector_deletion;
+      case insertion:
+        return constants.css_selector_insertion;
       case strand:
         return constants.css_selector_strand;
       case scaffold:
@@ -87,6 +93,8 @@ class SelectModeChoice extends EnumClass {
     end_3p_domain,
     crossover,
     loopout,
+    deletion,
+    insertion,
   ]);
 
   static final BuiltList<SelectModeChoice> ends = BuiltList<SelectModeChoice>([

lib/src/state/select_mode_state.dart

@@ -41,6 +41,12 @@ abstract class SelectModeState implements Built<SelectModeState, SelectModeState
   bool domains_selectable() =>
       modes.contains(SelectModeChoice.domain);
 
+  bool deletions_selectable() =>
+      modes.contains(SelectModeChoice.deletion);
+
+  bool insertions_selectable() =>
+      modes.contains(SelectModeChoice.insertion);
+
   String to_json() {
     List<String> lst = [for (var mode in modes) mode.name];
     var js = jsonEncode(lst);