NCBI C++ ToolKit
dll_register.cpp
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1 /* $Id: dll_register.cpp 47479 2023-05-02 13:24:02Z ucko $
2  * =========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
9  * the author's official duties as a United States Government employee and
10  * thus cannot be copyrighted. This software/database is freely available
11  * to the public for use. The National Library of Medicine and the U.S.
12  * Government have not placed any restriction on its use or reproduction.
13  *
14  * Although all reasonable efforts have been taken to ensure the accuracy
15  * and reliability of the software and data, the NLM and the U.S.
16  * Government do not and cannot warrant the performance or results that
17  * may be obtained by using this software or data. The NLM and the U.S.
18  * Government disclaim all warranties, express or implied, including
19  * warranties of performance, merchantability or fitness for any particular
20  * purpose.
21  *
22  * Please cite the author in any work or product based on this material.
23  *
24  * =========================================================================
25  *
26  * Authors: Andrey Yazhuk, Igor Filippov, Jie Chen
27  *
28  * File Description:
29  * Defines "Sequence Editing" package for GBENCH.
30  */
31 
32 #include <ncbi_pch.hpp>
33 #include <corelib/ncbiapp.hpp>
34 #include <objects/seqtable/SeqTable_column.hpp>
35 #include <objects/seqtable/SeqTable_multi_data.hpp>
36 #include <gui/objects/GBProject.hpp>
37 #include <objects/gbproj/ProjectItem.hpp>
38 #include <gui/core/project_tree_view.hpp>
39 #include <gui/core/object_loading_task.hpp>
40 #include <gui/framework/app_task_service.hpp>
41 #include <objects/submit/Seq_submit.hpp>
42 #include <objtools/edit/autodef_with_tax.hpp>
43 #include <objtools/edit/mail_report.hpp>
44 #include <objtools/edit/struc_comm_field.hpp>
45 #include <objtools/cleanup/cleanup.hpp>
46 #include <connect/ncbi_http_session.hpp>
47 
48 #include <gui/framework/gui_package.hpp>
49 #include <gui/framework/pkg_wb_connect.hpp>
50 #include <gui/framework/workbench_impl.hpp>
51 #include <gui/core/selection_service_impl.hpp>
52 
53 #include <gui/widgets/wx/ui_command.hpp>
54 #include <gui/widgets/wx/csv_exporter.hpp>
55 
56 #include <gui/utils/extension_impl.hpp>
57 #include <gui/utils/url_utils.hpp>
58 #include <gui/objutils/cmd_change_seq_feat.hpp>
59 #include <gui/objutils/cmd_change_align.hpp>
60 #include <gui/objutils/cmd_insert_bioseq_set.hpp>
61 #include <gui/objutils/cmd_change_seq_entry.hpp>
62 #include <gui/objutils/util_cmds.hpp>
63 #include <gui/objutils/utils.hpp>
64 #include <gui/objutils/macro_lib.hpp>
65 #include <gui/objutils/macro_fn_do.hpp>
66 #include <gui/objutils/macro_fn_entry.hpp>
67 #include <gui/objutils/table_data_base.hpp>
68 #include <gui/objutils/adjust_consensus_splicesite.hpp>
69 
70 
71 #include <gui/objects/GBWorkspace.hpp>
72 #include <gui/objects/WorkspaceFolder.hpp>
73 #include <gui/objects/gbench_version.hpp>
74 #include <gui/objects/GBenchVersionInfo.hpp>
75 
76 #include <gui/widgets/edit/init.hpp>
77 #include <gui/widgets/edit/edit_object.hpp>
78 #include <gui/widgets/edit/edit_object_seq_feat.hpp>
79 #include <gui/widgets/edit/edit_object_seq_desc.hpp>
80 
81 #include <gui/widgets/loaders/open_objects_dlg.hpp>
82 #include <gui/widgets/loaders/file_load_wizard.hpp>
83 #include "open_data_source_object_dlg.hpp"
84 #include <gui/utils/object_loader.hpp>
85 #include <gui/utils/execute_unit.hpp>
86 #include <gui/utils/app_popup.hpp>
87 #include <gui/utils/event_handler.hpp>
88 #include <gui/objutils/project_item_extra.hpp>
89 #include <gui/widgets/wx/async_call.hpp>
90 #include <gui/widgets/wx/sys_path.hpp>
91 #include <gui/widgets/wx/message_box.hpp>
92 
93 #include <gui/packages/pkg_sequence_edit/autodef_tool_manager.hpp>
94 #include <gui/packages/pkg_sequence_edit/srcedit_tool.hpp>
95 #include <gui/packages/pkg_sequence_edit/seqid_fix_dlg.hpp>
96 
97 #include <gui/widgets/edit/table_data_suc.hpp>
98 #include <gui/widgets/edit/table_data_validate.hpp>
99 #include <gui/widgets/edit/table_data_validate_params.hpp>
100 #include <gui/packages/pkg_sequence_edit/remove_desc_dlg.hpp>
101 #include <gui/packages/pkg_sequence_edit/remove_sequences_from_alignments.hpp>
102 #include <gui/packages/pkg_sequence_edit/remove_features_dlg.hpp>
103 #include <gui/packages/pkg_sequence_edit/remove_structured_comment.hpp>
104 #include <gui/packages/pkg_sequence_edit/remove_annot.hpp>
105 #include <gui/packages/pkg_sequence_edit/remove_genomeprojectdb.hpp>
106 #include <gui/packages/pkg_sequence_edit/add_citsubupdate.hpp>
107 #include <gui/packages/pkg_sequence_edit/pubdesc_editor.hpp>
108 #include <gui/packages/pkg_sequence_edit/modify_structured_comment.hpp>
109 #include <gui/packages/pkg_sequence_edit/remove_bankit_comment.hpp>
110 #include <gui/packages/pkg_sequence_edit/remove_structuredcomment_keyword.hpp>
111 #include <gui/packages/pkg_sequence_edit/reorder_sequences_dlg.hpp>
112 #include <gui/packages/pkg_sequence_edit/convert_comment.hpp>
113 #include <gui/packages/pkg_sequence_edit/modify_feature_id.hpp>
114 #include <gui/packages/pkg_sequence_edit/remove_sequences.hpp>
115 #include <gui/packages/pkg_sequence_edit/pcr-primers-edit.hpp>
116 #include <gui/packages/pkg_sequence_edit/fix_orgmod_institution.hpp>
117 #include <gui/packages/pkg_sequence_edit/parse_collectiondate_formats.hpp>
118 #include <gui/packages/pkg_sequence_edit/country_fixup.hpp>
119 #include <gui/packages/pkg_sequence_edit/bulk_feature_add_dlg_std.hpp>
120 #include <gui/packages/pkg_sequence_edit/srceditdialog.hpp>
121 #include <gui/packages/pkg_sequence_edit/molinfo_edit_dlg.hpp>
122 #include <gui/packages/pkg_sequence_edit/miscedit_util.hpp>
123 #include <gui/packages/pkg_sequence_edit/featedit_util.hpp>
124 #include <gui/packages/pkg_sequence_edit/autodef_dlg.hpp>
125 #include <gui/packages/pkg_sequence_edit/autodef_params.hpp>
126 #include <gui/packages/pkg_sequence_edit/autodef_functions.hpp>
127 #include <gui/packages/pkg_sequence_edit/strain_serotype_influenza.hpp>
128 #include <gui/packages/pkg_sequence_edit/qual_table_load_manager.hpp>
129 #include <gui/packages/pkg_sequence_edit/vectortrimdlg.hpp>
130 #include <gui/packages/pkg_sequence_edit/citem_util.hpp>
131 #include <gui/packages/pkg_sequence_edit/remove_unverified.hpp>
132 #include <gui/packages/pkg_sequence_edit/add_deflinedlg.hpp>
133 #include <gui/packages/pkg_sequence_edit/bulk_edit_feat_dlg_std.hpp>
134 #include <gui/packages/pkg_sequence_edit/convert_feat_dlg.hpp>
135 #include <gui/packages/pkg_sequence_edit/prefix_deflinedlg.hpp>
136 #include <gui/packages/pkg_sequence_edit/discrepancy_dlg.hpp>
137 #include <gui/packages/pkg_sequence_edit/edit_pub_dlg_std.hpp>
138 #include <gui/packages/pkg_sequence_edit/make_badspecifichost_tbl.hpp>
139 #include <gui/packages/pkg_sequence_edit/editingbtnspanel.hpp>
140 #include <gui/packages/pkg_sequence_edit/correct_rna_strand_dlg.hpp>
141 #include <gui/packages/pkg_sequence_edit/apply_rna_its_dlg.hpp>
142 #include <gui/packages/pkg_sequence_edit/trim_n.hpp>
143 #include <gui/packages/pkg_sequence_edit/label_rna.hpp>
144 #include <gui/packages/pkg_sequence_edit/rem_prot_titles.hpp>
145 #include <gui/packages/pkg_sequence_edit/add_transl_except_dlg.hpp>
146 #include <gui/packages/pkg_sequence_edit/bulk_cds_edit.hpp>
147 #include <gui/packages/pkg_sequence_edit/bulk_gene_edit.hpp>
148 #include <gui/packages/pkg_sequence_edit/bulk_rna_edit.hpp>
149 #include <gui/packages/pkg_sequence_edit/choose_set_class_dlg.hpp>
150 #include "test_dialog_view.hpp"
151 #include <gui/widgets/seq/text_panel.hpp>
152 #include <gui/packages/pkg_sequence_edit/retranslate_cds.hpp>
153 #include <gui/widgets/edit/generic_report_dlg.hpp>
154 #include <gui/packages/pkg_sequence_edit/segregate_sets.hpp>
155 #include <gui/packages/pkg_sequence_edit/sequester_sets.hpp>
156 #include <gui/widgets/edit/macrofloweditor.hpp>
157 #include <gui/packages/pkg_sequence_edit/suc_refresh_cntrl.hpp>
158 #include <gui/packages/pkg_sequence_edit/revcomp_sequences.hpp>
159 #include <gui/packages/pkg_sequence_edit/select_target_dlg.hpp>
160 #include <gui/packages/pkg_sequence_edit/withdraw_sequences.hpp>
161 #include <gui/packages/pkg_sequence_edit/uncul_tax_tool.hpp>
162 #include <gui/packages/pkg_sequence_edit/apply_indexer_comments.hpp>
163 #include <gui/packages/pkg_sequence_edit/correct_genes_dialog.hpp>
164 #include <gui/packages/pkg_sequence_edit/extend_partial_features.hpp>
165 #include <gui/packages/pkg_sequence_edit/convert_cds_to_misc_feat.hpp>
166 #include <gui/packages/pkg_sequence_edit/add_flu_comments.hpp>
167 #include <gui/packages/pkg_sequence_edit/lowercase_qualifiers.hpp>
168 #include <gui/packages/pkg_sequence_edit/add_sequences.hpp>
169 #include <gui/packages/pkg_sequence_edit/convert_set_type_dlg.hpp>
170 #include <gui/packages/pkg_sequence_edit/gene_features_from_other_features.hpp>
171 #include <gui/packages/pkg_sequence_edit/latlon_tool.hpp>
172 #include <gui/packages/pkg_sequence_edit/export_table.hpp>
173 #include <gui/widgets/edit/edit_sequence.hpp>
174 #include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_n.hpp>
175 #include <gui/packages/pkg_sequence_edit/update_replaced_ec_numbers.hpp>
176 #include <gui/packages/pkg_sequence_edit/update_seq_worker.hpp>
177 #include <gui/packages/pkg_sequence_edit/add_feature_between_dlg.hpp>
178 #include <gui/packages/pkg_sequence_edit/import_feat_table.hpp>
179 #include <gui/packages/pkg_sequence_edit/group_explode.hpp>
180 #include <gui/packages/pkg_sequence_edit/remove_text_inside_string_dlg.hpp>
181 #include <gui/packages/pkg_sequence_edit/find_asn1_dlg.hpp>
182 #include <gui/packages/pkg_sequence_edit/fuse_features.hpp>
183 #include <gui/packages/pkg_sequence_edit/remove_dup_feats_dlg.hpp>
184 #include <gui/packages/pkg_sequence_edit/remove_xrefs.hpp>
185 #include <gui/packages/pkg_sequence_edit/cds_from_gene_mrna_exon.hpp>
186 #include <gui/packages/pkg_sequence_edit/cds_to_mat_peptide.hpp>
187 #include <gui/packages/pkg_sequence_edit/select_features.hpp>
188 #include <gui/packages/pkg_sequence_edit/remove_set.hpp>
189 #include <gui/packages/pkg_sequence_edit/edit_seq_id.hpp>
190 #include <gui/packages/pkg_sequence_edit/edit_history.hpp>
191 #include <gui/packages/pkg_sequence_edit/exon_from_cds.hpp>
192 #include <gui/packages/pkg_sequence_edit/set_global_refgene_status.hpp>
193 #include <gui/packages/pkg_sequence_edit/clear_keywords.hpp>
194 #include <gui/packages/pkg_sequence_edit/convert_rpt_unit_range_to_location.hpp>
195 #include <gui/packages/pkg_sequence_edit/link_mrna_cds.hpp>
196 #include <gui/packages/pkg_sequence_edit/gene_feats_from_xrefs.hpp>
197 #include <gui/packages/pkg_sequence_edit/remove_gene_xrefs.hpp>
198 #include <gui/packages/pkg_sequence_edit/truncate_cds.hpp>
199 #include <gui/packages/pkg_sequence_edit/fix_product_names.hpp>
200 #include <gui/packages/pkg_sequence_edit/apply_gcode.hpp>
201 #include <gui/packages/pkg_sequence_edit/edit_seq_ends_with_align.hpp>
202 #include <gui/widgets/edit/field_type_constants.hpp>
203 #include <gui/packages/pkg_sequence_edit/update_align.hpp>
204 #include <gui/packages/pkg_sequence_edit/resolve_intersecting_feats.hpp>
205 #include <gui/packages/pkg_sequence_edit/create_protein_id.hpp>
206 #include <gui/packages/pkg_sequence_edit/genus_species_fixup.hpp>
207 #include <gui/packages/pkg_sequence_edit/country_conflict.hpp>
208 #include <gui/packages/pkg_sequence_edit/add_secondary.hpp>
209 #include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.hpp>
210 #include <gui/packages/pkg_sequence_edit/package_features_on_parts.hpp>
211 #include <gui/packages/pkg_sequence_edit/featuretbl_frame.hpp>
212 #include <gui/packages/pkg_sequence_edit/fix_structured_vouchers.hpp>
213 #include <gui/packages/pkg_sequence_edit/edit_seq_ends.hpp>
214 #include <gui/packages/pkg_sequence_edit/create_seq_hist_for_tpa.hpp>
215 #include <gui/widgets/edit/alignment_assistant.hpp>
216 #include <gui/packages/pkg_sequence_edit/adjust_features_for_gaps.hpp>
217 #include <gui/packages/pkg_sequence_edit/compare_with_biosample.hpp>
218 #include <gui/packages/pkg_sequence_edit/barcode_tool.hpp>
219 #include <gui/packages/pkg_sequence_edit/restore_local_file.hpp>
220 #include <gui/packages/pkg_sequence_edit/split_cds_with_too_many_n.hpp>
221 #include <gui/packages/pkg_sequence_edit/far_pointer_seq.hpp>
222 #include <gui/packages/pkg_sequence_edit/csuc_frame.hpp>
223 #include <gui/packages/pkg_sequence_edit/edit_cds_frame.hpp>
224 #include <gui/packages/pkg_sequence_edit/expand_gaps.hpp>
225 #include <gui/packages/pkg_sequence_edit/convert_cds_with_gaps_to_misc_feat.hpp>
226 #include <gui/packages/pkg_sequence_edit/convert_selected_gaps.hpp>
227 #include <gui/packages/pkg_sequence_edit/sorted_proteins.hpp>
228 #include <gui/packages/pkg_sequence_edit/add_linkage_to_gaps.hpp>
229 #include <gui/packages/pkg_sequence_edit/remove_srcnotes.hpp>
230 #include <gui/packages/pkg_sequence_edit/convert_second_prot_name.hpp>
231 #include <gui/packages/pkg_sequence_edit/mrna_from_gene_cds_exon.hpp>
232 #include <gui/packages/pkg_sequence_edit/trna_from_gene.hpp>
233 #include <gui/packages/pkg_sequence_edit/adjust_feats_for_introns.hpp>
234 #include <gui/packages/pkg_sequence_edit/clear_nomenclature.hpp>
235 #include <gui/packages/pkg_sequence_edit/merge_biosources.hpp>
236 #include <gui/packages/pkg_sequence_edit/suppress_genes.hpp>
237 #include <gui/packages/pkg_sequence_edit/extend_cds_to_stop.hpp>
238 #include <gui/packages/pkg_sequence_edit/recompute_intervals.hpp>
239 #include <gui/packages/pkg_sequence_edit/convert_bad_inference.hpp>
240 #include <gui/packages/pkg_sequence_edit/global_pubmedid_lookup.hpp>
241 #include <gui/packages/pkg_sequence_edit/remove_unindexed_features.hpp>
242 #include <gui/packages/pkg_sequence_edit/correct_interval_order.hpp>
243 #include <gui/packages/pkg_sequence_edit/load_secondary_accessions.hpp>
244 #include <gui/packages/pkg_sequence_edit/add_global_code_break.hpp>
245 #include <gui/packages/pkg_sequence_edit/convert_desc_to_feat.hpp>
246 #include <gui/packages/pkg_sequence_edit/validate_frame.hpp>
247 #include <gui/packages/pkg_sequence_edit/load_struct_comm_from_table.hpp>
248 #include <gui/packages/pkg_sequence_edit/suspect_product_rule_editor.hpp>
249 #include <gui/packages/pkg_sequence_edit/mixedstrands.hpp>
250 #include <gui/packages/pkg_sequence_edit/remove_unnecessary_exceptions.hpp>
251 #include <gui/packages/pkg_sequence_edit/restore_rna_edit.hpp>
252 #include <gui/packages/pkg_sequence_edit/fix_for_trans_splicing.hpp>
253 #include <gui/packages/pkg_sequence_edit/submission_wizard.hpp>
254 #include <gui/packages/pkg_sequence_edit/bulk_miscfeat_edit.hpp>
255 #include <gui/packages/pkg_sequence_edit/update_targeted_locus_name_dlg.hpp>
256 
257 #include <gui/widgets/edit/bioseq_editor.hpp>
258 #include <gui/core/simple_project_view.hpp>
259 #include <gui/widgets/edit/edit_obj_view_dlg.hpp>
260 #include <gui/widgets/edit/propagate_descriptors.hpp>
261 
262 #include "edit_project_item_extension.hpp"
263 #include "indexer_app_mode.hpp"
264 
265 #include <gui/packages/pkg_sequence_edit/sequin_desktop_view.hpp>
266 #include <gui/packages/pkg_sequence_edit/wrong_illegal_quals.hpp>
267 
268 #include <gui/packages/pkg_sequence_edit/editing_actions.hpp>
269 #include <gui/packages/pkg_sequence_edit/editing_action_constraint.hpp>
270 #include <gui/packages/pkg_sequence_edit/aecr_frame.hpp>
271 #include "attrib_table_column_id_panel.hpp"
272 
273 #include "gui_core_helper_impl.hpp"
274 
275 #include <gui/packages/pkg_sequence_edit/parse_text_dlg.hpp>
276 #include <gui/packages/pkg_sequence_edit/append_mod_to_org_dlg.hpp>
277 
278 #include <gui/widgets/edit/sequence_editing_cmds.hpp>
279 #include <gui/objutils/cmd_enable_hup_id.hpp>
280 #include <gui/core/cmd_change_projectitem.hpp>
281 
282 #include "cmd_feat_id_xrefs_from_qualifiers.hpp"
283 #include "cmd_convert_to_delayed_gen-prod-set_quals.hpp"
284 
285 #ifdef _DEBUG
286 #include <gui/packages/pkg_sequence_edit/debug_macro_tool.hpp>
287 #endif
288 
289 #include <wx/msgdlg.h>
290 #include <wx/statline.h>
291 #include <wx/clipbrd.h>
292 #include <gui/widgets/wx/file_extensions.hpp>
293 #include <wx/filedlg.h>
294 #include <wx/display.h>
295 #include <wx/evtloop.h>
296 #include <wx/uri.h>
297 #include <wx/utils.h>
298 
299 BEGIN_NCBI_SCOPE
300 
301 ///////////////////////////////////////////////////////////////////////////////
302 /// Declare the Package Object
303 class CSeqEditPackage
304  : public IGuiPackage
305  , public IUICommandContributor
306  , public IMenuContributor
307  , public IPackageWorkbenchConnector
308 {
309 public:
310  CSeqEditPackage();
311  virtual string GetName() const { return "Sequence Editing"; }
312  virtual void GetVersion(size_t& verMajor, size_t& verMinor, size_t& verPatch) const
313  {
314  verMajor = 1;
315  verMinor = 0;
316  verPatch = 0;
317  }
318  virtual bool Init();
319  virtual void Shut() {}
320 
321  // IUICommandContributor
322  virtual vector<CUICommand*> GetCommands();
323  virtual wxEvtHandler* GetEventHandler();
324 
325  // IPackageWorkbenchConnector
326  virtual void SetWorkbench(IWorkbench* wb);
327 
328 protected:
329  // IMenuContributor
330  virtual const SwxMenuItemRec* GetMenuDef() const;
331 
332  void x_UpdateValAuxFile(const string& fname) const;
333 
334  IWorkbench* m_Workbench;
335 };
336 
337 static const char* sMacroLibraries[] = {
338  "<std>/etc/macro_scripts/list_of_macros.mql",
339  "<std>/etc/macro_scripts/autofix_gb.mql",
340  "<std>/etc/macro_scripts/autofix_tsa.mql",
341  "<std>/etc/macro_scripts/autofix_wgs.mql",
342  NULL
343 };
344 
345 CSeqEditPackage::CSeqEditPackage()
346 {
347  m_Workbench = NULL;
348 }
349 
350 
351 bool CSeqEditPackage::Init()
352 {
353  // Declare you extension here
354 
355  // Examples:
356  //CExtensionDeclaration("view_manager_service::view_factory",
357  // new CTextViewFactory());
358 
359  //CExtensionDeclaration("ui_data_source_type",
360  // new CGenBankUIDataSourceType());
361  //CExtensionDeclaration ("file_format_loader_manager",
362  // new CFASTAFormatLoadManager());
363 
364  //CExtensionDeclaration("data_mining_tool", new CEntrezSearchTool());
365 
366  init_w_edit();
367 
368 // CExtensionDeclaration("ui_algo_tool_manager", new CAutodefToolManager());
369 
370  // Edit tools
371 // CExtensionDeclaration("ui_algo_tool_manager", new CEditingBtnsTool());
372 // CExtensionDeclaration("ui_algo_tool_manager", new CSrcEditTool());
373 
374 #ifdef _DEBUG
375  CExtensionDeclaration("ui_algo_tool_manager", new CDebugMacroTool());
376 #endif
377 
378  if (RunningInsideNCBI())
379  {
380  CExtensionDeclaration("view_manager_service::view_factory", new CSequinDesktopViewFactory());
381  }
382 
383  CExtensionDeclaration ("file_format_loader_manager", new CQualTableLoadManager());
384 
385 // IFileLoadPanelClient
386  CExtensionDeclaration ("file_load_panel_client", new CFileLoadPanelClientFactory<CQualTableLoadManager>());
387 
388  vector<string> filenames;
389  auto i = 0;
390  while (sMacroLibraries[i]) {
391  wxString path = CSysPath::ResolvePathExisting(wxString::FromUTF8(sMacroLibraries[i]));
392  if (!path.IsEmpty()) {
393  filenames.push_back(string(path.ToUTF8()));
394  }
395  else {
396  NcbiMessageBox(string(sMacroLibraries[i]) + " was not found");
397  }
398  ++i;
399  }
400 
401  if (!filenames.empty()) {
402  macro::CMacroLib& macroLib = macro::CMacroLib::GetInstance();
403  macroLib.ClearLibrary();
404  bool status = macroLib.AppendToLibrary(filenames);
405  if (!status) {
406  NcbiMessageBox(macroLib.GetLastError());
407  }
408 
409  wxString path = CSysPath::ResolvePathExisting(wxT("<std>/etc/synonyms.txt"));
410  if (!path.IsEmpty()) {
411  macroLib.StoreSynonymList(ToStdString(path));
412  }
413  }
414 
415  if (!RunningInsideNCBI()) {
416  x_UpdateValAuxFile("lat_lon_country.txt");
417  x_UpdateValAuxFile("lat_lon_water.txt");
418  }
419 
420  // needed to pick up the latest EC number lists
421  CNcbiApplication::Instance()->SetEnvironment("NCBI_ECNUM_USE_DATA_DIR_FIRST", "TRUE");
422 
423  //! Please don't register commands twice. Either you register them directly
424  //! with x_RegisterCommands(), or you use the interface IUICommandContributor.
425  //! Please never do both!
426  //!
