NCBI C++ ToolKit
Classes | Functions | Variables
dll_register.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <objects/seqtable/SeqTable_column.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <gui/objects/GBProject.hpp>
#include <objects/gbproj/ProjectItem.hpp>
#include <gui/core/project_tree_view.hpp>
#include <gui/core/object_loading_task.hpp>
#include <gui/framework/app_task_service.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objtools/edit/autodef_with_tax.hpp>
#include <objtools/edit/mail_report.hpp>
#include <objtools/edit/struc_comm_field.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include <connect/ncbi_http_session.hpp>
#include <gui/framework/gui_package.hpp>
#include <gui/framework/pkg_wb_connect.hpp>
#include <gui/framework/workbench_impl.hpp>
#include <gui/core/selection_service_impl.hpp>
#include <gui/widgets/wx/ui_command.hpp>
#include <gui/widgets/wx/csv_exporter.hpp>
#include <gui/utils/extension_impl.hpp>
#include <gui/utils/url_utils.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_change_align.hpp>
#include <gui/objutils/cmd_insert_bioseq_set.hpp>
#include <gui/objutils/cmd_change_seq_entry.hpp>
#include <gui/objutils/util_cmds.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/macro_lib.hpp>
#include <gui/objutils/macro_fn_do.hpp>
#include <gui/objutils/macro_fn_entry.hpp>
#include <gui/objutils/table_data_base.hpp>
#include <gui/objutils/adjust_consensus_splicesite.hpp>
#include <gui/objects/GBWorkspace.hpp>
#include <gui/objects/WorkspaceFolder.hpp>
#include <gui/objects/gbench_version.hpp>
#include <gui/objects/GBenchVersionInfo.hpp>
#include <gui/widgets/edit/init.hpp>
#include <gui/widgets/edit/edit_object.hpp>
#include <gui/widgets/edit/edit_object_seq_feat.hpp>
#include <gui/widgets/edit/edit_object_seq_desc.hpp>
#include <gui/widgets/loaders/open_objects_dlg.hpp>
#include <gui/widgets/loaders/file_load_wizard.hpp>
#include "open_data_source_object_dlg.hpp"
#include <gui/utils/object_loader.hpp>
#include <gui/utils/execute_unit.hpp>
#include <gui/utils/app_popup.hpp>
#include <gui/utils/event_handler.hpp>
#include <gui/objutils/project_item_extra.hpp>
#include <gui/widgets/wx/async_call.hpp>
#include <gui/widgets/wx/sys_path.hpp>
#include <gui/widgets/wx/message_box.hpp>
#include <gui/packages/pkg_sequence_edit/autodef_tool_manager.hpp>
#include <gui/packages/pkg_sequence_edit/srcedit_tool.hpp>
#include <gui/packages/pkg_sequence_edit/seqid_fix_dlg.hpp>
#include <gui/widgets/edit/table_data_suc.hpp>
#include <gui/widgets/edit/table_data_validate.hpp>
#include <gui/widgets/edit/table_data_validate_params.hpp>
#include <gui/packages/pkg_sequence_edit/remove_desc_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/remove_sequences_from_alignments.hpp>
#include <gui/packages/pkg_sequence_edit/remove_features_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/remove_structured_comment.hpp>
#include <gui/packages/pkg_sequence_edit/remove_annot.hpp>
#include <gui/packages/pkg_sequence_edit/remove_genomeprojectdb.hpp>
#include <gui/packages/pkg_sequence_edit/add_citsubupdate.hpp>
#include <gui/packages/pkg_sequence_edit/pubdesc_editor.hpp>
#include <gui/packages/pkg_sequence_edit/modify_structured_comment.hpp>
#include <gui/packages/pkg_sequence_edit/remove_bankit_comment.hpp>
#include <gui/packages/pkg_sequence_edit/remove_structuredcomment_keyword.hpp>
#include <gui/packages/pkg_sequence_edit/reorder_sequences_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/convert_comment.hpp>
#include <gui/packages/pkg_sequence_edit/modify_feature_id.hpp>
#include <gui/packages/pkg_sequence_edit/remove_sequences.hpp>
#include <gui/packages/pkg_sequence_edit/pcr-primers-edit.hpp>
#include <gui/packages/pkg_sequence_edit/fix_orgmod_institution.hpp>
#include <gui/packages/pkg_sequence_edit/parse_collectiondate_formats.hpp>
#include <gui/packages/pkg_sequence_edit/country_fixup.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_feature_add_dlg_std.hpp>
#include <gui/packages/pkg_sequence_edit/srceditdialog.hpp>
#include <gui/packages/pkg_sequence_edit/molinfo_edit_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/miscedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/featedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/autodef_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/autodef_params.hpp>
#include <gui/packages/pkg_sequence_edit/autodef_functions.hpp>
#include <gui/packages/pkg_sequence_edit/strain_serotype_influenza.hpp>
#include <gui/packages/pkg_sequence_edit/qual_table_load_manager.hpp>
#include <gui/packages/pkg_sequence_edit/vectortrimdlg.hpp>
#include <gui/packages/pkg_sequence_edit/citem_util.hpp>
