#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/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/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/PCRReactionSet.hpp>
#include <objects/seqfeat/PCRReaction.hpp>
#include <objects/seqfeat/PCRPrimerSet.hpp>
#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/PCRPrimerSeq.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/IUPACaa.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/widgets/object_list/object_list_widget.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/objutils/cmd_del_seq_feat.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>
#include <gui/objutils/cmd_change_bioseq_set.hpp>
#include <gui/widgets/wx/file_extensions.hpp>
#include <gui/widgets/wx/csv_exporter.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/widgets/edit/biosource_autocomplete.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_util.hpp>
#include <gui/packages/pkg_sequence_edit/featedit_util.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <algo/align/prosplign/prosplign.hpp>
#include <objtools/readers/source_mod_parser.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <wx/msgdlg.h>
#include <objtools/edit/cds_fix.hpp>

Include dependency graph for subprep_util.cpp:

Go to the SVN repository for this file.

Functions
TWizardNameList	GetWizardNameList ()

CSourceRequirements::EWizardType	GetWizardTypeFromName (string wizard_name)

static bool	OneRowOk (CRef< objects::CSeq_id > id, CRef< objects::CSeqTable_column > id_col, objects::CSeq_entry_Handle seh)

void	FixTableAfterImport (CRef< objects::CSeq_table > input_table)

string	FindBadRows (CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst, objects::CSeq_entry_Handle seh)

CRef< objects::CSeqTable_column >	FindSeqIDColumn (const objects::CSeq_table &table)

int	FindRowForSeqId (CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id)

int	CountColumnRowConflicts (CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)

int	CountTableColumnConflicts (CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)

void	DeleteTableRow (CRef< objects::CSeq_table > table, int row)

static void	CombineColumns (CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)

int	CombineTables (CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)

bool	SaveTableFile (wxWindow *parent, wxString &save_file_dir, wxString &save_file_name, CRef< objects::CSeq_table > values_table)

bool	AreAllColumnValuesTheSame (CRef< objects::CSeqTable_column > col, string default_val)

bool	AreAnyColumnValuesMissing (CRef< objects::CSeqTable_column > col)

bool	DoesColumnHaveValue (CRef< objects::CSeqTable_column > col, string val)

bool	AreAnyColumnValuesPresent (CRef< objects::CSeqTable_column > col, string default_val)

static void	s_ExtendIntervalToEnd (objects::CSeq_interval &ival, objects::CBioseq_Handle bsh)

bool	AddProteinToSeqEntry (const objects::CSeq_entry *protein, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool create_general_only)

static void	s_ReportMixError ()

void	ParseTitlesToNewSeqEntries (CRef< objects::CSeq_entry > entry)

bool	AddSeqEntryToSeqEntry (const objects::CSeq_entry *entry, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool &has_nuc, bool &has_prot, bool create_general_only)

string	CheckFeatureAnnotation (objects::CSeq_entry_Handle entry, bool &is_ok)

vector< string >	GetTrueFalseList ()

bool	IsSynonymForTrue (const string &val)

bool	IsSynonymForFalse (const string &val)

bool	IsTrueFalseList (const vector< string > &choices)

int	AddFeatureToSeqTable (const objects::CSeq_feat &f, CRef< objects::CSeq_table > table)

static bool	s_OkToAddFeature (const objects::CSeq_feat &f1, const objects::CSeq_feat &f2, const TFeatureSeqTableColumnList &reqs)

CRef< objects::CSeq_table >	GetFeaturesFromSeqEntry (objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)

void	AddFeatureSeqTableRowToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, unsigned int row, TFeatureSeqTableColumnList &vecColEditFactories, CRef< CCmdComposite > cmd)

CRef< CCmdComposite >	AddFeatureSeqTableToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)

void	MergeStringVectors (vector< string > &problems, vector< string > add)

static void	AddProblemsToColumn (CRef< objects::CSeqTable_column > val_col, CRef< CFeatureSeqTableColumnBase > rule_col, vector< string > &problems)

void	RemoveProblemsColumn (CRef< objects::CSeq_table > values_table)

CRef< CFeatureSeqTableColumnBase >	GetColumnRuleForFeatureSeqTable (CRef< objects::CSeqTable_column > col, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)

void	AddProblemsColumnToFeatureSeqTable (CRef< objects::CSeq_table > table, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)

bool	HasLocalIntFeatureId (const objects::CSeq_feat &feat)

CRef< CCmdComposite >	RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry (objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)

wxString	GetAsnSqnExtensions ()

bool	IsWizardObject (const objects::CUser_object &user)

CRef< objects::CUser_object >	MakeWizardObject ()

void	SetWizardFieldInSeqEntryNoUndo (objects::CSeq_entry_Handle entry, string field_name, string value)

bool	IsBankItSubmissionObject (const objects::CUser_object &user)