427  //x_RegisterCommands();
428 
429  CExtensionDeclaration(EXT_POINT__PROJECT_ITEM_EXTENSION, new CEditProjectItemExtension());
430  CExtensionDeclaration(EXT_POINT__APP_MODE_EXTENSION, new CIndexerAppModeExtension());
431  return true;
432 }
433 
434 void CSeqEditPackage::SetWorkbench(IWorkbench* wb)
435 {
436  m_Workbench = wb;
437 }
438 
439 static bool s_UpdateLocalFile(const string& url, const string& file_name)
440 {
441  CHttpResponse response = g_HttpGet(CUrl(url));
442  if (response.GetStatusCode() == 200 && response.CanGetContentStream()) {
443  CNcbiIstream& istr = response.ContentStream();
444  if (istr.good()) {
445  CNcbiOfstream ostr(file_name.c_str());
446  NcbiStreamCopy(ostr, istr);
447  LOG_POST(Info << "Downloaded " + file_name + " to be used by the validator");
448  return true;
449  }
450  }
451  return false;
452 }
453 
454 void CSeqEditPackage::x_UpdateValAuxFile(const string& fname) const
455 {
456  const string url = "https://anonsvn.ncbi.nlm.nih.gov/v1/trunk/c%2B%2B/src/objects/seqfeat/" + fname;
457 
458  const wxChar* kTempFilesDir = wxT("<home>/TempFiles");
459  wxString dir_path = CSysPath::ResolvePath(kTempFilesDir);
460  {
461  string path(dir_path.ToUTF8());
462  CNcbiApplication::Instance()->SetEnvironment("NCBI_LAT_LON_DATA_PATH", path);
463  }
464 
465  wxFileName wxfname;
466  wxfname.SetPath(dir_path);
467  wxfname.SetFullName(fname);
468  string filePath(wxfname.GetFullPath().ToUTF8());
469 
470  if (!wxfname.FileExists()) {
471  if (!wxFileName::DirExists(dir_path) && !wxFileName::Mkdir(dir_path)) {
472  LOG_POST(Error << "Failed to create directory: '" << dir_path << "'");
473  return;
474  }
475 
476  if (!s_UpdateLocalFile(url, filePath)) {
477  LOG_POST(Error << "Failed to download " + fname);
478  }
479  }
480  else {
481  try {
482  Uint8 remote_fsize = CUrlUtils::GetRemoteFileSize(url);
483  Uint8 existing_fsize = wxfname.GetSize().ToULong();
484  long diff = (long)abs((int)(existing_fsize - remote_fsize));
485 
486 #ifdef NCBI_OS_MSWIN
487 
488  CNcbiIfstream istr(filePath.c_str());
489  istr.unsetf(ios::skipws);
490  long count_lines = count(istream_iterator<char>(istr), istream_iterator<char>(), '\n');
491 
492  if (diff > 0 && count_lines == diff) {
493  // they are the same, no need to update
494  }
495  else {
496  s_UpdateLocalFile(url, filePath);
497  }
498 #else
499  if (diff > 0) {
500  s_UpdateLocalFile(url, filePath);
501  }
502 #endif
503  }
504  catch (const CException& e) {
505  LOG_POST(Error << "Failed to update " + fname + ": " + e.GetMsg());
506  }
507  catch (const exception& e) {
508  LOG_POST(Error << "Failed to update " + fname + ": " + e.what());
509  }
510  }
511 }
512 
513 ///////////////////////////////////////////////////////////////////////////////
514 /// Declare Package Entry Point
515 extern "C" {
516  NCBI_PACKAGEENTRYPOINT_EXPORT IGuiPackage* NCBIGBenchGetPackage()
517  {
518  return new CSeqEditPackage();
519  }
520 }
521 
522 
523 class CSequenceEditingEventHandler : public wxEvtHandler, public CEventHandler
524 {
525  DECLARE_EVENT_TABLE();
526  DECLARE_EVENT_MAP();
527 
528 public:
529  CSequenceEditingEventHandler(IWorkbench* wb = NULL);
530  void IsObjectSelected(wxUpdateUIEvent& event);
531  void IsLocationSelected(wxUpdateUIEvent& event);
532  bool TestHupIdEnabled();
533  void IsHupIdEnabled(wxUpdateUIEvent& event);
534  void ItemAction(wxCommandEvent& event, CRef <CItem> item, const string& title);
535  ~CSequenceEditingEventHandler();
536  void ShowAfter(wxWindow* dlg);
537 
538  // methods
539  void RemoveDescriptors(wxCommandEvent& evt);
540  void RemoveFeatures(wxCommandEvent& evt);
541  void RemoveUnindexedFeatures(wxCommandEvent& event);
542  void ApplyIndexerComments(wxCommandEvent& evt);
543  void RemoveSeqAnnotIds( wxCommandEvent& event );
544  void RemoveBankitComment( wxCommandEvent& event );
545  void RemoveDuplicateStructuredComments( wxCommandEvent& event );
546  void RemoveSequencesFromAlignments( wxCommandEvent& event );
547  void RemoveSequences( wxCommandEvent& event );
548  void RemoveSet( wxCommandEvent& event );
549  void RemoveSetsFromSet( wxCommandEvent& event );
550  void RevCompSequences( wxCommandEvent& event );
551  void BioseqFeatsRevComp( wxCommandEvent& event );
552  void BioseqOnlyRevComp( wxCommandEvent& event );
553  void UnculTaxTool( wxCommandEvent& event );
554  void MergeBiosources(wxCommandEvent& event);
555  void EditSequence( wxCommandEvent& event );
556  void AlignmentAssistant( wxCommandEvent& event );
557  void RemoveSeqAnnotAlign( wxCommandEvent& event );
558  void RemoveSeqAnnotGraph( wxCommandEvent& event );
559  void RemoveGenomeProjectsDB( wxCommandEvent& event );
560  void RemoveEmptyGenomeProjectsDB( wxCommandEvent& event );
561  void TaxFixCleanup( wxCommandEvent& event );
562  void SpecificHostCleanup( wxCommandEvent& event );
563  void FixNonReciprocalLinks( wxCommandEvent& event );
564  void DisableStrainForwarding( wxCommandEvent& event );
565  void EnableStrainForwarding(wxCommandEvent& event);
566  void EditPubs( wxCommandEvent& event );
567  void GlobalPubmedIdLookup(wxCommandEvent& event);
568  void FixCapitalizationAll( wxCommandEvent& event );
569  void FixCapitalizationAuthors( wxCommandEvent& event );
570  void FixCapitalizationTitles( wxCommandEvent& event );
571  void FixCapitalizationAffiliation( wxCommandEvent& event );
572  void FixCapitalizationCountry( wxCommandEvent& event );
573  void RemoveUnpublishedPublications( wxCommandEvent& event );
574  void RemoveInPressPublications( wxCommandEvent& event );
575  void RemovePublishedPublications( wxCommandEvent& event );
576  void RemoveCollidingPublications( wxCommandEvent& event );
577  void RemoveAllPublications( wxCommandEvent& event );
578  void RemoveAuthorConsortiums( wxCommandEvent& event );
579  void ReverseAuthorNames( wxCommandEvent& event );
580  void StripAuthorSuffixes( wxCommandEvent& event );
581  void TruncateAuthorMiddleInitials( wxCommandEvent& event );
582  void ConvertAuthorToConstortiumWhereLastName( wxCommandEvent& event );
583  void ConvertAuthorToConsortiumAll( wxCommandEvent& event );
584  void AddCitSubForUpdate( wxCommandEvent& event );
585  void FixUsaAndStates( wxCommandEvent& event );
586  void RetranslateCDS( wxCommandEvent& event );
587  void ResynchronizePartials( wxCommandEvent& event );
588  void AddTranslExcept( wxCommandEvent& event );
589  void RemoveAllStructuredComments( wxCommandEvent& event );
590  void RemoveEmptyStructuredComments( wxCommandEvent& event );
591  void ModifyStructuredComment( wxCommandEvent& event );
592  void SetGlobalRefGeneStatus( wxCommandEvent& event );
593  void ClearKeywords( wxCommandEvent& event );
594  void ClearNomenclature(wxCommandEvent& event);
595  void RemoveStructuredCommentKeyword( wxCommandEvent& event );
596  void AddStructuredCommentKeyword( wxCommandEvent& event );
597  void AddGenomeAssemblyStructuredComment( wxCommandEvent& event );
598  void AddAssemblyStructuredComment(wxCommandEvent& event);
599  void ReorderStructuredComment( wxCommandEvent& event );
600  void ConvertComment( wxCommandEvent& event );
601  void ParseComment( wxCommandEvent& event );
602  void IllegalQualsToNote( wxCommandEvent& event);
603  void RmIllegalQuals( wxCommandEvent& event);
604  void WrongQualsToNote( wxCommandEvent& event);
605  void ConvertBadInference(wxCommandEvent& event);
606  void RmWrongQuals( wxCommandEvent& event);
607  void LowercaseQuals( wxCommandEvent& event );
608  void AssignFeatureIds( wxCommandEvent& event );
609  void ClearFeatureIds( wxCommandEvent& event );
610  void ReassignFeatureIds( wxCommandEvent& event );
611  void UniqifyFeatureIds( wxCommandEvent& event );
612  void TrimJunkInPrimerSeqs( wxCommandEvent& event );
613  void FixiInPrimerSeqs( wxCommandEvent& event );
614 // J. Chen begin
615  void RemoveCddFeatDbxref(wxCommandEvent& event );
616  void PrefixAuthWithTax(wxCommandEvent& event );
617  void FocusSet( wxCommandEvent& event );
618  void FocusClear( wxCommandEvent& event );
619  void SetTransgSrcDesc( wxCommandEvent& event );
620  void SplitDblinkQuals(wxCommandEvent& evt);
621 // J. Chen end
622  void FixOrgModInstitution( wxCommandEvent& event );
623  void FixStructuredVouchers( wxCommandEvent& event );
624  void SwapPrimerSeqName( wxCommandEvent& event );
625  void MergePrimerSets( wxCommandEvent& event );
626  void SplitPrimerSets( wxCommandEvent& event );
627  void AppendModToOrg( wxCommandEvent& event );
628  void ParseCollectionDateMonthFirst( wxCommandEvent& event );
629  void ParseCollectionDateDayFirst( wxCommandEvent& event );
630  void CountryFixupCap( wxCommandEvent& event );
631  void CountryFixupNoCap( wxCommandEvent& event );
632  void VectorTrim( wxCommandEvent& event );
633  void SelectTarget( wxCommandEvent& event );
634  void SelectFeature( wxCommandEvent& event );
635  void AddCDS( wxCommandEvent& event );
636  void AddRNA( wxCommandEvent& event );
637  void AddOtherFeature( wxCommandEvent& event );
638  void AddFeatureBetween( wxCommandEvent& event );
639  void Validate( wxCommandEvent& event );
640  void SortUniqueCount( wxCommandEvent& event );
641  void SortUniqueCountTree(wxCommandEvent& event);
642  void Discrepancy(wxCommandEvent& event);
643  void Oncaller(wxCommandEvent& event);
644  void Submitter(wxCommandEvent& event);
645  void Mega(wxCommandEvent& event);
646  void DiscrepancyList(wxCommandEvent& event);
647  void RemoveAllFeatures(wxCommandEvent& event);
648  void RemoveDupFeats( wxCommandEvent& evt );
649  void RemoveDupFeatsWithOptions( wxCommandEvent& evt );
650  void ResolveIntersectingFeats( wxCommandEvent& evt );
651  void AddSequences ( wxCommandEvent& event );
652  void ApplyEditConvertRemove ( wxCommandEvent& event );
653  void ParseText ( wxCommandEvent& event );
654  void RemoveTextInsideStr( wxCommandEvent& event );
655  void ConvertFeatures ( wxCommandEvent& event );
656  void CdsToMatPeptide( wxCommandEvent& event );
657  void ConvertCdsToMiscFeat( wxCommandEvent& evt );
658  void ConvertCdsWithGapsToMiscFeat( wxCommandEvent& evt );
659  void ConvertCdsWithInternalStopToMiscFeat( wxCommandEvent& evt );
660  void ConvertCdsWithInternalStopToMiscFeatViral( wxCommandEvent& evt );
661  void ConvertCdsWithInternalStopToMiscFeatUnverified( wxCommandEvent& evt );
662  void TableReader ( wxCommandEvent& event );
663  void TableReaderClipboard ( wxCommandEvent& event );
664  void BulkEdit ( wxCommandEvent& event );
665  void MolInfoEdit ( wxCommandEvent& event );
666  void ExportTable ( wxCommandEvent& event );
667  void Autodef ( wxCommandEvent& event );
668  void PT_Cleanup ( wxCommandEvent& event );
669  void ParseStrainSerotypeFromNames ( wxCommandEvent& event);
670  void AddStrainSerotypeToNames ( wxCommandEvent& event);
671  void FixupOrganismNames ( wxCommandEvent& event);
672  void SplitQualifiersAtCommas ( wxCommandEvent& event);
673  void SplitStructuredCollections ( wxCommandEvent& event);
674  void TrimOrganismNames ( wxCommandEvent& event);
675  void RemoveUnverified( wxCommandEvent& event );
676  void RemoveUnreviewed(wxCommandEvent& event);
677  void AddNamedrRNA ( wxCommandEvent& event);
678  void AddControlRegion ( wxCommandEvent& event);
679  void AddMicrosatellite ( wxCommandEvent& event);
680  void CreateFeature ( wxCommandEvent& event);
681  void CreateRegulatory ( wxCommandEvent& evt);
682  void CreateDescriptor ( wxCommandEvent& event);
683  void CreateSpecificStructuredComment( wxCommandEvent& event );
684  void DeleteSpecificStructuredComment( wxCommandEvent& evt );
685  void EditFeature ( wxCommandEvent& evt);
686  void ExtendPartialsConstr( wxCommandEvent& evt);
687  void ExtendPartialsAll( wxCommandEvent& evt);
688  void AddDefLine ( wxCommandEvent& evt);
689  void PrefixDefLines ( wxCommandEvent& event);
690  void EditingButtons ( wxCommandEvent& event);
691  void MakeBadSpecificHostTable ( wxCommandEvent& event);
692  void CorrectRNAStrand ( wxCommandEvent& event);
693  void ApplyRNA_ITS ( wxCommandEvent& event);
694  void TrimNsRich( wxCommandEvent& event );
695  void TrimNsTerminal( wxCommandEvent& event );
696  void AddFluComments( wxCommandEvent& event );
697  void LabelRna( wxCommandEvent& event );
698  void RemProtTitles( wxCommandEvent& event );
699  void RemAllProtTitles( wxCommandEvent& event );
700  void BulkCdsEdit ( wxCommandEvent& event );
701  void BulkGeneEdit ( wxCommandEvent& event );
702  void BulkRnaEdit ( wxCommandEvent& event );
703  void BulkMiscFeatEdit(wxCommandEvent& event);
704  void CorrectGenes ( wxCommandEvent& event );
705  void SegregateSets ( wxCommandEvent& event );
706  void SequesterSets ( wxCommandEvent& event );
707  void DescriptorPropagateDown( wxCommandEvent& event );
708  void WithdrawSequences ( wxCommandEvent& event );
709  void AddSet ( wxCommandEvent& event );
710  void PropagateDBLink ( wxCommandEvent& event );
711  void ConvertSetType ( wxCommandEvent& event );
712  void ListMacroButtonNames ( wxCommandEvent& event );
713  void TestDialogView( wxCommandEvent& event );
714  void TestFormView( wxCommandEvent& event );
715  void PrepareSeqSubmit(wxCommandEvent& event);
716  CRef<CProjectItem> CreateSeqSubmit(CRef<CGBProjectHandle> ph, CRef<CProjectItem> pi, CIRef<CProjectService> srv);
717  void ChangeToGenomicDna();
718  void SetTopLevelBioseqSetClass();
719  void SaveSubmissionFile(wxCommandEvent& event);
720  void SaveASN1File(wxCommandEvent& event);
721  void MacroEditor( wxCommandEvent& event );
722  void AdjustForConsensusSpliceSites( wxCommandEvent& event );
723  void AdjustCDSForIntrons(wxCommandEvent& event);
724  void AdjustrRNAForIntrons(wxCommandEvent& event);
725  void AdjusttRNAForIntrons(wxCommandEvent& event);
726  void AdjustmRNAForIntrons(wxCommandEvent& event);
727  void CombineSelectedGenesIntoPseudogenes( wxCommandEvent& evt );
728  void GeneFromOtherFeat( wxCommandEvent& evt );
729  void CdsFromGeneMrnaExon( wxCommandEvent& evt );
730  void mRNAFromGeneCdsExon( wxCommandEvent& evt );
731  void tRNAFromGene( wxCommandEvent& evt );
732  void ExonFromCds( wxCommandEvent& evt );
733  void ExonFromMRNA( wxCommandEvent& evt );
734  void ExonFromTRNA( wxCommandEvent& evt );
735  void LatLonTool ( wxCommandEvent& event );
736  void CDSGeneRangeErrorSuppress( wxCommandEvent& event );
737  void CDSGeneRangeErrorRestore( wxCommandEvent& event );
738  void SuppressGenes(wxCommandEvent& evt);
739  void RemoveSegGaps( wxCommandEvent& event );
740  void RawSeqToDeltaByNs( wxCommandEvent& event );
741  void RawSeqToDeltaByLoc( wxCommandEvent& event );
742  void RawSeqToDeltaByAssemblyGapFeatures(wxCommandEvent& event);
743  void SplitCDSwithTooManyXs( wxCommandEvent& event );
744  void AdjustFeaturesForGaps( wxCommandEvent& event );
745  void DeltaSeqToRaw( wxCommandEvent& event );
746  void ExpandGaps(wxCommandEvent& event);
747  void ConvertSelectedGapsToKnown(wxCommandEvent& event);
748  void ConvertSelectedGapsToUnknown(wxCommandEvent& event);
749  void ConvertGapsBySize(wxCommandEvent& event);
750  void EditSelectedGaps(wxCommandEvent& event);
751  void CreateGapFeats(wxCommandEvent& event);
752  void AddLinkageToGaps(wxCommandEvent& event);
753  void ConvertFeatsToGaps(wxCommandEvent& event);
754  void CombineAdjacentGaps(wxCommandEvent& event);
755  void RmCultureNotes( wxCommandEvent& event );
756  void Update_Replaced_EC_numbers( wxCommandEvent& event );
757  void UpdateSingleSequence(wxCommandEvent& event);
758  void UpdateMultipleSequences(wxCommandEvent& event);
759  void ImportFeatureTable( wxCommandEvent& event );
760  void ImportFeatureTableClipboard( wxCommandEvent& event );
761  void ImportGFF3(wxCommandEvent& event);
762  void LoadSecondaryAccessions(wxCommandEvent& event);
763  void LoadSecondaryAccessionsHistoryTakeover(wxCommandEvent& event);
764  void AddGlobalCodeBreak( wxCommandEvent& event );
765  void GroupExplode( wxCommandEvent& event);
766  void FindASN1( wxCommandEvent& evt );
767  void FuseFeatures( wxCommandEvent& evt );
768  void FuseJoinsInLocs(wxCommandEvent& event);
769  void ExplodeRNAFeats(wxCommandEvent& event);
770  void ApplyStructuredCommentField( wxCommandEvent& evt );
771  void EditStructuredCommentPrefixSuffix( wxCommandEvent& evt );
772  void RemoveDbXrefsCDS( wxCommandEvent& evt );
773  void RemoveDbXrefsGenes( wxCommandEvent& evt );
774  void RemoveDbXrefsRNA( wxCommandEvent& evt );
775  void RemoveDbXrefsAllFeats( wxCommandEvent& evt );
776  void RemoveDbXrefsBioSource( wxCommandEvent& evt );
777  void RemoveDbXrefsBioSourceAndFeats( wxCommandEvent& evt );
778  void RemoveTaxonFeats( wxCommandEvent& event);
779  void RemoveTaxonFeatsAndBioSource( wxCommandEvent& event);
780  void AddKeywordGDS( wxCommandEvent& event );
781  void AddKeywordTPA_inferential( wxCommandEvent& event );
782  void AddKeywordTPA_experimental( wxCommandEvent& event );
783  void AddKeywordTPA_assembly( wxCommandEvent& event );
784  void AddKeywordWithConstraint( wxCommandEvent& event );
785  void EditSeqId( wxCommandEvent& event );
786  void RemoveLocalSeqIdsFromNuc(wxCommandEvent& event);
787  void RemoveLocalSeqIdsFromProt(wxCommandEvent& event);
788  void RemoveLocalSeqIdsFromAll(wxCommandEvent& event);
789  void RemoveGiSeqIdsFromAll(wxCommandEvent& event);
790  void RemoveGenbankSeqIdsFromProt(wxCommandEvent& event);
791  void RemoveGenbankSeqIdsFromAll(wxCommandEvent& event);
792  void RemoveSeqIdNamesFromProtFeats(wxCommandEvent& event);
793  void ConvertAccessionToLocalIdsAll(wxCommandEvent& event);
794  void ConvertAccessionToLocalIdsNuc(wxCommandEvent& event);
795  void ConvertAccessionToLocalIdsProt(wxCommandEvent& event);
796  void ConvertAccessionToLocalIdsName(wxCommandEvent& event);
797  void LocalToGeneralId(wxCommandEvent& event);
798  void GeneralToLocalId(wxCommandEvent& event);
799  void RemoveGeneralId( wxCommandEvent& event );
800  void RemoveUnnecessaryExceptions(wxCommandEvent& event);
801  void EditHistory( wxCommandEvent& event );
802  void ConvertToDelayedGenProdSetQuals( wxCommandEvent& event);
803  void ConvertRptUnitRangeToLoc( wxCommandEvent& event);
804  void ReorderSeqById( wxCommandEvent& event);
805  void LinkmRNACDS( wxCommandEvent& event );
806  void JustRemoveProteins( wxCommandEvent& event );
807  void RemoveProteinsAndRenormalizeNucProtSets( wxCommandEvent& event );
808  void RemoveOrphanedProteins( wxCommandEvent& event );
809  void GeneFeatFromXrefs( wxCommandEvent& event );
810  void GeneXrefsFromFeats( wxCommandEvent& event );
811  void RemoveAllGeneXrefs( wxCommandEvent& event );
812  void RemoveUnnecessaryGeneXrefs( wxCommandEvent& event );
813  void RemoveNonsuppressingGeneXrefs( wxCommandEvent& event );
814  void RemoveOrphanLocusGeneXrefs( wxCommandEvent& event );
815  void RemoveOrphanLocus_tagGeneXrefs( wxCommandEvent& event );
816  void RemoveGeneXrefs( wxCommandEvent& event );
817  void ExtendCDS( wxCommandEvent& event );
818  void TruncateCDS( wxCommandEvent& event );
819  void ExtendCDSToStop( wxCommandEvent& event );
820  void RecomputeIntervalsAndUpdateGenes(wxCommandEvent& event);
821  void RecomputeIntervals(wxCommandEvent& event);
822  void FixProductNamesDefault( wxCommandEvent& event );
823  void FixProductNamesOptions( wxCommandEvent& event );
824  void BulkApplyGenCode( wxCommandEvent& event );
825  void EditSeqEndsWithAlign( wxCommandEvent& event );
826  void EditSequenceEnds( wxCommandEvent& event );
827  void UpdateAlign( wxCommandEvent& event );
828  void CreateProteinId( wxCommandEvent& event );
829  void CreateLocusTagGene( wxCommandEvent& event );
830  void NormalizeGeneQuals(wxCommandEvent& event);
831  void GenusSpeciesFixup( wxCommandEvent& event );
832  void CountryConflict( wxCommandEvent& event );
833  void AddSecondary( wxCommandEvent& event );
834  void PackageFeaturesOnParts( wxCommandEvent& event );
835  void ShowFeatureTable ( wxCommandEvent& event );
836  void SaveDescriptors( wxCommandEvent& event );
837  void CreateSeqHistForTpaDetailed( wxCommandEvent& event );
838  void CreateSeqHistForTpa( wxCommandEvent& event );
839  void RemoveSeqHistAssembly( wxCommandEvent& event );
840  void CompareWithBiosample( wxCommandEvent& event );
841  void CompareWithBiosampleFirstOnly( wxCommandEvent& event );
842  void BarcodeTool( wxCommandEvent& event );
843  void ApplyFBOL(wxCommandEvent& event);
844  void RestoreLocalFile ( wxCommandEvent& event );
845  void FarPointerSeq( wxCommandEvent& event );
846  void ConvertBadCdsAndRnaToMiscFeat(wxCommandEvent& event);
847  void EditCdsFrame(wxCommandEvent& event);
848  void RestoreRNAediting(wxCommandEvent& event);
849  void ViewSortedProteins(wxCommandEvent& event);
850  void ConsolidateLikeModsWithSemicolon(wxCommandEvent& event);
851  void ConsolidateLikeModsWithoutSemicolon(wxCommandEvent& event);
852  void ConvertSecondProtNameToDesc(wxCommandEvent& event);
853  void ConvertDescToSecondProtName(wxCommandEvent& event);
854  void ConvertDescToFeatComment(wxCommandEvent& event);
855  void ConvertDescToFeatSource(wxCommandEvent& event);
856  void ConvertDescToFeatPub(wxCommandEvent& event);
857  void ConvertDescToFeatPubConstraint(wxCommandEvent& event);
858  void ConvertFeatToDescComment(wxCommandEvent& event);
859  void ConvertFeatToDescSource(wxCommandEvent& event);
860  void ConvertFeatToDescPub(wxCommandEvent& event);
861  void Duplicate(wxCommandEvent& event);
862  void ExportStructuredCommentsTable(wxCommandEvent& evt);
863  void LoadStructComments(wxCommandEvent& event);
864  void CorrectIntervalOrder( wxCommandEvent& event );
865  void SuspectProductRulesEditor(wxCommandEvent& event);
866  void CheckForMixedStrands(wxCommandEvent& event);
867  void EnableHupId(wxCommandEvent& event);
868  void IndexerTypeSelection(wxCommandEvent& event);
869  void FixForTransSplicing(wxCommandEvent& evt);
870  void RemoveDuplicateGoTerms(wxCommandEvent& evt);
871  void Help(wxCommandEvent& evt);
872  void UpdateTargetedLocusName(wxCommandEvent& evt);
873 
874 protected:
875  void x_OnSelectionEvent(CEvent* event);
876 
877 private:
878  ICommandProccessor* m_CmdProccessor;
879  CSeq_entry_Handle m_TopSeqEntry;
880  wxString m_WorkDir;
881  bool m_disable_hup_check;
882  bool m_disable_id_check;
883  CConstRef<CSeq_submit> m_SeqSubmit;
884  IWorkbench* m_Workbench;
885  TConstScopedObjects m_SelObjects;
886  vector<CRef<CSeq_loc> > m_CachedSelectedLocations;
887  bool m_attached;
888  bool m_IsAa;
889  bool m_IsSeq;
890  void x_SetUpTSEandUnDoManager(IWorkbench* wb);
891  vector<CRef<CSeq_loc> > &x_GetSelectedLocations();
892  void x_CacheSelectedLocations();
893  CSeq_align::TDim x_FindRelevantAlignRow(const CSeq_align& align, const CSeq_id* id);
894  bool x_IsLocationOkForFeatCmd(CSeqFeatData::ESubtype subtype, CRef<CSeq_loc> loc);
895  void SaveSettings(const string &regpath, wxWindow *dlg) const;
896  void LoadSettings(const string &regpath, wxWindow *dlg);
897  CRef<CSeq_loc> GetFeatureLocation(CSeqFeatData::ESubtype subtype);
898 };
899 
900 wxEvtHandler* CSeqEditPackage::GetEventHandler()
901 {
902  return new CSequenceEditingEventHandler(m_Workbench);
903 }
904 
905 CSequenceEditingEventHandler::CSequenceEditingEventHandler(IWorkbench* wb)
906 {
907  m_TopSeqEntry.Reset();
908  m_CmdProccessor = NULL;
909  m_Workbench = wb;
910  m_attached = false;
911  m_disable_hup_check = false;
912  m_disable_id_check = false;
913  wxWindow* main_window = NULL;
914  CWorkbench* wb_frame = dynamic_cast<CWorkbench*>(m_Workbench);
915  if (wb_frame)
916  main_window = wb_frame->GetMainWindow();
917  CEditingBtnsPanel::GetInstance(main_window, m_Workbench, true);
918 }
919 
920 CSequenceEditingEventHandler::~CSequenceEditingEventHandler()
921 {
922  if (m_Workbench && m_attached)
923  {
924  CSelectionService* service = m_Workbench->GetServiceByType<CSelectionService>();
925  if (service)
926  {
927  service->RemoveListener(this);
928  m_attached = false;
929  }
930  }
931 }
932 
933 void CSequenceEditingEventHandler::x_OnSelectionEvent(CEvent* event)
934 {
935  m_SelObjects.clear();
936  CSelectionService* service = m_Workbench->GetServiceByType<CSelectionService>();
937  if (service) {
938  service->GetActiveObjects(m_SelObjects);
939  if (m_SelObjects.empty())
940  {
941  GetViewObjects(m_Workbench, m_SelObjects);
942  }
943  x_CacheSelectedLocations();
944  }
945 }
946 
947 void CSequenceEditingEventHandler::x_SetUpTSEandUnDoManager(IWorkbench* wb)
948 {
949  m_TopSeqEntry.Reset();
950  m_WorkDir.Clear();
951  m_SeqSubmit.Reset(NULL);
952  m_CmdProccessor = NULL;
953  if (!wb) return;
954  if (!m_attached)
955  {
956  m_SelObjects.clear();
957  CSelectionService* service = wb->GetServiceByType<CSelectionService>();
958  if (service)
959  {
960  service->AddListener(this);
961  service->GetActiveObjects(m_SelObjects);
962  if (m_SelObjects.empty())
963  {
964  GetViewObjects(m_Workbench, m_SelObjects);
965  }
966  x_CacheSelectedLocations();
967  m_attached = true;
968  }
969  }
970 
971  TConstScopedObjects &objects = m_SelObjects;
972  if (objects.empty()) return;
973  NON_CONST_ITERATE (TConstScopedObjects, it, objects) {
974  const CSeq_submit* sub = dynamic_cast<const CSeq_submit*>((*it).object.GetPointer());
975  if (sub) {
976  m_SeqSubmit.Reset(sub);
977  }
978  if (!m_TopSeqEntry && it->object && it->scope) {
979  CSeq_entry_Handle seh = GetTopSeqEntryFromScopedObject(*it);
980  if (seh) {
981  m_TopSeqEntry = seh;
982  if (m_SeqSubmit) {
983  break;
984  }
985  }
986  }
987  }
988  if (!m_TopSeqEntry) return;
989  CIRef<CProjectService> srv = wb->GetServiceByType<CProjectService>();
990  if (srv)
991  {
992  CRef<CGBWorkspace> ws = srv->GetGBWorkspace();
993  if (!ws) return;
994 
995  CGBDocument* doc = dynamic_cast<CGBDocument*>(ws->GetProjectFromScope(m_TopSeqEntry.GetScope()));
996  if (doc) {
997  m_CmdProccessor = &doc->GetUndoManager();
998  m_WorkDir = doc->GetWorkDir();
999  }
1000  }
1001 
1002 }
1003 
1004 vector<CRef<CSeq_loc> >& CSequenceEditingEventHandler::x_GetSelectedLocations()
1005 {
1006  return m_CachedSelectedLocations;
1007 }
1008 
1009 
1010 void CSequenceEditingEventHandler::x_CacheSelectedLocations()
1011 {
1012  m_CachedSelectedLocations.clear();
1013  m_IsSeq = false;
1014 
1015  if (!m_Workbench) {
1016  return;
1017  }
1018 
1019  TConstScopedObjects &objects = m_SelObjects;
1020  if (objects.empty()) return;
1021  size_t count = 0;
1022  NON_CONST_ITERATE (TConstScopedObjects, it, objects) {
1023  const CObject* ptr = it->object.GetPointer();
1024 
1025  const CSeq_feat* seqfeat = dynamic_cast<const CSeq_feat*>(ptr);
1026  const CSeq_loc* seqloc = dynamic_cast<const CSeq_loc*>(ptr);
1027  const CBioseq* bioseq = dynamic_cast<const CBioseq*>(ptr);
1028  const CSeqdesc* seqdesc = dynamic_cast<const CSeqdesc*>(ptr);
1029  const CPubdesc* pubdesc = dynamic_cast<const CPubdesc*>(ptr);
1030 
1031  const CSeq_annot* annot = dynamic_cast<const CSeq_annot*>(ptr);
1032  const CBioseq_set* bioseqset = dynamic_cast<const CBioseq_set*>(ptr);
1033 
1034  const CSeq_align* align = dynamic_cast<const CSeq_align*>(ptr);
1035  const CSeq_id* seq_id = dynamic_cast<const CSeq_id*>(ptr);
1036 
1037  if (seqfeat) {
1038  if (seqfeat->IsSetLocation()) {
1039  CRef<CSeq_loc> loc(new CSeq_loc());
1040  loc->Assign(seqfeat->GetLocation());
1041  m_CachedSelectedLocations.push_back(loc);
1042  }
1043  m_IsSeq = false;
1044  } else if (seq_id && !CSeqUtils::IsVDBAccession(seq_id->GetSeqIdString())) {
1045  CBioseq_Handle bsh = it->scope->GetBioseqHandle(*seq_id);
1046  if (bsh) {
1047  CRef<CSeq_id> new_id(new CSeq_id());
1048  new_id->Assign(*seq_id);
1049  CRef<CSeq_loc> loc(new CSeq_loc(*new_id, 0, bsh.GetInst_Length() - 1));
1050  m_CachedSelectedLocations.push_back(loc);
1051  m_IsSeq = true;
1052  if (count == 0)
1053  m_IsAa = bsh.IsAa();
1054  }
1055  } else if (seqloc) {
1056 
1057  if (seqloc->IsWhole()) {
1058  CRef<CSeq_id> new_id(new CSeq_id());
1059  new_id->Assign(seqloc->GetWhole());
1060  CBioseq_Handle bsh = it->scope->GetBioseqHandle(*new_id);
1061  if (bsh) {
1062  CRef<CSeq_loc> loc(new CSeq_loc(*new_id, 0, bsh.GetInst_Length() - 1));
1063  m_CachedSelectedLocations.push_back(loc);
1064  }
1065  } else {
1066  CRef<CSeq_loc> loc(new CSeq_loc());
1067  loc->Assign(*seqloc);
1068  m_CachedSelectedLocations.push_back(loc);
1069  }
1070  CBioseq_Handle bsh = it->scope->GetBioseqHandle(*seqloc);
1071  if (bsh)
1072  {
1073  m_IsSeq = true;
1074  if (count == 0)
1075  m_IsAa = bsh.IsAa();
1076  }
1077  count++;
1078  } else if (bioseq) {
1079  CRef<CSeq_loc> loc(new CSeq_loc());
1080  loc->SetInt().SetId().Assign(*(bioseq->GetId().front()));