#include <gui/packages/pkg_sequence_edit/remove_unverified.hpp>
#include <gui/packages/pkg_sequence_edit/add_deflinedlg.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_edit_feat_dlg_std.hpp>
#include <gui/packages/pkg_sequence_edit/convert_feat_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/prefix_deflinedlg.hpp>
#include <gui/packages/pkg_sequence_edit/discrepancy_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/edit_pub_dlg_std.hpp>
#include <gui/packages/pkg_sequence_edit/make_badspecifichost_tbl.hpp>
#include <gui/packages/pkg_sequence_edit/editingbtnspanel.hpp>
#include <gui/packages/pkg_sequence_edit/correct_rna_strand_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/apply_rna_its_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/trim_n.hpp>
#include <gui/packages/pkg_sequence_edit/label_rna.hpp>
#include <gui/packages/pkg_sequence_edit/rem_prot_titles.hpp>
#include <gui/packages/pkg_sequence_edit/add_transl_except_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_cds_edit.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_gene_edit.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_rna_edit.hpp>
#include <gui/packages/pkg_sequence_edit/choose_set_class_dlg.hpp>
#include "test_dialog_view.hpp"
#include <gui/widgets/seq/text_panel.hpp>
#include <gui/packages/pkg_sequence_edit/retranslate_cds.hpp>
#include <gui/widgets/edit/generic_report_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/segregate_sets.hpp>
#include <gui/packages/pkg_sequence_edit/sequester_sets.hpp>
#include <gui/widgets/edit/macrofloweditor.hpp>
#include <gui/packages/pkg_sequence_edit/suc_refresh_cntrl.hpp>
#include <gui/packages/pkg_sequence_edit/revcomp_sequences.hpp>
#include <gui/packages/pkg_sequence_edit/select_target_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/withdraw_sequences.hpp>
#include <gui/packages/pkg_sequence_edit/uncul_tax_tool.hpp>
#include <gui/packages/pkg_sequence_edit/apply_indexer_comments.hpp>
#include <gui/packages/pkg_sequence_edit/correct_genes_dialog.hpp>
#include <gui/packages/pkg_sequence_edit/extend_partial_features.hpp>
#include <gui/packages/pkg_sequence_edit/convert_cds_to_misc_feat.hpp>
#include <gui/packages/pkg_sequence_edit/add_flu_comments.hpp>
#include <gui/packages/pkg_sequence_edit/lowercase_qualifiers.hpp>
#include <gui/packages/pkg_sequence_edit/add_sequences.hpp>
#include <gui/packages/pkg_sequence_edit/convert_set_type_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/gene_features_from_other_features.hpp>
#include <gui/packages/pkg_sequence_edit/latlon_tool.hpp>
#include <gui/packages/pkg_sequence_edit/export_table.hpp>
#include <gui/widgets/edit/edit_sequence.hpp>
#include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_n.hpp>
#include <gui/packages/pkg_sequence_edit/update_replaced_ec_numbers.hpp>
#include <gui/packages/pkg_sequence_edit/update_seq_worker.hpp>
#include <gui/packages/pkg_sequence_edit/add_feature_between_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/import_feat_table.hpp>
#include <gui/packages/pkg_sequence_edit/group_explode.hpp>
#include <gui/packages/pkg_sequence_edit/remove_text_inside_string_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/find_asn1_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/fuse_features.hpp>
#include <gui/packages/pkg_sequence_edit/remove_dup_feats_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/remove_xrefs.hpp>
#include <gui/packages/pkg_sequence_edit/cds_from_gene_mrna_exon.hpp>
#include <gui/packages/pkg_sequence_edit/cds_to_mat_peptide.hpp>
#include <gui/packages/pkg_sequence_edit/select_features.hpp>
#include <gui/packages/pkg_sequence_edit/remove_set.hpp>
#include <gui/packages/pkg_sequence_edit/edit_seq_id.hpp>
#include <gui/packages/pkg_sequence_edit/edit_history.hpp>
#include <gui/packages/pkg_sequence_edit/exon_from_cds.hpp>
#include <gui/packages/pkg_sequence_edit/set_global_refgene_status.hpp>
#include <gui/packages/pkg_sequence_edit/clear_keywords.hpp>
#include <gui/packages/pkg_sequence_edit/convert_rpt_unit_range_to_location.hpp>
#include <gui/packages/pkg_sequence_edit/link_mrna_cds.hpp>
#include <gui/packages/pkg_sequence_edit/gene_feats_from_xrefs.hpp>
#include <gui/packages/pkg_sequence_edit/remove_gene_xrefs.hpp>
#include <gui/packages/pkg_sequence_edit/truncate_cds.hpp>
#include <gui/packages/pkg_sequence_edit/fix_product_names.hpp>
#include <gui/packages/pkg_sequence_edit/apply_gcode.hpp>
#include <gui/packages/pkg_sequence_edit/edit_seq_ends_with_align.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/packages/pkg_sequence_edit/update_align.hpp>
#include <gui/packages/pkg_sequence_edit/resolve_intersecting_feats.hpp>
#include <gui/packages/pkg_sequence_edit/create_protein_id.hpp>
