Search Toolkit Book for CTable2AsnContext

#include "table2asn_context.hpp"
(Private to src/app/table2asn.)

Collaboration diagram for CTable2AsnContext:

Classes
struct	SPrtAlnOptions

Public Member Functions
	CTable2AsnContext ()

	~CTable2AsnContext ()

void	SetOrganismData (objects::CSeq_descr &SD, int genome_code, const string &taxname, int taxid, const string &strain) const

std::ostream &	GetOstream (eFiles suffix)

void	SetOutputFilename (eFiles kind, const string &filename)

void	SetOutputFile (eFiles kind, ostream &ostr)

void	OpenDiagnosticOutputs ()

void	OpenDataOutputs ()

void	DeleteOutputs ()

void	CloseDiagnosticOutputs ()

void	CloseDataOutputs ()

string	GenerateOutputFilename (eFiles kind, string_view basename=kEmptyStr) const

bool	ApplyCreateUpdateDates (objects::CSeq_entry &entry) const

void	ApplyUpdateDate (objects::CSeq_entry &entry) const

void	ApplyAccession (objects::CSeq_entry &entry) const

void	ApplyFileTracks (objects::CSeq_entry &entry) const

void	ApplyComments (objects::CSeq_entry &entry) const

CRef< CSerialObject >	CreateSubmitFromTemplate (CRef< objects::CSeq_entry > &object, CRef< objects::CSeq_submit > &submit) const

CRef< CSerialObject >	CreateSeqEntryFromTemplate (CRef< objects::CSeq_entry > object) const

void	UpdateSubmitObject (CRef< objects::CSeq_submit > &submit) const

void	MergeWithTemplate (objects::CSeq_entry &entry) const

void	SetSeqId (objects::CSeq_entry &entry) const

void	CopyFeatureIdsToComments (objects::CSeq_entry &entry) const

void	RemoveUnnecessaryXRef (objects::CSeq_entry &entry) const

void	SmartFeatureAnnotation (objects::CSeq_entry &entry) const

void	CorrectCollectionDates (objects::CSeq_entry &entry) const

void	MakeGenomeCenterId (objects::CSeq_entry &entry) const

void	RenameProteinIdsQuals (objects::CSeq_feat &feature) const

void	RemoveProteinIdsQuals (objects::CSeq_feat &feature) const

Static Public Member Functions
static void	AddUserTrack (objects::CSeq_descr &SD, const string &type, const string &label, const string &data)

static objects::CUser_object &	SetUserObject (objects::CSeq_descr &descr, const CTempString &type)

static bool	IsDBLink (const objects::CSeqdesc &desc)

static bool	GetOrgName (string &name, const objects::CSeq_entry &entry)

static CRef< objects::COrg_ref >	GetOrgRef (objects::CSeq_descr &descr)

static void	UpdateTaxonFromTable (objects::CBioseq &bioseq)

static void	MergeSeqDescr (objects::CSeq_entry &dest, const objects::CSeq_descr &src, bool only_set)

Public Attributes
string	m_current_file

string	m_ResultsDirectory

CNcbiOstream *	m_output { nullptr }

string	m_output_filename

string	m_base_name

CRef< objects::CSeq_id >	m_accession

string	m_OrganismName

string	m_single_source_qual_file

string	m_Comment

string	m_single_annot_file

string	m_ft_url

string	m_ft_url_mod

CTime	m_HoldUntilPublish

string	F

string	A

string	m_genome_center_id

string	m_validate

bool	m_delay_genprodset { false }

string	G

bool	R { false }

bool	S { false }

string	Q

bool	L { false }

bool	W { false }

bool	m_t { false }

bool	m_save_bioseq_set { false }

string	c

string	zOufFile

string	X

string	m_master_genome_flag

string	m

string	m_cleanup

string	m_single_structure_cmt

string	m_ProjectVersionNumber

string	m_disc_lineage

bool	m_RemoteTaxonomyLookup { false }

bool	m_RemotePubLookup { false }

bool	m_HandleAsSet { false }

objects::CBioseq_set::TClass	m_ClassValue { objects::CBioseq_set::eClass_genbank }