1081  loc->SetInt().SetFrom(0);
1082  loc->SetInt().SetTo(bioseq->GetLength() - 1);
1083  m_CachedSelectedLocations.push_back(loc);
1084  m_IsSeq = true;
1085  if (count == 0)
1086  m_IsAa = bioseq->IsAa();
1087  } else if (seqdesc) {
1088  CSeq_entry_Handle seh = edit::GetSeqEntryForSeqdesc(it->scope, *seqdesc);
1089  if (!seh) {
1090  CScope::TTSE_Handles tses;
1091  m_TopSeqEntry.GetScope().GetAllTSEs(tses, CScope::eAllTSEs);
1092  if (!tses.empty())
1093  seh = tses.front();
1094  }
1095 
1096  CBioseq_CI bi(seh);
1097  while (bi) {
1098  CRef<CSeq_loc> loc(new CSeq_loc());
1099  loc->SetInt().SetId().Assign(*(bi->GetId().front().GetSeqId()));
1100  loc->SetInt().SetFrom(0);
1101  loc->SetInt().SetTo(bi->GetInst_Length() - 1);
1102  m_CachedSelectedLocations.push_back(loc);
1103  ++bi;
1104  }
1105  m_IsSeq = false;
1106  } else if (pubdesc) {
1107  CSeq_entry_Handle seh = GetSeqEntryForPubdesc(it->scope, *pubdesc);
1108  CBioseq_CI bi(seh);
1109  while (bi) {
1110  CRef<CSeq_loc> loc(new CSeq_loc());
1111  loc->SetInt().SetId().Assign(*(bi->GetId().front().GetSeqId()));
1112  loc->SetInt().SetFrom(0);
1113  loc->SetInt().SetTo(bi->GetInst_Length() - 1);
1114  m_CachedSelectedLocations.push_back(loc);
1115  ++bi;
1116  }
1117  m_IsSeq = false;
1118  } else if (annot) {
1119  if (annot->IsSetData() &&
1120  annot->GetData().IsFtable() &&
1121  !annot->GetData().GetFtable().empty() &&
1122  annot->GetData().GetFtable().front()->IsSetLocation()) {
1123 
1124  CRef<CSeq_loc> loc(new CSeq_loc());
1125  loc->Assign(annot->GetData().GetFtable().front()->GetLocation());
1126  m_CachedSelectedLocations.push_back(loc);
1127  }
1128  m_IsSeq = false;
1129  } else if (bioseqset) {
1130  if (bioseqset->IsSetClass() && bioseqset->GetClass() == CBioseq_set::eClass_nuc_prot)
1131  {
1132  const CBioseq& bseq = bioseqset->GetNucFromNucProtSet();
1133  CRef<CSeq_loc> loc(new CSeq_loc());
1134  loc->SetInt().SetId().Assign(*(bseq.GetId().front()));
1135  loc->SetInt().SetFrom(0);
1136  loc->SetInt().SetTo(bseq.GetLength() - 1);
1137  m_CachedSelectedLocations.push_back(loc);
1138  }
1139  else
1140  {
1141  CSeq_entry* seq = bioseqset->GetParentEntry();
1142  if (seq)
1143  {
1144  m_CachedSelectedLocations.clear();
1145  }
1146  }
1147  m_IsSeq = false;
1148  } else if (align) {
1149  CSeq_align::TDim entry_row = x_FindRelevantAlignRow(*align, dynamic_cast<const CSeq_id*>(objects.back().object.GetPointer()));
1150  CRef<CSeq_loc> loc = align->CreateRowSeq_loc(entry_row);
1151  m_CachedSelectedLocations.push_back(loc);
1152  m_IsSeq = true;
1153  if (count == 0)
1154  m_IsAa = it->scope->GetBioseqHandle(*loc).IsAa();
1155  }
1156 
1157  }
1158  if (count > 1)
1159  {
1160  m_IsSeq = false;
1161  }
1162  if (!m_TopSeqEntry && !m_CachedSelectedLocations.empty()) {
1163  CBioseq_Handle bsh = objects.front().scope->GetBioseqHandle(*(m_CachedSelectedLocations.front()->GetId()));
1164  if (bsh)
1165  m_TopSeqEntry = bsh.GetTopLevelEntry();
1166  }
1167 }
1168 
1169 CSeq_align::TDim CSequenceEditingEventHandler::x_FindRelevantAlignRow(const CSeq_align& align, const CSeq_id* id)
1170 {
1171  // the relevant row corresponds to the subject sequence, which is the second one by default
1172  CSeq_align::TDim row = 1;
1173  if (align.GetSegs().IsSpliced()) {
1174  // looking for genomic sequence, which is always 1 in spliced-segs
1175  row = 1;
1176  }
1177  if (id)
1178  {
1179  CSeq_align::TDim num_rows = align.CheckNumRows();
1180  for (CSeq_align::TDim i = 0; i < num_rows; i++)
1181  {
1182  const CSeq_id &row_id = align.GetSeq_id(i);
1183  if (row_id.Match(*id))
1184  {
1185  row = i;
1186  break;
1187  }
1188  }
1189  }
1190  return row;
1191 }
1192 
1193 void CSequenceEditingEventHandler::IsObjectSelected(wxUpdateUIEvent& event)
1194 {
1195  x_SetUpTSEandUnDoManager(m_Workbench);
1196  event.Enable(m_TopSeqEntry && m_CmdProccessor);
1197 }
1198 
1199 bool CSequenceEditingEventHandler::TestHupIdEnabled()
1200 {
1201  if (m_TopSeqEntry && !m_disable_hup_check)
1202  {
1203  CRef<CSeq_id> id(new CSeq_id("MF358689", CSeq_id::fParse_Default));
1204  CBioseq_Handle bsh;
1205  try
1206  {
1207  bsh = m_TopSeqEntry.GetScope().GetBioseqHandle(*id);
1208  }
1209  catch (const exception&)
1210  {
1211  wxMessageBox(wxT("Error while attempting to connect to the ID server, restarting gbench is recommended"), wxT("Error"), wxOK | wxICON_ERROR, NULL);
1212  m_disable_hup_check = true;
1213  }
1214  if (bsh)
1215  return true;
1216  }
1217  return false;
1218 }
1219 
1220 void CSequenceEditingEventHandler::IsHupIdEnabled(wxUpdateUIEvent& event)
1221 {
1222  x_SetUpTSEandUnDoManager(m_Workbench);
1223  if (m_TopSeqEntry && m_CmdProccessor)
1224  {
1225  event.Enable(true);
1226  event.Check(TestHupIdEnabled());
1227  return;
1228  }
1229  event.Check(false);
1230  event.Enable(false);
1231 }
1232 
1233 void CSequenceEditingEventHandler::IsLocationSelected(wxUpdateUIEvent& evt)
1234 {
1235  vector<CRef<CSeq_loc> >& locs = x_GetSelectedLocations();
1236 
1237  if (!RunningInsideNCBI() && (m_TopSeqEntry || !locs.empty()))
1238  {
1239  evt.Enable(true);
1240  return;
1241  }
1242 
1243  if (!m_IsSeq)
1244  {
1245  evt.Enable(false);
1246  return;
1247  }
1248 
1249 
1250  bool rval = false;
1251  bool ok_for_something = false;
1252  CSeqFeatData::ESubtype subtype = CBioseqEditor::GetFeatTypeFromCmdID(evt.GetId());
1253  ITERATE(vector<CRef<CSeq_loc> >, lit, locs) {
1254  if (x_IsLocationOkForFeatCmd(subtype, *lit)) {
1255  rval = true;
1256  ok_for_something |= true;
1257  break;
1258  }
1259  if (x_IsLocationOkForFeatCmd(CSeqFeatData::eSubtype_gene, *lit)) {
1260  ok_for_something |= true;
1261  }
1262  if (x_IsLocationOkForFeatCmd(CSeqFeatData::eSubtype_prot, *lit)) {
1263  ok_for_something |= true;
1264  }
1265 
1266  }
1267  evt.Enable(rval);
1268 
1269  if (!ok_for_something && m_TopSeqEntry && !m_disable_id_check)
1270  {
1271  CRef<CSeq_id> id(new CSeq_id("U12345", CSeq_id::fParse_Default));
1272  CBioseq_Handle bsh;
1273  try
1274  {
1275  bsh = m_TopSeqEntry.GetScope().GetBioseqHandle(*id);
1276  }
1277  catch (const exception&)
1278  {
1279  wxMessageBox(wxT("Unable to connect to the ID server, restarting gbench is recommended"), wxT("Error"), wxOK | wxICON_ERROR, NULL);
1280  m_disable_id_check = true;
1281  }
1282  }
1283 }
1284 
1285 
1286 
1287 // Implementation
1288 vector<CUICommand*> CSeqEditPackage::GetCommands()
1289 {
1290  vector<CUICommand*> commands;
1291  commands.push_back(new CUICommand(eCmdRemoveDescriptors, "Remove Descriptors", "Remove Descriptors from Selected Object", "RDSO"));
1292  commands.push_back(new CUICommand(eCmdRemoveFeatures, "Remove Features", "Remove Features from Selected Object", "RFSO"));
1293  commands.push_back(new CUICommand(eCmdFixForTransSplicing, "Fix For Trans-splicing", "Fix For Trans-splicing", "FFTS"));
1294  commands.push_back(new CUICommand(eCmdRemoveUnindexedFeatures, "Remove Unindexed Features", "Remove Unindexed Features", "RUIF"));
1295  commands.push_back(new CUICommand(eCmdApplyIndexerComments, "Apply Indexer Comments", "Apply Indexer Comments", "AICS"));
1296  commands.push_back(new CUICommand(eCmdRemoveSeqAnnotIds, "Remove Seq-annot IDs", "Remove Seq-annot IDs from Selected Object", "RSAID"));
1297  commands.push_back(new CUICommand(eCmdRemoveCddFeatDbxref, "Remove All CDD Features and DBxrefs", "Remove All CDD Features and Dbxrefs", "RACFAD"));
1298  commands.push_back(new CUICommand(eCmdRemoveBankitComment, "Remove Bankit Comments", "Remove Bankit Comments from Selected Object", "RBC"));
1299  commands.push_back(new CUICommand(eCmdRemoveDuplicateStructuredComments, "Remove Duplicate Structured Comments", "Remove Duplicate Structured Comments from Selected Object", "RDSC"));
1300  commands.push_back(new CUICommand(eCmdRemoveSequencesFromAlignments, "Remove Sequences from Alignments", "Remove Sequences From Alignments from Selected Object", "RSFASO"));
1301  commands.push_back(new CUICommand(eCmdRemoveSequences, "Remove Sequences from Record", "Remove Sequences from Selected Object", "RSSO"));
1302  commands.push_back(new CUICommand(eCmdRemoveSequences_ext, "Remove Sequences", "Remove Sequences from Selected Object", "RSSO"));
1303  commands.push_back(new CUICommand(eCmdJustRemoveProteins, "Just Remove Proteins", "Just Remove Proteins", "JRP"));
1304  commands.push_back(new CUICommand(eCmdRemoveProteinsAndRenormalizeNucProtSets, "And Renormalize Nuc-Prot Sets", "And Renormalize Nuc-Prot Sets", "RPRNPS"));
1305  commands.push_back(new CUICommand(eCmdRemoveOrphanedProteins, "Orphaned Proteins", "Orphaned Proteins", "ROP"));
1306  commands.push_back(new CUICommand(eCmdRemoveSet,"RemoveSet", "RemoveSet","RSET"));
1307  commands.push_back(new CUICommand(eCmdRemoveSetsFromSet,"Remove Sets in Set", "Remove Sets in Set", "RSIS"));
1308  commands.push_back(new CUICommand(eCmdRevCompSequences, "Bioseq RevComp by ID", "Reverse Complement Sequences from Selected Object", "RVCS"));
1309  commands.push_back(new CUICommand(eCmdRevCompSequences_ext, "Reverse Complement Sequences by Sequence ID", "Reverse Complement Sequences from Selected Object", "RVCS"));
1310  commands.push_back(new CUICommand(eCmdBioseqFeatsRevComp, "BioseqFeatsRevComp", "Reverse Complement Sequences and Features", "RVCSF"));
1311  commands.push_back(new CUICommand(eCmdBioseqOnlyRevComp,"BioseqOnlyRevComp","Reverse Complement Sequences and Graphs", "RVCSG"));
1312  commands.push_back(new CUICommand(eCmdUnculTaxTool,"Uncultured Tax Tool", "Uncultured Tax Tool", "UCTT"));
1313  commands.push_back(new CUICommand(eCmdMergeBiosources, "Merge Multiple BioSources On Sequence", "Merge Multiple BioSources On Sequence", "MMBS"));
1314  commands.push_back(new CUICommand(eCmdCompareWithBiosample, "All Records", "Compare with Biosample", "CWBS"));
1315  commands.push_back(new CUICommand(eCmdCompareWithBiosampleFirstOnly, "First Record Only", "Compare with Biosample", "CWBSFO"));
1316  commands.push_back(new CUICommand(eCmdConsolidateLikeModsWithSemicolon, "With semicolons", "With semicolons", "CLMS"));
1317  commands.push_back(new CUICommand(eCmdConsolidateLikeModsWithoutSemicolon, "Without semicolons", "Without semicolons", "CLMWS"));
1318  commands.push_back(new CUICommand(eCmdBarcodeTool, "BARCODE Discrepancy Tool", "BARCODE Discrepancy Tool", "BDISTL"));
1319  commands.push_back(new CUICommand(eCmdApplyFBOL, "Apply FBOL Dbxrefs", "Apply FBOL Dbxrefs", "AFBOL"));
1320  commands.push_back(new CUICommand(eCmdEditSequence, "Edit Sequence", "Edit Sequence", "EDSEQ"));
1321  commands.push_back(new CUICommand(eCmdAlignmentAssistant, "Alignment Assistant", "Alignment Assistant", "ALAS"));
1322  commands.push_back(new CUICommand(eCmdRemoveAlignments, "Remove Alignments", "Remove Alignments from Selected Object", "RASO"));
1323  commands.push_back(new CUICommand(eCmdRemoveGraphs, "Remove Graphs", "Remove Graphs from Selected Object", "RGSO"));
1324  commands.push_back(new CUICommand(eCmdRemoveGenomeProjectId, "Remove All Genome Project IDs", "Remove All Genome Project Ids from Selected Object", "RGPIDSO"));
1325  commands.push_back(new CUICommand(eCmdRemoveEmptyGenomeProjectId, "Remove Empty Genome Project IDs", "Remove Empty Genome Project Ids from Selected Object", "REGPIDSO"));
1326  commands.push_back(new CUICommand(eCmdTaxFixCleanup, "Tax_fix/Cleanup", "Fix Taxonomy and Perform Basic and Extended Cleanup", "TFCU"));
1327  commands.push_back(new CUICommand(eCmdTaxFixCleanup_ext, "Lookup Taxonomy and Cleanup Record", "Lookup Taxonomy and Cleanup Record", "TFCU"));
1328  commands.push_back(new CUICommand(eCmdSpecificHostCleanup, "Specific Host Cleanup", "Specific Host Cleanup", "SHCU"));
1329  commands.push_back(new CUICommand(eCmdExtendedCleanup, "SeriousSeqEntryCleanup", "Perform Basic and Extended Cleanup", "SSEC"));
1330  commands.push_back(new CUICommand(eCmdFixNonReciprocalLinks, "Fix Non-Reciprocal Links", "Fix Non-Reciprocal Feature ID Links", "FNRL"));
1331  commands.push_back(new CUICommand(eCmdDisableStrainForwarding, "Globally Disable Strain Forwarding", "Globally Disable Strain Forwarding", "GDSF"));
1332  commands.push_back(new CUICommand(eCmdEnableStrainForwarding, "Globally Enable Strain Forwarding", "Globally Disable Strain Forwarding", "GESF"));
1333  commands.push_back(new CUICommand(eCmdEditPubs, "Edit Publications", "Edit Publications", "EP"));
1334  commands.push_back(new CUICommand(eCmdGlobalPubmedIdLookup, "Global PubMedId Lookup", "Global PubMedId Lookup", "GPMIDL"));
1335  commands.push_back(new CUICommand(eCmdFixCapitalizationAll, "Fix All Capitalization", "Fix All Capitalization for Selected Object", "FACSO"));
1336  commands.push_back(new CUICommand(eCmdFixCapitalizationAuthors, "Fix Capitalization in Authors", "Fix Capitalization in Authors for Selected Object", "FCASO"));
1337  commands.push_back(new CUICommand(eCmdFixCapitalizationTitles, "Fix Capitalization in Titles", "Fix Capitalization in Titles for Selected Object", "FCTSO"));
1338  commands.push_back(new CUICommand(eCmdFixCapitalizationAffiliation, "Fix Capitalization in Affiliations", "Fix Capitalization in Affiliations for Selected Object", "FCAfSO"));
1339  commands.push_back(new CUICommand(eCmdFixCapitalizationCountry, "Fix Capitalization in Countries", "Fix Capitalization in Countries for Selected Object", "FCCSO"));
1340  commands.push_back(new CUICommand(eCmdRemoveUnpublishedPublications, "Remove Unpublished Publications", "Remove Unpublished Publications from Selected Object", "RUPSO"));
1341  commands.push_back(new CUICommand(eCmdRemoveInPressPublications, "Remove In Press Publications", "Remove In Press Publications from Selected Object", "RIPSO"));
1342  commands.push_back(new CUICommand(eCmdRemovePublishedPublications, "Remove Published Publications", "Remove Published Publications from Selected Object", "RPPSO"));
1343  commands.push_back(new CUICommand(eCmdRemoveCollidingPublications, "Remove Colliding Publications", "Remove Colliding Publications from Selected Object", "RCPSO"));
1344  commands.push_back(new CUICommand(eCmdRemoveAllPublications, "Remove All Publications", "Remove All Publications from Selected Object", "RAPSO"));
1345  commands.push_back(new CUICommand(eCmdRemoveAuthorConsortiums, "Remove Author Consortiums", "Remove Author Consortiums from Selected Object", "RACSO"));
1346  commands.push_back(new CUICommand(eCmdReverseAuthorNames, "Reverse Author Names", "Reverse Author Names for Selected Object", "RANSO"));
1347  commands.push_back(new CUICommand(eCmdStripAuthorSuffixes, "Strip Author Suffixes", "Strip Author Suffixes from Selected Object", "SASSO"));
1348  commands.push_back(new CUICommand(eCmdTruncateAuthorMiddleInitials, "Truncate Author Middle Initials", "Truncate Author Middle Initials from Selected Object", "TAMISO"));
1349  commands.push_back(new CUICommand(eCmdConvertAuthorToConstortiumWhereLastName, "Convert Author to Consortium where Last Name Contains Consortium", "Convert Author To Consortium Where Last Name Contains Consortium For Selected Object", "CATCWLSO"));
1350  commands.push_back(new CUICommand(eCmdConvertAuthorToConsortiumAll, "Convert All Authors to Consortium", "Convert All Authors To Consortium For Selected Object", "CAATCSO"));
1351  commands.push_back(new CUICommand(eCmdAddCitSubForUpdate, "Add Cit-sub for Update", "Add Cit-sub For Update for Selected Object", "ACSFUSO"));
1352  commands.push_back(new CUICommand(eCmdFixUsaAndStates, "Fix USA and States", "Fix USA and States for Selected Object", "FUSSO"));
1353  commands.push_back(new CUICommand(eCmdRetranslateCDSObeyStop, "Obey Stop Codon", "Retranslate CDS, obey stop codon", "RCDSOSC"));
1354  commands.push_back(new CUICommand(eCmdRetranslateCDSIgnoreStopExceptEnd, "Ignore Stop Codon Except at End of Complete CDS", "Retranslate CDS, Ignore Stop Codon Except at End of Complete CDS", "RCDSISCEAE"));
1355  commands.push_back(new CUICommand(eCmdRetranslateCDSIgnoreStopExceptEnd_ext, "Retranslate Coding Regions", "Retranslate CDS, Ignore Stop Codon Except at End of Complete CDS", "RCDSISCEAE"));
1356  commands.push_back(new CUICommand(eCmdRetranslateCDSChooseFrame, "Choose Frame with No Stop Codon", "Retranslate CDS, Choose Frame With No Stop Codon", "RCDSCF"));
1357  commands.push_back(new CUICommand(eCmdEditCdsFrame, "Edit Coding Region Frame", "Edit Coding Region Frame", "ECRF"));
1358  commands.push_back(new CUICommand(eCmdRestoreRNAediting, "Restore RNA Editing of CDS", "Restore RNA Editing", "RRNAE"));
1359  commands.push_back(new CUICommand(eCmdResynchronizePartialsCDS, "Resynchronize CDS Partials", "Resynchronize CDS Partials", "RCDSP"));
1360  commands.push_back(new CUICommand(eCmdAddTranslExcept, "Add Translational Exceptions with Comment", "Add Translational Exceptions with Comment", "ATEWC"));
1361  commands.push_back(new CUICommand(eCmdRemoveAllStructuredComments,"Remove All Structured Comments","Remove All Structured Comments from Selected Object","RASCSO"));
1362  commands.push_back(new CUICommand(eCmdRemoveEmptyStructuredComments,"Remove Empty Structured Comments","Remove Empty Structured Comments from Selected Object","RESCSO"));
1363  commands.push_back(new CUICommand(eCmdModifyStructuredComment,"Remove Structured Comment Field","Remove Structured Comment Field from Selected Object","RSCFSO"));
1364  commands.push_back(new CUICommand(eCmdSetGlobalRefGeneStatus, "Set Global RefGene Status", "Set Global RefGene Status", "SGRGS"));
1365  commands.push_back(new CUICommand(eCmdClearKeywords, "Clear Keywords", "Clear Keywords", "CLKW"));
1366  commands.push_back(new CUICommand(eCmdClearNomenclature, "Clear Nomenclature", "Clear Nomenclature", "CLNMC"));
1367  commands.push_back(new CUICommand(eCmdConvertToDelayedGenProdSetQuals,"Convert to Delayed Gen-Prod-Set Qualifiers", "Convert to Delayed Gen-Prod-Set Qualifiers", "CDGPSQ"));
1368  commands.push_back(new CUICommand(eCmdConvertRptUnitRangeToLoc, "Convert Repeat-region Rpt-unit-range to Location", "Convert repeat-region rpt-unit-range to location", "CRRL"));
1369  commands.push_back(new CUICommand(eCmdRemoveStructuredCommentKeyword,"Remove Structured Comment Keyword","Remove Structured Comment Keyword from Selected Object","RSCKSO"));
1370  commands.push_back(new CUICommand(eCmdAddStructuredCommentKeyword ,"Add Structured Comment Keyword","Add Structured Comment Keyword to Selected Object","ASCKSO"));
1371  commands.push_back(new CUICommand(eCmdAddKeywordGDS,"GDS", "Add Keyword GDS", "AKG"));
1372  commands.push_back(new CUICommand(eCmdAddKeywordTPA_inferential,"TPA:inferential","Add Keyword TPA:inferential", "AKTI"));
1373  commands.push_back(new CUICommand(eCmdAddKeywordTPA_experimental,"TPA:experimental","Add Keyword TPA:experimental","AKTE"));
1374  commands.push_back(new CUICommand(eCmdAddKeywordTPA_assembly,"TPA:assembly","Add Keyword TPA:assembly","AKTA"));
1375  commands.push_back(new CUICommand(eCmdAddKeywordWithConstraint, "With Constraint", "Add Keyword With Constraint", "AKWC"));
1376  commands.push_back(new CUICommand(eCmdAddGenomeAssemblyStructuredComment, "Add Genome Assembly Structured Comment", "Add Genome Assembly Structured Comment", "AGASC"));
1377  commands.push_back(new CUICommand(eCmdAddAssemblyStructuredComment, "Add Assembly Structured Comment", "Add Assembly Structured Comment", "AASC"));
1378  commands.push_back(new CUICommand(eCmdReorderStructuredComment,"Reorder Structured Comment","Reorder Structured Comment in Selected Object","RSCSO"));
1379  commands.push_back(new CUICommand(eCmdConvertComment,"Convert Structured Comment","Convert Structured Comment in Selected Object","CSCSO"));
1380  commands.push_back(new CUICommand(eCmdParseComment,"Parse Structured Comment","Parse Structured Comment in Selected Object","PSCSO"));
1381  commands.push_back(new CUICommand(eCmdExportStructuredCommentsTable, "Export Structured Comment Table", "Export Structured Comment Table", "ESCT"));
1382  commands.push_back(new CUICommand(eCmdLoadStructComments, "Load Structured Comments from Table", "Load Structured Comments from Table", "LSCT"));
1383  commands.push_back(new CUICommand(eCmdIllegalQualsToNote, "Convert Illegal Qualifiers to Note", "Convert Illegal Qualifiers to Note", "CIQN"));
1384  commands.push_back(new CUICommand(eCmdRmIllegalQuals,"Remove Illegal Qualifiers", "Remove Illegal Qualifiers", "RMIQ"));
1385  commands.push_back(new CUICommand(eCmdWrongQualsToNote,"Convert Wrong Qualifiers to Note", "Convert Wrong Qualifiers to Note", "CWQN"));
1386  commands.push_back(new CUICommand(eCmdConvertBadInference, "Convert Bad Inference Qualifiers to Notes", "Convert Bad Inference Qualifiers to Notes", "CBIN"));
1387  commands.push_back(new CUICommand(eCmdRmWrongQuals,"Remove Wrong Qualifiers", "Remove Wrong Qualifiers", "RMWQ"));
1388  commands.push_back(new CUICommand(eCmdRemoveDbXrefsCDS,"From CDSs", "Remove DbXrefs from CDSs","RMDBXR"));
1389  commands.push_back(new CUICommand(eCmdRemoveDbXrefsGenes,"From Genes", "Remove DbXrefs from Genes","RMDBXR"));
1390  commands.push_back(new CUICommand(eCmdRemoveDbXrefsRNA,"From RNAs", "Remove DbXrefs from RNAs","RMDBXR"));
1391  commands.push_back(new CUICommand(eCmdRemoveDbXrefsAllFeats,"From All Features", "Remove DbXrefs from All Features","RMDBXR"));
1392  commands.push_back(new CUICommand(eCmdRemoveDbXrefsBioSource,"From All BioSources","Remove DbXrefs from All BioSources", "RMDBXR"));
1393  commands.push_back(new CUICommand(eCmdRemoveDbXrefsBioSourceAndFeats, "From All Features and BioSources", "Remove DbXrefs from All Features and BioSources", "RMDBXR"));
1394  commands.push_back(new CUICommand(eCmdRemoveTaxonFeats, "From Features", "Remove Taxons From Features", "RMTFF"));
1395  commands.push_back(new CUICommand(eCmdRemoveTaxonFeatsAndBioSource, "From Features And BioSources", "Remove Taxons From Features And BioSources", "RMTFFBS"));
1396  commands.push_back(new CUICommand(eCmdGroupExplode, "Group Explode", "Group Explode", "GREX"));
1397  commands.push_back(new CUICommand(eCmdFindASN1, "Find ASN.1", "Find ASN.1", "FA1"));
1398  commands.push_back(new CUICommand(eCmdFuseFeatures, "Fuse Features", "Fuse Features", "FUFE"));
1399  commands.push_back(new CUICommand(eCmdFuseJoinsInLocs, "Fuse Joins in Locations", "Fuse Joins in Locations", "FJIL"));
1400  commands.push_back(new CUICommand(eCmdExplodeRNAFeats, "Explode RNA Features", "Explode RNA Features", "ERNAF"));
1401  commands.push_back(new CUICommand(eCmdAssignFeatureIds,"Assign Feature IDs", "Assign Feature IDs for Selected Object","AFIDSO"));
1402  commands.push_back(new CUICommand(eCmdClearFeatureIds,"Clear Feature IDs and Xrefs", "Clear Feature IDs for Selected Object","CFIDSO"));
1403  commands.push_back(new CUICommand(eCmdReassignFeatureIds,"Reassign Feature IDs", "Reassign Feature IDs for Selected Object","RFIDSO"));
1404  commands.push_back(new CUICommand(eCmdUniqifyFeatureIds,"Uniqify Feature IDs", "Uniqify Feature IDs for Selected Object","UFIDSO"));
1405  commands.push_back(new CUICommand(eCmdTrimJunkInPrimerSeqs,"Trim Junk in Primer Sequences","Trim Junk In Primer Seqs for Selected Object","TJIPSSO"));
1406  commands.push_back(new CUICommand(eCmdFixiInPrimerSeqs,"Fix i in Primer Sequences","Fix i in Primer Seqs for Selected Object","FIIPSSO"));
1407  commands.push_back(new CUICommand(eCmdPrefixAuthWithTax, "Prefix Authority with Organism", "Prefix Authority with Organism", "PAWO"));
1408  commands.push_back(new CUICommand(eCmdFocusSet, "Set", "BioSource is_focus is set", "SFSET"));
1409  commands.push_back(new CUICommand(eCmdFocusClear, "Clear", "BioSource is_focus is clear", "SFCLE"));
1410  commands.push_back(new CUICommand(eCmdSetTransgSrcDesc, "Set Transgenic on Source Descriptor", "Set Transgenic on Source Desc when Source Feat present", "STOSD"));
1411  commands.push_back(new CUICommand(eCmdSplitDblinkQuals, "Split DBLink Qualifiers at Commas", "Split DBLink Quals at Commas", "SDQAC"));
1412  commands.push_back(new CUICommand(eCmdFixOrgModInstitution,"Fix OrgMod Institution Code","Fix OrgMod Institution Code for Selected Object","FOMICSO"));
1413  commands.push_back(new CUICommand(eCmdFixStructuredVouchers, "Fix Structured Vouchers", "Fix Structured Vouchers", "FSTV"));
1414  commands.push_back(new CUICommand(eCmdSwapPrimerSeqName,"Swap Primer Sequence and Name","Swap Primer Seq and Name for Selected Object","SPSNSO"));
1415  commands.push_back(new CUICommand(eCmdMergePrimerSets,"Merge Primer Sets","Merge Primer Sets for Selected Object","MPSSO"));
1416  commands.push_back(new CUICommand(eCmdSplitPrimerSets,"Split Primer Sets by Position","Split Primer Sets by Position for Selected Object","SPSBPSO"));
1417  commands.push_back(new CUICommand(eCmdAppendModToOrg,"Append Modifier to Organism","Append Mod To Org for Selected Object","AMTOSO"));
1418  commands.push_back(new CUICommand(eCmdParseCollectionDateMonthFirst,"Parse Collection Date Month First","Parse Collection Date Month First for Selected Object","PCDMFSO"));
1419  commands.push_back(new CUICommand(eCmdParseCollectionDateDayFirst,"Parse Collection Date Day First","Parse Collection Date Day First for Selected Object","PCDDFSO"));
1420  commands.push_back(new CUICommand(eCmdCountryFixupCap,"Country Fixup Fix Capitalization after Colon","Country Fixup Fix Capitalization After Colon","CFFCAC"));
1421  commands.push_back(new CUICommand(eCmdCountryFixupNoCap,"Country Fixup Do Not Fix Capitalization after Colon","Country Fixup Do Not Fix Capitalization After Colon","CFDNFCAC"));
1422  commands.push_back(new CUICommand(eCmdVectorTrim, "Vector Search and Trim Tool", "Vector Search and Trim Tool", "VSTT"));
1423  commands.push_back(new CUICommand(eCmdSelectTarget, "Select Target", "Select Target", "ST"));
1424  commands.push_back(new CUICommand(eCmdSelectTarget_ext, "Select Specific Sequence by Sequence ID", "Select Specific Sequence by Sequence ID", "ST"));
1425  commands.push_back(new CUICommand(eCmdSelectFeature, "Select Features", "Select Features", "SF"));
1426  commands.push_back(new CUICommand(eCmdApplyCDS, "Add CDS", "Add CDS", "AC"));
1427  commands.push_back(new CUICommand(eCmdApplyAddRNA, "Add RNA", "Add RNA", "AR"));
1428  commands.push_back(new CUICommand(eCmdApplyAddOther, "Add Other Feature", "Add other Feature", "AOF"));
1429  commands.push_back(new CUICommand(eCmdApplyAddOther_ext, "Add Other Feature (Non CDS, RNA)", "Add other Feature", "AOF"));
1430  commands.push_back(new CUICommand(eCmdAddFeatureBetween, "Add Feature Between", "Add Feature Between", "AFB"));
1431  commands.push_back(new CUICommand(eCmdValidate, "Validate", "Validate", "V"));
1432  commands.push_back(new CUICommand(eCmdValidate_ext, "Validation Report", "Validate", "V"));
1433  commands.push_back(new CUICommand(eCmdValidateNoAlignments, "Validate No Alignments", "Validate no Alignments", "VNA"));
1434  commands.push_back(new CUICommand(eCmdValidateCheckInferences, "Validate Check Inferences", "Validate Check Inferences", "VCI"));
1435 // commands.back()->AddAccelerator(wxACCEL_NORMAL, 'v');
1436  commands.push_back(new CUICommand(eCmdSortUniqueCountText, "SUC (Sort Unique Count)", "Sort Unique Count", "SUC"));
1437  commands.push_back(new CUICommand(eCmdSortUniqueCountTree, "cSUC (Clickable SUC)", "Clickable Sort Unique Count", "SUC"));
1438  commands.push_back(new CUICommand(eCmdSortUniqueCountTree_ext, "FlatFile Summary", "Clickable Sort Unique Count", "SUC"));
1439  commands.push_back(new CUICommand(eCmdDiscrepancy, "Discrepancy Report", "Discrepancy Report", "DR"));
1440  commands.push_back(new CUICommand(eCmdOncaller, "Oncaller Report", "Oncaller Report", "OR"));
1441  commands.push_back(new CUICommand(eCmdSubmitter_ext, "Submitter Report", "Submitter Report", "SR"));
1442  commands.push_back(new CUICommand(eCmdMega, "Mega Report", "Mega Report", "MR"));
1443  commands.push_back(new CUICommand(eCmdDiscrepancyList, "List Discrepancy Tests", "List Discrepancy Tests", "LDT"));
1444  commands.push_back(new CUICommand(eCmdAutodefDefaultOptions, "Autodef", "Autodef Default Options", "ADO"));
1445  commands.push_back(new CUICommand(eCmdAutodefOptions, "Autodef Select Options", "Autodef Select Options", "ADSO"));
1446  commands.push_back(new CUICommand(eCmdAutodefMisc, "Autodef Misc Feats", "Autodef Misc Feats", "ADMF"));
1447  commands.push_back(new CUICommand(eCmdAutodefId, "Autodef ID", "Autodef ID", "ADID"));
1448  commands.push_back(new CUICommand(eCmdAutodefNoMods, "Autodef No Modifiers", "Autodef No Modifiers", "ADNM"));
1449  commands.push_back(new CUICommand(eCmdAutodefPopset, "Add Popset Titles", "Add Popset Titles", "ADPT"));