#include <gui/packages/pkg_sequence_edit/genus_species_fixup.hpp>
#include <gui/packages/pkg_sequence_edit/country_conflict.hpp>
#include <gui/packages/pkg_sequence_edit/add_secondary.hpp>
#include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.hpp>
#include <gui/packages/pkg_sequence_edit/package_features_on_parts.hpp>
#include <gui/packages/pkg_sequence_edit/featuretbl_frame.hpp>
#include <gui/packages/pkg_sequence_edit/fix_structured_vouchers.hpp>
#include <gui/packages/pkg_sequence_edit/edit_seq_ends.hpp>
#include <gui/packages/pkg_sequence_edit/create_seq_hist_for_tpa.hpp>
#include <gui/widgets/edit/alignment_assistant.hpp>
#include <gui/packages/pkg_sequence_edit/adjust_features_for_gaps.hpp>
#include <gui/packages/pkg_sequence_edit/compare_with_biosample.hpp>
#include <gui/packages/pkg_sequence_edit/barcode_tool.hpp>
#include <gui/packages/pkg_sequence_edit/restore_local_file.hpp>
#include <gui/packages/pkg_sequence_edit/split_cds_with_too_many_n.hpp>
#include <gui/packages/pkg_sequence_edit/far_pointer_seq.hpp>
#include <gui/packages/pkg_sequence_edit/csuc_frame.hpp>
#include <gui/packages/pkg_sequence_edit/edit_cds_frame.hpp>
#include <gui/packages/pkg_sequence_edit/expand_gaps.hpp>
#include <gui/packages/pkg_sequence_edit/convert_cds_with_gaps_to_misc_feat.hpp>
#include <gui/packages/pkg_sequence_edit/convert_selected_gaps.hpp>
#include <gui/packages/pkg_sequence_edit/sorted_proteins.hpp>
#include <gui/packages/pkg_sequence_edit/add_linkage_to_gaps.hpp>
#include <gui/packages/pkg_sequence_edit/remove_srcnotes.hpp>
#include <gui/packages/pkg_sequence_edit/convert_second_prot_name.hpp>
#include <gui/packages/pkg_sequence_edit/mrna_from_gene_cds_exon.hpp>
#include <gui/packages/pkg_sequence_edit/trna_from_gene.hpp>
#include <gui/packages/pkg_sequence_edit/adjust_feats_for_introns.hpp>
#include <gui/packages/pkg_sequence_edit/clear_nomenclature.hpp>
#include <gui/packages/pkg_sequence_edit/merge_biosources.hpp>
#include <gui/packages/pkg_sequence_edit/suppress_genes.hpp>
#include <gui/packages/pkg_sequence_edit/extend_cds_to_stop.hpp>
#include <gui/packages/pkg_sequence_edit/recompute_intervals.hpp>
#include <gui/packages/pkg_sequence_edit/convert_bad_inference.hpp>
#include <gui/packages/pkg_sequence_edit/global_pubmedid_lookup.hpp>
#include <gui/packages/pkg_sequence_edit/remove_unindexed_features.hpp>
#include <gui/packages/pkg_sequence_edit/correct_interval_order.hpp>
#include <gui/packages/pkg_sequence_edit/load_secondary_accessions.hpp>
#include <gui/packages/pkg_sequence_edit/add_global_code_break.hpp>
#include <gui/packages/pkg_sequence_edit/convert_desc_to_feat.hpp>
#include <gui/packages/pkg_sequence_edit/validate_frame.hpp>
#include <gui/packages/pkg_sequence_edit/load_struct_comm_from_table.hpp>
#include <gui/packages/pkg_sequence_edit/suspect_product_rule_editor.hpp>
#include <gui/packages/pkg_sequence_edit/mixedstrands.hpp>
#include <gui/packages/pkg_sequence_edit/remove_unnecessary_exceptions.hpp>
#include <gui/packages/pkg_sequence_edit/restore_rna_edit.hpp>
#include <gui/packages/pkg_sequence_edit/fix_for_trans_splicing.hpp>
#include <gui/packages/pkg_sequence_edit/submission_wizard.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_miscfeat_edit.hpp>
#include <gui/packages/pkg_sequence_edit/update_targeted_locus_name_dlg.hpp>
#include <gui/widgets/edit/bioseq_editor.hpp>
#include <gui/core/simple_project_view.hpp>
#include <gui/widgets/edit/edit_obj_view_dlg.hpp>
#include <gui/widgets/edit/propagate_descriptors.hpp>
#include "edit_project_item_extension.hpp"
#include "indexer_app_mode.hpp"
#include <gui/packages/pkg_sequence_edit/sequin_desktop_view.hpp>
#include <gui/packages/pkg_sequence_edit/wrong_illegal_quals.hpp>
#include <gui/packages/pkg_sequence_edit/editing_actions.hpp>
#include <gui/packages/pkg_sequence_edit/editing_action_constraint.hpp>
#include <gui/packages/pkg_sequence_edit/aecr_frame.hpp>
#include "attrib_table_column_id_panel.hpp"
#include "gui_core_helper_impl.hpp"
#include <gui/packages/pkg_sequence_edit/parse_text_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/append_mod_to_org_dlg.hpp>
#include <gui/widgets/edit/sequence_editing_cmds.hpp>
#include <gui/objutils/cmd_enable_hup_id.hpp>
#include <gui/core/cmd_change_projectitem.hpp>
#include "cmd_feat_id_xrefs_from_qualifiers.hpp"
#include "cmd_convert_to_delayed_gen-prod-set_quals.hpp"
#include <gui/packages/pkg_sequence_edit/debug_macro_tool.hpp>
#include <wx/msgdlg.h>
#include <wx/statline.h>
#include <wx/clipbrd.h>
#include <gui/widgets/wx/file_extensions.hpp>
#include <wx/filedlg.h>
#include <wx/display.h>
#include <wx/evtloop.h>
#include <wx/uri.h>
#include <wx/utils.h>

