Merge pull request #1027 from UC-Davis-molecular-computing/984-replace-tuples-with-records-2

Fixes #984 - Replace Tuples with Records

Author: beanbeanjuice

lib/src/middleware/helices_positions_set_based_on_crossovers.dart

@@ -12,7 +12,6 @@ import '../state/domain.dart';
 import '../state/geometry.dart';
 import '../state/helix.dart';
 import '../state/position3d.dart';
-import 'package:tuple/tuple.dart';
 
 import '../state/address.dart';
 import '../actions/actions.dart' as actions;
@@ -60,7 +59,7 @@ List<actions.UndoableAction> get_helix_position_and_roll_actions(AppState state)
     var group = state.design.groups[group_name]!;
     var geometry = group.geometry ?? state.design.geometry;
     List<Helix> helices = _get_helices_to_process(state, group);
-    List<Tuple2<Address, Address>>? addresses = _get_addresses_to_process(state, helices);
+    List<(Address, Address)>? addresses = _get_addresses_to_process(state, helices);
     if (addresses == null) {
       continue;
     }
@@ -100,17 +99,17 @@ List<Helix> _get_helices_to_process(AppState state, HelixGroup group) {
 /// on the two helices it connects.
 /// returns null if two such crossovers are selected
 /// if none are selected, finds the first (one with lowest offset on helix earlier in order in [helices])
-List<Tuple2<Address, Address>>? _get_addresses_to_process(AppState state, List<Helix> helices) {
+List<(Address, Address)>? _get_addresses_to_process(AppState state, List<Helix> helices) {
   var design = state.design;
   var selected_crossovers = state.ui_state.selectables_store.selected_crossovers;
   var addresses_of_selected_crossovers_by_prev_helix_idx =
       _get_addresses_of_selected_crossovers_by_prev_helix_idx(selected_crossovers, helices, design);
 
-  List<Tuple2<Address, Address>> addresses = [];
+  List<(Address, Address)> addresses = [];
   for (int i = 0; i < helices.length - 1; i++) {
     var helix_top = helices[i];
     var helix_bot = helices[i + 1];
-    var helix_idx_top_bot = Tuple2<int, int>(helix_top.idx, helix_bot.idx);
+    (int, int) helix_idx_top_bot = (helix_top.idx, helix_bot.idx);
     var addresses_crossovers_this_helices_pair =
         addresses_of_selected_crossovers_by_prev_helix_idx[helix_idx_top_bot]!;
 
@@ -126,12 +125,11 @@ Please select only one, or select none to default to the first crossover between
       return null;
     } else if (addresses_crossovers_this_helices_pair.length == 1) {
       // first try selected crossovers between this pair of helices
-      address_top = addresses_crossovers_this_helices_pair.first.item1;
-      address_bot = addresses_crossovers_this_helices_pair.first.item2;
+      (address_top, address_bot) = addresses_crossovers_this_helices_pair.first;
     } else {
       // otherwise if none are selected, find the addresses of first crossover between this pair of helices
       // using boolean scaffold/staple settings from user to possible ignore one of those types
-      Tuple2<Address, Address>? address_top_bot;
+      (Address, Address)? address_top_bot;
       bool use_scaffold = state.ui_state.default_crossover_type_scaffold_for_setting_helix_rolls;
       bool use_staple = state.ui_state.default_crossover_type_staple_for_setting_helix_rolls;
 
@@ -151,50 +149,49 @@ Please select only one, or select none to default to the first crossover between
         util.async_alert(msg);
         return null;
       }
-      address_top = address_top_bot.item1;
-      address_bot = address_top_bot.item2;
+      (address_top, address_bot) = address_top_bot;
     }
-    addresses.add(Tuple2<Address, Address>(address_top, address_bot));
+    addresses.add((address_top, address_bot));
   }
   return addresses;
 }
 