1450  commands.push_back(new CUICommand(eCmdAutodefRefresh, "Refresh DefLine with Previous Options", "Refresh Definition Line", "RDEFL"));
1451  commands.push_back(new CUICommand(eCmdInstantiateProteinTitles, "PT_Cleanup", "PT_Cleanup Protein Titles", "PTCU"));
1452  commands.push_back(new CUICommand(eCmdRemoveAllFeatures, "Remove All Features", "Remove All Features", "RAF"));
1453  commands.push_back(new CUICommand(eCmdRemoveDupFeats, "All Feature Types", "Remove Duplicate Features", "RDF"));
1454  commands.push_back(new CUICommand(eCmdRemoveDupFeats_ext, "Remove Duplicate Features", "Remove Duplicate Features", "RDF"));
1455  commands.push_back(new CUICommand(eCmdRemoveDupFeatsWithOptions, "Features with Options", "Remove Duplicate Feats With Options", "RDFWO"));
1456  commands.push_back(new CUICommand(eCmdRemoveDupFeatsWithOptions_ext, "Remove Duplicate Features with Options", "Remove Duplicate Feats With Options", "RDFWO"));
1457  commands.push_back(new CUICommand(eCmdResolveIntersectingFeats, "Resolve Intersecting Feature Locations", "Resolve Intersecting Feature Locations", "RIFL"));
1458  commands.push_back(new CUICommand(eCmdAddSequences, "Add Sequences", "Add Sequences", "AS"));
1459  commands.push_back(new CUICommand(eCmdApplySourceQual, "Apply Source Qualifier", "Apply Source Qual", "ASQ"));
1460  commands.push_back(new CUICommand(eCmdEditSourceQual, "Edit Source Qualifier", "Edit Source Qual", "ESQ"));
1461  commands.push_back(new CUICommand(eCmdConvertSourceQual, "Convert Source Qualifier", "Convert Source Qual", "CSQ"));
1462  commands.push_back(new CUICommand(eCmdSwapSourceQual, "Swap Source Qualifiers", "Swap Source Qual", "SSQ"));
1463  commands.push_back(new CUICommand(eCmdRemoveSourceQual, "Remove Source Qualifier", "Remove Source Qual", "RSQ"));
1464  commands.push_back(new CUICommand(eCmdApplyRNAQual, "Apply RNA Qualifier", "Apply RNA Qual", "ARQ"));
1465  commands.push_back(new CUICommand(eCmdEditRNAQual, "Edit RNA Qualifier", "Edit RNA Qual", "ERQ"));
1466  commands.push_back(new CUICommand(eCmdConvertRNAQual, "Convert RNA Qualifier", "Convert RNA Qual", "CRQ"));
1467  commands.push_back(new CUICommand(eCmdSwapRNAQual, "Swap RNA Qualifiers", "Swap RNA Qual", "SRQ"));
1468  commands.push_back(new CUICommand(eCmdRemoveRNAQual, "Remove RNA Qualifier", "Remove RNA Qual", "RRQ"));
1469  commands.push_back(new CUICommand(eCmdApplyCGPQual, "Apply CDS-Gene-Prot-mRNA Qualifier", "Apply CDS-Gene-Prot-mRNA Qual", "ACGPQ"));
1470  commands.push_back(new CUICommand(eCmdEditCGPQual, "Edit CDS-Gene-Prot-mRNA Qualifier", "Edit CDS-Gene-Prot-mRNA Qual", "ECGPQ"));
1471  commands.push_back(new CUICommand(eCmdConvertCGPQual, "Convert CDS-Gene-Prot-mRNA Qualifier", "Convert CDS-Gene-Prot-mRNA Qual", "CCGPQ"));
1472  commands.push_back(new CUICommand(eCmdSwapCGPQual, "Swap CDS-Gene-Prot-mRNA Qualifiers", "Swap CDS-Gene-Prot-mRNA Qual", "SCGPQ"));
1473  commands.push_back(new CUICommand(eCmdRemoveCGPQual, "Remove CDS-Gene-Prot-mRNA Qualifier", "Remove CDS-Gene-Prot-mRNA Qual", "RCGPQ"));
1474  commands.push_back(new CUICommand(eCmdApplyFeatQual, "Apply Feature Qualifier", "Apply Feature Qual", "AFQ"));
1475  commands.push_back(new CUICommand(eCmdEditFeatQual, "Edit Feature Qualifier", "Edit Feature Qual", "EFQ"));
1476  commands.push_back(new CUICommand(eCmdConvertFeatQual, "Convert Feature Qualifier", "Convert Feature Qual", "CFQ"));
1477  commands.push_back(new CUICommand(eCmdConvertSecondProtNameToDesc, "Second Protein Name to Description", "Second Protein Name to Description", "CSPND"));
1478  commands.push_back(new CUICommand(eCmdConvertDescToSecondProtName, "Protein Description to Second Name", "Protein Description to Second Name", "PDSN"));
1479  commands.push_back(new CUICommand(eCmdConvertDescToFeatComment, "Comment", "Convert Desc to Feat Comment", "CDFC"));
1480  commands.push_back(new CUICommand(eCmdConvertDescToFeatSource, "Source", "Concert Desc to Feat Source", "CDFS"));
1481  commands.push_back(new CUICommand(eCmdConvertDescToFeatPub, "All", "Convert Desc to Feat Pub", "CDFP"));
1482  commands.push_back(new CUICommand(eCmdConvertDescToFeatPubConstraint, "By Constraint", "Convert Desc to Feat Pub", "CDFPC"));
1483  commands.push_back(new CUICommand(eCmdConvertFeatToDescComment, "Comment", "Convert Feat to Desc Comment", "CFDC"));
1484  commands.push_back(new CUICommand(eCmdConvertFeatToDescSource, "Source", "Convert Feat to Desc Source", "CFDS"));
1485  commands.push_back(new CUICommand(eCmdConvertFeatToDescPub, "Publication", "Convert Feat to Desc Pub", "CFDP"));
1486  commands.push_back(new CUICommand(eCmdSwapFeatQual, "Swap Feature Qualifiers", "Swap Feature Qual", "SFQ"));
1487  commands.push_back(new CUICommand(eCmdRemoveFeatQual, "Remove Feature Qualifier", "Remove Feature Qual", "RFQ"));
1488  commands.push_back(new CUICommand(eCmdRemoveTextOutsideString, "Remove Text Outside String", "Remove Text Outside String", "RTOS"));
1489  commands.push_back(new CUICommand(eCmdParseText, "Parse Text", "Parse Text", "PT"));
1490  commands.push_back(new CUICommand(eCmdParseTextFromDefline, "Parse Text", "Parse Text", "PTDL"));
1491  commands.push_back(new CUICommand(eCmdParseLocalToSrc, "Parse Local ID to Source", "Parse Local ID to Src", "PLIDTS"));
1492  commands.push_back(new CUICommand(eCmdRemoveTextInsideStr, "Remove Text Inside String", "Remove Text Inside String", "RTIS"));
1493  commands.push_back(new CUICommand(eCmdLowercaseQuals, "Lowercase Qualifiers", "Lowercase Qualifiers", "LQ"));
1494  commands.push_back(new CUICommand(eCmdConvertFeatures, "Convert Features", "Convert Features", "CF"));
1495  commands.push_back(new CUICommand(eCmdCdsToMatPeptide, "Convert CDS to Mat-peptide", "Convert CDS to mat-peptide", "CDSTMP"));
1496  commands.push_back(new CUICommand(eCmdConvertCdsToMiscFeat, "Convert CDS to Misc-feature or Pseudogene", "Convert CDS to misc-feat or Pseudogene", "CCDSMF"));
1497  commands.push_back(new CUICommand(eCmdConvertCdsWithInternalStopToMiscFeat, "To Misc-feature", "Convert CDS with Internal Stop Codon to Misc_feat", "CCDSWIMF"));
1498  commands.push_back(new CUICommand(eCmdConvertCdsWithInternalStopToMiscFeatViral, "To Misc-feature (Viral)", "Convert CDS with Internal Stop Codon to Misc_feat (Viral)", "CCDSWIMFV"));
1499  commands.push_back(new CUICommand(eCmdConvertCdsWithInternalStopToMiscFeatUnverified, "To Misc-feature with Unverified Comment", "Convert CDS with Internal Stop Codon to Misc_feat with Unverified Comment", "CCDSWIMFU"));
1500  commands.push_back(new CUICommand(eCmdConvertCdsWithGapsToMiscFeat, "Convert CDS with Internal Gaps to misc-feat", "Convert CDS with Internal Gaps to misc-feat", "CCDSWGMF"));
1501  commands.push_back(new CUICommand(eCmdTableReader, "Table Reader", "Table Reader", "TR"));
1502  commands.push_back(new CUICommand(eCmdTableReader_ext, "Use Table Reader", "Table Reader", "TR"));
1503  commands.push_back(new CUICommand(eCmdTableReaderClipboard, "Table Reader from Clipboard", "Table Reader from Clipboard", "TRFC"));
1504  commands.push_back(new CUICommand(eCmdBulkSourceEdit, "Bulk Source Edit", "Bulk Source Edit", "BE"));
1505  commands.push_back(new CUICommand(eCmdBulkCdsEdit, "Bulk CDS Edit", "Bulk CDS Edit", "BCDSE"));
1506  commands.push_back(new CUICommand(eCmdBulkGeneEdit, "Bulk Gene Edit", "Bulk Gene Edit", "BGENEE"));
1507  commands.push_back(new CUICommand(eCmdBulkRnaEdit, "Bulk RNA Edit", "Bulk RNA Edit", "BRNAE"));
1508  commands.push_back(new CUICommand(eCmdBulkMiscFeatEdit, "Bulk Misc Feat Edit", "Bulk Misc Feat Edit", "BMISCFE"));
1509  commands.push_back(new CUICommand(eCmdCorrectGenes, "Correct Genes for CDSs or mRNAs", "Correct Genes for CDSs or mRNAs", "CGFCOM"));
1510  commands.push_back(new CUICommand(eCmdSegregateSets, "Segregate Sets", "Segregate Sets", "SEGSET"));
1511  commands.push_back(new CUICommand(eCmdSequesterSets, "Sequester Sets", "Sequester Sets", "SEQSET"));
1512  commands.push_back(new CUICommand(eCmdDescriptorPropagateDown, "Propagate Descriptors", "Propagate Descriptors", "PRDS"));
1513  commands.push_back(new CUICommand(eCmdReorderSeqById, "Reorder by ID", "Reorder by ID", "RBID"));
1514  commands.push_back(new CUICommand(eCmdCombineSelectedGenesIntoPseudogenes,"Combine Selected Genes into Pseudogenes", "Combine selected genes into pseudogenes","CSGPG"));
1515  commands.push_back(new CUICommand(eCmdWithdrawSequences, "Withdraw Sequences", "Withdraw Sequences", "WSEQ"));
1516  commands.push_back(new CUICommand(eCmdAddSet, "Add Set", "Add Set", "AS"));
1517  commands.push_back(new CUICommand(eCmdPropagateDBLink, "Propagate DBLink Descriptors", "Propagate DBLink Descriptors", "PDBLD"));
1518  commands.push_back(new CUICommand(eCmdChangeSetClass, "Convert Set Type", "Convert Set Type", "CST"));
1519  commands.push_back(new CUICommand(eCmdMolInfoEdit, "MolInfo Edit", "MolInfo Edit", "MIE"));
1520  commands.push_back(new CUICommand(eCmdExportTable,"Export Table", "Export Table", "ETBL"));
1521  commands.push_back(new CUICommand(eCmdParseStrainSerotypeFromNames, "Parse Strain, Serotype from Names", "Parse Strain, Serotype from Names", "PSSFN"));
1522  commands.push_back(new CUICommand(eCmdAddStrainSerotypeToNames, "Add Strain, Serotype to Names", "Add Strain Serotype to Names", "ASSTN"));
1523  commands.push_back(new CUICommand(eCmdFixupOrganismNames, "Fixup Organism Names", "Fixup Organism Names", "FON"));
1524  commands.push_back(new CUICommand(eCmdSplitQualifiersAtCommas, "Split Qualifiers at Commas", "Split Quals at Commas", "SQAC"));
1525  commands.push_back(new CUICommand(eCmdSplitStructuredCollections, "Split Structured Collections", "Split Structured Collections", "SSC"));
1526  commands.push_back(new CUICommand(eCmdTrimOrganismNames, "Trim Organism Names", "Trim Organism Names", "TON"));
1527  commands.push_back(new CUICommand(eCmdRemoveUnverified, "Remove Unverified", "Remove Unverified from Selected Object", "RUNVER"));
1528  commands.push_back(new CUICommand(eCmdRemoveUnreviewed, "Remove Unreviewed", "Remove Unreviewed from selected Object", "RUNREV"));
1529  commands.push_back(new CUICommand(eCmdAddNamedrRNA12S, "12S", "Add Named rRNA 12S", "ANR12S"));
1530  commands.push_back(new CUICommand(eCmdAddNamedrRNA16S, "16S", "Add Named rRNA 16S", "ANR16S"));
1531  commands.push_back(new CUICommand(eCmdAddNamedrRNA23S, "23S", "Add Named rRNA 23S", "ANR23S"));
1532  commands.push_back(new CUICommand(eCmdAddNamedrRNA18S, "18S", "Add Named rRNA 18S", "ANR18S"));
1533  commands.push_back(new CUICommand(eCmdAddNamedrRNA28S, "28S", "Add Named rRNA 28S", "ANR28S"));
1534  commands.push_back(new CUICommand(eCmdAddNamedrRNA26S, "26S", "Add Named rRNA 26S", "ANR26S"));
1535  commands.push_back(new CUICommand(eCmdAddNamedrRNASmall, "Small", "Add Named rRNA Small", "ANRSmall"));
1536  commands.push_back(new CUICommand(eCmdAddNamedrRNALarge, "Large", "Add Named rRNA Large", "ANRLarge"));
1537  commands.push_back(new CUICommand(eCmdAddControlRegion, "Control Region", "Add Control Region", "ACR"));
1538  commands.push_back(new CUICommand(eCmdAddMicrosatellite, "Microsatellite", "Add Microsatellite", "AM"));
1539  commands.push_back(new CUICommand(eCmdEditFeatEv, "Evidence", "Edit Feature Evidence", "EFE"));
1540  commands.push_back(new CUICommand(eCmdEditFeatLoc, "Location", "Edit Feature Location", "EFL"));
1541  commands.push_back(new CUICommand(eCmdEditFeatLoc_ext, "Edit Feature Location", "Edit Feature Location", "EFL"));
1542  commands.push_back(new CUICommand(eCmdEditFeatStrand, "Strand", "Edit Feature Location Strand", "EFLS"));
1543  commands.push_back(new CUICommand(eCmdEditFeatStrand_ext, "Edit Feature Strand", "Edit Feature Location Strand", "EFLS"));
1544  commands.push_back(new CUICommand(eCmdEditFeatRevInt, "Reverse Location Interval Order", "Reverse Location Interval Order", "RLIO"));
1545  commands.push_back(new CUICommand(eCmdEditFeatPseudo,"Pseudo", "Edit Feature Pseudo", "EFP"));
1546  commands.push_back(new CUICommand(eCmdEditFeatException, "Exceptions", "Edit Feature Exception", "EFE"));
1547  commands.push_back(new CUICommand(eCmdEditFeatExperiment, "Experiment", "Edit Feature Experiment", "EFEX"));
1548  commands.push_back(new CUICommand(eCmdEditFeatInference, "Inference", "Edit Feature Inference", "EFINF"));
1549  commands.push_back(new CUICommand(eCmdExtendPartialsConstr, "With Constraint", "Extend Partials With Constraint", "EPWC"));
1550  commands.push_back(new CUICommand(eCmdExtendPartialsAll, "All to Ends", "Extend Partials All to Ends", "EPAE"));
1551  commands.push_back(new CUICommand(eCmdGeneFromOtherFeat,"Gene Features from Other Features","Gene Features From Other Features","GFFOF"));
1552  commands.push_back(new CUICommand(eCmdGeneFeatFromXrefs, "Gene Features from Xrefs", "Gene Features From Xrefs", "GFFX"));
1553  commands.push_back(new CUICommand(eCmdGeneXrefsFromFeats, "Gene Xrefs from Features", "Gene Xrefs from Features", "GXFF"));
1554  commands.push_back(new CUICommand(eCmdRemoveAllGeneXrefs, "All Gene Xrefs", "All Gene Xrefs", "RAGX"));
1555  commands.push_back(new CUICommand(eCmdRemoveUnnecessaryGeneXrefs, "Unnecessary Gene Xrefs", "Unnecessary Gene Xrefs", "RUGX"));
1556  commands.push_back(new CUICommand(eCmdRemoveNonsuppressingGeneXrefs, "Non-Suppressing Gene Xrefs","Non-Suppressing Gene Xrefs","RNSGX")); ///?????
1557  commands.push_back(new CUICommand(eCmdRemoveOrphanLocusGeneXrefs, "Gene Xrefs with Orphan Gene Locus","Gene Xrefs with Orphan Gene Locus","ROLGX"));
1558  commands.push_back(new CUICommand(eCmdRemoveOrphanLocus_tagGeneXrefs, "Gene Xrefs with Orphan Locus-tag", "Gene Xrefs with Orphan Locus-tag", "ROLTGX"));
1559  commands.push_back(new CUICommand(eCmdRemoveGeneXrefs, "Choose Types and Constraint", "Choose Types and Constraint", "RGXTC"));
1560  commands.push_back(new CUICommand(eCmdRemoveDuplicateGOTerms, "Remove Duplicate GO Terms", "Remove Duplicate GeneOntology Terms", "RDGOT"));
1561  commands.push_back(new CUICommand(eCmdExtendCDS, "Extend Coding Region Ends", "Extend Coding Region Ends", "ECDSE"));
1562  commands.push_back(new CUICommand(eCmdTruncateCDS, "Truncate Proteins and CDSs at Stops", "Truncate Proteins and CDSs at Stops", "TPCDSS"));
1563  commands.push_back(new CUICommand(eCmdExtendCDSToStop, "Extend Proteins to Stops", "Extend Proteins to Stops", "EPROTS"));
1564  commands.push_back(new CUICommand(eCmdRecomputeIntervalsAndUpdateGenes, "And Update Genes", "And Update Genes", "RIUPG"));
1565  commands.push_back(new CUICommand(eCmdRecomputeIntervals, "Do Not Update Genes" , "Do Not Update Genes", "RINUPG"));
1566  commands.push_back(new CUICommand(eCmdCdsFromGeneMrnaExon, "CDS Features from Gene, mRNA or Exon", "CDS Features from Gene, mRNA, or exon", "CDSFME"));
1567  commands.push_back(new CUICommand(eCmdmRNAFromGeneCdsExon, "mRNA Features from Gene, CDS, or exon", "mRNA Features from Gene, CDS, or exon", "MRNAFGCE"));
1568  commands.push_back(new CUICommand(eCmdtRNAFromGene, "tRNA/rRNA features from Gene", "tRNA/rRNA features from Gene",""));
1569  commands.push_back(new CUICommand(eCmdExonFromCds,"CDS Intervals", "Exon Features from CDS Intervals", "EFCDS"));
1570  commands.push_back(new CUICommand(eCmdExonFromMRNA,"mRNA Intervals", "Exon features from mRNA intervals", "EFMRNA"));
1571  commands.push_back(new CUICommand(eCmdExonFromTRNA,"tRNA Intervals", "Exon features from tRNA intervals", "EFTRNA"));
1572  commands.push_back(new CUICommand(eCmdFixProductNamesDefault, "Default","Fix Product Names Default", "FPND"));
1573  commands.push_back(new CUICommand(eCmdFixProductNamesOptions, "With Options","Fix Product Names With Options", "FPNWO"));
1574  commands.push_back(new CUICommand(eCmdBulkApplyGenCode, "Batch Apply Genetic Code", "Batch Apply Genetic Code", "BAGC"));
1575  commands.push_back(new CUICommand(eCmdEditSeqEndsWithAlign,"Edit Sequence Ends with Alignment","Edit Sequence Ends with Alignment", "ESEWA"));
1576  commands.push_back(new CUICommand(eCmdEditSequenceEnds,"Edit Sequence Ends","Edit Sequence Ends", "ESE"));
1577  commands.push_back(new CUICommand(eCmdUpdateAlign, "Update Sequence Alignment", "Update SeqAlign", "UPSA"));
1578  commands.push_back(new CUICommand(eCmdSaveDescriptors, "Save Descriptors", "Save Descriptors", "SD"));
1579  commands.push_back(new CUICommand(eCmdCreateSeqHistForTpaDetailed, "Create Seq-hist for TPA Detailed", "Create Seq-hist for TPA detailed", "CSHTPAD"));
1580  commands.push_back(new CUICommand(eCmdCreateSeqHistForTpa, "Create Seq-hist for TPA", "Create Seq-hist for TPA", "CSHTPA"));
1581  commands.push_back(new CUICommand(eCmdRemoveSeqHistAssembly, "Remove Seq-Hist Assembly", "Remove Seq-Hist Assembly", "RSHA"));
1582  commands.push_back(new CUICommand(eCmdFarPointerSeq, "Far Pointer Sequences", "Far Pointer Sequences", "FPSEQ"));
1583  commands.push_back(new CUICommand(eCmdConvertBadCdsAndRnaToMiscFeat, "Convert Bad Coding Regions and RNA features to misc-feat", "Convert Bad Coding Regions and RNA features to misc-feat", "CBCDSRNA"));
1584  commands.push_back(new CUICommand(eCmdCreateProteinId, "Create Protein IDs", "Create Protein IDs", "CPID"));
1585  commands.push_back(new CUICommand(eCmdCreateLocusTagGene, "Create Locus-tag Genes", "Create locus-tag genes", "CLTG"));
1586  commands.push_back(new CUICommand(eCmdNormalizeGeneQuals, "Normalize Gene Quals", "Copy gene qualifiers in xrefs on coding regions to parent genes", "NGQ"));
1587  commands.push_back(new CUICommand(eCmdGenusSpeciesFixup, "Genus-Species Fixup", "Genus-Species Fixup", "GSFU"));
1588  commands.push_back(new CUICommand(eCmdCountryConflict, "Lat-Lon Country Conflict Tool", "Lat-Lon Country Conflict Tool", "LLCCT"));
1589  commands.push_back(new CUICommand(eCmdDuplicate, "Duplicate", "Duplicate", "DUP"));
1590  commands.push_back(new CUICommand(eCmdCorrectIntervalOrder, "Correct Seq-loc Interval Order", "Correct Seq-loc Interval Order", "CLIO"));
1591  commands.push_back(new CUICommand(eCmdAddSecondary, "Add Secondary", "Add Secondary", "ADDS"));
1592  commands.push_back(new CUICommand(eCmdPackageFeaturesOnParts, "Package Features on Parts", "Package Features on Parts", "PFOP"));
1593  commands.push_back(new CUICommand(eCmdMakeBadSpecificHostTable, "Make Bad Specific-Host Table", "Make Bad Specific-Host Table", "MBSHT"));
1594  commands.push_back(new CUICommand(eCmdCorrectRNAStrand, "Correct RNA strandedness (Use SMART)", "Correct RNA strandedness", "CRSUS"));
1595  commands.push_back(new CUICommand(eCmdTrimNsRich, "Trim N-rich Sequence Ends", "Trim N-rich Sequence Ends", "TNR"));
1596  commands.push_back(new CUICommand(eCmdTrimNsTerminal, "Trim Terminal Ns", "Trim Terminal Ns", "TTN"));
1597  commands.push_back(new CUICommand(eCmdAddFluComments, "Add Flu Comments", "Add Flu Comments", "AFC"));
1598  commands.push_back(new CUICommand(eCmdLabelRna, "Label RNA", "Label RNA", "LRNA"));
1599  commands.push_back(new CUICommand(eCmdRemProtTitles, "All but RefSeq", "All but ReqSeq", "ABRS"));
1600  commands.push_back(new CUICommand(eCmdRemAllProtTitles, "All", "All", ""));
1601  commands.push_back(new CUICommand(eCmdApplyRNA_ITS, "Apply rRNA_ITS", "Apply rRNA_ITS", "ARNAITS"));
1602  commands.push_back(new CUICommand(eCmdEditingButtons, "Toolbar", "Sequin Special Editing Buttons", "SSEB"));
1603  commands.push_back(new CUICommand(eCmdMakeToolBarWindow, "Make ToolBar Window", "Make ToolBar Window", "MTBW"));
1604  commands.push_back(new CUICommand(eCmdEnableHupId, "Enable HUP-ID Loader", "Enable HUP-ID Loader", "", "", "", "", wxITEM_CHECK));
1605  commands.push_back(new CUICommand(eCmdIndexerTypeSelection, "Indexer Type", "Indexer Type", ""));
1606  commands.push_back(new CUICommand(eCmdTestDialogView, "Open Test DialogView", "Test DialogView", kEmptyStr));
1607  commands.push_back(new CUICommand(eCmdTestFormView, "Open Test FormView", "Test FormView", kEmptyStr));
1608  commands.push_back(new CUICommand(eCmdMacroEditor, "Macro Editor", "Macro Editor", "MACROE"));
1609  commands.push_back(new CUICommand(eCmdSuspectProductRulesEditor, "Suspect Product Rule Editor", "Suspect Product Rule Editor", "SPRE"));
1610  commands.push_back(new CUICommand(eCmdAdjustConsensusSpliceSitesStrict, "Strict", "Adjust Consensus Splice Sites Strict", "ACSS"));
1611  commands.push_back(new CUICommand(eCmdAdjustConsensusSpliceSitesStrict_ext, "Adjust CDS for Consensus Splice Sites (strict)", "Adjust Consensus Splice Sites Strict", "ACSS"));
1612  commands.push_back(new CUICommand(eCmdAdjustConsensusSpliceSitesRelaxed, "Relaxed", "Adjust Consensus Splice Sites Relaxed", "ACSR"));
1613  commands.push_back(new CUICommand(eCmdAdjustConsensusSpliceSitesRelaxed_ext, "Adjust CDS for Consensus Splice Sites (relaxed)", "Adjust Consensus Splice Sites Relaxed", "ACSR"));
1614  commands.push_back(new CUICommand(eCmdAdjustConsensusSpliceSitesConsensusEnds, "5' and 3' ends only", "Adjust Consensus Splice Sites Consensus Ends", "ACSENDS"));
1615  commands.push_back(new CUICommand(eCmdAdjustCDSForIntrons, "CDS", "Adjust CDS For Introns", "ACDSI"));
1616  commands.push_back(new CUICommand(eCmdAdjustrRNAForIntrons, "rRNA", "Adjust rRNA For Introns", "ARRNAI"));
1617  commands.push_back(new CUICommand(eCmdAdjusttRNAForIntrons, "tRNA", "Adjust tRNA For Introns", "ATRNAI"));
1618  commands.push_back(new CUICommand(eCmdAdjustmRNAForIntrons, "mRNA", "Adjust mRNA For Introns", "AMRNAI"));
1619  commands.push_back(new CUICommand(eCmdLatLonTool, "Lat-Lon Tool", "Lat-Lon Tool", "LLT"));
1620  commands.push_back(new CUICommand(eCmdCDSGeneRangeErrorSuppress, "Suppress", "CDS Gene Range Error Suppress", "CDSGRES"));
1621  commands.push_back(new CUICommand(eCmdCDSGeneRangeErrorRestore, "Restore", "CDS Gene Range Error Restore", "CDSGRER"));
1622  commands.push_back(new CUICommand(eCmdSuppressGenes, "Suppress Genes on Features", "Suppress Genes on Features", "SUPGF"));
1623  commands.push_back(new CUICommand(eCmdRemoveSegGaps, "Remove Seg Gaps", "Remove Seg Gaps", "RSEGGAPS"));
1624  commands.push_back(new CUICommand(eCmdRawSeqToDeltaByNs, "By Ns", "Raw Sequence To Delta By Ns", "RSDN"));
1625  commands.push_back(new CUICommand(eCmdRawSeqToDeltaByNs_ext, "Add Assembly Gaps to Sequence", "Add Assembly Gaps to Sequence" , "RSDN"));
1626  commands.push_back(new CUICommand(eCmdRawSeqToDeltaByLoc, "By Location", "By Location", "RSDL"));
1627  commands.push_back(new CUICommand(eCmdRawSeqToDeltaByAssemblyGapFeatures, "By Assembly_Gap Features", "By Assembly_Gap Features", ""));
1628  commands.push_back(new CUICommand(eCmdAdjustFeaturesForGaps, "Adjust Features for Gaps", "Adjust Features for Gaps", "AFFG"));
1629  commands.push_back(new CUICommand(eCmdDeltaSeqToRaw, "Delta Seq to Raw", "Delta Seq To Raw", "DSTR"));
1630  commands.push_back(new CUICommand(eCmdDeltaSeqToRaw_ext, "Remove Gap Features", "Remove Gap Features", "DSTR"));
1631  commands.push_back(new CUICommand(eCmdExpandGaps, "Expand Known Gaps to Include Flanking Ns", "Expand Known Gaps to Include Flanking Ns", "EKGFN"));
1632  commands.push_back(new CUICommand(eCmdConvertSelectedGapsToKnown, "To Known Length", "To Known Length", "CSGTK"));
1633  commands.push_back(new CUICommand(eCmdConvertSelectedGapsToUnknown, "To Unknown Length", "To Unknown Length", "CSGTU"));
1634  commands.push_back(new CUICommand(eCmdConvertGapsBySize, "Convert Known to Unknown (by Size)", "Convert Known to Unknown (by Size)", "CKTUS"));
1635  commands.push_back(new CUICommand(eCmdEditSelectedGaps, "Change Length of Selected Known Length Gaps", "Change Length of Selected Known Length Gaps", "CLSKG"));
1636  commands.push_back(new CUICommand(eCmdAddLinkageToGaps, "Add Linkage to All Gaps", "Add Linkage to All Gaps", "ALAG"));
1637  commands.push_back(new CUICommand(eCmdAddLinkageToGaps_ext, "Add Linkage Evidence to All Gaps", "Add Linkage to All Gaps", "ALAG"));
1638  commands.push_back(new CUICommand(eCmdCombineAdjacentGaps, "Combine Adjacent Gaps", "Combine Adjacent Gaps", "CAGAP"));
1639  commands.push_back(new CUICommand(eCmdSplitCDSwithTooManyXs, "Split CDS features with more than 50% N's", "Split CDS features with more than 50% N's", "SCDSN"));
1640  commands.push_back(new CUICommand(eCmdRmCultureNotes, "Remove Uncultured Notes", "Remove Uncultured Notes", "RUNN"));
1641  commands.push_back(new CUICommand(eCmdEditSeqId, "Edit Sequence IDs", "Edit Sequence IDs", "ESID"));
1642  commands.push_back(new CUICommand(eCmdRemoveLocalSeqIdsFromNuc, "From Nucleotides", "Remove Local Seq-id from Nucleotides", "RLIDN"));
1643  commands.push_back(new CUICommand(eCmdRemoveLocalSeqIdsFromProt, "From Proteins", "Remove Local Seq-id from Proteins", "RLIDP"));
1644  commands.push_back(new CUICommand(eCmdRemoveLocalSeqIdsFromAll, "From All Bioseqs", "Remove Local Seq-id from All Bioseqs", "RLIDA"));
1645  commands.push_back(new CUICommand(eCmdRemoveGiSeqIdsFromAll, "GI IDs from Bioseqs", "GI IDs from Bioseqs", "RGIB"));
1646  commands.push_back(new CUICommand(eCmdRemoveGenbankSeqIdsFromProt, "From Proteins", "From Proteins", "RGBP"));
1647  commands.push_back(new CUICommand(eCmdRemoveGenbankSeqIdsFromAll, "From All Bioseqs", "From All Bioseqs", "RGBA"));
1648  commands.push_back(new CUICommand(eCmdRemoveSeqIdNamesFromProtFeats, "Seq-ID Name From Prot Feats", "Seq-ID Name From Prot Feats", "RSINP"));
1649  commands.push_back(new CUICommand(eCmdConvertAccessionToLocalIdsAll, "For All Sequences", "For All Sequences", "CACCLA"));
1650  commands.push_back(new CUICommand(eCmdConvertAccessionToLocalIdsNuc, "For Nucleotide Sequences", "For Nucleotide Sequences", "CACCLN"));
1651  commands.push_back(new CUICommand(eCmdConvertAccessionToLocalIdsProt, "For Protein Sequences", "For Protein Sequences", "CACCLP"));
1652  commands.push_back(new CUICommand(eCmdConvertAccessionToLocalIdsName, "GenBank.name to LocalID", "GenBank.name to LocalID", "CNAML"));
1653  commands.push_back(new CUICommand(eCmdLocalToGeneralId, "LocalIDs to GeneralIDs", "Local Seq-id to General Seq-id", "LIDGID"));
1654  commands.push_back(new CUICommand(eCmdGeneralToLocalId, "GeneralIDs to LocalIDs", "GeneralIDs to LocalIDs", "GIDTOL"));
1655  commands.push_back(new CUICommand(eCmdRemoveGeneralId, "General IDs", "General IDs", "RGID"));
1656  commands.push_back(new CUICommand(eCmdRemoveUnnecessaryExceptions, "Remove Unnecessary Exceptions", "Remove Unnecessary Exceptions", "RUNE"));
1657  commands.push_back(new CUICommand(eCmdEditHistory, "Edit History", "Edit History", "EH"));
1658  commands.push_back(new CUICommand(eCmdUpdate_Replaced_EC_numbers,"Update Replaced EC Numbers", "Update Replaced EC Numbers", "URECN"));
1659  commands.push_back(new CUICommand(eCmdUpdateSequence, "Single Sequence", "Update Single Sequence", "USSSEQ"));
1660  commands.push_back(new CUICommand(eCmdUpdateSequence_ext, "Update Sequence", "Update Single Sequence", "USSSEQ"));
1661  commands.push_back(new CUICommand(eCmdUpdateSequenceClipboard, "Single Sequence (Clipboard)", "Update Single Sequence from Clipboard", "USSCLIP"));
1662  commands.push_back(new CUICommand(eCmdUpdateSequenceAccession, "Download Accession", "Update Single Sequence Accession", "USSACC"));
1663  commands.push_back(new CUICommand(eCmdUpdateMultiSequences, "Multiple Sequences", "Update Multiple Sequences from File", "UMSSFILE"));
1664  commands.push_back(new CUICommand(eCmdUpdateMultiSeqClipboard, "Multiple Sequences (Clipboard)", "Update Multiple Sequences from Clipboard", "UMSSCLIP"));
1665  commands.push_back(new CUICommand(eCmdImportFeatureTable, "Import Feature Table", "Import Feature Table", "IMPFTBL"));
1666  commands.push_back(new CUICommand(eCmdImportFeatureTable_ext, "5 Column Feature Table", "Import Feature Table", "IMPFTBL"));
1667  commands.push_back(new CUICommand(eCmdImportFeatureTableClipboard, "Import Feature Table from Clipboard", "Import Feature Table from Clipboard", "IMPFTBLC"));
1668  commands.push_back(new CUICommand(eCmdImportGFF3, "Import GFF3 File", "Import GFF3 File", "IMGFF"));
1669  commands.push_back(new CUICommand(eCmdImportGFF3_ext, "GFF3 File", "Import GFF3 File", "IMGFF"));
1670  commands.push_back(new CUICommand(eCmdLoadSecondaryAccessions, "Extra Accessions", "Extra Accessions", "LSAEA"));
1671  commands.push_back(new CUICommand(eCmdLoadSecondaryAccessionsHistoryTakeover, "History Takeover", "History Takeover", "LSAHT"));
1672  commands.push_back(new CUICommand(eCmdAddGlobalCodeBreak, "Add Global Code Break", "Add Global Code Break", "AGCB"));
1673  commands.push_back(new CUICommand(eCmdApplyStructuredCommentField, "Apply Structured Comment Field", "Apply Structured Comment Field", "ASTRCMNTFLD"));