CRef< objects::CUser_object >	MakeBankItSubmissionObject ()

string	GetFieldFromWizardObject (const objects::CUser_object &user, string field_name)

string	GetDescAlternateEmailAddress (const objects::CSeqdesc &desc)

string	GetAlternateEmailAddress (objects::CSeq_entry_Handle entry)

void	SetUserAlternateEmailAddress (objects::CUser_object &u, string alt_email)

void	SetAlternateEmailAddress (objects::CSeq_entry_Handle entry, string alt_email)

bool	IsValidEmail (string email)

static void	AddIdsFromSeqEntryToTable (const objects::CSeq_entry &entry, CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeqTable_column > pos_col, CRef< objects::CSeqTable_column > np_col, CRef< objects::CSeqTable_column > title_col, int &pos, size_t &row)

static CRef< objects::CSeqTable_column >	s_MakeIdTableIdCol ()

static CRef< objects::CSeqTable_column >	s_MakePosCol ()

static CRef< objects::CSeqTable_column >	s_MakeNpCol ()

static CRef< objects::CSeqTable_column >	s_MakeTitleCol ()

void	AddIdsFromSeqEntryToTable (const objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)

CRef< objects::CSeq_table >	GetIdsFromSeqEntry (const objects::CSeq_entry &entry)

static string	GetIdValueFromColumn (CRef< objects::CSeqTable_column > id_col, int pos)

CRef< objects::CSeqTable_column >	GetSeqIdProblems (CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)

string	SummarizeIdProblems (CRef< objects::CSeqTable_column > problems)

CRef< objects::CSeqTable_column >	GetReplacementSeqIds (CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)

static void	TransformSeqAnnot (objects::CSeq_annot &annot, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id)

static void	TransformSeqAnnots (objects::CBioseq &bioseq, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id)

void	ApplyReplacementIds (objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)

bool	AlreadyHasFeature (objects::CBioseq_Handle bh, string key, string comment)

bool	AlreadyHasFeature (objects::CBioseq_Handle bh, objects::CSeqFeatData::ESubtype subtype)

Variables
static TWizardName	s_WizardNames []

static int	k_NumWizardNames = sizeof (s_WizardNames) / sizeof (TWizardName)

const string	kBankitSubmissionLabel = "Submission"

const string	kBankItAltEmailPrefix = "ALT EMAIL:"

const string	kSMARTComment = "SmartComment"

const string	kIdTooLong = "ID is too long"

const string	kIdDuplicate = "duplicate"

const string	kIdMissing = "Missing ID"

Function Documentation

◆ AddFeatureSeqTableRowToSeqEntry()

void AddFeatureSeqTableRowToSeqEntry	(	CRef< objects::CSeq_table >	table,
		objects::CSeq_entry_Handle	entry,
		objects::CSeqFeatData::ESubtype	subtype,
		unsigned int	row,
		TFeatureSeqTableColumnList &	vecColEditFactories,
		CRef< CCmdComposite >	cmd
	)

Definition at line 1182 of file subprep_util.cpp.

References cmd, e_not_set, eExistingText_replace_old, eNa_strand_minus, eNa_strand_plus, FindSeqTableColumnByName(), i, NStr::IsBlank(), ncbi::grid::netcache::search::fields::key, kFeatureID, kSequenceIdColLabel, kSkipColumns, kStartColLabel, kStopColLabel, NULL, NStr::NumericToString(), row, ncbi::grid::netcache::search::fields::size, NStr::StringToInt(), table, and wxT.

Referenced by AddFeatureSeqTableToSeqEntry().

◆ AddFeatureSeqTableToSeqEntry()

CRef<CCmdComposite> AddFeatureSeqTableToSeqEntry	(	CRef< objects::CSeq_table >	table,
		objects::CSeq_entry_Handle	entry,
		objects::CSeqFeatData::ESubtype	subtype,
		const TFeatureSeqTableColumnList &	reqs,
		const TFeatureSeqTableColumnList &	opts
	)

Definition at line 1278 of file subprep_util.cpp.

References AddFeatureSeqTableRowToSeqEntry(), cmd, ctll::front(), GetColumnRuleForFeatureSeqTable(), i, kSkipColumns, ncbi::grid::netcache::search::fields::size, and table.

Referenced by CFeatureTableCommandConverter::GetCommandFromValuesTable().

◆ AddFeatureToSeqTable()

int AddFeatureToSeqTable	(	const objects::CSeq_feat &	f,
		CRef< objects::CSeq_table >	table
	)

Definition at line 1089 of file subprep_util.cpp.

References AddValueToTable(), eExtreme_Biological, NStr::EqualNocase(), f, i, ITERATE, kFeatureID, kNumSatelliteTypes, kPartialStart, kPartialStop, kSatelliteTypes, kStartColLabel, kStopColLabel, NStr::NumericToString(), row, NStr::StartsWith(), table, NStr::TruncateSpacesInPlace(), and val.

Referenced by GetFeaturesFromSeqEntry(), and CFeatureTableCommandConverter::GetValuesTableFromSeqEntry().

◆ AddIdsFromSeqEntryToTable() [1/2]

void AddIdsFromSeqEntryToTable	(	const objects::CSeq_entry &	entry,
		CRef< objects::CSeq_table >	table
	)

Definition at line 1698 of file subprep_util.cpp.

References AddIdsFromSeqEntryToTable(), FindSeqTableColumnByName(), kSequenceIdColLabel, row, s_MakeIdTableIdCol(), s_MakeNpCol(), s_MakePosCol(), s_MakeTitleCol(), and table.

◆ AddIdsFromSeqEntryToTable() [2/2]

static void AddIdsFromSeqEntryToTable	(	const objects::CSeq_entry &	entry,
		CRef< objects::CSeqTable_column >	id_col,
		CRef< objects::CSeqTable_column >	pos_col,
		CRef< objects::CSeqTable_column >	np_col,
		CRef< objects::CSeqTable_column >	title_col,
		int &	pos,
		size_t &	row
	)

static

Definition at line 1621 of file subprep_util.cpp.

