Merge pull request #971 from UC-Davis-molecular-computing/588-export-…

…to-oxview-format

closes #588: export to oxView format

lib/src/actions/actions.dart

@@ -4523,3 +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/middleware/oxdna_export.dart

@@ -1,6 +1,8 @@
+import 'dart:convert';
 import 'dart:html';
 import 'dart:math';
 import 'package:path/path.dart' as path;
+import 'package:quiver/iterables.dart' as quiver;
 
 import 'package:redux/redux.dart';
 import 'package:scadnano/src/state/design.dart';
@@ -16,9 +18,11 @@ import '../state/app_state.dart';
 import '../actions/actions.dart' as actions;
 import '../state/helix.dart';
 import '../util.dart' as util;
+import 'export_cadnano_or_codenano_file.dart' as export_cadnano;
+import '../constants.dart' as constants;
 
 oxdna_export_middleware(Store<AppState> store, dynamic action, NextDispatcher next) {
-  if (action is actions.OxdnaExport) {
+  if (action is actions.OxdnaExport || action is actions.OxviewExport) {
     AppState state = store.state;
 
     List<Strand> strands_to_export;
@@ -34,18 +38,160 @@ First select some strands, or choose Export🡒oxDNA to export all strands in th
       strands_to_export = state.design.strands.toList();
     }
 
-    Tuple2<String, String> dat_top = to_oxdna_format(state.design, strands_to_export);
-    String dat = dat_top.item1;
-    String top = dat_top.item2;
+    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;
+
+      String default_filename = state.ui_state.loaded_filename;
+      String default_filename_dat = path.setExtension(default_filename, '.dat');
+      String default_filename_top = path.setExtension(default_filename, '.top');
+
+      util.save_file(default_filename_dat, dat);
+      util.save_file(default_filename_top, top);
+    } else if (action is actions.OxviewExport) {
+      String content = to_oxview_format(state.design, strands_to_export);
+      String default_filename = state.ui_state.loaded_filename;
+      String default_filename_ext = path.setExtension(default_filename, '.oxview');
+      util.save_file(default_filename_ext, content);
+    }
+  }
+  next(action);
+}
 
-    String default_filename = state.ui_state.loaded_filename;
-    String default_filename_dat = path.setExtension(default_filename, '.dat');
-    String default_filename_top = path.setExtension(default_filename, '.top');
+String to_oxview_format(Design design, List<Strand> strands_to_export) {
+  OxdnaSystem system = convert_design_to_oxdna_system(design, strands_to_export);
+  List<Map<String, dynamic>> oxview_strands = [];
+  int nuc_count = 0;
+  int strand_count = 0;
+  List<int> strand_nuc_start = [-1];
+  assert(strands_to_export.length == system.strands.length);
+
+  for (int i = 0; i < strands_to_export.length; i++) {
+    Strand sc_strand = strands_to_export[i];
+    OxdnaStrand oxdna_strand = system.strands[i];
+
+    strand_count += 1;
+    List<Map<String, dynamic>> oxvnucs = [];
+    strand_nuc_start.add(nuc_count);
+    Map<String, dynamic> oxvstrand = {
+      'id': strand_count,
+      'class': 'NucleicAcidStrand',
+      'end5': nuc_count,
+      'end3': nuc_count + system.strands[i].nucleotides.length,
+      'monomers': oxvnucs
+    };
+
+    int scolor;
+    if (sc_strand.color != null) {
+      scolor = export_cadnano.to_cadnano_v2_int_hex(sc_strand.color);
+    } else {
+      scolor = null;
+    }
 