1674  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixHIVData, "HIVData", "Replace Structured Comment to HIVData", "RSTRCMNT1"));
1675  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixFluData, "FluData", "Replace Structured Comment to FluData", "RSTRCMNT2"));
1676  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixMIGSData, "MIGSData", "Replace Structured Comment to MIGSData", "RSTRCMNT3"));
1677  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixMIMSData, "MIMSData", "Replace Structured Comment to MIMSData", "RSTRCMNT4"));
1678  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixMIENSData, "MIENSData", "Replace Structured Comment to MIENSData", "RSTRCMNT5"));
1679  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixMIMARKS3_0, "MIMARKS:3.0", "Replace Structured Comment to MIMARKS:3.0", "RSTRCMNT6"));
1680  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixMIGS3_0, "MIGS:3.0", "Replace Structured Comment to MIGS:3.0", "RSTRCMNT7"));
1681  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixMIMS3_0, "MIMS:3.0", "Replace Structured Comment to MIMS:3.0", "RSTRCMNT8"));
1682  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixAssemblyData, "AssemblyData", "Replace Structured Comment to AssemblyData", "RSTRCMNT9"));
1683  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixGenAssData, "GenomeAssemblyData", "Replace Structured Comment to GAssemblyData", "RSTRCMNT10"));
1684  commands.push_back(new CUICommand(eCmdEditStructuredCommentPrefixSuffixiBol, "iBOL", "Replace Structured Comment to iBOL", "RSTRCMNT11"));
1685  commands.push_back(new CUICommand(eCmdLinkSelectedmRNACDS, "Link Selected CDS and mRNA Pair", "Link Selected CDS and mRNA Pair", "LSCDSMRNAP"));
1686  commands.push_back(new CUICommand(eCmdLinkmRNACDSOverlap, "By Overlap", "Link CDS and mRNA by Overlap", "LCDSMRNAO"));
1687  commands.push_back(new CUICommand(eCmdLinkmRNACDSProduct, "By Product", "Link CDS and mRNA by Product", "LCDSMRNAP"));
1688  commands.push_back(new CUICommand(eCmdLinkmRNACDSLabel, "By Label", "Link CDS and mRNA by Label", "LCDSMRNALAB"));
1689  commands.push_back(new CUICommand(eCmdLinkmRNACDSLabelLocation, "By Label and Location", "Link CDS and mRNA by Label and Location", "LCDSMRNALABLOC"));
1690  commands.push_back(new CUICommand(eCmdLinkmRNACDSProteinID, "By Protein-ID Qualifier", "Link CDS and mRNA by protein-id qualifier", "LCDSMRNAPRQUAL"));
1691  commands.push_back(new CUICommand(eCmdLinkmRNACDSTranscriptID, "By Transcript-ID Qualifier", "Link CDS and mRNA by transcript-id qualifier", "LCDSMRNATRQUAL"));
1692  commands.push_back(new CUICommand(eCmdLinkmRNACDSUnidirectional, "From Unidirectional Xrefs", "Link CDS and mRNA from unidirectional Xrefs", "LSCDSMRNAUNID"));
1693  commands.push_back(new CUICommand(eCmdShowLinkedmRNACDS, "Show Linked CDS or mRNA Feature", "Show Linked CDS or mRNA Feature", "SLINKCDSMRNA"));
1694  commands.push_back(new CUICommand(eCmdShowFeatureTable, "Show Feature Table", "Show Feature Table", "SFEATTBL"));
1695  commands.push_back(new CUICommand(eCmdShowFeatureTable_ext, "Feature Table", "Show Feature Table", "SFEATTBL"));
1696  commands.push_back(new CUICommand(eCmdRestoreFromFile, "Restore from File", "Restore from Local File", "RFFILE"));
1697  commands.push_back(new CUICommand(eCmdRestoreAndConvertSeqSubmit, "Restore and Convert SeqSubmit", "Restore and Convert SeqSubmit", "RCVFFILE"));
1698  commands.push_back(new CUICommand(eCmdViewSortedProteins, "View Sorted Proteins (FASTA)", "View Sorted Proteins (FASTA)", "VSPF"));
1699  commands.push_back(new CUICommand(eCmdCheckForMixedStrands, "Check for Mixed Strands", "Check for Mixed Strands", "CMSTRAND"));
1700  commands.push_back(new CUICommand(eCmdPrepareSeqSubmit, "Genome Submission Wizard", "Prepare a Submission", "PREPASUB"));
1701  commands.push_back(new CUICommand(eCmdSaveSubmissionFile, "Save Submission File", "Save Submission File", "SSUBF"));
1702  commands.push_back(new CUICommand(eCmdSaveASN1File, "Save ASN.1 File", "Save ASN.1 File", "SVASN"));
1703  commands.push_back(new CUICommand(eCmdHelpReports_ext, "Help", "Help Reports", "HELPR"));
1704  commands.push_back(new CUICommand(eCmdHelpImport_ext, "Help", "Help Import", "HELPI"));
1705  commands.push_back(new CUICommand(eCmdHelpSequences_ext, "Help", "Help Sequences", "HELPS"));
1706  commands.push_back(new CUICommand(eCmdHelpFeatures_ext, "Help", "Help Features", "HELPF"));
1707  commands.push_back(new CUICommand(eCmdHelpComments_ext, "Help", "Help Comments", "HELPC"));
1708  commands.push_back(new CUICommand(eCmdHelpEditingTools_ext, "Help", "Help Editing Tools", "HELPET"));
1709  commands.push_back(new CUICommand(eCmdUpdateTLSName, "Update Targeted Locus Name", "Update Targeted Locus Name", "UPTLSNAME"));
1710 
1711 
1712  CBioseqEditorFactory::CollectBioseqEditorCommands(commands);
1713 
1714  commands.push_back(new CUICommand(eCmdAddDefLine, "Add Definition Line", "Add Definition Line", "ADL"));
1715  commands.push_back(new CUICommand(eCmdPrefixOrgToDefLine, "Organism", "Prefix Defline With Organism", "PDLORG"));
1716  commands.push_back(new CUICommand(eCmdPrefixStrainToDefLine, "Strain", "Prefix Defline With Strain", "PDLSTR"));
1717  commands.push_back(new CUICommand(eCmdPrefixCloneToDefLine, "Clone", "Prefix Defline With Clone", "PDLCLO"));
1718  commands.push_back(new CUICommand(eCmdPrefixIsolateToDefLine, "Isolate", "Prefix Defline With Isolate", "PDLISO"));
1719  commands.push_back(new CUICommand(eCmdPrefixHaplotToDefLine, "Haplotype", "Prefix Defline With Haplotype", "PDLH"));
1720  commands.push_back(new CUICommand(eCmdPrefixCultivarToDefLine, "Cultivar", "Prefix Defline With Cultivar", "PDLCULT"));
1721  commands.push_back(new CUICommand(eCmdPrefixListToDefLine, "List", "Prefix Defline From List", "PDLLIST"));
1722 
1723  // annotate descriptors commands
1724  commands.push_back(new CUICommand(eCmdCreateDescTPAAssembly, "TPA Assembly", "TPA Assembly", "TPAA"));
1725  commands.push_back(new CUICommand(eCmdCreateDescStructuredComment, "Structured Comment", "Structured Comment", "SCD"));
1726  commands.push_back(new CUICommand(eCmdCreateDescRefGeneTracking, "RefGene Tracking", "RefGene Tracking", "RGT"));
1727  commands.push_back(new CUICommand(eCmdCreateDescDBLink, "DBLink", "DBLink", "DBLD"));
1728  commands.push_back(new CUICommand(eCmdCreateDescUnverified, "Unverified", "Unverified", "UVD"));
1729  commands.push_back(new CUICommand(eCmdCreateDescUnreviewed, "Unreviewed", "Unreviewed", "UNREV"));
1730  commands.push_back(new CUICommand(eCmdCreateDescAuthorizedAccess, "Authorized Access", "Authorized Access", "AAD"));
1731  commands.push_back(new CUICommand(eCmdCreateDescGenomeAssemblyComment, "Genome Assembly", "Genome Assembly", "GAD"));
1732  commands.push_back(new CUICommand(eCmdCreateDescGenBankBlock, "GenBank Block", "GenBank Block", "GBBD"));
1733  commands.push_back(new CUICommand(eCmdCreateDescComment, "Comment", "Comment", "CD"));
1734  commands.push_back(new CUICommand(eCmdCreateDescComment_ext, "Add Free Text Comment", "Comment", "CD"));
1735  commands.push_back(new CUICommand(eCmdCreateDescTitle, "Title", "Title", "TD"));
1736  commands.push_back(new CUICommand(eCmdCreateDescMolinfo, "Molecule Description", "Molinfo", "MIDD"));
1737  commands.push_back(new CUICommand(eCmdCreateDescSource, "Biological Source", "BioSource", "BSD"));
1738  commands.push_back(new CUICommand(eCmdCreateDescPub, "Publication Descriptor", "Publication", "PD"));
1739  commands.push_back(new CUICommand(eCmdCreateDescPub_ext, "Add Publication", "Publication", "PD"));
1740  commands.push_back(new CUICommand(eCmdSubmitter, "Submitter Report", "Submitter Report", "SDR"));
1741 
1742  commands.push_back(new CUICommand(eCmdCreateStructuredCommentPrefixSuffixMIMS, "Add", "MIMS Comment", "AMIMC"));
1743  commands.push_back(new CUICommand(eCmdCreateStructuredCommentPrefixSuffixMIGS, "Add", "MIGS Comment", "AMIGC"));
1744  commands.push_back(new CUICommand(eCmdCreateStructuredCommentPrefixSuffixMIMARKS, "Add", "MIMARKS Comment", "AMIMARC"));
1745  commands.push_back(new CUICommand(eCmdCreateStructuredCommentPrefixSuffixMIENSData, "Add", "MIENS Comment", "AMIENC"));
1746  commands.push_back(new CUICommand(eCmdCreateStructuredCommentPrefixSuffixGenAnnData, "Add", "Genome Annotation Comment", "AGANNC"));
1747  commands.push_back(new CUICommand(eCmdCreateStructuredCommentPrefixSuffixGenAssData, "Add", "Genome Assembly Comment", "AGASSC"));
1748  commands.push_back(new CUICommand(eCmdDeleteStructuredCommentPrefixSuffixMIMS, "Remove", "MIMS Comment", "RMIMC"));
1749  commands.push_back(new CUICommand(eCmdDeleteStructuredCommentPrefixSuffixMIGS, "Remove", "MIGS Comment", "RMIGC"));
1750  commands.push_back(new CUICommand(eCmdDeleteStructuredCommentPrefixSuffixMIMARKS, "Remove", "MIMARKS Comment", "RMIMARC"));
1751  commands.push_back(new CUICommand(eCmdDeleteStructuredCommentPrefixSuffixMIENSData, "Remove", "MIENS Comment", "RMIENC"));
1752  commands.push_back(new CUICommand(eCmdDeleteStructuredCommentPrefixSuffixGenAnnData, "Remove", "Genome Annotation Comment", "RGANNC"));
1753  commands.push_back(new CUICommand(eCmdDeleteStructuredCommentPrefixSuffixGenAssData, "Remove", "Genome Assembly Comment", "RGASSC"));
1754 
1755  return commands;
1756 }
1757 
1758 BEGIN_EVENT_TABLE(CSequenceEditingEventHandler, wxEvtHandler)
1759  EVT_MENU( eCmdRemoveDescriptors, CSequenceEditingEventHandler::RemoveDescriptors )
1760  EVT_MENU( eCmdRemoveFeatures, CSequenceEditingEventHandler::RemoveFeatures )
1761  EVT_MENU( eCmdFixForTransSplicing, CSequenceEditingEventHandler::FixForTransSplicing )
1762  EVT_MENU( eCmdRemoveDuplicateGOTerms, CSequenceEditingEventHandler::RemoveDuplicateGoTerms)
1763  EVT_MENU( eCmdRemoveUnindexedFeatures, CSequenceEditingEventHandler::RemoveUnindexedFeatures )
1764  EVT_MENU( eCmdApplyIndexerComments, CSequenceEditingEventHandler::ApplyIndexerComments )
1765  EVT_MENU( eCmdRemoveSeqAnnotIds, CSequenceEditingEventHandler::RemoveSeqAnnotIds )
1766  EVT_MENU( eCmdRemoveCddFeatDbxref, CSequenceEditingEventHandler::RemoveCddFeatDbxref )
1767  EVT_MENU( eCmdRemoveBankitComment, CSequenceEditingEventHandler::RemoveBankitComment )
1768  EVT_MENU( eCmdRemoveDuplicateStructuredComments, CSequenceEditingEventHandler::RemoveDuplicateStructuredComments )
1769  EVT_MENU( eCmdRemoveSequencesFromAlignments, CSequenceEditingEventHandler::RemoveSequencesFromAlignments )
1770  EVT_MENU( eCmdRemoveSequences, CSequenceEditingEventHandler::RemoveSequences )
1771  EVT_MENU( eCmdRemoveSequences_ext, CSequenceEditingEventHandler::RemoveSequences )
1772  EVT_MENU( eCmdJustRemoveProteins, CSequenceEditingEventHandler::JustRemoveProteins )
1773  EVT_MENU( eCmdRemoveProteinsAndRenormalizeNucProtSets, CSequenceEditingEventHandler::RemoveProteinsAndRenormalizeNucProtSets )
1774  EVT_MENU( eCmdRemoveOrphanedProteins, CSequenceEditingEventHandler::RemoveOrphanedProteins )
1775  EVT_MENU( eCmdRemoveSet, CSequenceEditingEventHandler::RemoveSet)
1776  EVT_MENU( eCmdRemoveSetsFromSet, CSequenceEditingEventHandler::RemoveSetsFromSet)
1777  EVT_MENU( eCmdRevCompSequences, CSequenceEditingEventHandler::RevCompSequences )
1778  EVT_MENU( eCmdRevCompSequences_ext, CSequenceEditingEventHandler::RevCompSequences )
1779  EVT_MENU( eCmdBioseqFeatsRevComp, CSequenceEditingEventHandler::BioseqFeatsRevComp)
1780  EVT_MENU( eCmdBioseqOnlyRevComp, CSequenceEditingEventHandler::BioseqOnlyRevComp)
1781  EVT_MENU( eCmdUnculTaxTool, CSequenceEditingEventHandler::UnculTaxTool )
1782  EVT_MENU( eCmdMergeBiosources, CSequenceEditingEventHandler::MergeBiosources)
1783  EVT_MENU( eCmdCompareWithBiosample, CSequenceEditingEventHandler::CompareWithBiosample)
1784  EVT_MENU( eCmdCompareWithBiosampleFirstOnly, CSequenceEditingEventHandler::CompareWithBiosampleFirstOnly)
1785  EVT_MENU( eCmdConsolidateLikeModsWithSemicolon, CSequenceEditingEventHandler::ConsolidateLikeModsWithSemicolon)
1786  EVT_MENU( eCmdConsolidateLikeModsWithoutSemicolon, CSequenceEditingEventHandler::ConsolidateLikeModsWithoutSemicolon)
1787  EVT_MENU( eCmdBarcodeTool, CSequenceEditingEventHandler::BarcodeTool)
1788  EVT_MENU( eCmdApplyFBOL, CSequenceEditingEventHandler::ApplyFBOL)
1789  EVT_MENU( eCmdEditSequence, CSequenceEditingEventHandler::EditSequence )
1790  EVT_MENU( eCmdAlignmentAssistant, CSequenceEditingEventHandler::AlignmentAssistant )
1791  EVT_MENU( eCmdRemoveAlignments, CSequenceEditingEventHandler::RemoveSeqAnnotAlign )
1792  EVT_MENU( eCmdRemoveGraphs, CSequenceEditingEventHandler::RemoveSeqAnnotGraph )
1793  EVT_MENU( eCmdRemoveGenomeProjectId, CSequenceEditingEventHandler::RemoveGenomeProjectsDB )
1794  EVT_MENU( eCmdRemoveEmptyGenomeProjectId, CSequenceEditingEventHandler::RemoveEmptyGenomeProjectsDB )
1795  EVT_MENU( eCmdTaxFixCleanup, CSequenceEditingEventHandler::TaxFixCleanup )
1796  EVT_MENU( eCmdTaxFixCleanup_ext, CSequenceEditingEventHandler::TaxFixCleanup )
1797  EVT_MENU( eCmdSpecificHostCleanup, CSequenceEditingEventHandler::SpecificHostCleanup )
1798  EVT_MENU( eCmdExtendedCleanup, CSequenceEditingEventHandler::TaxFixCleanup )
1799  EVT_MENU( eCmdFixNonReciprocalLinks, CSequenceEditingEventHandler::FixNonReciprocalLinks )
1800  EVT_MENU( eCmdDisableStrainForwarding, CSequenceEditingEventHandler::DisableStrainForwarding )
1801  EVT_MENU (eCmdEnableStrainForwarding, CSequenceEditingEventHandler::EnableStrainForwarding)
1802  EVT_MENU( eCmdEditPubs, CSequenceEditingEventHandler::EditPubs )
1803  EVT_MENU( eCmdGlobalPubmedIdLookup, CSequenceEditingEventHandler::GlobalPubmedIdLookup )
1804  EVT_MENU( eCmdFixCapitalizationAll, CSequenceEditingEventHandler::FixCapitalizationAll )
1805  EVT_MENU( eCmdFixCapitalizationAuthors, CSequenceEditingEventHandler::FixCapitalizationAuthors )
1806  EVT_MENU( eCmdFixCapitalizationTitles, CSequenceEditingEventHandler::FixCapitalizationTitles )
1807  EVT_MENU( eCmdFixCapitalizationAffiliation, CSequenceEditingEventHandler::FixCapitalizationAffiliation )
1808  EVT_MENU( eCmdFixCapitalizationCountry, CSequenceEditingEventHandler::FixCapitalizationCountry )
1809  EVT_MENU( eCmdRemoveUnpublishedPublications, CSequenceEditingEventHandler::RemoveUnpublishedPublications )
1810  EVT_MENU( eCmdRemoveInPressPublications, CSequenceEditingEventHandler::RemoveInPressPublications )
1811  EVT_MENU( eCmdRemovePublishedPublications, CSequenceEditingEventHandler::RemovePublishedPublications )
1812  EVT_MENU( eCmdRemoveCollidingPublications, CSequenceEditingEventHandler::RemoveCollidingPublications )
1813  EVT_MENU( eCmdRemoveAllPublications, CSequenceEditingEventHandler::RemoveAllPublications )
1814  EVT_MENU( eCmdRemoveAuthorConsortiums, CSequenceEditingEventHandler::RemoveAuthorConsortiums )
1815  EVT_MENU( eCmdReverseAuthorNames, CSequenceEditingEventHandler::ReverseAuthorNames )
1816  EVT_MENU( eCmdStripAuthorSuffixes, CSequenceEditingEventHandler::StripAuthorSuffixes )
1817  EVT_MENU( eCmdTruncateAuthorMiddleInitials, CSequenceEditingEventHandler::TruncateAuthorMiddleInitials )
1818  EVT_MENU( eCmdConvertAuthorToConstortiumWhereLastName, CSequenceEditingEventHandler::ConvertAuthorToConstortiumWhereLastName )
1819  EVT_MENU( eCmdConvertAuthorToConsortiumAll, CSequenceEditingEventHandler::ConvertAuthorToConsortiumAll )
1820  EVT_MENU( eCmdAddCitSubForUpdate, CSequenceEditingEventHandler::AddCitSubForUpdate )
1821  EVT_MENU( eCmdFixUsaAndStates, CSequenceEditingEventHandler::FixUsaAndStates )
1822  EVT_MENU( eCmdRetranslateCDSObeyStop, CSequenceEditingEventHandler::RetranslateCDS )
1823  EVT_MENU( eCmdRetranslateCDSIgnoreStopExceptEnd, CSequenceEditingEventHandler::RetranslateCDS )
1824  EVT_MENU( eCmdRetranslateCDSIgnoreStopExceptEnd_ext, CSequenceEditingEventHandler::RetranslateCDS )
1825  EVT_MENU( eCmdRetranslateCDSChooseFrame, CSequenceEditingEventHandler::RetranslateCDS )
1826  EVT_MENU( eCmdEditCdsFrame, CSequenceEditingEventHandler::EditCdsFrame)
1827  EVT_MENU( eCmdRestoreRNAediting, CSequenceEditingEventHandler::RestoreRNAediting)
1828  EVT_MENU( eCmdResynchronizePartialsCDS, CSequenceEditingEventHandler::ResynchronizePartials )
1829  EVT_MENU( eCmdAddTranslExcept, CSequenceEditingEventHandler::AddTranslExcept )
1830  EVT_MENU( eCmdRemoveAllStructuredComments, CSequenceEditingEventHandler::RemoveAllStructuredComments )
1831  EVT_MENU( eCmdRemoveEmptyStructuredComments, CSequenceEditingEventHandler::RemoveEmptyStructuredComments )
1832  EVT_MENU( eCmdModifyStructuredComment, CSequenceEditingEventHandler::ModifyStructuredComment )
1833  EVT_MENU( eCmdSetGlobalRefGeneStatus, CSequenceEditingEventHandler::SetGlobalRefGeneStatus )
1834  EVT_MENU( eCmdClearKeywords, CSequenceEditingEventHandler::ClearKeywords )
1835  EVT_MENU( eCmdClearNomenclature, CSequenceEditingEventHandler::ClearNomenclature )
1836  EVT_MENU( eCmdConvertToDelayedGenProdSetQuals, CSequenceEditingEventHandler::ConvertToDelayedGenProdSetQuals )
1837  EVT_MENU( eCmdConvertRptUnitRangeToLoc, CSequenceEditingEventHandler::ConvertRptUnitRangeToLoc )
1838  EVT_MENU( eCmdRemoveStructuredCommentKeyword, CSequenceEditingEventHandler::RemoveStructuredCommentKeyword )
1839  EVT_MENU( eCmdAddStructuredCommentKeyword, CSequenceEditingEventHandler::AddStructuredCommentKeyword )
1840  EVT_MENU( eCmdAddKeywordGDS, CSequenceEditingEventHandler::AddKeywordGDS )
1841  EVT_MENU( eCmdAddKeywordTPA_inferential, CSequenceEditingEventHandler::AddKeywordTPA_inferential )
1842  EVT_MENU( eCmdAddKeywordTPA_experimental, CSequenceEditingEventHandler::AddKeywordTPA_experimental )
1843  EVT_MENU( eCmdAddKeywordTPA_assembly, CSequenceEditingEventHandler::AddKeywordTPA_assembly )
1844  EVT_MENU( eCmdAddKeywordWithConstraint, CSequenceEditingEventHandler::AddKeywordWithConstraint )
1845  EVT_MENU( eCmdAddGenomeAssemblyStructuredComment, CSequenceEditingEventHandler::AddGenomeAssemblyStructuredComment )
1846  EVT_MENU( eCmdAddAssemblyStructuredComment, CSequenceEditingEventHandler::AddAssemblyStructuredComment )
1847  EVT_MENU( eCmdReorderStructuredComment, CSequenceEditingEventHandler::ReorderStructuredComment )
1848  EVT_MENU( eCmdConvertComment, CSequenceEditingEventHandler::ConvertComment )
1849  EVT_MENU( eCmdParseComment, CSequenceEditingEventHandler::ParseComment )
1850  EVT_MENU( eCmdExportStructuredCommentsTable, CSequenceEditingEventHandler::ExportStructuredCommentsTable)
1851  EVT_MENU( eCmdLoadStructComments, CSequenceEditingEventHandler::LoadStructComments)
1852  EVT_MENU( eCmdIllegalQualsToNote, CSequenceEditingEventHandler::IllegalQualsToNote )
1853  EVT_MENU( eCmdRmIllegalQuals, CSequenceEditingEventHandler::RmIllegalQuals )
1854  EVT_MENU( eCmdWrongQualsToNote, CSequenceEditingEventHandler::WrongQualsToNote )
1855  EVT_MENU( eCmdConvertBadInference, CSequenceEditingEventHandler::ConvertBadInference)
1856  EVT_MENU( eCmdRmWrongQuals, CSequenceEditingEventHandler::RmWrongQuals )
1857  EVT_MENU( eCmdRemoveDbXrefsCDS, CSequenceEditingEventHandler::RemoveDbXrefsCDS )
1858  EVT_MENU( eCmdRemoveDbXrefsGenes, CSequenceEditingEventHandler::RemoveDbXrefsGenes )
1859  EVT_MENU( eCmdRemoveDbXrefsRNA, CSequenceEditingEventHandler::RemoveDbXrefsRNA )
1860  EVT_MENU( eCmdRemoveDbXrefsAllFeats, CSequenceEditingEventHandler::RemoveDbXrefsAllFeats )
1861  EVT_MENU( eCmdRemoveDbXrefsBioSource, CSequenceEditingEventHandler::RemoveDbXrefsBioSource )
1862  EVT_MENU( eCmdRemoveDbXrefsBioSourceAndFeats, CSequenceEditingEventHandler::RemoveDbXrefsBioSourceAndFeats )
1863  EVT_MENU( eCmdRemoveTaxonFeats, CSequenceEditingEventHandler::RemoveTaxonFeats)
1864  EVT_MENU( eCmdRemoveTaxonFeatsAndBioSource, CSequenceEditingEventHandler::RemoveTaxonFeatsAndBioSource)
1865  EVT_MENU( eCmdGroupExplode, CSequenceEditingEventHandler::GroupExplode )
1866  EVT_MENU( eCmdFindASN1, CSequenceEditingEventHandler::FindASN1 )
1867  EVT_MENU( eCmdFuseFeatures, CSequenceEditingEventHandler::FuseFeatures )
1868  EVT_MENU( eCmdFuseJoinsInLocs, CSequenceEditingEventHandler::FuseJoinsInLocs )
1869  EVT_MENU( eCmdExplodeRNAFeats, CSequenceEditingEventHandler::ExplodeRNAFeats )
1870  EVT_MENU( eCmdAssignFeatureIds, CSequenceEditingEventHandler::AssignFeatureIds )
1871  EVT_MENU( eCmdClearFeatureIds, CSequenceEditingEventHandler::ClearFeatureIds )
1872  EVT_MENU( eCmdReassignFeatureIds, CSequenceEditingEventHandler::ReassignFeatureIds )
1873  EVT_MENU( eCmdUniqifyFeatureIds, CSequenceEditingEventHandler::UniqifyFeatureIds )
1874  EVT_MENU( eCmdTrimJunkInPrimerSeqs, CSequenceEditingEventHandler::TrimJunkInPrimerSeqs )
1875  EVT_MENU( eCmdFixiInPrimerSeqs, CSequenceEditingEventHandler::FixiInPrimerSeqs )
1876  EVT_MENU( eCmdPrefixAuthWithTax, CSequenceEditingEventHandler::PrefixAuthWithTax)
1877  EVT_MENU( eCmdFocusSet, CSequenceEditingEventHandler::FocusSet )
1878  EVT_MENU( eCmdFocusClear, CSequenceEditingEventHandler::FocusClear )
1879  EVT_MENU( eCmdSetTransgSrcDesc, CSequenceEditingEventHandler::SetTransgSrcDesc )
1880  EVT_MENU( eCmdSplitDblinkQuals, CSequenceEditingEventHandler::SplitDblinkQuals )
1881  EVT_MENU( eCmdFixOrgModInstitution, CSequenceEditingEventHandler::FixOrgModInstitution )
1882  EVT_MENU( eCmdFixStructuredVouchers, CSequenceEditingEventHandler::FixStructuredVouchers )
1883  EVT_MENU( eCmdSwapPrimerSeqName, CSequenceEditingEventHandler::SwapPrimerSeqName )
1884  EVT_MENU( eCmdMergePrimerSets, CSequenceEditingEventHandler::MergePrimerSets )
1885  EVT_MENU( eCmdSplitPrimerSets, CSequenceEditingEventHandler::SplitPrimerSets )
1886  EVT_MENU( eCmdAppendModToOrg, CSequenceEditingEventHandler::AppendModToOrg )
1887  EVT_MENU( eCmdParseCollectionDateMonthFirst, CSequenceEditingEventHandler::ParseCollectionDateMonthFirst )
1888  EVT_MENU( eCmdParseCollectionDateDayFirst, CSequenceEditingEventHandler::ParseCollectionDateDayFirst )
1889  EVT_MENU( eCmdCountryFixupCap, CSequenceEditingEventHandler::CountryFixupCap )
1890  EVT_MENU( eCmdCountryFixupNoCap, CSequenceEditingEventHandler::CountryFixupNoCap )
1891  EVT_MENU( eCmdVectorTrim, CSequenceEditingEventHandler::VectorTrim )
1892  EVT_MENU( eCmdSelectTarget, CSequenceEditingEventHandler::SelectTarget )
1893  EVT_MENU( eCmdSelectTarget_ext, CSequenceEditingEventHandler::SelectTarget )
1894  EVT_MENU( eCmdSelectFeature, CSequenceEditingEventHandler::SelectFeature )
1895  EVT_MENU( eCmdApplyCDS, CSequenceEditingEventHandler::AddCDS )
1896  EVT_MENU( eCmdApplyAddRNA, CSequenceEditingEventHandler::AddRNA )
1897  EVT_MENU( eCmdApplyAddOther, CSequenceEditingEventHandler::AddOtherFeature )
1898  EVT_MENU( eCmdApplyAddOther_ext, CSequenceEditingEventHandler::AddOtherFeature )
1899  EVT_MENU( eCmdAddFeatureBetween, CSequenceEditingEventHandler::AddFeatureBetween )
1900  EVT_MENU( eCmdValidate, CSequenceEditingEventHandler::Validate )
1901  EVT_MENU( eCmdValidate_ext, CSequenceEditingEventHandler::Validate)
1902  EVT_MENU( eCmdValidateNoAlignments, CSequenceEditingEventHandler::Validate )
1903  EVT_MENU( eCmdValidateCheckInferences, CSequenceEditingEventHandler::Validate )
1904  EVT_MENU( eCmdSortUniqueCountText, CSequenceEditingEventHandler::SortUniqueCount )
1905  EVT_MENU( eCmdSortUniqueCountTree, CSequenceEditingEventHandler::SortUniqueCountTree )
1906  EVT_MENU( eCmdSortUniqueCountTree_ext, CSequenceEditingEventHandler::SortUniqueCountTree )
1907  EVT_MENU( eCmdDiscrepancy, CSequenceEditingEventHandler::Discrepancy)
1908  EVT_MENU( eCmdOncaller, CSequenceEditingEventHandler::Oncaller)
1909  EVT_MENU( eCmdSubmitter, CSequenceEditingEventHandler::Submitter)
1910  EVT_MENU( eCmdSubmitter_ext, CSequenceEditingEventHandler::Submitter)
1911  EVT_MENU( eCmdMega, CSequenceEditingEventHandler::Mega)
1912  EVT_MENU( eCmdDiscrepancyList, CSequenceEditingEventHandler::DiscrepancyList)
1913  EVT_MENU( eCmdAutodefDefaultOptions, CSequenceEditingEventHandler::Autodef)
1914  EVT_MENU( eCmdAutodefOptions, CSequenceEditingEventHandler::Autodef )
1915  EVT_MENU( eCmdAutodefMisc, CSequenceEditingEventHandler::Autodef )
1916  EVT_MENU( eCmdAutodefId, CSequenceEditingEventHandler::Autodef )
1917  EVT_MENU( eCmdAutodefNoMods, CSequenceEditingEventHandler::Autodef )
1918  EVT_MENU( eCmdAutodefPopset, CSequenceEditingEventHandler::Autodef )
1919  EVT_MENU( eCmdAutodefRefresh, CSequenceEditingEventHandler::Autodef)
1920  EVT_MENU( eCmdInstantiateProteinTitles, CSequenceEditingEventHandler::PT_Cleanup )
1921  EVT_MENU( eCmdRemoveAllFeatures, CSequenceEditingEventHandler::RemoveAllFeatures )
1922  EVT_MENU( eCmdRemoveDupFeats, CSequenceEditingEventHandler::RemoveDupFeats )
1923  EVT_MENU( eCmdRemoveDupFeats_ext, CSequenceEditingEventHandler::RemoveDupFeats )
1924  EVT_MENU( eCmdRemoveDupFeatsWithOptions, CSequenceEditingEventHandler::RemoveDupFeatsWithOptions )
1925  EVT_MENU( eCmdRemoveDupFeatsWithOptions_ext, CSequenceEditingEventHandler::RemoveDupFeatsWithOptions )
1926  EVT_MENU( eCmdResolveIntersectingFeats, CSequenceEditingEventHandler::ResolveIntersectingFeats )
1927  EVT_MENU( eCmdAddSequences, CSequenceEditingEventHandler::AddSequences )
1928  EVT_MENU (eCmdApplySourceQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1929  EVT_MENU (eCmdEditSourceQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1930  EVT_MENU (eCmdConvertSourceQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1931  EVT_MENU (eCmdSwapSourceQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1932  EVT_MENU (eCmdRemoveSourceQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1933  EVT_MENU (eCmdApplyRNAQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1934  EVT_MENU (eCmdEditRNAQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1935  EVT_MENU (eCmdConvertRNAQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1936  EVT_MENU (eCmdSwapRNAQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1937  EVT_MENU (eCmdRemoveRNAQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1938  EVT_MENU (eCmdApplyCGPQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1939  EVT_MENU (eCmdEditCGPQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1940  EVT_MENU (eCmdConvertCGPQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1941  EVT_MENU (eCmdSwapCGPQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1942  EVT_MENU (eCmdRemoveCGPQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1943  EVT_MENU (eCmdApplyFeatQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1944  EVT_MENU (eCmdEditFeatQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1945  EVT_MENU (eCmdConvertFeatQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1946  EVT_MENU (eCmdConvertSecondProtNameToDesc, CSequenceEditingEventHandler::ConvertSecondProtNameToDesc)
1947  EVT_MENU (eCmdConvertDescToSecondProtName, CSequenceEditingEventHandler::ConvertDescToSecondProtName)
1948  EVT_MENU (eCmdConvertDescToFeatComment, CSequenceEditingEventHandler::ConvertDescToFeatComment)
1949  EVT_MENU (eCmdConvertDescToFeatSource, CSequenceEditingEventHandler::ConvertDescToFeatSource)
1950  EVT_MENU (eCmdConvertDescToFeatPub, CSequenceEditingEventHandler::ConvertDescToFeatPub)
1951  EVT_MENU (eCmdConvertDescToFeatPubConstraint, CSequenceEditingEventHandler::ConvertDescToFeatPubConstraint)
1952  EVT_MENU (eCmdConvertFeatToDescComment, CSequenceEditingEventHandler::ConvertFeatToDescComment)
1953  EVT_MENU (eCmdConvertFeatToDescSource, CSequenceEditingEventHandler::ConvertFeatToDescSource)
1954  EVT_MENU (eCmdConvertFeatToDescPub, CSequenceEditingEventHandler::ConvertFeatToDescPub)
1955  EVT_MENU (eCmdSwapFeatQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1956  EVT_MENU (eCmdRemoveFeatQual, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1957  EVT_MENU (eCmdRemoveTextOutsideString, CSequenceEditingEventHandler::ApplyEditConvertRemove )
1958  EVT_MENU (eCmdEditFeatEv, CSequenceEditingEventHandler::EditFeature )
1959  EVT_MENU (eCmdEditFeatLoc, CSequenceEditingEventHandler::EditFeature )
1960  EVT_MENU (eCmdEditFeatLoc_ext, CSequenceEditingEventHandler::EditFeature )
1961  EVT_MENU (eCmdEditFeatStrand, CSequenceEditingEventHandler::EditFeature )
1962  EVT_MENU (eCmdEditFeatStrand_ext, CSequenceEditingEventHandler::EditFeature )
1963  EVT_MENU (eCmdEditFeatRevInt, CSequenceEditingEventHandler::EditFeature )
1964  EVT_MENU (eCmdEditFeatPseudo, CSequenceEditingEventHandler::EditFeature )
1965  EVT_MENU (eCmdEditFeatException, CSequenceEditingEventHandler::EditFeature )
1966  EVT_MENU (eCmdEditFeatExperiment, CSequenceEditingEventHandler::EditFeature )
1967  EVT_MENU (eCmdEditFeatInference, CSequenceEditingEventHandler::EditFeature )
1968  EVT_MENU (eCmdExtendPartialsConstr, CSequenceEditingEventHandler::ExtendPartialsConstr )
1969  EVT_MENU (eCmdExtendPartialsAll, CSequenceEditingEventHandler::ExtendPartialsAll )
