Merge branch '2-extensions-on-end-of-strand' of https://github.com/UC…

…-Davis-molecular-computing/scadnano into 2-extensions-on-end-of-strand

lib/src/constants.dart

@@ -8,12 +8,13 @@ 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 = "0.17.4";
+const String CURRENT_VERSION = "0.17.5";
 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 =[
   // "0.17.3", // accidentally skipped this version
+  "0.17.4",
   "0.17.2",
   "0.17.1",
   "0.17.0",

lib/src/middleware/helix_idxs_change.dart

@@ -12,6 +12,35 @@ helix_idxs_change_middleware(Store<AppState> store, dynamic action, NextDispatch
     Set<int> existing_idxs = store.state.design.helices.keys.toSet();
     Set<int> old_idxs = action.idx_replacements.keys.toSet();
     Set<int> remaining_idxs = existing_idxs.difference(old_idxs);
+    var new_indices = action.idx_replacements.values.toSet();
+
+    if (new_indices.length != action.idx_replacements.length) {
+      Map<int, List<int>> key_to_idxs = new Map<int, List<int>>();
+
+      for (var old_index in old_idxs) {
+        var new_index = action.idx_replacements[old_index];
+        if (key_to_idxs.containsKey(new_index))
+          key_to_idxs[new_index].add(old_index);
+        else
+          key_to_idxs[new_index] = [ old_index ];
+      }
+
+      if (key_to_idxs.length != action.idx_replacements.length) {
+        var msg = 'You tried to assign existing helices ';
+
+        msg += key_to_idxs.entries.where((element) => element.value.length != 1).map((element) {
+          return element.value.join(', ') + " to " + element.key.toString();
+        }).join(" and helices ");
+
+        msg += ". Each helix must have a unique new index; make sure all the integers you write are distinct from each other and do not appear elsewhere in the design";
+
+        window.alert(msg);
+        return;
+      }
+
+
+    }
+
     for (int new_idx in action.idx_replacements.values) {
       if (remaining_idxs.contains(new_idx)) {
         var msg = 'Index ${new_idx} is already taken.';

lib/src/reducers/helices_reducer.dart

@@ -89,12 +89,13 @@ Design helix_idx_change_reducer(Design design, AppState state, actions.HelixIdxs
   var strands = design.strands.toList();
 
   Map<String, HelixGroup> new_groups = change_groups(action, helices, design);
-
+  var copy_helices = design.helices.toMap();
   // change helices
+
+  helices.removeWhere((key, _) => action.idx_replacements.containsKey(key));
   for (int old_idx in action.idx_replacements.keys) {
     int new_idx = action.idx_replacements[old_idx];
-    var helix = helices[old_idx].rebuild((b) => b..idx = new_idx);
-    helices.remove(old_idx);
+    var helix = copy_helices[old_idx].rebuild((b) => b..idx = new_idx);
     helices[new_idx] = helix;
   }
 

lib/src/serializers.dart

@@ -288,6 +288,7 @@ part 'serializers.g.dart';
   DialogShow,
   DialogHide,
   DialogLink,
+  DialogLabel,
   StrandOrder,
   StrandColorSet,
   StrandColorPickerShow,

lib/src/state/dialog.dart

@@ -305,6 +305,8 @@ abstract class DialogLink
       ..tooltip = tooltip);
   }
 
+
+
   /************************ end BuiltValue boilerplate ************************/
 
   String get label;
@@ -314,6 +316,33 @@ abstract class DialogLink
   String get value;
 }
 