-    util.save_file(default_filename_dat, dat);
-    util.save_file(default_filename_top, top);
+    for (int index_in_strand = 0; index_in_strand < oxdna_strand.nucleotides.length; index_in_strand++) {
+      OxdnaNucleotide nuc = oxdna_strand.nucleotides[index_in_strand];
+      Map<String, dynamic> oxvnuc = {
+        'id': nuc_count,
+        'p': [nuc.r.x, nuc.r.y, nuc.r.z],
+        'a1': [nuc.b.x, nuc.b.y, nuc.b.z],
+        'a3': [nuc.n.x, nuc.n.y, nuc.n.z],
+        'class': 'DNA',
+        'type': nuc.base,
+        'cluster': 1,
+      };
+      if (index_in_strand != 0) {
+        oxvnuc['n5'] = nuc_count - 1;
+      }
+      if (index_in_strand != oxdna_strand.nucleotides.length - 1) {
+        oxvnuc['n3'] = nuc_count + 1;
+      }
+      if (scolor != null) {
+        oxvnuc['color'] = scolor;
+      }
+      nuc_count += 1;
+      oxvnucs.add(oxvnuc);
+    }
+    oxview_strands.add(oxvstrand);
   }
-  next(action);
+
+  for (int si1 = 0; si1 < strands_to_export.length; si1++) {
+    Strand sc_strand1 = strands_to_export[si1];
+    Map<String, dynamic> oxv_strand1 = oxview_strands[si1];
+    for (int si2 = 0; si2 < strands_to_export.length; si2++) {
+      Strand sc_strand2 = strands_to_export[si2];
+      if (!sc_strand1.overlaps(sc_strand2)) {
+        continue;
+      }
+      int s1_nuc_idx = strand_nuc_start[si1 + 1];
+      for (var domain1 in sc_strand1.domains) {
+        if (domain1 is Loopout || domain1 is Extension) {
+          continue;
+        }
+        int s2_nuc_idx = strand_nuc_start[si2 + 1];
+        for (var domain2 in sc_strand2.domains) {
+          if (domain2 is Loopout || domain2 is Extension) {
+            continue;
+          }
+          if (!domain1.overlaps(domain2)) {
+            continue;
+          }
+          Tuple2<int, int> overlap = domain1.compute_overlap(domain2);
+          int overlap_left = overlap.item1;
+          int overlap_right = overlap.item2;
+          int s1_left = sc_strand1.domain_offset_to_strand_dna_idx(domain1, overlap_left, false);
+          int s1_right = sc_strand1.domain_offset_to_strand_dna_idx(domain1, overlap_right, false);
+          int s2_left = sc_strand2.domain_offset_to_strand_dna_idx(domain2, overlap_left, false);
+          int s2_right = sc_strand2.domain_offset_to_strand_dna_idx(domain2, overlap_right, false);
+          List<int> d1range;
+          List<int> d2range;
+          if (domain1.forward) {
+            d1range = List<int>.from(quiver.range(s1_left, s1_right));
+            d2range = List<int>.from(quiver.range(s2_left, s2_right, -1));
+          } else {
+            d1range = List<int>.from(quiver.range(s1_right + 1, s1_left + 1));
+            d2range = List<int>.from(quiver.range(s2_right - 1, s2_left - 1, -1));
+          }
+          assert(d1range.length == d2range.length);
+
+          // Check for mismatches, and do not add a pair if the bases are *known*
+          // to mismatch.  (FIXME: this must be changed if scadnano later supports
+          // degenerate base codes.)
+          for (int i = 0; i < d1range.length; i++) {
+            int d1 = d1range[i];
+            int d2 = d2range[i];
+            if (sc_strand1.dna_sequence != null &&
+                sc_strand2.dna_sequence != null &&
+                sc_strand1.dna_sequence[d1] != constants.DNA_BASE_WILDCARD &&
+                sc_strand2.dna_sequence[d2] != constants.DNA_BASE_WILDCARD &&
+                util.wc(sc_strand1.dna_sequence[d1]) != sc_strand2.dna_sequence[d2]) {
+              continue;
+            }
+            oxv_strand1['monomers'][d1]['bp'] = s2_nuc_idx + d2;
+            if (oxview_strands[si2]['monomers'][d2].containsKey('bp')) {
+              if (oxview_strands[si2]['monomers'][d2]['bp'] != s1_nuc_idx + d1) {
+                print('${s2_nuc_idx + d2} ${s1_nuc_idx + d1} '
+                    '${oxview_strands[si2]['monomers'][d2]['bp']} ${domain1} ${domain2}');
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+  var b = system.compute_bounding_box();
+  Map<String, dynamic> oxvsystem = {
+    'box': [b.x, b.y, b.z],
+    'date': DateTime.now().toIso8601String(),
+    'systems': [
+      {'id': 0, 'strands': oxview_strands}
+    ],
+    'forces': [],
+    'selections': [],
+  };
+  String content = jsonEncode(oxvsystem);
+
+  return content;
 }
 