1970  EVT_MENU (eCmdGeneFromOtherFeat, CSequenceEditingEventHandler::GeneFromOtherFeat )
1971  EVT_MENU (eCmdGeneFeatFromXrefs, CSequenceEditingEventHandler::GeneFeatFromXrefs )
1972  EVT_MENU (eCmdGeneXrefsFromFeats, CSequenceEditingEventHandler::GeneXrefsFromFeats)
1973  EVT_MENU (eCmdRemoveAllGeneXrefs, CSequenceEditingEventHandler::RemoveAllGeneXrefs )
1974  EVT_MENU (eCmdRemoveUnnecessaryGeneXrefs, CSequenceEditingEventHandler::RemoveUnnecessaryGeneXrefs )
1975  EVT_MENU (eCmdRemoveNonsuppressingGeneXrefs, CSequenceEditingEventHandler::RemoveNonsuppressingGeneXrefs )
1976  EVT_MENU (eCmdRemoveOrphanLocusGeneXrefs, CSequenceEditingEventHandler::RemoveOrphanLocusGeneXrefs )
1977  EVT_MENU (eCmdRemoveOrphanLocus_tagGeneXrefs, CSequenceEditingEventHandler::RemoveOrphanLocus_tagGeneXrefs )
1978  EVT_MENU (eCmdRemoveGeneXrefs, CSequenceEditingEventHandler::RemoveGeneXrefs )
1979  EVT_MENU (eCmdExtendCDS, CSequenceEditingEventHandler::ExtendCDS )
1980  EVT_MENU (eCmdTruncateCDS, CSequenceEditingEventHandler::TruncateCDS )
1981  EVT_MENU (eCmdExtendCDSToStop, CSequenceEditingEventHandler::ExtendCDSToStop)
1982  EVT_MENU (eCmdRecomputeIntervalsAndUpdateGenes, CSequenceEditingEventHandler::RecomputeIntervalsAndUpdateGenes)
1983  EVT_MENU (eCmdRecomputeIntervals, CSequenceEditingEventHandler::RecomputeIntervals)
1984  EVT_MENU (eCmdCdsFromGeneMrnaExon, CSequenceEditingEventHandler::CdsFromGeneMrnaExon )
1985  EVT_MENU (eCmdmRNAFromGeneCdsExon, CSequenceEditingEventHandler::mRNAFromGeneCdsExon)
1986  EVT_MENU (eCmdtRNAFromGene, CSequenceEditingEventHandler::tRNAFromGene)
1987  EVT_MENU (eCmdExonFromCds, CSequenceEditingEventHandler::ExonFromCds )
1988  EVT_MENU (eCmdExonFromMRNA, CSequenceEditingEventHandler::ExonFromMRNA )
1989  EVT_MENU (eCmdExonFromTRNA, CSequenceEditingEventHandler::ExonFromTRNA )
1990  EVT_MENU (eCmdFixProductNamesDefault, CSequenceEditingEventHandler::FixProductNamesDefault )
1991  EVT_MENU (eCmdFixProductNamesOptions, CSequenceEditingEventHandler::FixProductNamesOptions)
1992  EVT_MENU (eCmdBulkApplyGenCode, CSequenceEditingEventHandler::BulkApplyGenCode)
1993  EVT_MENU (eCmdEditSeqEndsWithAlign, CSequenceEditingEventHandler::EditSeqEndsWithAlign)
1994  EVT_MENU (eCmdEditSequenceEnds, CSequenceEditingEventHandler::EditSequenceEnds)
1995  EVT_MENU (eCmdUpdateAlign, CSequenceEditingEventHandler::UpdateAlign)
1996  EVT_MENU (eCmdSaveDescriptors, CSequenceEditingEventHandler::SaveDescriptors)
1997  EVT_MENU (eCmdCreateSeqHistForTpaDetailed, CSequenceEditingEventHandler::CreateSeqHistForTpaDetailed)
1998  EVT_MENU (eCmdCreateSeqHistForTpa, CSequenceEditingEventHandler::CreateSeqHistForTpa)
1999  EVT_MENU (eCmdRemoveSeqHistAssembly, CSequenceEditingEventHandler::RemoveSeqHistAssembly)
2000  EVT_MENU (eCmdFarPointerSeq, CSequenceEditingEventHandler::FarPointerSeq)
2001  EVT_MENU (eCmdConvertBadCdsAndRnaToMiscFeat, CSequenceEditingEventHandler::ConvertBadCdsAndRnaToMiscFeat)
2002  EVT_MENU (eCmdCreateProteinId, CSequenceEditingEventHandler::CreateProteinId)
2003  EVT_MENU (eCmdCreateLocusTagGene, CSequenceEditingEventHandler::CreateLocusTagGene)
2004  EVT_MENU (eCmdNormalizeGeneQuals, CSequenceEditingEventHandler::NormalizeGeneQuals)
2005  EVT_MENU (eCmdGenusSpeciesFixup, CSequenceEditingEventHandler::GenusSpeciesFixup)
2006  EVT_MENU (eCmdCountryConflict, CSequenceEditingEventHandler::CountryConflict)
2007  EVT_MENU (eCmdDuplicate, CSequenceEditingEventHandler::Duplicate)
2008  EVT_MENU (eCmdCorrectIntervalOrder, CSequenceEditingEventHandler::CorrectIntervalOrder)
2009  EVT_MENU (eCmdAddSecondary, CSequenceEditingEventHandler::AddSecondary)
2010  EVT_MENU (eCmdPackageFeaturesOnParts, CSequenceEditingEventHandler::PackageFeaturesOnParts)
2011  EVT_MENU (eCmdParseText, CSequenceEditingEventHandler::ParseText )
2012  EVT_MENU (eCmdParseTextFromDefline, CSequenceEditingEventHandler::ParseText )
2013  EVT_MENU (eCmdRemoveTextInsideStr, CSequenceEditingEventHandler::RemoveTextInsideStr )
2014  EVT_MENU (eCmdParseLocalToSrc, CSequenceEditingEventHandler::ParseText )
2015  EVT_MENU (eCmdLowercaseQuals, CSequenceEditingEventHandler::LowercaseQuals )
2016  EVT_MENU (eCmdConvertFeatures, CSequenceEditingEventHandler::ConvertFeatures )
2017  EVT_MENU (eCmdCdsToMatPeptide, CSequenceEditingEventHandler::CdsToMatPeptide )
2018  EVT_MENU (eCmdConvertCdsToMiscFeat, CSequenceEditingEventHandler::ConvertCdsToMiscFeat )
2019  EVT_MENU (eCmdConvertCdsWithInternalStopToMiscFeat, CSequenceEditingEventHandler::ConvertCdsWithInternalStopToMiscFeat )
2020  EVT_MENU (eCmdConvertCdsWithInternalStopToMiscFeatViral, CSequenceEditingEventHandler::ConvertCdsWithInternalStopToMiscFeatViral )
2021  EVT_MENU (eCmdConvertCdsWithInternalStopToMiscFeatUnverified, CSequenceEditingEventHandler::ConvertCdsWithInternalStopToMiscFeatUnverified )
2022  EVT_MENU (eCmdConvertCdsWithGapsToMiscFeat, CSequenceEditingEventHandler::ConvertCdsWithGapsToMiscFeat )
2023  EVT_MENU (eCmdTableReader, CSequenceEditingEventHandler::TableReader )
2024  EVT_MENU (eCmdTableReader_ext, CSequenceEditingEventHandler::TableReader)
2025  EVT_MENU (eCmdTableReaderClipboard, CSequenceEditingEventHandler::TableReaderClipboard )
2026  EVT_MENU (eCmdBulkSourceEdit, CSequenceEditingEventHandler::BulkEdit )
2027  EVT_MENU (eCmdBulkCdsEdit, CSequenceEditingEventHandler::BulkCdsEdit )
2028  EVT_MENU (eCmdBulkGeneEdit, CSequenceEditingEventHandler::BulkGeneEdit )
2029  EVT_MENU (eCmdBulkRnaEdit, CSequenceEditingEventHandler::BulkRnaEdit )
2030  EVT_MENU (eCmdBulkMiscFeatEdit, CSequenceEditingEventHandler::BulkMiscFeatEdit)
2031  EVT_MENU (eCmdLatLonTool, CSequenceEditingEventHandler::LatLonTool )
2032  EVT_MENU (eCmdCDSGeneRangeErrorSuppress, CSequenceEditingEventHandler::CDSGeneRangeErrorSuppress )
2033  EVT_MENU (eCmdCDSGeneRangeErrorRestore, CSequenceEditingEventHandler::CDSGeneRangeErrorRestore )
2034  EVT_MENU (eCmdSuppressGenes, CSequenceEditingEventHandler::SuppressGenes)
2035  EVT_MENU (eCmdCorrectGenes, CSequenceEditingEventHandler::CorrectGenes )
2036  EVT_MENU (eCmdSegregateSets, CSequenceEditingEventHandler::SegregateSets )
2037  EVT_MENU (eCmdSequesterSets, CSequenceEditingEventHandler::SequesterSets )
2038  EVT_MENU (eCmdDescriptorPropagateDown, CSequenceEditingEventHandler::DescriptorPropagateDown )
2039  EVT_MENU (eCmdReorderSeqById, CSequenceEditingEventHandler::ReorderSeqById )
2040  EVT_MENU (eCmdCombineSelectedGenesIntoPseudogenes, CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes )
2041  EVT_MENU (eCmdWithdrawSequences, CSequenceEditingEventHandler::WithdrawSequences )
2042  EVT_MENU (eCmdAddSet, CSequenceEditingEventHandler::AddSet )
2043  EVT_MENU (eCmdPropagateDBLink, CSequenceEditingEventHandler::PropagateDBLink )
2044  EVT_MENU (eCmdChangeSetClass, CSequenceEditingEventHandler::ConvertSetType )
2045  EVT_MENU (eCmdMolInfoEdit, CSequenceEditingEventHandler::MolInfoEdit )
2046  EVT_MENU (eCmdExportTable, CSequenceEditingEventHandler::ExportTable )
2047  EVT_MENU (eCmdParseStrainSerotypeFromNames, CSequenceEditingEventHandler::ParseStrainSerotypeFromNames)
2048  EVT_MENU (eCmdAddStrainSerotypeToNames, CSequenceEditingEventHandler::AddStrainSerotypeToNames )
2049  EVT_MENU (eCmdFixupOrganismNames, CSequenceEditingEventHandler::FixupOrganismNames)
2050  EVT_MENU (eCmdSplitQualifiersAtCommas, CSequenceEditingEventHandler::SplitQualifiersAtCommas)
2051  EVT_MENU (eCmdSplitStructuredCollections, CSequenceEditingEventHandler::SplitStructuredCollections)
2052  EVT_MENU (eCmdTrimOrganismNames, CSequenceEditingEventHandler::TrimOrganismNames)
2053  EVT_MENU (eCmdRemoveUnverified, CSequenceEditingEventHandler::RemoveUnverified )
2054  EVT_MENU (eCmdRemoveUnreviewed, CSequenceEditingEventHandler::RemoveUnreviewed )
2055  EVT_MENU (eCmdAddNamedrRNA12S, CSequenceEditingEventHandler::AddNamedrRNA)
2056  EVT_MENU (eCmdAddNamedrRNA16S, CSequenceEditingEventHandler::AddNamedrRNA)
2057  EVT_MENU (eCmdAddNamedrRNA23S, CSequenceEditingEventHandler::AddNamedrRNA)
2058  EVT_MENU (eCmdAddNamedrRNA18S, CSequenceEditingEventHandler::AddNamedrRNA)
2059  EVT_MENU (eCmdAddNamedrRNA28S, CSequenceEditingEventHandler::AddNamedrRNA)
2060  EVT_MENU (eCmdAddNamedrRNA26S, CSequenceEditingEventHandler::AddNamedrRNA)
2061  EVT_MENU (eCmdAddNamedrRNASmall, CSequenceEditingEventHandler::AddNamedrRNA)
2062  EVT_MENU (eCmdAddNamedrRNALarge, CSequenceEditingEventHandler::AddNamedrRNA)
2063  EVT_MENU (eCmdAddControlRegion, CSequenceEditingEventHandler::AddControlRegion)
2064  EVT_MENU (eCmdAddMicrosatellite, CSequenceEditingEventHandler::AddMicrosatellite)
2065  EVT_MENU (eCmdCreateGene, CSequenceEditingEventHandler::CreateFeature)
2066  EVT_MENU (eCmdCreateLTR, CSequenceEditingEventHandler::CreateFeature)
2067  EVT_MENU (eCmdCreateProt, CSequenceEditingEventHandler::CreateFeature)
2068  EVT_MENU (eCmdCreateSecondaryStructure, CSequenceEditingEventHandler::CreateFeature)
2069  EVT_MENU (eCmdCreateRegion, CSequenceEditingEventHandler::CreateFeature)
2070  EVT_MENU (eCmdCreatePubFeatureLabeled, CSequenceEditingEventHandler::CreateFeature)
2071  EVT_MENU (eCmdCreateStemLoop, CSequenceEditingEventHandler::CreateFeature)
2072  EVT_MENU (eCmdCreateSTS, CSequenceEditingEventHandler::CreateFeature)
2073  EVT_MENU (eCmdCreateCodingRegion, CSequenceEditingEventHandler::CreateFeature)
2074  EVT_MENU (eCmdCreateCodingRegion_ext, CSequenceEditingEventHandler::CreateFeature)
2075  EVT_MENU (eCmdCreateRepeatRegion, CSequenceEditingEventHandler::CreateFeature)
2076  EVT_MENU (eCmdCreateVariation, CSequenceEditingEventHandler::CreateFeature)
2077  EVT_MENU (eCmdCreateOperon, CSequenceEditingEventHandler::CreateFeature)
2078  EVT_MENU (eCmdCreateMobileElement, CSequenceEditingEventHandler::CreateFeature)
2079  EVT_MENU (eCmdCreateCentromere, CSequenceEditingEventHandler::CreateFeature)
2080  EVT_MENU (eCmdCreateTelomere, CSequenceEditingEventHandler::CreateFeature)
2081  EVT_MENU (eCmdCreateRegulatory, CSequenceEditingEventHandler::CreateFeature)
2082  EVT_MENU (eCmdCreateRegulatory_promoter, CSequenceEditingEventHandler::CreateRegulatory)
2083  EVT_MENU (eCmdCreateRegulatory_enhancer, CSequenceEditingEventHandler::CreateRegulatory)
2084  EVT_MENU (eCmdCreateRegulatory_ribosome_binding_site, CSequenceEditingEventHandler::CreateRegulatory)
2085  EVT_MENU (eCmdCreateRegulatory_riboswitch, CSequenceEditingEventHandler::CreateRegulatory)
2086  EVT_MENU (eCmdCreateRegulatory_terminator, CSequenceEditingEventHandler::CreateRegulatory)
2087  EVT_MENU (eCmdCreatePreRNA, CSequenceEditingEventHandler::CreateFeature)
2088  EVT_MENU (eCmdCreateMRNA, CSequenceEditingEventHandler::CreateFeature)
2089  EVT_MENU (eCmdCreateExon, CSequenceEditingEventHandler::CreateFeature)
2090  EVT_MENU (eCmdCreateIntron, CSequenceEditingEventHandler::CreateFeature)
2091  EVT_MENU (eCmdCreate3UTR, CSequenceEditingEventHandler::CreateFeature)
2092  EVT_MENU (eCmdCreate5UTR, CSequenceEditingEventHandler::CreateFeature)
2093  EVT_MENU (eCmdCreatetRNA, CSequenceEditingEventHandler::CreateFeature)
2094  EVT_MENU (eCmdCreaterRNA, CSequenceEditingEventHandler::CreateFeature)
2095  EVT_MENU (eCmdCreateRNA, CSequenceEditingEventHandler::CreateFeature)
2096  EVT_MENU (eCmdCreatemiscRNA, CSequenceEditingEventHandler::CreateFeature)
2097  EVT_MENU (eCmdCreatepreRNA, CSequenceEditingEventHandler::CreateFeature)
2098  EVT_MENU (eCmdCreatencRNA, CSequenceEditingEventHandler::CreateFeature)
2099  EVT_MENU (eCmdCreatetmRNA, CSequenceEditingEventHandler::CreateFeature)
2100  EVT_MENU (eCmdCreateCommentDescriptor, CSequenceEditingEventHandler::CreateFeature)
2101  EVT_MENU (eCmdCreateBiosourceFeat, CSequenceEditingEventHandler::CreateFeature)
2102  EVT_MENU (eCmdCreatePolyASite, CSequenceEditingEventHandler::CreateFeature)
2103  EVT_MENU (eCmdCreatePrimerBind, CSequenceEditingEventHandler::CreateFeature)
2104  EVT_MENU (eCmdCreateProteinBind, CSequenceEditingEventHandler::CreateFeature)
2105  EVT_MENU (eCmdCreateRepOrigin, CSequenceEditingEventHandler::CreateFeature)
2106  EVT_MENU (eCmdCreateOriT, CSequenceEditingEventHandler::CreateFeature)
2107  EVT_MENU (eCmdCreateCRegion, CSequenceEditingEventHandler::CreateFeature)
2108  EVT_MENU (eCmdCreateDLoop, CSequenceEditingEventHandler::CreateFeature)
2109  EVT_MENU (eCmdCreateDSegment, CSequenceEditingEventHandler::CreateFeature)
2110  EVT_MENU (eCmdCreateiDNA, CSequenceEditingEventHandler::CreateFeature)
2111  EVT_MENU (eCmdCreateJSegment, CSequenceEditingEventHandler::CreateFeature)
2112  EVT_MENU (eCmdCreateMiscBinding, CSequenceEditingEventHandler::CreateFeature)
2113  EVT_MENU (eCmdCreateMiscDifference, CSequenceEditingEventHandler::CreateFeature)
2114  EVT_MENU (eCmdCreateMiscFeature, CSequenceEditingEventHandler::CreateFeature)
2115  EVT_MENU (eCmdCreateMiscRecomb, CSequenceEditingEventHandler::CreateFeature)
2116  EVT_MENU (eCmdCreateMiscStructure, CSequenceEditingEventHandler::CreateFeature)
2117  EVT_MENU (eCmdCreateModifiedBase, CSequenceEditingEventHandler::CreateFeature)
2118  EVT_MENU (eCmdCreateNRegion, CSequenceEditingEventHandler::CreateFeature)
2119  EVT_MENU (eCmdCreatePrimTranscript, CSequenceEditingEventHandler::CreateFeature)
2120  EVT_MENU (eCmdCreateSRegion, CSequenceEditingEventHandler::CreateFeature)
2121  EVT_MENU (eCmdCreateUnsure, CSequenceEditingEventHandler::CreateFeature)
2122  EVT_MENU (eCmdCreateVRegion, CSequenceEditingEventHandler::CreateFeature)
2123  EVT_MENU (eCmdCreateVSegment, CSequenceEditingEventHandler::CreateFeature)
2124  EVT_MENU (eCmdCreateProprotein, CSequenceEditingEventHandler::CreateFeature)
2125  EVT_MENU (eCmdCreateMatPeptide, CSequenceEditingEventHandler::CreateFeature)
2126  EVT_MENU (eCmdCreateSigPeptide, CSequenceEditingEventHandler::CreateFeature)
2127  EVT_MENU (eCmdCreateTransitPeptide, CSequenceEditingEventHandler::CreateFeature)
2128  EVT_MENU (eCmdCreateBond, CSequenceEditingEventHandler::CreateFeature)
2129  EVT_MENU (eCmdCreateSite, CSequenceEditingEventHandler::CreateFeature)
2130  EVT_MENU (eCmdCreateAssemblyGap, CSequenceEditingEventHandler::CreateFeature)
2131  EVT_MENU (eCmdAddDefLine, CSequenceEditingEventHandler::AddDefLine)
2132  EVT_MENU (eCmdPrefixOrgToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2133  EVT_MENU (eCmdPrefixStrainToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2134  EVT_MENU (eCmdPrefixCloneToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2135  EVT_MENU (eCmdPrefixIsolateToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2136  EVT_MENU (eCmdPrefixHaplotToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2137  EVT_MENU (eCmdPrefixCultivarToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2138  EVT_MENU (eCmdPrefixListToDefLine, CSequenceEditingEventHandler::PrefixDefLines)
2139  EVT_MENU (eCmdCreateDescTPAAssembly, CSequenceEditingEventHandler::CreateDescriptor)
2140  EVT_MENU (eCmdCreateDescStructuredComment, CSequenceEditingEventHandler::CreateDescriptor)
2141  EVT_MENU (eCmdCreateDescRefGeneTracking, CSequenceEditingEventHandler::CreateDescriptor)
2142  EVT_MENU (eCmdCreateDescDBLink, CSequenceEditingEventHandler::CreateDescriptor)
2143  EVT_MENU (eCmdCreateDescUnverified, CSequenceEditingEventHandler::CreateDescriptor)
2144  EVT_MENU (eCmdCreateDescUnreviewed, CSequenceEditingEventHandler::CreateDescriptor)
2145  EVT_MENU (eCmdCreateDescAuthorizedAccess, CSequenceEditingEventHandler::CreateDescriptor)
2146  EVT_MENU (eCmdCreateDescGenomeAssemblyComment, CSequenceEditingEventHandler::CreateDescriptor)
2147  EVT_MENU (eCmdCreateDescGenBankBlock, CSequenceEditingEventHandler::CreateDescriptor)
2148  EVT_MENU (eCmdCreateDescComment, CSequenceEditingEventHandler::CreateDescriptor)
2149  EVT_MENU (eCmdCreateDescComment_ext, CSequenceEditingEventHandler::CreateDescriptor)
2150  EVT_MENU (eCmdCreateDescTitle, CSequenceEditingEventHandler::CreateDescriptor)
2151  EVT_MENU (eCmdCreateDescMolinfo, CSequenceEditingEventHandler::CreateDescriptor)
2152  EVT_MENU (eCmdCreateDescSource, CSequenceEditingEventHandler::CreateDescriptor)
2153  EVT_MENU (eCmdMakeBadSpecificHostTable, CSequenceEditingEventHandler::MakeBadSpecificHostTable)
2154  EVT_MENU (eCmdEditingButtons, CSequenceEditingEventHandler::EditingButtons)
2155  EVT_MENU (eCmdMakeToolBarWindow, CSequenceEditingEventHandler::EditingButtons)
2156  EVT_MENU (eCmdEnableHupId, CSequenceEditingEventHandler::EnableHupId)
2157  EVT_MENU (eCmdIndexerTypeSelection, CSequenceEditingEventHandler::IndexerTypeSelection)
2158  EVT_MENU (eCmdCreateDescPub, CSequenceEditingEventHandler::CreateDescriptor)
2159  EVT_MENU (eCmdCreateDescPub_ext, CSequenceEditingEventHandler::CreateDescriptor)
2160  EVT_MENU (eCmdCreateStructuredCommentPrefixSuffixMIENSData, CSequenceEditingEventHandler::CreateSpecificStructuredComment)
2161  EVT_MENU (eCmdCreateStructuredCommentPrefixSuffixMIMARKS, CSequenceEditingEventHandler::CreateSpecificStructuredComment)
2162  EVT_MENU (eCmdCreateStructuredCommentPrefixSuffixMIGS, CSequenceEditingEventHandler::CreateSpecificStructuredComment)
2163  EVT_MENU (eCmdCreateStructuredCommentPrefixSuffixMIMS, CSequenceEditingEventHandler::CreateSpecificStructuredComment)
2164  EVT_MENU (eCmdCreateStructuredCommentPrefixSuffixGenAssData, CSequenceEditingEventHandler::CreateSpecificStructuredComment)
2165  EVT_MENU (eCmdCreateStructuredCommentPrefixSuffixGenAnnData, CSequenceEditingEventHandler::CreateSpecificStructuredComment)
2166  EVT_MENU (eCmdDeleteStructuredCommentPrefixSuffixMIENSData, CSequenceEditingEventHandler::DeleteSpecificStructuredComment)
2167  EVT_MENU (eCmdDeleteStructuredCommentPrefixSuffixMIMARKS, CSequenceEditingEventHandler::DeleteSpecificStructuredComment)
2168  EVT_MENU (eCmdDeleteStructuredCommentPrefixSuffixMIGS, CSequenceEditingEventHandler::DeleteSpecificStructuredComment)
2169  EVT_MENU (eCmdDeleteStructuredCommentPrefixSuffixMIMS, CSequenceEditingEventHandler::DeleteSpecificStructuredComment)
2170  EVT_MENU (eCmdDeleteStructuredCommentPrefixSuffixGenAssData, CSequenceEditingEventHandler::DeleteSpecificStructuredComment)
2171  EVT_MENU (eCmdDeleteStructuredCommentPrefixSuffixGenAnnData, CSequenceEditingEventHandler::DeleteSpecificStructuredComment)
2172  EVT_MENU (eCmdCorrectRNAStrand, CSequenceEditingEventHandler::CorrectRNAStrand)
2173  EVT_MENU (eCmdTrimNsRich, CSequenceEditingEventHandler::TrimNsRich)
2174  EVT_MENU (eCmdTrimNsTerminal, CSequenceEditingEventHandler::TrimNsTerminal)
2175  EVT_MENU (eCmdAddFluComments, CSequenceEditingEventHandler::AddFluComments)
2176  EVT_MENU (eCmdLabelRna, CSequenceEditingEventHandler::LabelRna)
2177  EVT_MENU (eCmdRemProtTitles, CSequenceEditingEventHandler::RemProtTitles)
2178  EVT_MENU (eCmdRemAllProtTitles, CSequenceEditingEventHandler::RemAllProtTitles)
2179  EVT_MENU (eCmdApplyRNA_ITS, CSequenceEditingEventHandler::ApplyRNA_ITS)
2180  EVT_MENU (eCmdTestDialogView, CSequenceEditingEventHandler::TestDialogView)
2181  EVT_MENU (eCmdTestFormView, CSequenceEditingEventHandler::TestFormView)
2182  EVT_MENU (eCmdMacroEditor, CSequenceEditingEventHandler::MacroEditor)
2183  EVT_MENU (eCmdSuspectProductRulesEditor, CSequenceEditingEventHandler::SuspectProductRulesEditor)
2184  EVT_MENU (eCmdAdjustConsensusSpliceSitesStrict, CSequenceEditingEventHandler::AdjustForConsensusSpliceSites)
2185  EVT_MENU (eCmdAdjustConsensusSpliceSitesStrict_ext, CSequenceEditingEventHandler::AdjustForConsensusSpliceSites)
2186  EVT_MENU (eCmdAdjustConsensusSpliceSitesRelaxed, CSequenceEditingEventHandler::AdjustForConsensusSpliceSites)
2187  EVT_MENU (eCmdAdjustConsensusSpliceSitesRelaxed_ext, CSequenceEditingEventHandler::AdjustForConsensusSpliceSites)
2188  EVT_MENU (eCmdAdjustConsensusSpliceSitesConsensusEnds, CSequenceEditingEventHandler::AdjustForConsensusSpliceSites)
2189  EVT_MENU (eCmdAdjustCDSForIntrons, CSequenceEditingEventHandler::AdjustCDSForIntrons)
2190  EVT_MENU (eCmdAdjustrRNAForIntrons, CSequenceEditingEventHandler::AdjustrRNAForIntrons)
2191  EVT_MENU (eCmdAdjusttRNAForIntrons, CSequenceEditingEventHandler::AdjusttRNAForIntrons)
2192  EVT_MENU (eCmdAdjustmRNAForIntrons, CSequenceEditingEventHandler::AdjustmRNAForIntrons)
2193  EVT_MENU (eCmdRemoveSegGaps, CSequenceEditingEventHandler::RemoveSegGaps)
2194  EVT_MENU (eCmdRawSeqToDeltaByNs, CSequenceEditingEventHandler::RawSeqToDeltaByNs)
2195  EVT_MENU (eCmdRawSeqToDeltaByNs_ext, CSequenceEditingEventHandler::RawSeqToDeltaByNs)
2196  EVT_MENU (eCmdRawSeqToDeltaByLoc, CSequenceEditingEventHandler::RawSeqToDeltaByLoc)
2197  EVT_MENU (eCmdRawSeqToDeltaByAssemblyGapFeatures, CSequenceEditingEventHandler::RawSeqToDeltaByAssemblyGapFeatures)
2198  EVT_MENU (eCmdAdjustFeaturesForGaps, CSequenceEditingEventHandler::AdjustFeaturesForGaps )
2199  EVT_MENU (eCmdDeltaSeqToRaw, CSequenceEditingEventHandler::DeltaSeqToRaw)
2200  EVT_MENU (eCmdDeltaSeqToRaw_ext, CSequenceEditingEventHandler::DeltaSeqToRaw)
2201  EVT_MENU (eCmdExpandGaps, CSequenceEditingEventHandler::ExpandGaps )
2202  EVT_MENU (eCmdConvertSelectedGapsToKnown, CSequenceEditingEventHandler::ConvertSelectedGapsToKnown )
2203  EVT_MENU (eCmdConvertSelectedGapsToUnknown, CSequenceEditingEventHandler::ConvertSelectedGapsToUnknown )
2204  EVT_MENU (eCmdConvertGapsBySize, CSequenceEditingEventHandler::ConvertGapsBySize)
2205  EVT_MENU (eCmdEditSelectedGaps, CSequenceEditingEventHandler::EditSelectedGaps)
2206  EVT_MENU (eCmdAddLinkageToGaps, CSequenceEditingEventHandler::AddLinkageToGaps)
2207  EVT_MENU (eCmdAddLinkageToGaps_ext, CSequenceEditingEventHandler::AddLinkageToGaps)
2208  EVT_MENU (eCmdCombineAdjacentGaps, CSequenceEditingEventHandler::CombineAdjacentGaps)
2209  EVT_MENU (eCmdSplitCDSwithTooManyXs, CSequenceEditingEventHandler::SplitCDSwithTooManyXs)
2210  EVT_MENU (eCmdRmCultureNotes, CSequenceEditingEventHandler::RmCultureNotes)
2211  EVT_MENU (eCmdEditSeqId, CSequenceEditingEventHandler::EditSeqId)
2212  EVT_MENU (eCmdRemoveLocalSeqIdsFromNuc, CSequenceEditingEventHandler::RemoveLocalSeqIdsFromNuc)
2213  EVT_MENU (eCmdRemoveLocalSeqIdsFromProt, CSequenceEditingEventHandler::RemoveLocalSeqIdsFromProt)
2214  EVT_MENU (eCmdRemoveLocalSeqIdsFromAll, CSequenceEditingEventHandler::RemoveLocalSeqIdsFromAll)
2215  EVT_MENU (eCmdRemoveGiSeqIdsFromAll, CSequenceEditingEventHandler::RemoveGiSeqIdsFromAll)
2216  EVT_MENU (eCmdRemoveGenbankSeqIdsFromProt, CSequenceEditingEventHandler::RemoveGenbankSeqIdsFromProt)
2217  EVT_MENU (eCmdRemoveGenbankSeqIdsFromAll, CSequenceEditingEventHandler::RemoveGenbankSeqIdsFromAll)
2218  EVT_MENU (eCmdRemoveSeqIdNamesFromProtFeats, CSequenceEditingEventHandler::RemoveSeqIdNamesFromProtFeats)
2219  EVT_MENU (eCmdConvertAccessionToLocalIdsAll, CSequenceEditingEventHandler::ConvertAccessionToLocalIdsAll)
2220  EVT_MENU (eCmdConvertAccessionToLocalIdsNuc, CSequenceEditingEventHandler::ConvertAccessionToLocalIdsNuc)
2221  EVT_MENU (eCmdConvertAccessionToLocalIdsProt, CSequenceEditingEventHandler::ConvertAccessionToLocalIdsProt)
2222  EVT_MENU (eCmdConvertAccessionToLocalIdsName, CSequenceEditingEventHandler::ConvertAccessionToLocalIdsName)
2223  EVT_MENU (eCmdLocalToGeneralId, CSequenceEditingEventHandler::LocalToGeneralId)
2224  EVT_MENU (eCmdGeneralToLocalId, CSequenceEditingEventHandler::GeneralToLocalId)
2225  EVT_MENU (eCmdRemoveGeneralId, CSequenceEditingEventHandler::RemoveGeneralId)
2226  EVT_MENU (eCmdRemoveUnnecessaryExceptions, CSequenceEditingEventHandler::RemoveUnnecessaryExceptions)
2227  EVT_MENU (eCmdEditHistory, CSequenceEditingEventHandler:: EditHistory)
2228  EVT_MENU (eCmdUpdate_Replaced_EC_numbers, CSequenceEditingEventHandler::Update_Replaced_EC_numbers)
2229  EVT_MENU (eCmdUpdateSequence, CSequenceEditingEventHandler::UpdateSingleSequence)
2230  EVT_MENU (eCmdUpdateSequence_ext, CSequenceEditingEventHandler::UpdateSingleSequence)
2231  EVT_MENU (eCmdUpdateSequenceClipboard, CSequenceEditingEventHandler::UpdateSingleSequence)
2232  EVT_MENU (eCmdUpdateSequenceAccession, CSequenceEditingEventHandler::UpdateSingleSequence)
2233  EVT_MENU (eCmdUpdateMultiSeqClipboard, CSequenceEditingEventHandler::UpdateMultipleSequences)
2234  EVT_MENU (eCmdUpdateMultiSequences, CSequenceEditingEventHandler::UpdateMultipleSequences)
2235  EVT_MENU (eCmdImportFeatureTable, CSequenceEditingEventHandler::ImportFeatureTable)
2236  EVT_MENU (eCmdImportFeatureTable_ext, CSequenceEditingEventHandler::ImportFeatureTable)
2237  EVT_MENU (eCmdImportFeatureTableClipboard, CSequenceEditingEventHandler::ImportFeatureTableClipboard)
2238  EVT_MENU (eCmdImportGFF3, CSequenceEditingEventHandler::ImportGFF3)
2239  EVT_MENU (eCmdImportGFF3_ext, CSequenceEditingEventHandler::ImportGFF3)
2240  EVT_MENU (eCmdLoadSecondaryAccessions, CSequenceEditingEventHandler::LoadSecondaryAccessions)
2241  EVT_MENU (eCmdLoadSecondaryAccessionsHistoryTakeover, CSequenceEditingEventHandler::LoadSecondaryAccessionsHistoryTakeover)
2242  EVT_MENU (eCmdAddGlobalCodeBreak, CSequenceEditingEventHandler::AddGlobalCodeBreak )
2243  EVT_MENU (eCmdApplyStructuredCommentField, CSequenceEditingEventHandler::ApplyStructuredCommentField)
2244  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixHIVData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2245  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixFluData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2246  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixMIGSData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2247  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixMIMSData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2248  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixMIENSData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2249  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixMIMARKS3_0, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2250  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixMIGS3_0, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2251  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixMIMS3_0, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2252  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixAssemblyData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2253  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixGenAssData, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2254  EVT_MENU (eCmdEditStructuredCommentPrefixSuffixiBol, CSequenceEditingEventHandler::EditStructuredCommentPrefixSuffix)
2255  EVT_MENU (eCmdLinkSelectedmRNACDS, CSequenceEditingEventHandler::LinkmRNACDS)
2256  EVT_MENU (eCmdLinkmRNACDSOverlap, CSequenceEditingEventHandler::LinkmRNACDS)
2257  EVT_MENU (eCmdLinkmRNACDSProduct, CSequenceEditingEventHandler::LinkmRNACDS)
2258  EVT_MENU (eCmdLinkmRNACDSLabel, CSequenceEditingEventHandler::LinkmRNACDS)
2259  EVT_MENU (eCmdLinkmRNACDSLabelLocation, CSequenceEditingEventHandler::LinkmRNACDS)
2260  EVT_MENU (eCmdLinkmRNACDSProteinID, CSequenceEditingEventHandler::LinkmRNACDS)
2261  EVT_MENU (eCmdLinkmRNACDSTranscriptID, CSequenceEditingEventHandler::LinkmRNACDS)
2262  EVT_MENU (eCmdLinkmRNACDSUnidirectional, CSequenceEditingEventHandler::LinkmRNACDS)
2263  EVT_MENU (eCmdShowLinkedmRNACDS, CSequenceEditingEventHandler::LinkmRNACDS)
2264  EVT_MENU (eCmdShowFeatureTable, CSequenceEditingEventHandler::ShowFeatureTable)
2265  EVT_MENU (eCmdShowFeatureTable_ext, CSequenceEditingEventHandler::ShowFeatureTable)
2266  EVT_MENU (eCmdRestoreFromFile, CSequenceEditingEventHandler::RestoreLocalFile)
2267  EVT_MENU (eCmdRestoreAndConvertSeqSubmit, CSequenceEditingEventHandler::RestoreLocalFile)
2268  EVT_MENU (eCmdViewSortedProteins, CSequenceEditingEventHandler::ViewSortedProteins)
2269  EVT_MENU (eCmdCheckForMixedStrands, CSequenceEditingEventHandler::CheckForMixedStrands)
2270  EVT_MENU (eCmdPrepareSeqSubmit, CSequenceEditingEventHandler::PrepareSeqSubmit)
2271  EVT_MENU (eCmdSaveSubmissionFile, CSequenceEditingEventHandler::SaveSubmissionFile)
2272  EVT_MENU (eCmdSaveASN1File, CSequenceEditingEventHandler::SaveASN1File)
2273  EVT_MENU (eCmdHelpReports_ext, CSequenceEditingEventHandler::Help)
2274  EVT_MENU (eCmdHelpImport_ext, CSequenceEditingEventHandler::Help)
2275  EVT_MENU (eCmdHelpSequences_ext, CSequenceEditingEventHandler::Help)
2276  EVT_MENU (eCmdHelpFeatures_ext, CSequenceEditingEventHandler::Help)
2277  EVT_MENU (eCmdHelpComments_ext, CSequenceEditingEventHandler::Help)
2278  EVT_MENU (eCmdHelpEditingTools_ext, CSequenceEditingEventHandler::Help)
2279  EVT_MENU (eCmdUpdateTLSName, CSequenceEditingEventHandler::UpdateTargetedLocusName)
2280 
2281 
2282 // Please do not make overlapping UPDATE_UI_RANGEs. Every time there is an overlapping range here a cute kitten dies in horror!!!