 // "First" refers to having the lowest offset on helix h1.
-Tuple2<Address, Address>? _first_crossover_addresses_between_helices(
+(Address, Address)? _first_crossover_addresses_between_helices(
   Helix helix_top,
   Helix helix_bot,
   Design design, {
   required bool use_scaffold,
   required bool use_staple,
 }) {
-  BuiltList<Tuple2<Address, Crossover>> address_crossovers_on_top =
+  BuiltList<(Address, Crossover)> address_crossovers_on_top =
       design.address_crossover_pairs_by_helix_idx[helix_top.idx]!;
-  BuiltList<Tuple2<Address, Crossover>> address_crossovers_on_bot =
+  BuiltList<(Address, Crossover)> address_crossovers_on_bot =
       design.address_crossover_pairs_by_helix_idx[helix_bot.idx]!;
 
   // if not using scaffold or crossovers when finding leftmost, filter those out
   if (!use_scaffold) {
     address_crossovers_on_bot =
         address_crossovers_on_bot
-            .where((address_crossover) => !address_crossover.item2.is_scaffold)
+            .where((address_crossover) => !address_crossover.$2.is_scaffold)
             .toBuiltList();
   }
   if (!use_staple) {
     address_crossovers_on_bot =
         address_crossovers_on_bot
-            .where((address_crossover) => address_crossover.item2.is_scaffold)
+            .where((address_crossover) => address_crossover.$2.is_scaffold)
             .toBuiltList();
   }
 
   // find first crossover on h1 that also goes to h2
-  for (Tuple2<Address, Crossover> address_crossover_top in address_crossovers_on_top) {
-    Crossover crossover_top = address_crossover_top.item2;
+  for ((Address, Crossover) address_crossover_top in address_crossovers_on_top) {
+    Crossover crossover_top = address_crossover_top.$2;
     for (var address_crossover_bot in address_crossovers_on_bot) {
-      var crossover_bot = address_crossover_bot.item2;
+      var crossover_bot = address_crossover_bot.$2;
       if (crossover_bot == crossover_top) {
-        Address address_top = address_crossover_top.item1;
-        Address address_bot = address_crossover_bot.item1;
-        return Tuple2<Address, Address>(address_top, address_bot);
+        Address address_top = address_crossover_top.$1;
+        Address address_bot = address_crossover_bot.$1;
+        return (address_top, address_bot);
       }
     }
   }
@@ -213,20 +210,20 @@ Tuple2<Address, Address>? _first_crossover_addresses_between_helices(
 //   (7,5): [... (offset,crossover) pairs between 5 and 7, offset is where crossover touches helix 7]
 // }
 // Sorts each list by the offset on its first helix (first meaning first in order in helices)
-Map<Tuple2<int, int>, List<Tuple2<Address, Address>>> _get_addresses_of_selected_crossovers_by_prev_helix_idx(
+Map<(int, int), List<(Address, Address)>> _get_addresses_of_selected_crossovers_by_prev_helix_idx(
   BuiltSet<Crossover> selected_crossovers,
   List<Helix> helices,
   Design design,
 ) {
   // this is essentially what we return, but each crossover also carries with it the start offset of
   // the helix earlier in the ordering, which helps to sort the lists of crossovers before returning
-  Map<Tuple2<int, int>, List<Tuple2<Address, Address>>> addresses_top_bot_crossovers = {};
+  Map<(int, int), List<(Address, Address)>> addresses_top_bot_crossovers = {};
 
   // initialize internal map to have empty lists
   for (int i = 0; i < helices.length - 1; i++) {
     int idx1 = helices[i].idx;
     int idx2 = helices[i + 1].idx;
-    var pair_idxs = Tuple2<int, int>(idx1, idx2);
+    (int, int) pair_idxs = (idx1, idx2);
     addresses_top_bot_crossovers[pair_idxs] = [];
   }
 
@@ -240,8 +237,8 @@ Map<Tuple2<int, int>, List<Tuple2<Address, Address>>> _get_addresses_of_selected
     var next_dom = strand.substrands[crossover.next_domain_idx] as Domain;
     var prev_idx = prev_dom.helix;
     var next_idx = next_dom.helix;
-    var pair_idxs = Tuple2<int, int>(prev_idx, next_idx);
-    var pair_idxs_rev = Tuple2<int, int>(next_idx, prev_idx);
+    (int, int) pair_idxs = (prev_idx, next_idx);
+    (int, int) pair_idxs_rev = (next_idx, prev_idx);
 