 Tuple2<String, String> to_oxdna_format(Design design, [List<Strand> strands_to_export = null]) {

lib/src/reducers/app_ui_state_reducer.dart

@@ -244,6 +244,9 @@ bool show_base_pair_lines_with_mismatches_reducer(
 bool export_svg_text_separately_reducer(bool _, actions.ExportSvgTextSeparatelySet action) =>
     action.export_svg_text_separately;
 
+bool ox_export_only_selected_strands_reducer(bool _, actions.OxExportOnlySelectedStrandsSet action) =>
+    action.only_selected;
+
 bool display_major_tick_widths_reducer(bool _, actions.SetDisplayMajorTickWidths action) => action.show;
 
 bool strand_paste_keep_color_reducer(bool _, actions.StrandPasteKeepColorSet action) => action.keep;
@@ -460,6 +463,7 @@ AppUIStateStorables app_ui_state_storable_local_reducer(AppUIStateStorables stor
     ..show_base_pair_lines = TypedReducer<bool, actions.ShowBasePairLinesSet>(show_base_pair_lines_reducer)(storables.show_base_pair_lines, action)
     ..show_base_pair_lines_with_mismatches = TypedReducer<bool, actions.ShowBasePairLinesWithMismatchesSet>(show_base_pair_lines_with_mismatches_reducer)(storables.show_base_pair_lines_with_mismatches, action)
     ..export_svg_text_separately = TypedReducer<bool, actions.ExportSvgTextSeparatelySet>(export_svg_text_separately_reducer)(storables.export_svg_text_separately, action)
+    ..ox_export_only_selected_strands = TypedReducer<bool, actions.OxExportOnlySelectedStrandsSet>(ox_export_only_selected_strands_reducer)(storables.ox_export_only_selected_strands, action)
     ..only_display_selected_helices = TypedReducer<bool, actions.SetOnlyDisplaySelectedHelices>(only_display_selected_helices_reducer)(storables.only_display_selected_helices, action)
     ..default_crossover_type_scaffold_for_setting_helix_rolls = TypedReducer<bool, actions.DefaultCrossoverTypeForSettingHelixRollsSet>(default_crossover_type_scaffold_for_setting_helix_rolls_reducer)(storables.default_crossover_type_scaffold_for_setting_helix_rolls, action)
     ..default_crossover_type_staple_for_setting_helix_rolls = TypedReducer<bool, actions.DefaultCrossoverTypeForSettingHelixRollsSet>(default_crossover_type_staple_for_setting_helix_rolls_reducer)(storables.default_crossover_type_staple_for_setting_helix_rolls, action)

lib/src/serializers.dart

@@ -363,6 +363,8 @@ part 'serializers.g.dart';
   ZoomSpeedSet,
   NewDesignSet,
   OxdnaExport,
+  OxviewExport,
+  OxExportOnlySelectedStrandsSet,
   Design,
   AssignDomainNameComplementFromBoundStrands,
   AssignDomainNameComplementFromBoundDomains,

lib/src/state/app_ui_state.dart

@@ -246,6 +246,8 @@ abstract class AppUIState with BuiltJsonSerializable implements Built<AppUIState
 
   bool get selection_box_intersection => storables.selection_box_intersection;
 