2283  EVT_UPDATE_UI_RANGE(eCmdRemoveDescriptors, eCmdCreateDescPub, CSequenceEditingEventHandler::IsObjectSelected )
2284 
2285  EVT_UPDATE_UI_RANGE(eCmdCreateBiosourceFeat, eCmdCreatePubFeatureLabeled, CSequenceEditingEventHandler::IsLocationSelected )
2286 
2287  EVT_UPDATE_UI_RANGE(eCmdTestDialogView, eCmdTestFormView, CSequenceEditingEventHandler::IsObjectSelected )
2288 
2289  EVT_UPDATE_UI(eCmdEnableHupId, CSequenceEditingEventHandler::IsHupIdEnabled)
2290 END_EVENT_TABLE()
2291 
2292 BEGIN_EVENT_MAP(CSequenceEditingEventHandler, CEventHandler)
2293  ON_EVENT_RANGE(CSelectionServiceEvent,
2294  CSelectionServiceEvent::eClientAttached, CSelectionServiceEvent::eSelectionChanged,
2295  &CSequenceEditingEventHandler::x_OnSelectionEvent)
2296 END_EVENT_MAP()
2297 
2298 static
2299 WX_DEFINE_MENU(kEditingMenu)
2300  WX_SUBMENU("&Edit")
2301  WX_MENU_ITEM_INT(eCmdRemoveSequences)
2302  WX_MENU_ITEM_INT(eCmdAddSequences)
2303  WX_SUBMENU_INT("Update Sequences")
2304  WX_MENU_ITEM_INT(eCmdUpdateSequence)
2305  WX_MENU_ITEM_INT(eCmdUpdateSequenceClipboard)
2306  WX_MENU_ITEM_INT(eCmdUpdateSequenceAccession)
2307  WX_MENU_ITEM_INT(eCmdUpdateMultiSequences)
2308  WX_MENU_ITEM_INT(eCmdUpdateMultiSeqClipboard)
2309  WX_END_SUBMENU()
2310  WX_MENU_ITEM_INT(eCmdRestoreFromFile)
2311  WX_MENU_ITEM_INT(eCmdRestoreAndConvertSeqSubmit)
2312  WX_END_SUBMENU()
2313  WX_MENU_SEPARATOR_L("Contribs")
2314  WX_SUBMENU_INT("Sea&rch")
2315  WX_SUBMENU_INT("&Validate")
2316  WX_MENU_ITEM_INT(eCmdValidate)
2317  WX_MENU_ITEM_INT(eCmdValidateNoAlignments)
2318  WX_MENU_ITEM_INT(eCmdValidateCheckInferences)
2319  WX_END_SUBMENU()
2320  WX_MENU_ITEM_INT(eCmdVectorTrim)
2321  WX_MENU_ITEM_INT(eCmdSelectTarget)
2322  WX_END_SUBMENU()
2323 
2324  WX_SUBMENU_EXT("Submission")
2325  WX_MENU_ITEM_EXT(eCmdPrepareSeqSubmit)
2326  WX_MENU_ITEM_EXT(eCmdSaveSubmissionFile)
2327  WX_SUBMENU_EXT("Reports")
2328  WX_MENU_ITEM_EXT(eCmdShowFeatureTable_ext)
2329  WX_MENU_ITEM_EXT(eCmdValidate_ext)
2330  WX_MENU_ITEM_EXT(eCmdSortUniqueCountTree_ext)
2331  WX_MENU_ITEM_EXT(eCmdSubmitter_ext)
2332  WX_MENU_ITEM_EXT(eCmdVectorTrim)
2333  WX_MENU_SEPARATOR_EXT()
2334  WX_MENU_ITEM_EXT(eCmdHelpReports_ext)
2335  WX_END_SUBMENU()
2336  WX_SUBMENU_EXT("Import")
2337  WX_MENU_ITEM_EXT(eCmdTableReader_ext)
2338  WX_MENU_ITEM_EXT(eCmdImportFeatureTable_ext)
2339  WX_MENU_ITEM_EXT(eCmdImportGFF3_ext)
2340  WX_MENU_SEPARATOR_EXT()
2341  WX_MENU_ITEM_EXT(eCmdHelpImport_ext)
2342  WX_END_SUBMENU()
2343  WX_SUBMENU_EXT("Sequences")
2344  WX_MENU_ITEM_EXT(eCmdAddSequences)
2345  WX_MENU_ITEM_EXT(eCmdEditSequence)
2346  WX_MENU_ITEM_EXT(eCmdUpdateSequence_ext)
2347  WX_MENU_ITEM_EXT(eCmdRemoveSequences_ext)
2348  WX_MENU_ITEM_EXT(eCmdRevCompSequences_ext)
2349  WX_MENU_ITEM_EXT(eCmdTrimNsTerminal)
2350  WX_MENU_ITEM_EXT(eCmdExpandGaps)
2351  WX_MENU_ITEM_EXT(eCmdAddLinkageToGaps_ext)
2352  WX_MENU_ITEM_EXT(eCmdRawSeqToDeltaByNs_ext)
2353  WX_MENU_ITEM_EXT(eCmdDeltaSeqToRaw_ext)
2354  WX_MENU_SEPARATOR_EXT()
2355  WX_MENU_ITEM_EXT(eCmdHelpSequences_ext)
2356  WX_END_SUBMENU()
2357  WX_SUBMENU_EXT("Add Features")
2358  WX_SUBMENU_EXT("gene/mRNA/CDS")
2359  WX_MENU_ITEM_EXT(eCmdCreateGene)
2360  WX_MENU_ITEM_EXT(eCmdCreateMRNA)
2361  WX_MENU_ITEM_EXT(eCmdCreateCodingRegion_ext)
2362  WX_MENU_ITEM_EXT(eCmdCreateOperon)
2363  WX_MENU_ITEM_EXT(eCmdCreateIntron)
2364  WX_MENU_ITEM_EXT(eCmdCreateExon)
2365  WX_MENU_ITEM_EXT(eCmdCreate5UTR)
2366  WX_MENU_ITEM_EXT(eCmdCreate3UTR)
2367  WX_END_SUBMENU()
2368  WX_SUBMENU_EXT("Structural RNAs")
2369  WX_MENU_ITEM_EXT(eCmdCreaterRNA)
2370  WX_MENU_ITEM_EXT(eCmdCreatetRNA)
2371  WX_MENU_ITEM_EXT(eCmdCreatencRNA)
2372  WX_MENU_ITEM_EXT(eCmdCreatepreRNA)
2373  WX_MENU_ITEM_EXT(eCmdCreatetmRNA)
2374  WX_MENU_ITEM_EXT(eCmdCreatemiscRNA)
2375  WX_END_SUBMENU()
2376  WX_SUBMENU_EXT("Regulatory")
2377  WX_MENU_ITEM_EXT(eCmdCreateRegulatory_promoter)
2378  WX_MENU_ITEM_EXT(eCmdCreateRegulatory_enhancer)
2379  WX_MENU_ITEM_EXT(eCmdCreateRegulatory_ribosome_binding_site)
2380  WX_MENU_ITEM_EXT(eCmdCreateRegulatory_riboswitch)
2381  WX_MENU_ITEM_EXT(eCmdCreateRegulatory_terminator)
2382  WX_MENU_ITEM_EXT(eCmdCreateRegulatory)
2383  WX_END_SUBMENU()
2384  WX_SUBMENU_EXT("Protein Features")
2385  WX_MENU_ITEM_EXT(eCmdCreateMatPeptide)
2386  WX_MENU_ITEM_EXT(eCmdCreateSigPeptide)
2387  WX_MENU_ITEM_EXT(eCmdCreateProprotein)
2388  WX_MENU_ITEM_EXT(eCmdCreateTransitPeptide)
2389  WX_END_SUBMENU()
2390  WX_SUBMENU_EXT("Other Features")
2391  WX_MENU_ITEM_EXT(eCmdCreateCentromere)
2392  WX_MENU_ITEM_EXT(eCmdCreateDLoop)
2393  WX_MENU_ITEM_EXT(eCmdCreateMiscBinding)
2394  WX_MENU_ITEM_EXT(eCmdCreateMiscDifference)
2395  WX_MENU_ITEM_EXT(eCmdCreateMiscFeature)
2396  WX_MENU_ITEM_EXT(eCmdCreateMiscRecomb)
2397  WX_MENU_ITEM_EXT(eCmdCreateMobileElement)
2398  WX_MENU_ITEM_EXT(eCmdCreateOriT)
2399  WX_MENU_ITEM_EXT(eCmdCreateProteinBind)
2400  WX_MENU_ITEM_EXT(eCmdCreateRepOrigin)
2401  WX_MENU_ITEM_EXT(eCmdCreateRepeatRegion)
2402  WX_MENU_ITEM_EXT(eCmdCreateSite)
2403  WX_MENU_ITEM_EXT(eCmdCreateTelomere)
2404  WX_MENU_ITEM_EXT(eCmdCreateVariation)
2405  WX_END_SUBMENU()
2406  WX_MENU_SEPARATOR_EXT()
2407  WX_MENU_ITEM_EXT(eCmdHelpFeatures_ext)
2408  WX_END_SUBMENU()
2409  WX_MENU_ITEM_EXT(eCmdCreateDescPub_ext)
2410  WX_SUBMENU_EXT("Comments")
2411  WX_MENU_ITEM_EXT(eCmdCreateDescComment_ext)
2412  WX_SUBMENU_EXT("MIMS Comment")
2413  WX_MENU_ITEM_EXT(eCmdCreateStructuredCommentPrefixSuffixMIMS)
2414  WX_MENU_ITEM_EXT(eCmdDeleteStructuredCommentPrefixSuffixMIMS)
2415  WX_END_SUBMENU()
2416  WX_SUBMENU_EXT("MIGS Comment")
2417  WX_MENU_ITEM_EXT(eCmdCreateStructuredCommentPrefixSuffixMIGS)
2418  WX_MENU_ITEM_EXT(eCmdDeleteStructuredCommentPrefixSuffixMIGS)
2419  WX_END_SUBMENU()
2420  WX_SUBMENU_EXT("MIMARKS Comment")
2421  WX_MENU_ITEM_EXT(eCmdCreateStructuredCommentPrefixSuffixMIMARKS)
2422  WX_MENU_ITEM_EXT(eCmdDeleteStructuredCommentPrefixSuffixMIMARKS)
2423  WX_END_SUBMENU()
2424  WX_SUBMENU_EXT("MIENS Comment")
2425  WX_MENU_ITEM_EXT(eCmdCreateStructuredCommentPrefixSuffixMIENSData)
2426  WX_MENU_ITEM_EXT(eCmdDeleteStructuredCommentPrefixSuffixMIENSData)
2427  WX_END_SUBMENU()
2428  WX_SUBMENU_EXT("GenomeAnnotation Comment")
2429  WX_MENU_ITEM_EXT(eCmdCreateStructuredCommentPrefixSuffixGenAnnData)
2430  WX_MENU_ITEM_EXT(eCmdDeleteStructuredCommentPrefixSuffixGenAnnData)
2431  WX_END_SUBMENU()
2432  WX_SUBMENU_EXT("GenomeDataAssembly Comment")
2433  WX_MENU_ITEM_EXT(eCmdCreateStructuredCommentPrefixSuffixGenAssData)
2434  WX_MENU_ITEM_EXT(eCmdDeleteStructuredCommentPrefixSuffixGenAssData)
2435  WX_END_SUBMENU()
2436  WX_MENU_SEPARATOR_EXT()
2437  WX_MENU_ITEM_EXT(eCmdHelpComments_ext)
2438  WX_END_SUBMENU()
2439  WX_SUBMENU_EXT("Editing Tools")
2440  WX_MENU_ITEM_EXT(eCmdSelectTarget_ext)
2441  WX_MENU_ITEM_EXT(eCmdTaxFixCleanup_ext)
2442  WX_MENU_ITEM_EXT(eCmdBulkApplyGenCode)
2443  WX_MENU_ITEM_EXT(eCmdBulkSourceEdit)
2444  WX_MENU_ITEM_EXT(eCmdBulkCdsEdit)
2445  WX_MENU_ITEM_EXT(eCmdBulkGeneEdit)
2446  WX_MENU_ITEM_EXT(eCmdBulkRnaEdit)
2447  WX_MENU_ITEM_EXT(eCmdRemoveFeatures)
2448  WX_MENU_ITEM_EXT(eCmdRemoveAllFeatures)
2449  WX_MENU_ITEM_EXT(eCmdSelectFeature)
2450  WX_MENU_ITEM_EXT(eCmdConvertFeatures)
2451  WX_MENU_ITEM_EXT(eCmdRetranslateCDSIgnoreStopExceptEnd_ext)
2452  WX_MENU_ITEM_EXT(eCmdAdjustFeaturesForGaps)
2453  WX_MENU_SEPARATOR_EXT()
2454  WX_MENU_ITEM_EXT(eCmdHelpEditingTools_ext)
2455  WX_END_SUBMENU()
2456  WX_END_SUBMENU()
2457 
2458  WX_SUBMENU_INT("Advan&ced Editing")
2459  WX_SUBMENU_INT("Def Line")
2460  WX_SUBMENU_INT("Automatic Def Line")
2461  WX_MENU_ITEM_INT(eCmdAutodefDefaultOptions)
2462  WX_MENU_ITEM_INT(eCmdAutodefNoMods)
2463  WX_MENU_ITEM_INT(eCmdAutodefOptions)
2464  WX_MENU_ITEM_INT(eCmdAutodefMisc)
2465  WX_MENU_ITEM_INT(eCmdAutodefId)
2466  WX_MENU_ITEM_INT(eCmdAutodefPopset)
2467  WX_MENU_ITEM_INT(eCmdAutodefRefresh)
2468  WX_END_SUBMENU()
2469  WX_MENU_ITEM_INT(eCmdAddDefLine)
2470  WX_SUBMENU_INT("Prefix Def Line With")
2471  WX_MENU_ITEM_INT(eCmdPrefixOrgToDefLine)
2472  WX_MENU_ITEM_INT(eCmdPrefixStrainToDefLine)
2473  WX_MENU_ITEM_INT(eCmdPrefixCloneToDefLine)
2474  WX_MENU_ITEM_INT(eCmdPrefixIsolateToDefLine)
2475  WX_MENU_ITEM_INT(eCmdPrefixHaplotToDefLine)
2476  WX_MENU_ITEM_INT(eCmdPrefixCultivarToDefLine)
2477  WX_MENU_ITEM_INT(eCmdPrefixListToDefLine)
2478  WX_END_SUBMENU()
2479  WX_MENU_ITEM_INT(eCmdParseTextFromDefline)
2480  WX_END_SUBMENU()
2481  WX_SUBMENU_INT("Organism")
2482  WX_MENU_ITEM_INT(eCmdPrefixAuthWithTax)
2483  WX_MENU_ITEM_INT(eCmdAppendModToOrg)
2484  WX_MENU_ITEM_INT(eCmdCountryFixupCap)
2485  WX_MENU_ITEM_INT(eCmdCountryFixupNoCap)
2486  WX_MENU_ITEM_INT(eCmdParseCollectionDateMonthFirst)
2487  WX_MENU_ITEM_INT(eCmdParseCollectionDateDayFirst)
2488  WX_MENU_ITEM_INT(eCmdMakeBadSpecificHostTable)
2489  WX_MENU_SEPARATOR_INT()
2490  WX_SUBMENU_INT("Source Focus")
2491  WX_MENU_ITEM_INT(eCmdFocusSet)
2492  WX_MENU_ITEM_INT(eCmdFocusClear)
2493  WX_END_SUBMENU()
2494  WX_MENU_ITEM_INT(eCmdSetTransgSrcDesc)
2495  WX_MENU_ITEM_INT(eCmdFixOrgModInstitution)
2496  WX_MENU_ITEM_INT(eCmdFixStructuredVouchers)
2497  WX_MENU_ITEM_INT(eCmdTrimOrganismNames)
2498  WX_MENU_ITEM_INT(eCmdSplitStructuredCollections)
2499  WX_MENU_ITEM_INT(eCmdSplitQualifiersAtCommas)
2500  WX_MENU_ITEM_INT(eCmdSplitDblinkQuals)
2501  WX_SUBMENU_INT("PCR Fixes")
2502  WX_MENU_ITEM_INT(eCmdSwapPrimerSeqName)
2503  WX_MENU_ITEM_INT(eCmdTrimJunkInPrimerSeqs)
2504  WX_MENU_ITEM_INT(eCmdSplitPrimerSets)
2505  WX_MENU_ITEM_INT(eCmdMergePrimerSets)
2506  WX_MENU_ITEM_INT(eCmdFixiInPrimerSeqs)
2507  WX_END_SUBMENU()
2508  WX_SUBMENU_INT("Influenza Virus Names")
2509  WX_MENU_ITEM_INT(eCmdParseStrainSerotypeFromNames)
2510  WX_MENU_ITEM_INT(eCmdAddStrainSerotypeToNames)
2511  WX_MENU_ITEM_INT(eCmdFixupOrganismNames)
2512  WX_END_SUBMENU()
2513  WX_MENU_ITEM_INT(eCmdDisableStrainForwarding)
2514  WX_MENU_ITEM_INT(eCmdEnableStrainForwarding)
2515  WX_MENU_ITEM_INT(eCmdUnculTaxTool)
2516  WX_MENU_ITEM_INT(eCmdGenusSpeciesFixup)
2517  WX_MENU_ITEM_INT(eCmdLatLonTool)
2518  WX_MENU_ITEM_INT(eCmdCountryConflict)
2519  WX_SUBMENU_INT("Compare with Biosample")
2520  WX_MENU_ITEM_INT(eCmdCompareWithBiosample)
2521  WX_MENU_ITEM_INT(eCmdCompareWithBiosampleFirstOnly)
2522  WX_END_SUBMENU()
2523  WX_MENU_ITEM_INT(eCmdMergeBiosources)
2524  WX_SUBMENU_INT("Parse Organism Modifiers")
2525  WX_MENU_ITEM_INT(eCmdExportTable)
2526  WX_END_SUBMENU()
2527  WX_SUBMENU_INT("Consolidate Like Modifiers")
2528  WX_MENU_ITEM_INT(eCmdConsolidateLikeModsWithSemicolon)
2529  WX_MENU_ITEM_INT(eCmdConsolidateLikeModsWithoutSemicolon)
2530  WX_END_SUBMENU()
2531  WX_END_SUBMENU()
2532  WX_SUBMENU_INT("&Apply")
2533  WX_MENU_ITEM_INT(eCmdApplyCDS)
2534  WX_MENU_ITEM_INT(eCmdApplyAddRNA)
2535  WX_SUBMENU_INT("Add Named rRNA")
2536  WX_MENU_ITEM_INT(eCmdAddNamedrRNA12S)
2537  WX_MENU_ITEM_INT(eCmdAddNamedrRNA16S)
2538  WX_MENU_ITEM_INT(eCmdAddNamedrRNA23S)
2539  WX_MENU_ITEM_INT(eCmdAddNamedrRNA18S)
2540  WX_MENU_ITEM_INT(eCmdAddNamedrRNA28S)
2541  WX_MENU_ITEM_INT(eCmdAddNamedrRNA26S)
2542  WX_MENU_ITEM_INT(eCmdAddNamedrRNASmall)
2543  WX_MENU_ITEM_INT(eCmdAddNamedrRNALarge)
2544  WX_END_SUBMENU()
2545  WX_MENU_ITEM_INT(eCmdApplyRNA_ITS)
2546  WX_MENU_ITEM_INT(eCmdApplyAddOther)
2547  WX_MENU_ITEM_INT(eCmdAddFeatureBetween)
2548  WX_SUBMENU_INT("Add Common Feature")
2549  WX_MENU_ITEM_INT(eCmdAddMicrosatellite)
2550  WX_MENU_ITEM_INT(eCmdAddControlRegion)
2551  WX_END_SUBMENU()
2552  WX_MENU_ITEM_INT(eCmdApplyFeatQual)
2553  WX_MENU_ITEM_INT(eCmdApplySourceQual)
2554  WX_MENU_ITEM_INT(eCmdApplyCGPQual)
2555  WX_MENU_ITEM_INT(eCmdApplyRNAQual)
2556  WX_MENU_ITEM_INT(eCmdTableReader)
2557  WX_MENU_ITEM_INT(eCmdTableReaderClipboard)
2558  WX_MENU_ITEM_INT(eCmdExportTable)
2559  WX_MENU_ITEM_INT(eCmdMolInfoEdit)
2560  WX_MENU_ITEM_INT(eCmdLabelRna)
2561  WX_MENU_ITEM_INT(eCmdPropagateDBLink)
2562  WX_MENU_ITEM_INT(eCmdApplyIndexerComments)
2563  WX_MENU_ITEM_INT(eCmdImportGFF3)
2564  WX_MENU_ITEM_INT(eCmdImportFeatureTable)
2565  WX_MENU_ITEM_INT(eCmdImportFeatureTableClipboard)
2566  WX_SUBMENU_INT("Add Keyword")
2567  WX_MENU_ITEM_INT(eCmdAddStructuredCommentKeyword)
2568  WX_MENU_ITEM_INT(eCmdAddKeywordGDS)
2569  WX_MENU_ITEM_INT(eCmdAddKeywordTPA_inferential)
2570  WX_MENU_ITEM_INT(eCmdAddKeywordTPA_experimental)
2571  WX_MENU_ITEM_INT(eCmdAddKeywordTPA_assembly)
2572  WX_MENU_ITEM_INT(eCmdAddKeywordWithConstraint)
2573  WX_END_SUBMENU()
2574  WX_SUBMENU_INT("Load Secondary Accessions from File")
2575  WX_MENU_ITEM_INT(eCmdLoadSecondaryAccessions)
2576  WX_MENU_ITEM_INT(eCmdLoadSecondaryAccessionsHistoryTakeover)
2577  WX_END_SUBMENU()
2578  WX_MENU_ITEM_INT(eCmdAddGlobalCodeBreak)
2579  WX_END_SUBMENU()
2580  WX_SUBMENU_INT("&Remove")
2581  WX_MENU_ITEM_INT(eCmdRemoveDescriptors)
2582  WX_MENU_ITEM_INT(eCmdRemoveFeatures)
2583  WX_MENU_ITEM_INT(eCmdRemoveAllFeatures)
2584  WX_MENU_ITEM_INT(eCmdRemoveUnindexedFeatures)
2585  WX_MENU_ITEM_INT(eCmdRemoveFeatQual)
2586  WX_MENU_ITEM_INT(eCmdRemoveSourceQual)
2587  WX_MENU_ITEM_INT(eCmdRemoveCGPQual)
2588  WX_MENU_ITEM_INT(eCmdRemoveRNAQual)
2589  WX_MENU_ITEM_INT(eCmdRemoveSeqAnnotIds)
2590  WX_MENU_ITEM_INT(eCmdRemoveCddFeatDbxref)
2591  WX_MENU_ITEM_INT(eCmdRemoveBankitComment)
2592  WX_MENU_ITEM_INT(eCmdRemoveUnverified)
2593  WX_MENU_ITEM_INT(eCmdRemoveUnreviewed)
2594  WX_SUBMENU_INT("Remove Text")
2595  WX_MENU_ITEM_INT(eCmdRemoveTextOutsideString)
2596  WX_MENU_ITEM_INT(eCmdRemoveTextInsideStr)
2597  WX_END_SUBMENU()
2598  WX_SUBMENU_INT("Remove Duplicate")
2599  WX_MENU_ITEM_INT(eCmdRemoveDuplicateStructuredComments)
2600  WX_MENU_ITEM_INT(eCmdRemoveDupFeats)
2601  WX_MENU_ITEM_INT(eCmdRemoveDupFeatsWithOptions)
2602  WX_END_SUBMENU()
2603  WX_MENU_ITEM_INT(eCmdRemoveSequencesFromAlignments)
2604  WX_MENU_ITEM_INT(eCmdRemoveSequences)
2605  WX_MENU_ITEM_INT(eCmdRemoveAlignments)
2606  WX_MENU_ITEM_INT(eCmdRemoveGraphs)
2607  WX_MENU_ITEM_INT(eCmdRemoveGenomeProjectId)
2608  WX_MENU_ITEM_INT(eCmdRemoveEmptyGenomeProjectId)
2609  WX_SUBMENU_INT("Remove Titles")
2610  WX_SUBMENU_INT("Protein")
2611  WX_MENU_ITEM_INT(eCmdRemProtTitles)
2612  WX_MENU_ITEM_INT(eCmdRemAllProtTitles)
2613  WX_END_SUBMENU()
2614  WX_END_SUBMENU()
2615  WX_MENU_ITEM_INT(eCmdWithdrawSequences)
2616  WX_MENU_ITEM_INT(eCmdRmCultureNotes)
2617  WX_MENU_ITEM_INT(eCmdRmIllegalQuals)
2618  WX_MENU_ITEM_INT(eCmdRmWrongQuals)
2619  WX_SUBMENU_INT("Remove Xrefs")
2620  WX_SUBMENU_INT("Db_xrefs")
2621  WX_MENU_ITEM_INT(eCmdRemoveDbXrefsCDS)
2622  WX_MENU_ITEM_INT(eCmdRemoveDbXrefsGenes)
2623  WX_MENU_ITEM_INT(eCmdRemoveDbXrefsRNA)
2624  WX_MENU_ITEM_INT(eCmdRemoveDbXrefsAllFeats)
2625  WX_MENU_ITEM_INT(eCmdRemoveDbXrefsBioSource)
2626  WX_MENU_ITEM_INT(eCmdRemoveDbXrefsBioSourceAndFeats)
2627  WX_END_SUBMENU()
2628  WX_SUBMENU_INT("Taxon Xrefs")
2629  WX_MENU_ITEM_INT(eCmdRemoveTaxonFeats)
2630  WX_MENU_ITEM_INT(eCmdRemoveTaxonFeatsAndBioSource)
2631  WX_END_SUBMENU()
2632  WX_SUBMENU_INT("Gene Xrefs")
2633  WX_MENU_ITEM_INT(eCmdRemoveAllGeneXrefs)
2634  WX_MENU_ITEM_INT(eCmdRemoveUnnecessaryGeneXrefs)
2635  WX_MENU_ITEM_INT(eCmdRemoveNonsuppressingGeneXrefs)
2636  WX_MENU_ITEM_INT(eCmdRemoveOrphanLocusGeneXrefs)
2637  WX_MENU_ITEM_INT(eCmdRemoveOrphanLocus_tagGeneXrefs)
2638  WX_MENU_ITEM_INT(eCmdRemoveGeneXrefs)
2639  WX_END_SUBMENU()
2640  WX_END_SUBMENU()
2641  WX_MENU_ITEM_INT(eCmdClearKeywords)
2642  WX_MENU_ITEM_INT(eCmdClearNomenclature)
2643  WX_SUBMENU_INT("Remove Proteins")
2644  WX_MENU_ITEM_INT(eCmdJustRemoveProteins)
2645  WX_MENU_ITEM_INT(eCmdRemoveProteinsAndRenormalizeNucProtSets)
2646  WX_MENU_ITEM_INT(eCmdRemoveOrphanedProteins)
2647  WX_END_SUBMENU()
2648  WX_SUBMENU_INT("Remove IDs, SeqIDs, GI_IDs, LOCUS")
2649  WX_SUBMENU_INT("Local")
2650  WX_MENU_ITEM_INT(eCmdRemoveLocalSeqIdsFromNuc)
2651  WX_MENU_ITEM_INT(eCmdRemoveLocalSeqIdsFromProt)
2652  WX_MENU_ITEM_INT(eCmdRemoveLocalSeqIdsFromAll)
2653  WX_END_SUBMENU()
2654  WX_SUBMENU_INT("GenBank")
2655  WX_MENU_ITEM_INT(eCmdRemoveGenbankSeqIdsFromProt)
2656  WX_MENU_ITEM_INT(eCmdRemoveGenbankSeqIdsFromAll)
2657  WX_END_SUBMENU()
2658  WX_MENU_ITEM_INT(eCmdRemoveGiSeqIdsFromAll)
2659  WX_MENU_ITEM_INT(eCmdRemoveSeqIdNamesFromProtFeats)
2660  WX_MENU_ITEM_INT(eCmdRemoveGeneralId)
2661  WX_END_SUBMENU()
2662  WX_MENU_ITEM_INT(eCmdRemoveUnnecessaryExceptions)
2663  WX_END_SUBMENU()
2664  WX_SUBMENU_INT("&Convert")
2665  WX_MENU_ITEM_INT(eCmdConvertFeatures)
2666  WX_MENU_ITEM_INT(eCmdConvertCdsToMiscFeat)
2667  WX_SUBMENU_INT("Convert CDS with Internal Stop Codon")
2668  WX_MENU_ITEM_INT(eCmdConvertCdsWithInternalStopToMiscFeat)
2669  WX_MENU_ITEM_INT(eCmdConvertCdsWithInternalStopToMiscFeatViral)
2670  WX_MENU_ITEM_INT(eCmdConvertCdsWithInternalStopToMiscFeatUnverified)
2671  WX_END_SUBMENU()
2672  WX_MENU_ITEM_INT(eCmdConvertFeatQual)
2673  WX_MENU_ITEM_INT(eCmdConvertSourceQual)
2674  WX_MENU_ITEM_INT(eCmdConvertCGPQual)