+abstract class DialogLabel
+    with BuiltJsonSerializable
+    implements DialogItem, Built<DialogLabel, DialogLabelBuilder> {
+  DialogLabel._();
+
+  factory DialogLabel.from([void Function(DialogLabelBuilder) updates]) = _$DialogLabel;
+
+  static Serializer<DialogLabel> get serializer => _$dialogLabelSerializer;
+
+  @memoized
+  int get hashCode;
+
+  factory DialogLabel({String label, String tooltip}) {
+    return DialogLabel.from((b) => b
+      ..label = label
+      ..value = ""
+      ..tooltip = tooltip);
+  }
+
+
+  /************************ end BuiltValue boilerplate ************************/
+
+  String get label;
+
+  String get value;
+}
+
 // abstract class DialogLink
 //     with BuiltJsonSerializable
 //     implements DialogItem, Built<DialogLink, DialogLinkBuilder> {

lib/src/view/design_dialog_form.dart

@@ -318,6 +318,13 @@ class DesignDialogFormComponent extends UiStatefulComponent2<DesignDialogFormPro
         ..href = item.link
         ..target = '_blank')(item.label);
     }
+    else if (item is DialogLabel) {
+      return (Dom.span()
+        ..title = item.tooltip
+        )(item.label);
+    }
+
+
     return null;
   }
 

lib/src/view/design_main_error_boundary.dart

@@ -120,5 +120,6 @@ class DesignMainErrorBoundaryComponent<T extends DesignMainErrorBoundaryProps,
 
 send_error(String escaped_error_message) async{
   app.dispatch(actions.ErrorMessageSet(escaped_error_message));
+  app.dispatch(actions.LoadingDialogHide());    // close loading dialog if it's currently being shown
   app.view.design_view.render(app.state);
 }

lib/src/view/menu_side.dart

@@ -96,6 +96,11 @@ class SideMenuComponent extends UiComponent2<SideMenuProps> with RedrawCounterMi
         ..disabled = props.groups.length == 1
         ..on_click = ((ev) => app.dispatch(actions.GroupRemove(name: props.displayed_group_name)))
         ..key = 'remove-current-group')(),
+      (MenuDropdownItem()
+        ..display = 'adjust helix indices'
+        ..disabled = props.groups[props.displayed_group_name].helices_view_order.length == 0
+        ..on_click = ((ev) => adjust_helix_indices_for_current_group())
+        ..key = 'adjust-helix-indices')(),
     ]);
     return NavDropdown({
       'title': 'Group',
@@ -125,6 +130,9 @@ class SideMenuComponent extends UiComponent2<SideMenuProps> with RedrawCounterMi
   set_new_parameters_for_current_group() =>
       app.disable_keyboard_shortcuts_while(ask_new_parameters_for_current_group);
 
+  adjust_helix_indices_for_current_group() =>
+    app.disable_keyboard_shortcuts_while(ask_new_helix_indices_for_current_group);
+
   add_new_group(Iterable<String> existing_names) =>
       app.disable_keyboard_shortcuts_while(() => ask_about_new_group(existing_names));
 
@@ -262,4 +270,31 @@ class SideMenuComponent extends UiComponent2<SideMenuProps> with RedrawCounterMi
     app.dispatch(
         actions.GroupChange(old_name: props.displayed_group_name, new_name: new_name, new_group: new_group));
   }
+
+  Future<void> ask_new_helix_indices_for_current_group() async {
+    var group = props.groups[props.displayed_group_name];
+    var existing_grid = group.grid;
+
+    List<DialogItem> items = []; 
+    items.add(DialogLabel(label: 'current view order: ' + group.helices_view_order.join(' ')));
+
+    for (var helix_index in group.helices_view_order) {
+      items.add(DialogInteger(label: helix_index.toString(), value: helix_index));
+    }
+
+    var dialog =
+        Dialog(title: 'adjust Helix indices', items: items);
+    List<DialogItem> results = await util.dialog(dialog);
+    if (results == null) return;
+
+    Map<int, int> new_indices_map = {}; 
+    for (int i = 1; i < results.length; i++) {
+      new_indices_map[group.helices_view_order[i-1]] = (results[i] as DialogInteger).value; 
+    }
+
+   app.dispatch(actions.HelixIdxsChange(idx_replacements: new_indices_map));
+  }
+
 }
+
+