subprep_panel.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objects/submit/Contact_info.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/biblio/Cit_sub.hpp>
#include <objects/biblio/Cit_gen.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/general/Name_std.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <gui/framework/workbench_impl.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_panel.hpp>
#include <gui/widgets/object_list/object_list_widget.hpp>
#include <gui/objutils/cmd_change_bioseq_set.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/util_cmds.hpp>
#include <gui/packages/pkg_sequence_edit/srceditdialog.hpp>
#include <gui/packages/pkg_sequence_edit/seqtechdlg.hpp>
#include <gui/packages/pkg_sequence_edit/submitblockdlg.hpp>
#include <gui/packages/pkg_sequence_edit/import_feat_table.hpp>
#include <gui/packages/pkg_sequence_edit/molinfoedit_util.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_molinfo_edit_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/vectortrimdlg.hpp>
#include <gui/packages/pkg_sequence_edit/tbl_edit_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/remove_sequences.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_util.hpp>
#include <gui/packages/pkg_sequence_edit/reorder_sequences_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/seqid_fix_dlg.hpp>
#include <gui/packages/pkg_sequence_edit/bulk_feature_add_dlg_std.hpp>
#include <wx/sizer.h>
#include <wx/statbox.h>
#include <wx/radiobox.h>
#include <wx/msgdlg.h>
#include <wx/choice.h>
#include <wx/filedlg.h>
#include <gui/widgets/wx/file_extensions.hpp>
#include <gui/widgets/loaders/open_objects_dlg.hpp>
#include <gui/widgets/loaders/file_load_wizard.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/utils/object_loader.hpp>
#include <gui/utils/execute_unit.hpp>
#include <gui/utils/app_popup.hpp>
#include <gui/widgets/wx/async_call.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/table_data_base.hpp>
#include "subprep_event.hpp"
#include <gui/widgets/grid_widget/grid_event.hpp>
#include <objtools/validator/validator.hpp>
#include <objmgr/object_manager.hpp>
#include <objects/valerr/ValidError.hpp>
#include <objects/valerr/ValidErrItem.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include "cmd_place_protein_feats.hpp"

Include dependency graph for subprep_panel.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions
static bool	s_MatchesFieldName (string field_name, string label)

Variables
static CSubPrep_panel::TWizardKeyword	s_keywords []
static int	num_keywords = sizeof (s_keywords) / sizeof (CSubPrep_panel::TWizardKeyword)
static const string	kAssemblyDescription = "Assembly Description"
const string	kChimeraLabel = "Program and Version"
const string	kChimeraField = "Chimera Screening"
const string	kGenome = "genome"
const string	kWizardType = "WizardType"
const string	kSrcType = "SrcType"
static const char *	kTableTag = "Table"
const string	kNotReadyForSubmission = "Warning: This submission is not ready to be submitted to GenBank. Do not submit this file until all required information is provided."
const string	kSubmissionStatus = "Submission Status"
const string	kSubmissionOk = "OK"

Function Documentation

s_MatchesFieldName()

static bool s_MatchesFieldName ( string  field_name, string  label  )

static

Definition at line 1682 of file subprep_panel.cpp.

References NStr::EqualNocase(), label, and NStr::ReplaceInPlace().

Referenced by CSubPrep_panel::GetConverterForFieldName().

Variable Documentation

kAssemblyDescription

const string kAssemblyDescription = "Assembly Description"

static

Definition at line 380 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GetConverterForFieldName(), CSubPrep_panel::x_ClearWizardSpecificData(), and CSubPrep_panel::x_CreateWizardExtras().

kChimeraField

const string kChimeraField = "Chimera Screening"

Definition at line 553 of file subprep_panel.cpp.

kChimeraLabel

const string kChimeraLabel = "Program and Version"

Definition at line 552 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GetConverterForFieldName().

kGenome

const string kGenome = "genome"

Definition at line 591 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GetConverterForFieldName(), and CSubPrep_panel::x_CreateGenomeOptions().

kNotReadyForSubmission

const string kNotReadyForSubmission = "Warning: This submission is not ready to be submitted to GenBank. Do not submit this file until all required information is provided."

Definition at line 1819 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::OnSaveBtnClick().

kSrcType

const string kSrcType = "SrcType"

Definition at line 708 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GetWizardSrcTypeField(), CSubPrep_panel::SetSourceType(), and CSubPrep_panel::x_GetWizardSrcTypefromSeqEntry().

kSubmissionOk

const string kSubmissionOk = "OK"

Definition at line 1821 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::OnSaveBtnClick().

kSubmissionStatus

const string kSubmissionStatus = "Submission Status"

Definition at line 1820 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::OnSaveBtnClick().

kTableTag

const char* kTableTag = "Table"

static

Transfer data from the window

Definition at line 1093 of file subprep_panel.cpp.

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

kWizardType

const string kWizardType = "WizardType"

Definition at line 707 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GetWizardTypeField(), CSubPrep_panel::GetWizardTypefromSeqEntry(), and CSubPrep_panel::SetWizardType().

num_keywords

int num_keywords = sizeof (s_keywords) / sizeof (CSubPrep_panel::TWizardKeyword)

static

Definition at line 235 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GuessWizardTypefromSeqEntry(), and CSubPrep_panel::Init().

s_keywords

CSubPrep_panel::TWizardKeyword s_keywords[]

static

Initial value:

= {
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_uncultured_samples, "uncultured"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_rrna_its_igs, "cultured"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_tsa, "TSA"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_microsatellite, "Microsatellite"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_igs, "intergenic"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_d_loop, "D-loop"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_viruses, "virus"),
  CSubPrep_panel::TWizardKeyword(CSourceRequirements::eWizardType_standard, "standard")
}

Member initialisation

Definition at line 225 of file subprep_panel.cpp.

Referenced by CSubPrep_panel::GuessWizardTypefromSeqEntry(), and CSubPrep_panel::Init().