bool	m_SetIDFromFile { false }

TSeqPos	m_gapNmin { 0 }

TSeqPos	m_gap_Unknown_length { 0 }

TSeqPos	m_minimal_sequence_length { 0 }

objects::CGapsEditor::TEvidenceSet	m_DefaultEvidence

objects::CGapsEditor::TCountToEvidenceMap	m_GapsizeToEvidence

int	m_gap_type { -1 }

bool	m_fcs_trim { false }

bool	m_split_log_files { false }

bool	m_postprocess_pubs { false }

string	m_asn1_suffix

string	m_locus_tag_prefix

bool	m_locus_tags_needed

bool	m_use_hypothetic_protein { false }

bool	m_eukaryote { false }

bool	m_di_fasta { false }

bool	m_d_fasta { false }

bool	m_allow_accession { false }

bool	m_verbose { false }

SPrtAlnOptions	prtAlnOptions

bool	m_make_flatfile { false }

bool	m_run_discrepancy { false }

bool	m_split_discrepancy { false }

bool	m_accumulate_mods { false }

bool	m_binary_asn1_output { false }

bool	m_can_use_huge_files { false }

bool	m_huge_files_mode { false }

bool	m_disable_huge_files { false }

optional< size_t >	m_use_threads {}

NDiscrepancy::EGroup	m_discrepancy_group { NDiscrepancy::eOncaller }

unique_ptr< objects::edit::CRemoteUpdater >	m_remote_updater

unique_ptr< objects::CFixSuspectProductName >	m_suspect_rules

CRef< objects::CSeq_submit >	m_submit_template

CRef< objects::CSeq_entry >	m_entry_template

objects::ILineErrorListener *	m_logger { nullptr }

unique_ptr< CValidMessageHandler >	pValMsgHandler

CRef< objects::CObjectManager >	m_ObjMgr

string	mCommandLineMods

std::mutex	m_mutex

Static Private Member Functions
static void	x_ApplyAccession (const CTable2AsnContext &context, objects::CBioseq &bioseq)

Private Attributes
CDiagnosticFileSet	mDiagnosticWriters

CDataFileSet	mDataWriters

CDiagnosticFileSet::fileset_type	mCurrentDiagnosticOutputs

CDataFileSet::fileset_type	mCurrentDataOutputs

Detailed Description

Definition at line 90 of file table2asn_context.hpp.

Constructor & Destructor Documentation

◆ CTable2AsnContext()

CTable2AsnContext::CTable2AsnContext ( )

Definition at line 179 of file table2asn_context.cpp.

References mDataWriters, mDiagnosticWriters, and TMultiSourceFileSet< _Enum, _options >::SetUseMT().

◆ ~CTable2AsnContext()

CTable2AsnContext::~CTable2AsnContext ( )

Definition at line 186 of file table2asn_context.cpp.

Member Function Documentation

◆ AddUserTrack()

void CTable2AsnContext::AddUserTrack	(	objects::CSeq_descr &	SD,
		const string &	type,
		const string &	label,
		const string &	data
	)

static

Definition at line 190 of file table2asn_context.cpp.

References data, SD, CUser_field_Base::SetData(), CUser_field_Base::SetLabel(), CUser_field_Base::SetNum(), and SetUserObject().

Referenced by ApplyFileTracks().

◆ ApplyAccession()

void CTable2AsnContext::ApplyAccession ( objects::CSeq_entry & entry ) const

Definition at line 355 of file table2asn_context.cpp.

References CSeq_id::Assign(), CRef< C, Locker >::Empty(), m_accession, CBioseq_Base::SetId(), and objects::VisitAllBioseqs().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ ApplyComments()

void CTable2AsnContext::ApplyComments ( objects::CSeq_entry & entry ) const

Definition at line 865 of file table2asn_context.cpp.

References CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::GetClass(), CBioseq_set_Base::IsSetClass(), m_Comment, CSeqdesc_Base::SetComment(), CBioseq_set_Base::SetDescr(), and objects::VisitAllSetandSeq().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ ApplyCreateUpdateDates()

bool CTable2AsnContext::ApplyCreateUpdateDates ( objects::CSeq_entry & entry ) const

Definition at line 712 of file table2asn_context.cpp.