+  bool get ox_export_only_selected_strands => storables.ox_export_only_selected_strands;
+
   static void _initializeBuilder(AppUIStateBuilder b) {
     b.copy_info = null;
     b.last_mod_5p = null;

lib/src/state/app_ui_state_storables.dart

@@ -130,6 +130,8 @@ abstract class AppUIStateStorables
 
   bool get export_svg_text_separately;
 
+  bool get ox_export_only_selected_strands;
+
   static void _initializeBuilder(AppUIStateStorablesBuilder b) {
     // This ensures that even if these keys are not in localStorage (e.g., due to upgrading),
     // then they will be populated with a default value instead of raising an exception.
@@ -188,6 +190,7 @@ abstract class AppUIStateStorables
     b.show_mouseover_data = false;
     b.selection_box_intersection = false;
     b.export_svg_text_separately = false;
+    b.ox_export_only_selected_strands = false;
   }
 
   /************************ begin BuiltValue boilerplate ************************/

lib/src/state/strand.dart

@@ -753,6 +753,59 @@ abstract class Strand
     return rebuild((strand) => strand..substrands.replace(substrands_new));
   }
 
+  /// Convert from offset on the given Domain's Helix to string index on the parent Strand's DNA sequence.
+  /// If `offset_closer_to_5p` is ``true``, (this only matters if `offset` contains an insertion)
+  /// then the only leftmost string index corresponding to this offset is included,
+  /// otherwise up to the rightmost string index (including all insertions) is included.
+  int domain_offset_to_strand_dna_idx(Domain domain, int offset, bool offset_closer_to_5p) {
+    if (domain.deletions.contains(offset)) {
+      throw ArgumentError('offset ${offset} illegally contains a deletion from ${domain.deletions}');
+    }
+
+    int len_adjust = this._net_ins_del_length_increase_from_5p_to(domain, offset, offset_closer_to_5p);
+
+    int domain_str_idx;
+    if (domain.forward) {
+      offset += len_adjust;
+      domain_str_idx = offset - domain.start;
+    } else {
+      offset -= len_adjust;
+      domain_str_idx = domain.end - 1 - offset;
+    }
+
+    return domain_str_idx + get_seq_start_idx(domain);
+  }
+
+  /// Net number of insertions from 5'/3' end to offset_edge,
+  /// INCLUSIVE on 5'/3' end, EXCLUSIVE on offset_edge.
+  /// Set `five_p` ``= False`` to test from 3' end to `offset_edge`.
+  int _net_ins_del_length_increase_from_5p_to(Domain domain, int offset_edge, bool offset_closer_to_5p) {
+    int length_increase = 0;
+    for (int deletion in domain.deletions) {
+      if (_between_5p_and_offset(domain, deletion, offset_edge)) {
+        length_increase -= 1;
+      }
+    }
+    for (var insertion in domain.insertions) {
+      if (_between_5p_and_offset(domain, insertion.offset, offset_edge)) {
+        length_increase += insertion.length;
+      }
+    }
+    if (!offset_closer_to_5p) {
+      Map<int, int> insertion_map =
+          Map<int, int>.fromIterable(domain.insertions, key: (e) => e.offset, value: (e) => e.length);
+      if (insertion_map.containsKey(offset_edge)) {
+        int insertion_length = insertion_map[offset_edge];
+        length_increase += insertion_length;
+      }
+    }
+    return length_increase;
+  }
+
+  bool _between_5p_and_offset(Domain domain, int offset_to_test, int offset_edge) =>
+      (domain.forward && domain.start <= offset_to_test && offset_to_test < offset_edge) ||
+      (!domain.forward && offset_edge < offset_to_test && offset_to_test < domain.end);
+
   String _trim_or_pad_sequence_to_desired_length(String dna_sequence_new, int desired_length) {
     // truncate dna_sequence_new if too long; pad with ?'s if to short
     int seq_len = dna_sequence_new.length;