References ITERATE, and row.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ AddProblemsColumnToFeatureSeqTable()

void AddProblemsColumnToFeatureSeqTable	(	CRef< objects::CSeq_table >	table,
		const TFeatureSeqTableColumnList &	reqs,
		const TFeatureSeqTableColumnList &	opts
	)

Definition at line 1367 of file subprep_util.cpp.

References AddProblemsToColumn(), GetColumnRuleForFeatureSeqTable(), i, ITERATE, kProblems, kSkipColumns, RemoveProblemsColumn(), ncbi::grid::netcache::search::fields::size, and table.

Referenced by CFeatureTableCommandConverter::GetValuesTableFromSeqEntry().

◆ AddProblemsToColumn()

static void AddProblemsToColumn	(	CRef< objects::CSeqTable_column >	val_col,
		CRef< CFeatureSeqTableColumnBase >	rule_col,
		vector< string > &	problems
	)

static

Definition at line 1322 of file subprep_util.cpp.

References CFeatureSeqTableColumnBase::IsValid(), and MergeStringVectors().

Referenced by AddProblemsColumnToFeatureSeqTable().

◆ AddProteinToSeqEntry()

bool AddProteinToSeqEntry	(	const objects::CSeq_entry *	protein,
		objects::CSeq_entry_Handle	seh,
		CRef< CCmdComposite >	cmd,
		bool	create_general_only
	)

Definition at line 719 of file subprep_util.cpp.

References AddProteinFeatureToProtein(), cmd, eContent, eExtreme_Biological, CProSplignOutputOptions::ePassThrough, CProSplign::FindAlignment(), GetNewProtId(), ITERATE, label, NULL, offset, s_ExtendIntervalToEnd(), SetMolinfoForProtein(), ToWxString(), and wxT.

Referenced by AddSeqEntryToSeqEntry().

◆ AddSeqEntryToSeqEntry()

bool AddSeqEntryToSeqEntry	(	const objects::CSeq_entry *	entry,
		objects::CSeq_entry_Handle	seh,
		CRef< CCmdComposite >	cmd,
		bool &	has_nuc,
		bool &	has_prot,
		bool	create_general_only
	)

Definition at line 893 of file subprep_util.cpp.

References AddProteinToSeqEntry(), cmd, ITERATE, ParseTitlesToNewSeqEntries(), and s_ReportMixError().

Referenced by CAddSequences::apply(), CSubPrep_panel::OnAddSequenceBtnClick(), and CPromote::x_PromoteCdregion().

◆ AlreadyHasFeature() [1/2]

bool AlreadyHasFeature	(	objects::CBioseq_Handle	bh,
		objects::CSeqFeatData::ESubtype	subtype
	)

Definition at line 2051 of file subprep_util.cpp.

References f.

◆ AlreadyHasFeature() [2/2]

bool AlreadyHasFeature	(	objects::CBioseq_Handle	bh,
		string	key,
		string	comment
	)

Definition at line 2033 of file subprep_util.cpp.

References NStr::Equal(), NStr::EqualNocase(), f, NStr::IsBlank(), and ncbi::grid::netcache::search::fields::key.

Referenced by CBulkCDSAddPanel::AddOneCmd(), CBulkOtherAddPanel::AddOneCommand(), CBulkRNAAddPanel::AddOneCommand(), CIGSPanel::GetCommand(), CRNANamePanel::GetCommand(), CVirusNonCodingFeaturesPanel::GetCommand(), and CBulkFeatureAddDlgStd::x_CreateImportFeatures().

◆ ApplyReplacementIds()

void ApplyReplacementIds	(	objects::CSeq_entry &	entry,
		CRef< objects::CSeq_table >	table
	)

Definition at line 1999 of file subprep_util.cpp.

References FindSeqTableColumnByName(), kNewId, kSequenceIdColLabel, NON_CONST_ITERATE, table, and TransformSeqAnnots().

Referenced by CAddSequences::apply(), and CSubPrep_panel::OnAddSequenceBtnClick().

◆ AreAllColumnValuesTheSame()

bool AreAllColumnValuesTheSame	(	CRef< objects::CSeqTable_column >	col,
		string	default_val
	)

Definition at line 596 of file subprep_util.cpp.

References NStr::Equal(), NStr::IsBlank(), row, and val.

Referenced by CCommentDescriptorTableCommandConverter::CheckForMixedValues(), CChimeraCommentDescriptorTableCommandConverter::CheckForMixedValues(), CTableCommandConverter::CheckForMixedValues(), CGenomeTableCommandConverter::CheckForMixedValues(), CPrimerTableCommandConverter::CheckForMixedValues(), CSubPrep_panel::OkToBulkEditSeqTech(), CSubPrep_panel::SetWizardType(), CSubmissionPrepMainPanel::UpdateSeqTechCtrls(), and CSubPrepFieldEditor::UpdateValues().

◆ AreAnyColumnValuesMissing()

bool AreAnyColumnValuesMissing ( CRef< objects::CSeqTable_column > col )

Definition at line 634 of file subprep_util.cpp.

References NStr::IsBlank(), and row.