References ApplyUpdateDate(), CSeq_entry_Base::e_Seq, CSeq_entry_Base::e_Set, CSeqdesc_Base::e_Update_date, CBioseq_set_Base::eClass_nuc_prot, CAutoAddDesc::EraseDesc(), CBioseq_set_Base::GetClass(), CSeq_entry::GetParentEntry(), CSeq_entry_Base::GetSet(), CBioseq_set_Base::IsSetClass(), CSeq_entry::SetDescr(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeq_entry_Base::Which().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ ApplyFileTracks()

void CTable2AsnContext::ApplyFileTracks ( objects::CSeq_entry & entry ) const

Definition at line 751 of file table2asn_context.cpp.

References AddUserTrack(), m_ft_url, m_ft_url_mod, and CSeq_entry::SetDescr().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ ApplyUpdateDate()

void CTable2AsnContext::ApplyUpdateDate ( objects::CSeq_entry & entry ) const

Definition at line 348 of file table2asn_context.cpp.

References CSeqdesc_Base::e_Update_date, CTime::eCurrent, CDate::ePrecision_day, CAutoAddDesc::Set(), CSeq_entry::SetDescr(), and CSeqdesc_Base::SetUpdate_date().

Referenced by ApplyCreateUpdateDates().

◆ CloseDataOutputs()

void CTable2AsnContext::CloseDataOutputs ( )

Definition at line 257 of file table2asn_context.cpp.

References mCurrentDataOutputs, mDataWriters, TFileSet< _Stream, _Enum, _options >::Reset(), and TMultiSourceFileSet< _Enum, _options >::Reset().

Referenced by DeleteOutputs().

◆ CloseDiagnosticOutputs()

void CTable2AsnContext::CloseDiagnosticOutputs ( )

Definition at line 250 of file table2asn_context.cpp.

References mCurrentDiagnosticOutputs, mDiagnosticWriters, TFileSet< _Stream, _Enum, _options >::Reset(), and TMultiSourceFileSet< _Enum, _options >::Reset().

Referenced by DeleteOutputs().

◆ CopyFeatureIdsToComments()

void CTable2AsnContext::CopyFeatureIdsToComments ( objects::CSeq_entry & entry ) const

Definition at line 553 of file table2asn_context.cpp.

References CScope::AddTopLevelSeqEntry(), NStr::Compare(), CSeqFeatData_Base::e_Rna, CObjectManager::GetInstance(), CSeq_feat_Base::IsSetComment(), and CSeq_feat_Base::SetComment().

◆ CorrectCollectionDates()

void CTable2AsnContext::CorrectCollectionDates ( objects::CSeq_entry & entry ) const

Definition at line 844 of file table2asn_context.cpp.

References m_cleanup, and objects::VisitAllSetandSeq().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ CreateSeqEntryFromTemplate()

CRef< CSerialObject > CTable2AsnContext::CreateSeqEntryFromTemplate ( CRef< objects::CSeq_entry > object ) const

Definition at line 406 of file table2asn_context.cpp.

References CSerialObject::Assign(), m_submit_template, CRef< C, Locker >::NotEmpty(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), and CPub_Base::SetSub().

◆ CreateSubmitFromTemplate()

CRef< CSerialObject > CTable2AsnContext::CreateSubmitFromTemplate	(	CRef< objects::CSeq_entry > &	object,
		CRef< objects::CSeq_submit > &	submit
	)		const

Definition at line 382 of file table2asn_context.cpp.

References CSerialObject::Assign(), m_submit_template, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CSeq_submit_Base::SetData(), and UpdateSubmitObject().

Referenced by CTbl2AsnApp::ProcessHugeFile().

◆ DeleteOutputs()

void CTable2AsnContext::DeleteOutputs ( )

Definition at line 264 of file table2asn_context.cpp.

References CloseDataOutputs(), CloseDiagnosticOutputs(), f, CDirEntry::fIgnoreMissing, mDataWriters, mDiagnosticWriters, and CDirEntry::Remove().

◆ GenerateOutputFilename()

string CTable2AsnContext::GenerateOutputFilename	(	eFiles	kind,
		string_view	basename = `kEmptyStr`
	)		const

Definition at line 280 of file table2asn_context.cpp.