     if (addresses_top_bot_crossovers.containsKey(pair_idxs) ||
         addresses_top_bot_crossovers.containsKey(pair_idxs_rev)) {
@@ -280,7 +277,7 @@ Map<Tuple2<int, int>, List<Tuple2<Address, Address>>> _get_addresses_of_selected
       }
       var address_top = Address(helix_idx: dom_top.helix, offset: offset_top, forward: dom_top.forward);
       var address_bot = Address(helix_idx: dom_bot.helix, offset: offset_bot, forward: dom_bot.forward);
-      addresses_top_bot_crossovers[pair_idxs]!.add(Tuple2<Address, Address>(address_top, address_bot));
+      addresses_top_bot_crossovers[pair_idxs]!.add((address_top, address_bot));
     }
   }
 
@@ -307,7 +304,7 @@ List<RollXY> _calculate_rolls_and_positions(
   Design design,
   Geometry geometry,
   List<Helix> helices,
-  List<Tuple2<Address, Address>> addresses,
+  List<(Address, Address)> addresses,
   double first_roll,
 ) {
   assert(helices.length == addresses.length + 1);
@@ -317,8 +314,8 @@ List<RollXY> _calculate_rolls_and_positions(
   List<RollXY> rollxys = [RollXY(roll: first_roll, x: x, y: y)];
 
   for (int i = 0; i < addresses.length; i++) {
-    var address_top = addresses[i].item1;
-    var address_bot = addresses[i].item2;
+    var (address_top, address_bot) = addresses[i];
+
     var roll = rollxys[i].roll;
     var x = rollxys[i].x;
     var y = rollxys[i].y;

lib/src/middleware/oxdna_export.dart

@@ -15,7 +15,6 @@ import 'package:scadnano/src/state/grid.dart';
 import 'package:scadnano/src/state/loopout.dart';
 import 'package:scadnano/src/state/position3d.dart';
 import 'package:scadnano/src/state/strand.dart';
-import 'package:tuple/tuple.dart';
 import '../state/app_state.dart';
 import '../actions/actions.dart' as actions;
 import '../state/helix.dart';
@@ -41,9 +40,7 @@ First select some strands, or choose Export🡒oxDNA to export all strands in th
     }
 
     if (action is actions.OxdnaExport) {
-      Tuple2<String, String> dat_top = to_oxdna_format(state.design, strands_to_export);
-      String dat = dat_top.item1;
-      String top = dat_top.item2;
+      var (dat, top) = to_oxdna_format(state.design, strands_to_export); // (String, String)
 
       String default_filename = state.ui_state.loaded_filename;
       String default_filename_dat = path.setExtension(default_filename, '.dat');
@@ -152,11 +149,9 @@ String to_oxview_format(Design design, List<Strand> strands_to_export) {
   );
   for (int helix in base_pairs_map.keys) {
     for (var offset_dom_strands in base_pairs_map[helix]!) {
-      int offset = offset_dom_strands.item1;
-      Domain domain1 = offset_dom_strands.item2;
-      Domain domain2 = offset_dom_strands.item3;
-      Strand sc_strand1 = offset_dom_strands.item4;
-      Strand sc_strand2 = offset_dom_strands.item5;
+      // (int, Domain, Domain, Strand, Strand)
+      var (offset, domain1, domain2, sc_strand1, sc_strand2) = offset_dom_strands;
+
       Map<String, dynamic> oxv_strand1 = oxview_strand_map[sc_strand1.id];
       Map<String, dynamic> oxv_strand2 = oxview_strand_map[sc_strand2.id];
       int d1 = sc_strand1.domain_offset_to_strand_dna_idx(domain1, offset, false);
@@ -195,10 +190,9 @@ String to_oxview_format(Design design, List<Strand> strands_to_export) {
   return content;
 }
 
-Tuple2<String, String> to_oxdna_format(Design design, [List<Strand>? strands_to_export = null]) {
+(String, String) to_oxdna_format(Design design, [List<Strand>? strands_to_export = null]) {
   OxdnaSystem system = convert_design_to_oxdna_system(design, strands_to_export);
-  Tuple2<String, String> dat_top = system.oxdna_output();
-  return dat_top;
+  return system.oxdna_output();
 }
 
 class OxdnaVector {
@@ -320,7 +314,7 @@ class OxdnaSystem {
     }
   }
 
-  Tuple2<String, String> oxdna_output() {
+  (String, String) oxdna_output() {
     OxdnaVector bbox = compute_bounding_box();
 