Referenced by CChimeraCommentDescriptorTableCommandConverter::CheckForMixedValues(), CSubPrep_panel::SetWizardType(), CSubmissionPrepMainPanel::UpdateSeqTechCtrls(), and CSubPrepFieldEditor::UpdateValues().

◆ AreAnyColumnValuesPresent()

bool AreAnyColumnValuesPresent	(	CRef< objects::CSeqTable_column >	col,
		string	default_val
	)

Definition at line 678 of file subprep_util.cpp.

References NStr::EqualNocase(), NStr::IsBlank(), and row.

Referenced by CSubPrep_panel::x_ClearWizardSpecificData(), and CSubPrepFieldEditor::x_SetOneValue().

◆ CheckFeatureAnnotation()

string CheckFeatureAnnotation	(	objects::CSeq_entry_Handle	entry,
		bool &	is_ok
	)

Definition at line 968 of file subprep_util.cpp.

References all, and NStr::NumericToString().

Referenced by CSubPrep_panel::x_UpdateFeatureStatus().

◆ CombineColumns()

static void CombineColumns	(	CRef< objects::CSeqTable_column >	dst_id,
		CRef< objects::CSeqTable_column >	dst_col,
		CRef< objects::CSeqTable_column >	src_id,
		CRef< objects::CSeqTable_column >	src_col
	)

static

Definition at line 483 of file subprep_util.cpp.

References FindRowForSeqId(), i, and row.

Referenced by CombineTables().

◆ CombineTables()

int CombineTables	(	CRef< objects::CSeq_table >	dst,
		const objects::CSeq_table &	src
	)

Definition at line 505 of file subprep_util.cpp.

References CombineColumns(), FindSeqIDColumn(), FindSeqTableColumnByName(), and ITERATE.

Referenced by CTblEditDlg::OnImportTableClick().

◆ CountColumnRowConflicts()

int CountColumnRowConflicts	(	CRef< objects::CSeqTable_column >	dst_id,
		CRef< objects::CSeqTable_column >	dst_col,
		CRef< objects::CSeqTable_column >	src_id,
		CRef< objects::CSeqTable_column >	src_col
	)

Definition at line 393 of file subprep_util.cpp.

References count, NStr::Equal(), FindRowForSeqId(), i, NStr::IsBlank(), and row.

Referenced by CountTableColumnConflicts().

◆ CountTableColumnConflicts()

int CountTableColumnConflicts	(	CRef< objects::CSeq_table >	dst,
		const objects::CSeq_table &	src
	)

Definition at line 411 of file subprep_util.cpp.

References CountColumnRowConflicts(), FindSeqIDColumn(), FindSeqTableColumnByName(), and ITERATE.

Referenced by CTblEditDlg::OnImportTableClick().

◆ DeleteTableRow()

void DeleteTableRow	(	CRef< objects::CSeq_table >	table,
		int	row
	)

Definition at line 432 of file subprep_util.cpp.

References NON_CONST_ITERATE, row, and table.

Referenced by FixTableAfterImport().

◆ DoesColumnHaveValue()

bool DoesColumnHaveValue	(	CRef< objects::CSeqTable_column >	col,
		string	val
	)

Definition at line 656 of file subprep_util.cpp.

References NStr::Equal(), row, and val.

Referenced by CSubmissionPrepMainPanel::CreateVirusMoleculeOptions().

◆ FindBadRows()

string FindBadRows	(	CRef< objects::CSeq_table >	src,
		CRef< objects::CSeq_table >	dst,
		objects::CSeq_entry_Handle	seh
	)

Definition at line 327 of file subprep_util.cpp.

References eContent, FindSeqIDColumn(), NStr::IsBlank(), ITERATE, NStr::NumericToString(), OneRowOk(), and row.

Referenced by CTblEditDlg::OnImportTableClick().

◆ FindRowForSeqId()

int FindRowForSeqId	(	CRef< objects::CSeqTable_column >	id_col,
		CRef< objects::CSeq_id >	id
	)

Definition at line 377 of file subprep_util.cpp.

References row.

Referenced by CombineColumns(), and CountColumnRowConflicts().

◆ FindSeqIDColumn()

CRef<objects::CSeqTable_column> FindSeqIDColumn ( const objects::CSeq_table & table )

Definition at line 365 of file subprep_util.cpp.

References ITERATE, NULL, and table.

Referenced by CombineTables(), CountTableColumnConflicts(), FindBadRows(), and FixTableAfterImport().

◆ FixTableAfterImport()

void FixTableAfterImport ( CRef< objects::CSeq_table > input_table )

Definition at line 219 of file subprep_util.cpp.

References DeleteTableRow(), eContent, NStr::Equal(), NStr::EqualNocase(), FindSeqIDColumn(), NStr::IsBlank(), ITERATE, NON_CONST_ITERATE, NStr::NumericToString(), NStr::ReplaceInPlace(), ncbi::grid::netcache::search::fields::size, and val.

Referenced by CTblEditDlg::OnImportTableClick().

◆ GetAlternateEmailAddress()

string GetAlternateEmailAddress ( objects::CSeq_entry_Handle entry )

Definition at line 1549 of file subprep_util.cpp.

References GetDescAlternateEmailAddress(), and NStr::IsBlank().

Referenced by CSubPrep_panel::GetAltEmailAddress().

◆ GetAsnSqnExtensions()

wxString GetAsnSqnExtensions ( )

Definition at line 1419 of file subprep_util.cpp.