2675  WX_MENU_ITEM_INT(eCmdConvertRNAQual)
2676  WX_MENU_ITEM_INT(eCmdSwapFeatQual)
2677  WX_MENU_ITEM_INT(eCmdSwapSourceQual)
2678  WX_MENU_ITEM_INT(eCmdSwapCGPQual)
2679  WX_MENU_ITEM_INT(eCmdSwapRNAQual)
2680  WX_MENU_ITEM_INT(eCmdParseText)
2681  WX_MENU_ITEM_INT(eCmdIllegalQualsToNote)
2682  WX_MENU_ITEM_INT(eCmdWrongQualsToNote)
2683  WX_MENU_ITEM_INT(eCmdConvertBadInference)
2684  WX_MENU_ITEM_INT(eCmdConvertToDelayedGenProdSetQuals)
2685  WX_MENU_ITEM_INT(eCmdConvertRptUnitRangeToLoc)
2686  WX_SUBMENU_INT("Convert IDs, Accessions, or GenBank.names")
2687  WX_MENU_ITEM_INT(eCmdLocalToGeneralId)
2688  WX_MENU_ITEM_INT(eCmdGeneralToLocalId)
2689  WX_SUBMENU_INT("Accession to LocalIDs")
2690  WX_MENU_ITEM_INT(eCmdConvertAccessionToLocalIdsAll)
2691  WX_MENU_ITEM_INT(eCmdConvertAccessionToLocalIdsNuc)
2692  WX_MENU_ITEM_INT(eCmdConvertAccessionToLocalIdsProt)
2693  WX_MENU_ITEM_INT(eCmdConvertAccessionToLocalIdsName)
2694  WX_END_SUBMENU()
2695  WX_END_SUBMENU()
2696  WX_SUBMENU_INT("Convert Second Protein Name and Description")
2697  WX_MENU_ITEM_INT(eCmdConvertSecondProtNameToDesc)
2698  WX_MENU_ITEM_INT(eCmdConvertDescToSecondProtName)
2699  WX_END_SUBMENU()
2700  WX_SUBMENU_INT("Convert Descriptors and Features")
2701  WX_SUBMENU_INT("Descriptor to Feature")
2702  WX_MENU_ITEM_INT(eCmdConvertDescToFeatComment)
2703  WX_MENU_ITEM_INT(eCmdConvertDescToFeatSource)
2704  WX_SUBMENU_INT("Publication")
2705  WX_MENU_ITEM_INT(eCmdConvertDescToFeatPub)
2706  WX_MENU_ITEM_INT(eCmdConvertDescToFeatPubConstraint)
2707  WX_END_SUBMENU()
2708  WX_END_SUBMENU()
2709  WX_SUBMENU_INT("Convert Full Length Feature to Descriptor")
2710  WX_MENU_ITEM_INT(eCmdConvertFeatToDescSource)
2711  WX_MENU_ITEM_INT(eCmdConvertFeatToDescComment)
2712  WX_MENU_ITEM_INT(eCmdConvertFeatToDescPub)
2713  WX_END_SUBMENU()
2714  WX_END_SUBMENU()
2715  WX_END_SUBMENU()
2716  WX_SUBMENU_INT("&Edit")
2717  WX_MENU_ITEM_INT(eCmdEditFeatQual)
2718  WX_MENU_ITEM_INT(eCmdEditSourceQual)
2719  WX_MENU_ITEM_INT(eCmdEditCGPQual)
2720  WX_MENU_ITEM_INT(eCmdEditRNAQual)
2721  WX_MENU_ITEM_INT(eCmdMolInfoEdit)
2722  WX_MENU_ITEM_INT(eCmdTrimNsRich)
2723  WX_MENU_ITEM_INT(eCmdTrimNsTerminal)
2724  WX_SUBMENU_INT("Edit Feature")
2725  WX_MENU_ITEM_INT(eCmdEditFeatEv)
2726  WX_MENU_ITEM_INT(eCmdEditFeatLoc)
2727  WX_MENU_ITEM_INT(eCmdEditFeatStrand)
2728  WX_MENU_ITEM_INT(eCmdEditFeatRevInt)
2729  WX_MENU_ITEM_INT(eCmdEditFeatPseudo)
2730  WX_MENU_ITEM_INT(eCmdEditFeatException)
2731  WX_MENU_ITEM_INT(eCmdEditFeatExperiment)
2732  WX_MENU_ITEM_INT(eCmdEditFeatInference)
2733  WX_MENU_ITEM_INT(eCmdExtendCDS)
2734  WX_MENU_ITEM_INT(eCmdResolveIntersectingFeats)
2735  WX_END_SUBMENU()
2736  WX_SUBMENU_INT("Bulk Edit")
2737  WX_MENU_ITEM_INT(eCmdBulkSourceEdit)
2738  WX_MENU_ITEM_INT(eCmdBulkCdsEdit)
2739  WX_MENU_ITEM_INT(eCmdBulkGeneEdit)
2740  WX_MENU_ITEM_INT(eCmdBulkRnaEdit)
2741  WX_MENU_ITEM_INT(eCmdBulkMiscFeatEdit)
2742  WX_END_SUBMENU()
2743  WX_SUBMENU_INT("Extend Partial Features")
2744  WX_MENU_ITEM_INT(eCmdExtendPartialsConstr)
2745  WX_MENU_ITEM_INT(eCmdExtendPartialsAll)
2746  WX_END_SUBMENU()
2747  WX_MENU_ITEM_INT(eCmdCorrectGenes)
2748  WX_MENU_ITEM_INT(eCmdLowercaseQuals)
2749  WX_MENU_ITEM_INT(eCmdEditSequence)
2750  WX_MENU_ITEM_INT(eCmdEditSeqId)
2751  WX_MENU_ITEM_INT(eCmdEditHistory)
2752  WX_MENU_ITEM_INT(eCmdEditSeqEndsWithAlign)
2753  WX_MENU_ITEM_INT(eCmdEditSequenceEnds)
2754  WX_MENU_ITEM_INT(eCmdAddSecondary)
2755  WX_MENU_ITEM_INT(eCmdDuplicate)
2756  WX_MENU_ITEM_INT(eCmdCorrectIntervalOrder)
2757  WX_MENU_ITEM_INT(eCmdSuspectProductRulesEditor)
2758  WX_END_SUBMENU()
2759  WX_SUBMENU_INT("Authors and Publications")
2760  WX_MENU_ITEM_INT(eCmdEditPubs)
2761  WX_MENU_ITEM_INT(eCmdGlobalPubmedIdLookup)
2762  WX_SUBMENU_INT("Fix Capitalization")
2763  WX_MENU_ITEM_INT(eCmdFixCapitalizationAll)
2764  WX_MENU_ITEM_INT(eCmdFixCapitalizationAuthors)
2765  WX_MENU_ITEM_INT(eCmdFixCapitalizationTitles)
2766  WX_MENU_ITEM_INT(eCmdFixCapitalizationAffiliation)
2767  WX_MENU_ITEM_INT(eCmdFixCapitalizationCountry)
2768  WX_END_SUBMENU()
2769  WX_SUBMENU_INT("Remove Publications")
2770  WX_MENU_ITEM_INT(eCmdRemoveUnpublishedPublications)
2771  WX_MENU_ITEM_INT(eCmdRemoveInPressPublications)
2772  WX_MENU_ITEM_INT(eCmdRemovePublishedPublications)
2773  WX_MENU_ITEM_INT(eCmdRemoveCollidingPublications)
2774  WX_MENU_ITEM_INT(eCmdRemoveAllPublications)
2775  WX_END_SUBMENU()
2776  WX_MENU_ITEM_INT(eCmdRemoveAuthorConsortiums)
2777  WX_MENU_ITEM_INT(eCmdReverseAuthorNames)
2778  WX_MENU_ITEM_INT(eCmdStripAuthorSuffixes)
2779  WX_MENU_ITEM_INT(eCmdTruncateAuthorMiddleInitials)
2780  WX_SUBMENU_INT("Convert Author to Consortium")
2781  WX_MENU_ITEM_INT(eCmdConvertAuthorToConstortiumWhereLastName)
2782  WX_MENU_ITEM_INT(eCmdConvertAuthorToConsortiumAll)
2783  WX_END_SUBMENU()
2784  WX_MENU_ITEM_INT(eCmdAddCitSubForUpdate)
2785  WX_MENU_ITEM_INT(eCmdFixUsaAndStates)
2786  WX_END_SUBMENU()
2787  WX_SUBMENU_INT("CDS, Protein, and RNA")
2788  WX_SUBMENU_INT("Retranslate Coding Regions")
2789  WX_MENU_ITEM_INT(eCmdRetranslateCDSObeyStop)
2790  WX_MENU_ITEM_INT(eCmdRetranslateCDSIgnoreStopExceptEnd)
2791  WX_MENU_ITEM_INT(eCmdRetranslateCDSChooseFrame)
2792  WX_END_SUBMENU()
2793  WX_MENU_ITEM_INT(eCmdEditCdsFrame)
2794  WX_MENU_ITEM_INT(eCmdResynchronizePartialsCDS)
2795  WX_MENU_ITEM_INT(eCmdAddTranslExcept)
2796  WX_SUBMENU_INT("Adjust CDS for Consensus Splice Sites")
2797  WX_MENU_ITEM_INT(eCmdAdjustConsensusSpliceSitesStrict)
2798  WX_MENU_ITEM_INT(eCmdAdjustConsensusSpliceSitesRelaxed)
2799  WX_MENU_ITEM_INT(eCmdAdjustConsensusSpliceSitesConsensusEnds)
2800  WX_END_SUBMENU()
2801  WX_SUBMENU_INT("Adjust Features for Introns")
2802  WX_MENU_ITEM_INT(eCmdAdjustCDSForIntrons)
2803  WX_MENU_ITEM_INT(eCmdAdjustrRNAForIntrons)
2804  WX_MENU_ITEM_INT(eCmdAdjusttRNAForIntrons)
2805  WX_MENU_ITEM_INT(eCmdAdjustmRNAForIntrons)
2806  WX_END_SUBMENU()
2807  WX_MENU_ITEM_INT(eCmdCdsToMatPeptide)
2808  WX_MENU_ITEM_INT(eCmdTruncateCDS)
2809  WX_MENU_ITEM_INT(eCmdExtendCDSToStop)
2810  WX_SUBMENU_INT("Recompute Suggested Intervals")
2811  WX_MENU_ITEM_INT(eCmdRecomputeIntervalsAndUpdateGenes)
2812  WX_MENU_ITEM_INT(eCmdRecomputeIntervals)
2813  WX_END_SUBMENU()
2814  WX_SUBMENU_INT("Fix Product Name Capitalization")
2815  WX_MENU_ITEM_INT(eCmdFixProductNamesDefault)
2816  WX_MENU_ITEM_INT(eCmdFixProductNamesOptions)
2817  WX_END_SUBMENU()
2818  WX_MENU_ITEM_INT(eCmdRestoreRNAediting)
2819  WX_MENU_ITEM_INT(eCmdFixForTransSplicing)
2820  WX_END_SUBMENU()
2821  WX_SUBMENU_INT("Structured Comments")
2822  WX_MENU_ITEM_INT(eCmdApplyStructuredCommentField)
2823  WX_SUBMENU_INT("Edit Structured Comment Prefix-Suffix")
2824  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixHIVData)
2825  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixFluData)
2826  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixMIGSData)
2827  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixMIMSData)
2828  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixMIENSData)
2829  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixMIMARKS3_0)
2830  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixMIGS3_0)
2831  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixMIMS3_0)
2832  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixAssemblyData)
2833  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixGenAssData)
2834  WX_MENU_ITEM_INT(eCmdEditStructuredCommentPrefixSuffixiBol)
2835  WX_END_SUBMENU()
2836  WX_MENU_ITEM_INT(eCmdRemoveDuplicateStructuredComments)
2837  WX_MENU_ITEM_INT(eCmdRemoveAllStructuredComments)
2838  WX_MENU_ITEM_INT(eCmdRemoveEmptyStructuredComments)
2839  WX_MENU_ITEM_INT(eCmdModifyStructuredComment)
2840  WX_MENU_ITEM_INT(eCmdRemoveStructuredCommentKeyword)
2841  WX_MENU_ITEM_INT(eCmdAddStructuredCommentKeyword)
2842  WX_MENU_ITEM_INT(eCmdAddGenomeAssemblyStructuredComment)
2843  WX_MENU_ITEM_INT(eCmdAddAssemblyStructuredComment)
2844  WX_MENU_ITEM_INT(eCmdReorderStructuredComment)
2845  WX_MENU_ITEM_INT(eCmdConvertComment)
2846  WX_MENU_ITEM_INT(eCmdParseComment)
2847  WX_MENU_ITEM_INT(eCmdExportStructuredCommentsTable)
2848  WX_MENU_ITEM_INT(eCmdLoadStructComments)
2849  WX_END_SUBMENU()
2850  WX_SUBMENU_INT("Cleanup and Fixup")
2851  WX_MENU_ITEM_INT(eCmdTaxFixCleanup)
2852  WX_MENU_ITEM_INT(eCmdExtendedCleanup)
2853  WX_MENU_ITEM_INT(eCmdSpecificHostCleanup)
2854  WX_MENU_ITEM_INT(eCmdInstantiateProteinTitles)
2855  WX_MENU_ITEM_INT(eCmdUpdate_Replaced_EC_numbers)
2856  WX_MENU_ITEM_INT(eCmdRemoveDuplicateGOTerms)
2857  WX_END_SUBMENU()
2858  WX_SUBMENU_INT("Display")
2859  WX_MENU_ITEM_INT(eCmdViewSortedProteins)
2860  WX_MENU_ITEM_INT(eCmdShowFeatureTable)
2861  WX_MENU_ITEM_INT(eCmdMakeToolBarWindow)
2862  WX_MENU_CHECK_ITEM_INT(eCmdEnableHupId)
2863  WX_MENU_ITEM_INT(eCmdIndexerTypeSelection)
2864  WX_END_SUBMENU()
2865  WX_SUBMENU_INT("Desktop")
2866  WX_MENU_ITEM_INT(eCmdCorrectRNAStrand)
2867  WX_MENU_ITEM_INT(eCmdSegregateSets)
2868  WX_MENU_ITEM_INT(eCmdSequesterSets)
2869  WX_MENU_ITEM_INT(eCmdAddSet)
2870  WX_MENU_ITEM_INT(eCmdRemoveSegGaps)
2871  WX_MENU_ITEM_INT(eCmdRevCompSequences)
2872  WX_MENU_ITEM_INT(eCmdChangeSetClass)
2873  WX_MENU_ITEM_INT(eCmdGroupExplode)
2874  WX_MENU_ITEM_INT(eCmdFindASN1)
2875  WX_MENU_ITEM_INT(eCmdRemoveSetsFromSet)
2876  WX_MENU_ITEM_INT(eCmdReorderSeqById)
2877  WX_MENU_ITEM_INT(eCmdUpdateAlign)
2878  WX_MENU_ITEM_INT(eCmdAlignmentAssistant)
2879  WX_MENU_ITEM_INT(eCmdSaveDescriptors)
2880  WX_MENU_ITEM_INT(eCmdDescriptorPropagateDown)
2881  WX_SUBMENU_INT("Utilities")
2882  WX_MENU_ITEM_INT(eCmdBioseqFeatsRevComp)
2883  WX_MENU_ITEM_INT(eCmdBioseqOnlyRevComp)
2884  WX_MENU_ITEM_INT(eCmdCheckForMixedStrands)
2885  WX_END_SUBMENU()
2886  WX_SUBMENU_INT("Indexer")
2887  WX_MENU_ITEM_INT(eCmdRemoveSet)
2888  WX_END_SUBMENU()
2889  WX_END_SUBMENU()
2890  WX_SUBMENU_INT("Link")
2891  WX_SUBMENU_INT("Feature IDs")
2892  WX_MENU_ITEM_INT(eCmdAssignFeatureIds)
2893  WX_MENU_ITEM_INT(eCmdClearFeatureIds)
2894  WX_MENU_ITEM_INT(eCmdReassignFeatureIds)
2895  WX_MENU_ITEM_INT(eCmdUniqifyFeatureIds)
2896  WX_MENU_ITEM_INT(eCmdFixNonReciprocalLinks)
2897  WX_END_SUBMENU()
2898  WX_SUBMENU_INT("Create CDS-mRNA Links")
2899  WX_MENU_ITEM_INT(eCmdLinkmRNACDSOverlap)
2900  WX_MENU_ITEM_INT(eCmdLinkmRNACDSProduct)
2901  WX_MENU_ITEM_INT(eCmdLinkmRNACDSLabel)
2902  WX_MENU_ITEM_INT(eCmdLinkmRNACDSLabelLocation)
2903  WX_MENU_ITEM_INT(eCmdLinkmRNACDSProteinID)
2904  WX_MENU_ITEM_INT(eCmdLinkmRNACDSTranscriptID)
2905  WX_MENU_ITEM_INT(eCmdLinkmRNACDSUnidirectional)
2906  WX_END_SUBMENU()
2907  WX_MENU_ITEM_INT(eCmdLinkSelectedmRNACDS)
2908  WX_MENU_ITEM_INT(eCmdShowLinkedmRNACDS)
2909  WX_END_SUBMENU()
2910  WX_SUBMENU_INT("Projects")
2911  WX_MENU_ITEM_INT(eCmdAddFluComments)
2912  WX_MENU_ITEM_INT(eCmdSetGlobalRefGeneStatus)
2913  WX_MENU_ITEM_INT(eCmdCreateSeqHistForTpaDetailed)
2914  WX_MENU_ITEM_INT(eCmdCreateSeqHistForTpa)
2915  WX_MENU_ITEM_INT(eCmdRemoveSeqHistAssembly)
2916  WX_MENU_ITEM_INT(eCmdBarcodeTool)
2917  WX_MENU_ITEM_INT(eCmdApplyFBOL)
2918  WX_MENU_ITEM_INT(eCmdFarPointerSeq)
2919  WX_MENU_ITEM_INT(eCmdConvertBadCdsAndRnaToMiscFeat)
2920  WX_MENU_ITEM_INT(eCmdUpdateTLSName)
2921  WX_END_SUBMENU()
2922  WX_SUBMENU_INT("Make Features and Fuse")
2923  WX_MENU_ITEM_INT(eCmdCombineSelectedGenesIntoPseudogenes)
2924  WX_MENU_ITEM_INT(eCmdGeneFromOtherFeat)
2925  WX_MENU_ITEM_INT(eCmdGeneFeatFromXrefs)
2926  WX_MENU_ITEM_INT(eCmdGeneXrefsFromFeats)
2927  WX_MENU_ITEM_INT(eCmdCdsFromGeneMrnaExon)
2928  WX_MENU_ITEM_INT(eCmdmRNAFromGeneCdsExon)
2929  WX_MENU_ITEM_INT(eCmdtRNAFromGene)
2930  WX_MENU_ITEM_INT(eCmdFuseFeatures)
2931  WX_MENU_ITEM_INT(eCmdFuseJoinsInLocs)
2932  WX_MENU_ITEM_INT(eCmdExplodeRNAFeats)
2933  WX_SUBMENU_INT("Exon features from")
2934  WX_MENU_ITEM_INT(eCmdExonFromCds)
2935  WX_MENU_ITEM_INT(eCmdExonFromMRNA)
2936  WX_MENU_ITEM_INT(eCmdExonFromTRNA)
2937  WX_END_SUBMENU()
2938  WX_END_SUBMENU()
2939  WX_SUBMENU_INT("Normalize, Map, Package")
2940  WX_SUBMENU_INT("CDSGeneRangeError")
2941  WX_MENU_ITEM_INT(eCmdCDSGeneRangeErrorSuppress)
2942  WX_MENU_ITEM_INT(eCmdCDSGeneRangeErrorRestore)
2943  WX_END_SUBMENU()
2944  WX_MENU_ITEM_INT(eCmdSuppressGenes)
2945  WX_MENU_ITEM_INT(eCmdPackageFeaturesOnParts)
2946  WX_END_SUBMENU()
2947  WX_SUBMENU_INT("Gap Sequences")
2948  WX_SUBMENU_INT("Raw Sequence To Delta")
2949  WX_MENU_ITEM_INT(eCmdRawSeqToDeltaByNs)
2950  WX_MENU_ITEM_INT(eCmdRawSeqToDeltaByLoc)
2951  WX_MENU_ITEM_INT(eCmdRawSeqToDeltaByAssemblyGapFeatures)
2952  WX_END_SUBMENU()
2953  WX_MENU_ITEM_INT(eCmdDeltaSeqToRaw)
2954  WX_MENU_ITEM_INT(eCmdExpandGaps)
2955  WX_SUBMENU_INT("Convert Selected Gaps")
2956  WX_MENU_ITEM_INT(eCmdConvertSelectedGapsToKnown)
2957  WX_MENU_ITEM_INT(eCmdConvertSelectedGapsToUnknown)
2958  WX_END_SUBMENU()
2959  WX_MENU_ITEM_INT(eCmdConvertGapsBySize)
2960  WX_MENU_ITEM_INT(eCmdEditSelectedGaps)
2961  WX_MENU_ITEM_INT(eCmdAddLinkageToGaps)
2962  WX_MENU_ITEM_INT(eCmdCombineAdjacentGaps)
2963  WX_MENU_ITEM_INT(eCmdAdjustFeaturesForGaps)
2964  WX_MENU_ITEM_INT(eCmdConvertCdsWithGapsToMiscFeat)
2965  WX_MENU_ITEM_INT(eCmdSplitCDSwithTooManyXs)
2966  WX_END_SUBMENU()
2967  WX_MENU_ITEM_INT(eCmdSortUniqueCountTree)
2968  WX_MENU_ITEM_INT(eCmdSortUniqueCountText)
2969  WX_MENU_ITEM_INT(eCmdDiscrepancy)
2970  WX_MENU_ITEM_INT(eCmdOncaller)
2971  WX_MENU_ITEM_INT(eCmdSubmitter)
2972  WX_MENU_ITEM_INT(eCmdMega)
2973  WX_MENU_ITEM_INT(eCmdDiscrepancyList)
2974  WX_MENU_ITEM_INT(eCmdValidate)
2975  WX_MENU_ITEM_INT(eCmdMacroEditor)
2976 #ifdef _DEBUG
2977  WX_MENU_ITEM_INT(eCmdPrepareSeqSubmit)
2978  WX_MENU_ITEM_INT(eCmdTestDialogView)
2979  WX_MENU_ITEM_INT(eCmdTestFormView)
2980 #endif
2981  WX_SUBMENU_INT("Select")
2982  WX_MENU_ITEM_INT(eCmdSelectFeature)
2983  WX_END_SUBMENU()
2984  WX_SUBMENU_INT("Locus-tags")
2985  WX_MENU_ITEM_INT(eCmdCreateProteinId)
2986  WX_MENU_ITEM_INT(eCmdCreateLocusTagGene)
2987  WX_MENU_ITEM_INT(eCmdNormalizeGeneQuals)
2988  WX_END_SUBMENU()
2989  WX_MENU_ITEM_INT(eCmdEditingButtons)
2990  WX_MENU_ITEM_INT(eCmdSaveASN1File)
2991  WX_END_SUBMENU()
2992  WX_SUBMENU_INT("&Annotate")
2993  WX_SUBMENU_INT("Genes and Named Regions")
2994  WX_MENU_ITEM_INT(eCmdCreateGene)
2995  WX_MENU_ITEM_INT(eCmdCreateProt)
2996  WX_MENU_ITEM_INT(eCmdCreateRepeatRegion)
2997  WX_MENU_ITEM_INT(eCmdCreateStemLoop)
2998  WX_MENU_ITEM_INT(eCmdCreateSTS)
2999  WX_MENU_ITEM_INT(eCmdCreateRegion)
3000  WX_MENU_ITEM_INT(eCmdCreateSecondaryStructure)
3001  WX_MENU_ITEM_INT(eCmdCreateProprotein)
3002  WX_MENU_ITEM_INT(eCmdCreateMatPeptide)
3003  WX_MENU_ITEM_INT(eCmdCreateSigPeptide)
3004  WX_MENU_ITEM_INT(eCmdCreateTransitPeptide)
3005  WX_MENU_ITEM_INT(eCmdCreateOperon)
3006  WX_MENU_ITEM_INT(eCmdCreateMobileElement)
3007  WX_MENU_ITEM_INT(eCmdCreateCentromere)
3008  WX_MENU_ITEM_INT(eCmdCreateTelomere)
3009  WX_MENU_ITEM_INT(eCmdCreateRegulatory)
3010  WX_END_SUBMENU()
3011  WX_SUBMENU_INT("Coding Regions and Transcripts")
3012  WX_MENU_ITEM_INT(eCmdCreateCodingRegion)
3013  WX_MENU_ITEM_INT(eCmdCreatePreRNA)
3014  WX_MENU_ITEM_INT(eCmdCreateMRNA)
3015  WX_MENU_ITEM_INT(eCmdCreateExon)
3016  WX_MENU_ITEM_INT(eCmdCreateIntron)
3017  WX_MENU_ITEM_INT(eCmdCreate3UTR)
3018  WX_MENU_ITEM_INT(eCmdCreate5UTR)
3019  WX_END_SUBMENU()
3020  WX_SUBMENU_INT("Structural RNAs")
3021  WX_MENU_ITEM_INT(eCmdCreatetRNA)
3022  WX_MENU_ITEM_INT(eCmdCreaterRNA)
3023  WX_MENU_ITEM_INT(eCmdCreateRNA)
3024  WX_MENU_ITEM_INT(eCmdCreatencRNA)
3025  WX_MENU_ITEM_INT(eCmdCreatetmRNA)
3026  WX_END_SUBMENU()
3027  WX_SUBMENU_INT("Bibliographic and Comments")
3028  WX_MENU_ITEM_INT(eCmdCreateCommentDescriptor)
3029  WX_MENU_ITEM_INT(eCmdCreateBiosourceFeat)
3030  WX_END_SUBMENU()
3031  WX_SUBMENU_INT("Sites and Bonds")
3032  WX_MENU_ITEM_INT(eCmdCreatePolyASite)
3033  WX_MENU_ITEM_INT(eCmdCreatePrimerBind)
3034  WX_MENU_ITEM_INT(eCmdCreateProteinBind)
3035  WX_MENU_ITEM_INT(eCmdCreateRepOrigin)
3036  WX_MENU_ITEM_INT(eCmdCreateBond)
3037  WX_MENU_ITEM_INT(eCmdCreateSite)
3038  WX_MENU_ITEM_INT(eCmdCreateOriT)
3039  WX_END_SUBMENU()
3040  WX_SUBMENU_INT("Remaining Features")
3041  WX_MENU_ITEM_INT(eCmdCreateCRegion)
3042  WX_MENU_ITEM_INT(eCmdCreateDLoop)
3043  WX_MENU_ITEM_INT(eCmdCreateDSegment)
3044  WX_MENU_ITEM_INT(eCmdCreateiDNA)
3045  WX_MENU_ITEM_INT(eCmdCreateJSegment)
3046  WX_MENU_ITEM_INT(eCmdCreateMiscBinding)
3047  WX_MENU_ITEM_INT(eCmdCreateMiscDifference)
3048  WX_MENU_ITEM_INT(eCmdCreateMiscFeature)
3049  WX_MENU_ITEM_INT(eCmdCreateMiscRecomb)
3050  WX_MENU_ITEM_INT(eCmdCreateMiscStructure)
3051  WX_MENU_ITEM_INT(eCmdCreateModifiedBase)
3052  WX_MENU_ITEM_INT(eCmdCreateNRegion)
3053  WX_MENU_ITEM_INT(eCmdCreatePrimTranscript)
3054  WX_MENU_ITEM_INT(eCmdCreateSRegion)
3055  WX_MENU_ITEM_INT(eCmdCreateUnsure)
3056  WX_MENU_ITEM_INT(eCmdCreateVRegion)
3057  WX_MENU_ITEM_INT(eCmdCreateVSegment)
3058  WX_MENU_ITEM_INT(eCmdCreateVariation)
3059