     List<String> dat_list = ['t = 0', 'b = ${bbox.x} ${bbox.y} ${bbox.z}', 'E = 0 0 0'];
@@ -358,14 +352,14 @@ class OxdnaSystem {
 
     top = '${nuc_count} ${strand_count}\n' + top;
 
-    return Tuple2<String, String>(dat, top);
+    return (dat, top);
   }
 }
 
 const NM_TO_OX_UNITS = 1.0 / 0.8518;
 
 // returns the origin, forward, and normal vectors of a helix
-Tuple3<OxdnaVector, OxdnaVector, OxdnaVector> oxdna_get_helix_vectors(Design design, Helix helix) {
+(OxdnaVector, OxdnaVector, OxdnaVector) oxdna_get_helix_vectors(Design design, Helix helix) {
   /*
   TODO: document functions/methods with docstrings
   :param helix:
@@ -426,7 +420,7 @@ Tuple3<OxdnaVector, OxdnaVector, OxdnaVector> oxdna_get_helix_vectors(Design des
 
   var origin = (position_in_helix_group_rotated + helix_group_offset) * NM_TO_OX_UNITS;
 
-  return Tuple3<OxdnaVector, OxdnaVector, OxdnaVector>(origin, forward, normal);
+  return (origin, forward, normal);
 }
 
 OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands_to_export = null]) {
@@ -472,7 +466,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
   };
 
   for (var strand in strands_to_export) {
-    List<Tuple2<OxdnaStrand, bool>> strand_domains = [];
+    List<(OxdnaStrand, bool)> strand_domains = [];
     for (int ss_idx = 0; ss_idx < strand.substrands.length; ss_idx++) {
       var domain = strand.substrands[ss_idx];
       var ox_strand = OxdnaStrand();
@@ -487,10 +481,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
         var group = design.groups[helix.group]!;
         var geometry = group.geometry ?? design.geometry;
         var step_rot = -360 / geometry.bases_per_turn;
-        var origin_forward_normal = helix_vectors[helix.idx]!;
-        var origin = origin_forward_normal.item1;
-        var forward = origin_forward_normal.item2;
-        var normal = origin_forward_normal.item3;
+        var (origin, forward, normal) = helix_vectors[helix.idx]!; // (OxdnaVector, OxdnaVector, OxdnaVector)
 
         if (!domain.forward) {
           normal = normal.rotate(-geometry.minor_groove_angle, forward);
@@ -545,7 +536,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
         if (!domain.forward) {
           ox_strand.nucleotides = List<OxdnaNucleotide>.from(ox_strand.nucleotides.reversed);
         }
-        strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, false));
+        strand_domains.add((ox_strand, false));
         // because we need to know the positions of nucleotides before and after the loopout
         // we temporarily store domain strands with a boolean that is true if it's a loopout
         // handle loopouts
@@ -560,7 +551,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
           var nuc = OxdnaNucleotide(center, normal, forward, base);
           ox_strand.nucleotides.add(nuc);
         }
-        strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, true));
+        strand_domains.add((ox_strand, true));
       } else if (domain is Extension) {
         bool is_5p = ss_idx == 0;
         var helix = design.helices[domain.adjacent_domain.helix]!;
@@ -575,7 +566,7 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
           mod_map: mod_map,
         );
         ox_strand.nucleotides.addAll(nucleotides);
-        strand_domains.add(Tuple2<OxdnaStrand, bool>(ox_strand, false));
+        strand_domains.add((ox_strand, false));
       } else {
         throw AssertionError('unreachable');
       }
@@ -584,12 +575,11 @@ OxdnaSystem convert_design_to_oxdna_system(Design design, [List<Strand>? strands
     var sstrand = OxdnaStrand();
     // process loopouts and join strands
     for (int i = 0; i < strand_domains.length; i++) {
-      var dstrand_is_loopout = strand_domains[i];
-      var dstrand = dstrand_is_loopout.item1;
-      var is_loopout = dstrand_is_loopout.item2;
+      var (dstrand, is_loopout) = strand_domains[i]; // (OxdnaStrand, bool)
+
       if (is_loopout) {
-        var prev_nuc = strand_domains[i - 1].item1.nucleotides.last;
-        var next_nuc = strand_domains[i + 1].item1.nucleotides.first;
+        var prev_nuc = strand_domains[i - 1].$1.nucleotides.last;
+        var next_nuc = strand_domains[i + 1].$1.nucleotides.first;
 
         int strand_length = dstrand.nucleotides.length;
 