References wxT.

Referenced by CSubmitBlockDlg::OnExportBtnClick(), and CSubPrep_panel::OnSaveBtnClick().

◆ GetColumnRuleForFeatureSeqTable()

CRef<CFeatureSeqTableColumnBase> GetColumnRuleForFeatureSeqTable	(	CRef< objects::CSeqTable_column >	col,
		const TFeatureSeqTableColumnList &	reqs,
		const TFeatureSeqTableColumnList &	opts
	)

Definition at line 1350 of file subprep_util.cpp.

References CFeatureSeqTableColumnBaseFactory::Create(), ITERATE, and MatchColumnName().

Referenced by AddFeatureSeqTableToSeqEntry(), AddProblemsColumnToFeatureSeqTable(), and CFeatureTableCommandConverter::MakeProblemsColumn().

◆ GetDescAlternateEmailAddress()

string GetDescAlternateEmailAddress ( const objects::CSeqdesc & desc )

Definition at line 1535 of file subprep_util.cpp.

References NStr::Find(), GetFieldFromWizardObject(), IsBankItSubmissionObject(), kBankItAltEmailPrefix, kSMARTComment, and str().

Referenced by GetAlternateEmailAddress(), and CSubmitBlockDlg::OnImportBtnClick().

◆ GetFeaturesFromSeqEntry()

CRef<objects::CSeq_table> GetFeaturesFromSeqEntry	(	objects::CSeq_entry_Handle	entry,
		const objects::CSeq_feat &	feat,
		const TFeatureSeqTableColumnList &	reqs
	)

Definition at line 1159 of file subprep_util.cpp.

References AddFeatureToSeqTable(), AddIntColumnToTable(), AddStringColumnToTable(), kFeatureID, kSequenceIdColLabel, kStartColLabel, kStopColLabel, s_OkToAddFeature(), and table.

Referenced by CFeatureTableCommandConverter::GetValuesTableFromSeqEntry().

◆ GetFieldFromWizardObject()

string GetFieldFromWizardObject	(	const objects::CUser_object &	user,
		string	field_name
	)

Definition at line 1516 of file subprep_util.cpp.

References NStr::EqualNocase(), ITERATE, and rapidjson::value.

Referenced by GetDescAlternateEmailAddress(), CSubPrep_panel::GetWizardFieldFromSeqEntry(), CSubPrep_panel::GetWizardSrcTypeField(), CSubPrep_panel::GetWizardTypeField(), CSubPrep_panel::GetWizardTypefromSeqEntry(), and CSubPrep_panel::x_GetWizardSrcTypefromSeqEntry().

◆ GetIdsFromSeqEntry()

CRef<objects::CSeq_table> GetIdsFromSeqEntry ( const objects::CSeq_entry & entry )

Definition at line 1731 of file subprep_util.cpp.

References AddIdsFromSeqEntryToTable(), row, s_MakeIdTableIdCol(), s_MakeNpCol(), s_MakePosCol(), s_MakeTitleCol(), and table.

Referenced by CAddSequences::apply(), CSeqIdFixDlg::CreateControls(), and CSubPrep_panel::OnAddSequenceBtnClick().

◆ GetIdValueFromColumn()

static string GetIdValueFromColumn	(	CRef< objects::CSeqTable_column >	id_col,
		int	pos
	)

static

Definition at line 1756 of file subprep_util.cpp.

References eContent, and str().

Referenced by GetSeqIdProblems().

◆ GetReplacementSeqIds()

CRef<objects::CSeqTable_column> GetReplacementSeqIds	(	CRef< objects::CSeq_table >	new_ids,
		CRef< objects::CSeq_table >	old_ids,
		size_t	max_len
	)

Definition at line 1873 of file subprep_util.cpp.

References eContent, NStr::EqualNocase(), FindNonUniqueStrings(), FindSeqTableColumnByName(), i, ITERATE, kSequenceIdColLabel, log, NULL, NStr::NumericToString(), offset, CRef< C, Locker >::Reset(), NStr::StartsWith(), str(), and NStr::StringToInt().

◆ GetSeqIdProblems()

CRef<objects::CSeqTable_column> GetSeqIdProblems	(	CRef< objects::CSeq_table >	new_ids,
		CRef< objects::CSeq_table >	old_ids,
		size_t	max_len
	)

Definition at line 1769 of file subprep_util.cpp.

References eContent, NStr::EqualNocase(), FindNonUniqueStrings(), FindSeqTableColumnByName(), GetIdValueFromColumn(), i, NStr::IsBlank(), ITERATE, kIdDuplicate, kIdMissing, kIdTooLong, kNewId, kSequenceIdColLabel, NULL, CRef< C, Locker >::Reset(), str(), and val.

Referenced by CAddSequences::apply(), CSeqIdFixDlg::CreateControls(), CSeqIdFixDlg::GetReplacementTable(), CSubPrep_panel::OnAddSequenceBtnClick(), and CSeqIdFixDlg::x_RefreshProblems().

◆ GetTrueFalseList()

vector<string> GetTrueFalseList ( )

Definition at line 1041 of file subprep_util.cpp.

Referenced by CFeatureTableCommandConverter::GetChoices().

◆ GetWizardNameList()

TWizardNameList GetWizardNameList ( )

Definition at line 121 of file subprep_util.cpp.