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Classes

class  CSeqEditPackage
 Declare the Package Object. More...
 
class  CSequenceEditingEventHandler
 
class  CDoOnIdleTask
 

Functions

static bool s_UpdateLocalFile (const string &url, const string &file_name)
 
IGuiPackage * NCBIGBenchGetPackage ()
 Declare Package Entry Point. More...
 
 ON_EVENT_RANGE (CSelectionServiceEvent, CSelectionServiceEvent::eClientAttached, CSelectionServiceEvent::eSelectionChanged, &CSequenceEditingEventHandler::x_OnSelectionEvent) static const SwxMenuItemRec *CSeqEditPackage
 
static bool CompLoc (CRef< CSeq_loc > first, CRef< CSeq_loc > second)
 
static bool EqualLoc (CRef< CSeq_loc > first, CRef< CSeq_loc > second)
 
static wxString IndexerTypeToName (int i)
 
static CRef< CUser_object > GetParams ()
 
static tuple< CRef< CGBProjectHandle >, CRef< CProjectItem > > LoadFileForSubmission (wxWindow *parent, CIRef< CProjectService > srv, CRef< CGBWorkspace > ws)
 

Variables

static const char * sMacroLibraries []
 
static const char * kFrameWidth = "Frame Width"
 
static const char * kFrameHeight = "Frame Height"
 
static const char * kFramePosX = "Frame Position X"
 
static const char * kFramePosY = "Frame Position Y"
 

Function Documentation

◆ CompLoc()

static bool CompLoc ( CRef< CSeq_loc >  first,
CRef< CSeq_loc >  second 
)
static

Definition at line 4719 of file dll_register.cpp.

References CSeq_loc::fCompare_Default, and first().

Referenced by CSequenceEditingEventHandler::Autodef().