References asn, basename, m_asn1_suffix, m_current_file, m_output_filename, m_ResultsDirectory, and CDirEntry::SplitPath().

Referenced by CTbl2AsnApp::ProcessHugeFile(), and CTable2AsnValidator::x_PopulateDiscrepancy().

◆ GetOrgName()

bool CTable2AsnContext::GetOrgName	(	string &	name,
		const objects::CSeq_entry &	entry
	)

static

Definition at line 780 of file table2asn_context.cpp.

References CSeq_descr_Base::Get(), CBioseq_set_Base::GetDescr(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::IsSetDescr(), and rapidjson::source.

Referenced by CFeatureTableReader::xAddProteinToSeqEntry(), and CFeatTableEdit::xGenerate_mRNA_Product().

◆ GetOrgRef()

CRef< COrg_ref > CTable2AsnContext::GetOrgRef ( objects::CSeq_descr & descr )

static

Definition at line 760 of file table2asn_context.cpp.

References Ref(), CSeq_descr_Base::Set(), and rapidjson::source.

Referenced by UpdateTaxonFromTable().

◆ GetOstream()

std::ostream & CTable2AsnContext::GetOstream ( eFiles suffix )

Definition at line 214 of file table2asn_context.cpp.

References asn, mCurrentDataOutputs, and mCurrentDiagnosticOutputs.

Referenced by CTable2AsnValidator::CollectDiscrepancies(), CUpdateECNumbers::operator()(), CTbl2AsnApp::ProcessHugeFile(), CTable2AsnValidator::ReportDiscrepancies(), and CTable2AsnValidator::ValReportErrors().

◆ IsDBLink()

bool CTable2AsnContext::IsDBLink ( const objects::CSeqdesc & desc )

static

Definition at line 426 of file table2asn_context.cpp.

References NStr::CompareNocase(), CObject_id_Base::GetStr(), CUser_object_Base::GetType(), CSeqdesc_Base::GetUser(), CUser_object_Base::IsSetType(), CObject_id_Base::IsStr(), and CSeqdesc_Base::IsUser().

Referenced by MergeSeqDescr().

◆ MakeGenomeCenterId()

void CTable2AsnContext::MakeGenomeCenterId ( objects::CSeq_entry & entry ) const

Definition at line 620 of file table2asn_context.cpp.

References for(), if(), m_genome_center_id, CBioseq_Base::SetId(), and objects::VisitAllBioseqs().

Referenced by CHugeFastaReader::xLoadNextSeq(), and CMultiReader::xReadFasta().

◆ MergeSeqDescr()

void CTable2AsnContext::MergeSeqDescr	(	objects::CSeq_entry &	dest,
		const objects::CSeq_descr &	src,
		bool	only_set
	)

static

◆ MergeWithTemplate()

void CTable2AsnContext::MergeWithTemplate ( objects::CSeq_entry & entry ) const

Definition at line 503 of file table2asn_context.cpp.

References CSeq_entry::GetParentEntry(), CRef< C, Locker >::IsNull(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), m_entry_template, MergeSeqDescr(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by CMultiReader::xApplyTemplate().

◆ OpenDataOutputs()

void CTable2AsnContext::OpenDataOutputs ( )

Definition at line 208 of file table2asn_context.cpp.

References TMultiSourceFileSet< _Enum, _options >::MakeNewFileset(), mCurrentDataOutputs, mDataWriters, and TFileSet< _Stream, _Enum, _options >::Reset().

◆ OpenDiagnosticOutputs()

void CTable2AsnContext::OpenDiagnosticOutputs ( )

Definition at line 202 of file table2asn_context.cpp.

References TMultiSourceFileSet< _Enum, _options >::MakeNewFileset(), mCurrentDiagnosticOutputs, mDiagnosticWriters, and TFileSet< _Stream, _Enum, _options >::Reset().

◆ RemoveProteinIdsQuals()

void CTable2AsnContext::RemoveProteinIdsQuals ( objects::CSeq_feat & feature ) const

Definition at line 690 of file table2asn_context.cpp.

References CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::ResetQual(), and CSeq_feat_Base::SetQual().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ RemoveUnnecessaryXRef()

void CTable2AsnContext::RemoveUnnecessaryXRef ( objects::CSeq_entry & entry ) const

◆ RenameProteinIdsQuals()

void CTable2AsnContext::RenameProteinIdsQuals ( objects::CSeq_feat & feature ) const

Definition at line 661 of file table2asn_context.cpp.

References CGb_qual_Base::CanGetVal(), CGb_qual_Base::GetQual(), CSeq_feat_Base::IsSetQual(), CSeq_feat_Base::ResetQual(), CGb_qual_Base::SetQual(), and CSeq_feat_Base::SetQual().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ SetOrganismData()

void CTable2AsnContext::SetOrganismData	(	objects::CSeq_descr &	SD,
		int	genome_code,
		const string &	taxname,
		int	taxid,
		const string &	strain
	)		const

◆ SetOutputFile()

void CTable2AsnContext::SetOutputFile	(	eFiles	kind,
		ostream &	ostr
	)

Definition at line 240 of file table2asn_context.cpp.

References asn, mDataWriters, mDiagnosticWriters, and TMultiSourceFileSet< _Enum, _options >::Open().

◆ SetOutputFilename()

void CTable2AsnContext::SetOutputFilename	(	eFiles	kind,
		const string &	filename
	)

Definition at line 230 of file table2asn_context.cpp.

References asn, mDataWriters, mDiagnosticWriters, and TMultiSourceFileSet< _Enum, _options >::SetFilename().

◆ SetSeqId()

void CTable2AsnContext::SetSeqId ( objects::CSeq_entry & entry ) const

Definition at line 529 of file table2asn_context.cpp.

References _ASSERT, CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), m_current_file, CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CDirEntry::SplitPath().

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ SetUserObject()

CUser_object & CTable2AsnContext::SetUserObject	(	objects::CSeq_descr &	descr,
		const CTempString &	type
	)

static

Definition at line 322 of file table2asn_context.cpp.

References CSeqdesc_Base::e_User, CSeqdesc_Base::Select(), CSeq_descr_Base::Set(), CObject_id_Base::SetStr(), CUser_object_Base::SetType(), and CSeqdesc_Base::SetUser().

Referenced by AddUserTrack(), and MergeSeqDescr().

◆ SmartFeatureAnnotation()

void CTable2AsnContext::SmartFeatureAnnotation ( objects::CSeq_entry & entry ) const

Definition at line 585 of file table2asn_context.cpp.

References CScope::AddTopLevelSeqEntry(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, and CObjectManager::GetInstance().

◆ UpdateSubmitObject()

void CTable2AsnContext::UpdateSubmitObject ( CRef< objects::CSeq_submit > & submit ) const

Definition at line 368 of file table2asn_context.cpp.

References CDate::ePrecision_day, CSubmit_block_Base::eSubtype_new, CNcbiApplicationAPI::GetVersion(), CNcbiApplication::Instance(), CTime::IsEmpty(), m_HoldUntilPublish, CVersionInfo::Print(), and CSeq_submit_Base::SetSub().

Referenced by CreateSubmitFromTemplate().

◆ UpdateTaxonFromTable()

void CTable2AsnContext::UpdateTaxonFromTable ( objects::CBioseq & bioseq )

static

Definition at line 823 of file table2asn_context.cpp.

References CBioseq_Base::GetDescr(), GetOrgRef(), CSeq_descr_Base::IsSet(), CBioseq_Base::IsSetDescr(), CRef< C, Locker >::NotEmpty(), CBioseq_Base::SetDescr(), and COrg_ref::UpdateFromTable().

Referenced by CTbl2AsnApp::ProcessOneEntry(), and CTbl2AsnApp::ProcessSingleEntry().

◆ x_ApplyAccession()

static void CTable2AsnContext::x_ApplyAccession	(	const CTable2AsnContext &	context,
		objects::CBioseq &	bioseq
	)

staticprivate

Member Data Documentation

◆ A

string CTable2AsnContext::A

Definition at line 107 of file table2asn_context.hpp.

◆ c

string CTable2AsnContext::c

Definition at line 119 of file table2asn_context.hpp.

◆ F

string CTable2AsnContext::F

Definition at line 106 of file table2asn_context.hpp.