References i, k_NumWizardNames, and s_WizardNames.

Referenced by CSubPrepIntroPanel::CreateControls(), and CSubPrep_panel::Init().

◆ GetWizardTypeFromName()

CSourceRequirements::EWizardType GetWizardTypeFromName ( string wizard_name )

Definition at line 132 of file subprep_util.cpp.

References NStr::EqualNocase(), CSourceRequirements::eWizardType_standard, k_NumWizardNames, and s_WizardNames.

Referenced by CSubPrep_panel::GetWizardTypefromSeqEntry(), and CSubPrepIntroPanel::SetWizardTypeCtrl().

◆ HasLocalIntFeatureId()

bool HasLocalIntFeatureId ( const objects::CSeq_feat & feat )

Definition at line 1393 of file subprep_util.cpp.

Referenced by RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry().

◆ IsBankItSubmissionObject()

bool IsBankItSubmissionObject ( const objects::CUser_object & user )

Definition at line 1498 of file subprep_util.cpp.

References NStr::EqualNocase(), and kBankitSubmissionLabel.

Referenced by GetDescAlternateEmailAddress(), CSubmitBlockDlg::OnImportBtnClick(), and SetAlternateEmailAddress().

◆ IsSynonymForFalse()

bool IsSynonymForFalse ( const string & val )

Definition at line 1061 of file subprep_util.cpp.

References NStr::EqualNocase(), NStr::IsBlank(), and val.

Referenced by IsTrueFalseList(), CSeqTableGridPanel::SetColumnSizesAndChoices(), and CSeqTableGridPanel::UpdateColumnChoices().

◆ IsSynonymForTrue()

bool IsSynonymForTrue ( const string & val )

Definition at line 1049 of file subprep_util.cpp.

References NStr::EqualNocase(), and val.

Referenced by IsTrueFalseList(), CSeqTableGridPanel::SetColumnSizesAndChoices(), and CSeqTableGridPanel::UpdateColumnChoices().

◆ IsTrueFalseList()

bool IsTrueFalseList ( const vector< string > & choices )

Definition at line 1074 of file subprep_util.cpp.

References IsSynonymForFalse(), and IsSynonymForTrue().

◆ IsValidEmail()

bool IsValidEmail ( string email )

Definition at line 1602 of file subprep_util.cpp.

References NStr::Find(), NStr::IsBlank(), and tmp.

Referenced by CSubmitBlockDlg::GetBlockProblems(), CSubPrepIntroPanel::RefreshSubmitterInfoStatus(), and CSubPrepIntroPanel::x_LaunchSubmitEditor().

◆ IsWizardObject()

bool IsWizardObject ( const objects::CUser_object & user )

Definition at line 1443 of file subprep_util.cpp.

References NStr::EqualNocase(), and kWizardLabel.

Referenced by CSubPrep_panel::GetWizardFieldFromSeqEntry(), CSubPrep_panel::GetWizardSrcTypeField(), CSubPrep_panel::GetWizardTypeField(), CSubPrep_panel::GetWizardTypefromSeqEntry(), CSubPrep_panel::SetWizardFieldInSeqEntry(), SetWizardFieldInSeqEntryNoUndo(), and CSubPrep_panel::x_GetWizardSrcTypefromSeqEntry().

◆ MakeBankItSubmissionObject()

CRef<objects::CUser_object> MakeBankItSubmissionObject ( )

Definition at line 1508 of file subprep_util.cpp.

References kBankitSubmissionLabel.

Referenced by CSubmitBlockDlg::OnExportBtnClick(), and SetAlternateEmailAddress().

◆ MakeWizardObject()

CRef<objects::CUser_object> MakeWizardObject ( )

Definition at line 1453 of file subprep_util.cpp.

References kWizardLabel.

Referenced by CSubPrep_panel::SetWizardFieldInSeqEntry(), and SetWizardFieldInSeqEntryNoUndo().

◆ MergeStringVectors()

void MergeStringVectors	(	vector< string > &	problems,
		vector< string >	add
	)

Definition at line 1297 of file subprep_util.cpp.

References NStr::IsBlank().

Referenced by AddProblemsToColumn().

◆ OneRowOk()

static bool OneRowOk	(	CRef< objects::CSeq_id >	id,
		CRef< objects::CSeqTable_column >	id_col,
		objects::CSeq_entry_Handle	seh
	)

static

Definition at line 170 of file subprep_util.cpp.

References b, ITERATE, RelaxedMatch(), and row.

Referenced by FindBadRows().

◆ ParseTitlesToNewSeqEntries()

void ParseTitlesToNewSeqEntries ( CRef< objects::CSeq_entry > entry )

Definition at line 866 of file subprep_util.cpp.

References NON_CONST_ITERATE.

Referenced by AddSeqEntryToSeqEntry().

◆ RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry()

CRef<CCmdComposite> RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry	(	objects::CSeq_entry_Handle	entry,
		const objects::CSeq_feat &	feat,
		const TFeatureSeqTableColumnList &	reqs
	)

Definition at line 1403 of file subprep_util.cpp.

References cmd, HasLocalIntFeatureId(), and s_OkToAddFeature().

Referenced by CFeatureTableCommandConverter::GetCommandFromValuesTable().

◆ RemoveProblemsColumn()

void RemoveProblemsColumn ( CRef< objects::CSeq_table > values_table )

Definition at line 1336 of file subprep_util.cpp.