◆ EqualLoc()

static bool EqualLoc ( CRef< CSeq_loc >  first,
CRef< CSeq_loc >  second 
)
static

Definition at line 4725 of file dll_register.cpp.

References first().

Referenced by CSequenceEditingEventHandler::Autodef().

◆ GetParams()

static CRef<CUser_object> GetParams ( )
static

Definition at line 8395 of file dll_register.cpp.

References data, label, CUser_field_Base::SetData(), CUser_object_Base::SetData(), CUser_field_Base::SetLabel(), CUser_object_Base::SetType(), and type.

Referenced by CSequenceEditingEventHandler::PrepareSeqSubmit().

◆ IndexerTypeToName()

static wxString IndexerTypeToName ( int  i)
static

Definition at line 8304 of file dll_register.cpp.

References _, e_GenBankIndexer, e_RefSeqIndexer, and i.

Referenced by CSequenceEditingEventHandler::IndexerTypeSelection().

◆ LoadFileForSubmission()

static tuple<CRef<CGBProjectHandle>,CRef<CProjectItem> > LoadFileForSubmission ( wxWindow *  parent,
CIRef< CProjectService >  srv,
CRef< CGBWorkspace >  ws 
)
static

Definition at line 8429 of file dll_register.cpp.

References CObjectLoadingTask::AddObjects(), GetExtensionAsInterface(), COpenObjectsDlg::GetObjectLoader(), CRef< C, Locker >::GetPointer(), GUI_AsyncExecUnit(), Info(), CBioseq::IsAa(), kEmptyStr, LOG_POST, MSerial_AsnText, pi, IExecuteUnit::PostExecute(), IExecuteUnit::PreExecute(), CSelectProjectOptions::Set_CreateNewProject(), COpenObjectsDlg::SetManagers(), CDialog::SetRegistryPath(), and wxT.

Referenced by CSequenceEditingEventHandler::PrepareSeqSubmit().

◆ NCBIGBenchGetPackage()

IGuiPackage* NCBIGBenchGetPackage ( )

Declare Package Entry Point.

Definition at line 516 of file dll_register.cpp.

◆ ON_EVENT_RANGE()

ON_EVENT_RANGE ( CSelectionServiceEvent  ,
CSelectionServiceEvent::eClientAttached  ,
CSelectionServiceEvent::eSelectionChanged  ,
&CSequenceEditingEventHandler::x_OnSelectionEvent   
) const

Definition at line 2296 of file dll_register.cpp.

◆ s_UpdateLocalFile()

static bool s_UpdateLocalFile ( const string &  url,
const string &  file_name 
)
static

Definition at line 439 of file dll_register.cpp.

References CHttpResponse::CanGetContentStream(), CHttpResponse::ContentStream(), file_name, g_HttpGet(), CHttpResponse::GetStatusCode(), Info(), LOG_POST, and NcbiStreamCopy().

Referenced by CSeqEditPackage::x_UpdateValAuxFile().

Variable Documentation

◆ kFrameHeight

const char* kFrameHeight = "Frame Height"
static

Definition at line 4379 of file dll_register.cpp.

Referenced by CSequenceEditingEventHandler::LoadSettings(), and CSequenceEditingEventHandler::SaveSettings().

◆ kFramePosX

const char* kFramePosX = "Frame Position X"
static

Definition at line 4380 of file dll_register.cpp.

Referenced by CSequenceEditingEventHandler::LoadSettings(), and CSequenceEditingEventHandler::SaveSettings().

◆ kFramePosY

const char* kFramePosY = "Frame Position Y"
static

Definition at line 4381 of file dll_register.cpp.

Referenced by CSequenceEditingEventHandler::LoadSettings(), and CSequenceEditingEventHandler::SaveSettings().

◆ kFrameWidth

const char* kFrameWidth = "Frame Width"
static

Definition at line 4378 of file dll_register.cpp.

Referenced by CSequenceEditingEventHandler::LoadSettings(), and CSequenceEditingEventHandler::SaveSettings().

◆ sMacroLibraries

const char* sMacroLibraries[]
static
Initial value:
= {
"<std>/etc/macro_scripts/list_of_macros.mql",
"<std>/etc/macro_scripts/autofix_gb.mql",
"<std>/etc/macro_scripts/autofix_tsa.mql",
"<std>/etc/macro_scripts/autofix_wgs.mql",
NULL
}
NULL
#define NULL
Definition: ncbistd.hpp:225

Definition at line 337 of file dll_register.cpp.

Referenced by CSeqEditPackage::Init().

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Modified on Fri Sep 20 14:57:22 2024 by modify_doxy.py rev. 669887