@@ -618,7 +608,7 @@ List<OxdnaNucleotide> _compute_extension_nucleotides({
   required Geometry geometry,
   required Strand strand,
   required bool is_5p,
-  required Map<int, Tuple3<OxdnaVector, OxdnaVector, OxdnaVector>> helix_vectors,
+  required Map<int, (OxdnaVector, OxdnaVector, OxdnaVector)> helix_vectors,
   required Map<int, List<int>> mod_map,
 }) {
   var step_rot = -360 / geometry.bases_per_turn;
@@ -628,9 +618,8 @@ List<OxdnaNucleotide> _compute_extension_nucleotides({
   var offset = is_5p ? adj_dom.offset_5p : adj_dom.offset_3p; // offset of attached end of domain
 
   var origin_forward_normal = helix_vectors[adj_dom.helix]!;
-  var origin_ = origin_forward_normal.item1;
-  var forward = origin_forward_normal.item2;
-  var normal = origin_forward_normal.item3;
+
+  var (origin_, forward, normal) = origin_forward_normal; // (OxdnaVector, OxdnaVector, OxdnaVector)
 
   if (!adj_dom.forward) {
     normal = normal.rotate(-geometry.minor_groove_angle, forward);

lib/src/middleware/oxview_update_view.dart

@@ -17,7 +17,6 @@ import 'package:scadnano/src/state/grid.dart';
 import 'package:scadnano/src/state/loopout.dart';
 import 'package:scadnano/src/state/position3d.dart';
 import 'package:scadnano/src/state/strand.dart';
-import 'package:tuple/tuple.dart';
 import '../state/app_state.dart';
 import '../actions/actions.dart' as actions;
 import '../state/helix.dart';
@@ -67,9 +66,7 @@ void update_oxview_view(Design design, [IFrameElement? frame = null]) {
   List<Strand> strands_to_export = design.strands.toList();
 
   // String content = to_oxview_format(design, strands_to_export);
-  Tuple2<String, String> dat_top = to_oxdna_format(design, strands_to_export);
-  String dat = dat_top.item1;
-  String top = dat_top.item2;
+  var (dat, top) = to_oxdna_format(design, strands_to_export); // (String, String)
 
   Blob blob_dat = new Blob([dat], blob_type_to_string(BlobType.text));
   Blob blob_top = new Blob([top], blob_type_to_string(BlobType.text));

lib/src/middleware/reselect_moved_dna_extension_ends.dart

@@ -2,7 +2,6 @@ import 'package:react/react.dart';
 import 'package:redux/redux.dart';
 import 'package:built_collection/built_collection.dart';
 import 'package:scadnano/src/state/extension.dart';
-import 'package:tuple/tuple.dart';
 
 import '../state/domain.dart';
 import '../state/dna_end.dart';

lib/src/middleware/selections_intersect_box_compute.dart

@@ -5,7 +5,6 @@ import 'dart:svg' as svg;
 import 'package:built_collection/built_collection.dart';
 import 'package:redux/redux.dart';
 import 'package:scadnano/src/state/selection_rope.dart';
-import 'package:tuple/tuple.dart';
 
 import '../state/select_mode.dart';
 import '../state/selection_box.dart';

lib/src/middleware/system_clipboard.dart

@@ -127,8 +127,7 @@ bool paste_is_impossible_from_clipboard(String clipboard_content, bool in_browse
   var strands_and_helices_view_order = parse_strands_and_helices_view_order_from_clipboard(clipboard_content);
   if (strands_and_helices_view_order == null) return true;
 
-  List<Strand> strands = strands_and_helices_view_order.item1;
-  List<int>? helices_view_order = strands_and_helices_view_order.item2;
+  var (strands, helices_view_order) = strands_and_helices_view_order; // (List<Strand>, List<int>?)
 
   if (strands.isEmpty) return true;