References NStr::Equal(), and kProblems.

Referenced by AddProblemsColumnToFeatureSeqTable(), and CTblEditDlg::OnUpdateProblems().

◆ s_ExtendIntervalToEnd()

static void s_ExtendIntervalToEnd	(	objects::CSeq_interval &	ival,
		objects::CBioseq_Handle	bsh
	)

static

Definition at line 700 of file subprep_util.cpp.

References eNa_strand_minus, and len.

Referenced by AddProteinToSeqEntry(), and s_GetCDSLoc().

◆ s_MakeIdTableIdCol()

static CRef<objects::CSeqTable_column> s_MakeIdTableIdCol ( )

static

Definition at line 1662 of file subprep_util.cpp.

References kSequenceIdColLabel.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_MakeNpCol()

static CRef<objects::CSeqTable_column> s_MakeNpCol ( )

static

Definition at line 1680 of file subprep_util.cpp.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_MakePosCol()

static CRef<objects::CSeqTable_column> s_MakePosCol ( )

static

Definition at line 1671 of file subprep_util.cpp.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_MakeTitleCol()

static CRef<objects::CSeqTable_column> s_MakeTitleCol ( )

static

Definition at line 1689 of file subprep_util.cpp.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_OkToAddFeature()

static bool s_OkToAddFeature	(	const objects::CSeq_feat &	f1,
		const objects::CSeq_feat &	f2,
		const TFeatureSeqTableColumnList &	reqs
	)

static

Definition at line 1145 of file subprep_util.cpp.

References ITERATE, and ok.

Referenced by GetFeaturesFromSeqEntry(), and RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry().

◆ s_ReportMixError()

static void s_ReportMixError ( )

static

Definition at line 859 of file subprep_util.cpp.

References NULL, and wxT.

Referenced by AddSeqEntryToSeqEntry().

◆ SaveTableFile()

bool SaveTableFile	(	wxWindow *	parent,
		wxString &	save_file_dir,
		wxString &	save_file_name,
		CRef< objects::CSeq_table >	values_table
	)

Definition at line 533 of file subprep_util.cpp.

References eContent, CCSVExporter::Field(), CFileExtensions::GetDialogFilter(), i, ITERATE, CFileExtensions::kAllFiles, CFileExtensions::kTable, label, CCSVExporter::NewRow(), out(), and wxT.

Referenced by CAssemblyTrackingPanel::OnExportIntervalsBtnClick(), and CTblEditDlg::OnExportTableClick().

◆ SetAlternateEmailAddress()

void SetAlternateEmailAddress	(	objects::CSeq_entry_Handle	entry,
		string	alt_email
	)

Definition at line 1572 of file subprep_util.cpp.

References IsBankItSubmissionObject(), MakeBankItSubmissionObject(), and SetUserAlternateEmailAddress().

Referenced by CSubPrep_panel::SetAltEmailAddress().

◆ SetUserAlternateEmailAddress()

void SetUserAlternateEmailAddress	(	objects::CUser_object &	u,
		string	alt_email
	)

Definition at line 1562 of file subprep_util.cpp.

References NStr::eNocase, kBankItAltEmailPrefix, kSMARTComment, and NStr::StartsWith().

Referenced by CSubmitBlockDlg::OnExportBtnClick(), and SetAlternateEmailAddress().

◆ SetWizardFieldInSeqEntryNoUndo()

void SetWizardFieldInSeqEntryNoUndo	(	objects::CSeq_entry_Handle	entry,
		string	field_name,
		string	value
	)

Definition at line 1461 of file subprep_util.cpp.

References IsWizardObject(), MakeWizardObject(), and rapidjson::value.

Referenced by CSubPrep_panel::OnSaveBtnClick(), and CSubPrep_panel::UpdateSubmitBlock().

◆ SummarizeIdProblems()

string SummarizeIdProblems ( CRef< objects::CSeqTable_column > problems )

Definition at line 1843 of file subprep_util.cpp.

References NStr::FindNoCase(), ITERATE, kIdDuplicate, kIdTooLong, and NStr::NumericToString().

Referenced by CAddSequences::apply(), CSeqIdFixDlg::GetReplacementTable(), and CSubPrep_panel::OnAddSequenceBtnClick().

◆ TransformSeqAnnot()

static void TransformSeqAnnot	(	objects::CSeq_annot &	annot,
		CRef< objects::CSeq_id >	seq_id,
		CRef< objects::CSeq_id >	new_seq_id
	)

static

Definition at line 1959 of file subprep_util.cpp.

References Begin().

Referenced by TransformSeqAnnots().

◆ TransformSeqAnnots()

static void TransformSeqAnnots	(	objects::CBioseq &	bioseq,
		CRef< objects::CSeq_id >	seq_id,
		CRef< objects::CSeq_id >	new_seq_id
	)

static

Definition at line 1973 of file subprep_util.cpp.

References NON_CONST_ITERATE, and TransformSeqAnnot().

Referenced by ApplyReplacementIds().

Variable Documentation

◆ k_NumWizardNames

int k_NumWizardNames = sizeof (s_WizardNames) / sizeof (TWizardName)

static

Definition at line 118 of file subprep_util.cpp.

Referenced by GetWizardNameList(), and GetWizardTypeFromName().

◆ kBankItAltEmailPrefix

const string kBankItAltEmailPrefix = "ALT EMAIL:"

Definition at line 1496 of file subprep_util.cpp.

Referenced by GetDescAlternateEmailAddress(), and SetUserAlternateEmailAddress().

◆ kBankitSubmissionLabel

const string kBankitSubmissionLabel = "Submission"

Definition at line 1495 of file subprep_util.cpp.

Referenced by IsBankItSubmissionObject(), and MakeBankItSubmissionObject().

◆ kIdDuplicate

const string kIdDuplicate = "duplicate"

Definition at line 1752 of file subprep_util.cpp.

Referenced by GetSeqIdProblems(), and SummarizeIdProblems().

◆ kIdMissing

const string kIdMissing = "Missing ID"

Definition at line 1753 of file subprep_util.cpp.

Referenced by GetSeqIdProblems().

◆ kIdTooLong

const string kIdTooLong = "ID is too long"

Definition at line 1751 of file subprep_util.cpp.

Referenced by GetSeqIdProblems(), and SummarizeIdProblems().

◆ kSMARTComment

const string kSMARTComment = "SmartComment"

Definition at line 1533 of file subprep_util.cpp.

Referenced by GetDescAlternateEmailAddress(), and SetUserAlternateEmailAddress().

◆ s_WizardNames

TWizardName s_WizardNames[]

static

Initial value:

= {
    TWizardName(CSourceRequirements::eWizardType_standard, "Standard"),
    TWizardName(CSourceRequirements::eWizardType_viruses, "Viruses"),
    TWizardName(CSourceRequirements::eWizardType_uncultured_samples, "Uncultured Samples"),
    TWizardName(CSourceRequirements::eWizardType_rrna_its_igs, "rRNA-ITS-IGS sequences"),
    TWizardName(CSourceRequirements::eWizardType_tsa, "TSA"),
    TWizardName(CSourceRequirements::eWizardType_igs, "Intergenic Spacer (IGS) sequences"),
    TWizardName(CSourceRequirements::eWizardType_microsatellite, "Microsatellite sequences"),
    TWizardName(CSourceRequirements::eWizardType_d_loop, "D-loops and control regions")
}

Definition at line 108 of file subprep_util.cpp.

Referenced by GetWizardNameList(), and GetWizardTypeFromName().

Functions

Variables

Function Documentation

◆ AddFeatureSeqTableRowToSeqEntry()

◆ AddFeatureSeqTableToSeqEntry()

◆ AddFeatureToSeqTable()

◆ AddIdsFromSeqEntryToTable() [1/2]

◆ AddIdsFromSeqEntryToTable() [2/2]

◆ AddProblemsColumnToFeatureSeqTable()

◆ AddProblemsToColumn()

◆ AddProteinToSeqEntry()

◆ AddSeqEntryToSeqEntry()

◆ AlreadyHasFeature() [1/2]

◆ AlreadyHasFeature() [2/2]

◆ ApplyReplacementIds()

◆ AreAllColumnValuesTheSame()

◆ AreAnyColumnValuesMissing()

◆ AreAnyColumnValuesPresent()

◆ CheckFeatureAnnotation()

◆ CombineColumns()

◆ CombineTables()

◆ CountColumnRowConflicts()

◆ CountTableColumnConflicts()

◆ DeleteTableRow()

◆ DoesColumnHaveValue()

◆ FindBadRows()

◆ FindRowForSeqId()

◆ FindSeqIDColumn()

◆ FixTableAfterImport()

◆ GetAlternateEmailAddress()

◆ GetAsnSqnExtensions()

◆ GetColumnRuleForFeatureSeqTable()

◆ GetDescAlternateEmailAddress()

◆ GetFeaturesFromSeqEntry()

◆ GetFieldFromWizardObject()

◆ GetIdsFromSeqEntry()

◆ GetIdValueFromColumn()

◆ GetReplacementSeqIds()

◆ GetSeqIdProblems()

◆ GetTrueFalseList()

◆ GetWizardNameList()

◆ GetWizardTypeFromName()

◆ HasLocalIntFeatureId()

◆ IsBankItSubmissionObject()

◆ IsSynonymForFalse()

◆ IsSynonymForTrue()

◆ IsTrueFalseList()

◆ IsValidEmail()

◆ IsWizardObject()

◆ MakeBankItSubmissionObject()

◆ MakeWizardObject()

◆ MergeStringVectors()

◆ OneRowOk()

◆ ParseTitlesToNewSeqEntries()

◆ RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry()

◆ RemoveProblemsColumn()

◆ s_ExtendIntervalToEnd()

◆ s_MakeIdTableIdCol()

◆ s_MakeNpCol()

◆ s_MakePosCol()

◆ s_MakeTitleCol()

◆ s_OkToAddFeature()

◆ s_ReportMixError()

◆ SaveTableFile()

◆ SetAlternateEmailAddress()

◆ SetUserAlternateEmailAddress()

◆ SetWizardFieldInSeqEntryNoUndo()

◆ SummarizeIdProblems()

◆ TransformSeqAnnot()

◆ TransformSeqAnnots()

Variable Documentation

◆ k_NumWizardNames

◆ kBankItAltEmailPrefix

◆ kBankitSubmissionLabel

◆ kIdDuplicate

◆ kIdMissing

◆ kIdTooLong

◆ kSMARTComment

◆ s_WizardNames