◆ G

string CTable2AsnContext::G

Definition at line 111 of file table2asn_context.hpp.

◆ L

bool CTable2AsnContext::L { false }

Definition at line 115 of file table2asn_context.hpp.

◆ m

string CTable2AsnContext::m

Definition at line 123 of file table2asn_context.hpp.

◆ m_accession

CRef<objects::CSeq_id> CTable2AsnContext::m_accession

Definition at line 98 of file table2asn_context.hpp.

Referenced by ApplyAccession().

◆ m_accumulate_mods

bool CTable2AsnContext::m_accumulate_mods { false }

Definition at line 164 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSecretFiles1Phase().

◆ m_allow_accession

bool CTable2AsnContext::m_allow_accession { false }

Definition at line 151 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), and CMultiReader::xReadFasta().

◆ m_asn1_suffix

string CTable2AsnContext::m_asn1_suffix

Definition at line 144 of file table2asn_context.hpp.

Referenced by GenerateOutputFilename().

◆ m_base_name

string CTable2AsnContext::m_base_name

Definition at line 97 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile().

◆ m_binary_asn1_output

bool CTable2AsnContext::m_binary_asn1_output { false }

Definition at line 165 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile(), and CMultiReader::WriteObject().

◆ m_can_use_huge_files

bool CTable2AsnContext::m_can_use_huge_files { false }

Definition at line 166 of file table2asn_context.hpp.

◆ m_ClassValue

objects::CBioseq_set::TClass CTable2AsnContext::m_ClassValue { objects::CBioseq_set::eClass_genbank }

Definition at line 131 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile(), CHugeFastaReader::xLoadNextSeq(), and CMultiReader::xReadFasta().

◆ m_cleanup

string CTable2AsnContext::m_cleanup

Definition at line 124 of file table2asn_context.hpp.

Referenced by CorrectCollectionDates(), and CTbl2AsnApp::ProcessSingleEntry().

◆ m_Comment

string CTable2AsnContext::m_Comment

Definition at line 101 of file table2asn_context.hpp.

Referenced by ApplyComments().

◆ m_current_file

string CTable2AsnContext::m_current_file

Definition at line 93 of file table2asn_context.hpp.

Referenced by GenerateOutputFilename(), SetSeqId(), and CMultiReader::xReadFasta().

◆ m_d_fasta

bool CTable2AsnContext::m_d_fasta { false }

Definition at line 150 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), CHugeFastaReader::xLoadNextSeq(), and CMultiReader::xReadFasta().

◆ m_DefaultEvidence

objects::CGapsEditor::TEvidenceSet CTable2AsnContext::m_DefaultEvidence

Definition at line 137 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), CTbl2AsnApp::ProcessHugeFile(), CMultiReader::xReadASN1Text(), and CMultiReader::xReadFasta().

◆ m_delay_genprodset

bool CTable2AsnContext::m_delay_genprodset { false }

Definition at line 110 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ m_di_fasta

bool CTable2AsnContext::m_di_fasta { false }

Definition at line 149 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::xLoadNextSeq(), and CMultiReader::xReadFasta().

◆ m_disable_huge_files

bool CTable2AsnContext::m_disable_huge_files { false }

Definition at line 168 of file table2asn_context.hpp.

◆ m_disc_lineage

string CTable2AsnContext::m_disc_lineage

Definition at line 127 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::x_PopulateDiscrepancy().

◆ m_discrepancy_group

NDiscrepancy::EGroup CTable2AsnContext::m_discrepancy_group { NDiscrepancy::eOncaller }

Definition at line 172 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::x_PopulateDiscrepancy().

◆ m_entry_template

CRef<objects::CSeq_entry> CTable2AsnContext::m_entry_template

Definition at line 229 of file table2asn_context.hpp.

Referenced by CMultiReader::LoadTemplate(), MergeWithTemplate(), and CTbl2AsnApp::ProcessHugeFile().

◆ m_eukaryote

bool CTable2AsnContext::m_eukaryote { false }

Definition at line 148 of file table2asn_context.hpp.

Referenced by CMultiReader::x_PostProcessAnnots().

◆ m_fcs_trim

bool CTable2AsnContext::m_fcs_trim { false }

Definition at line 141 of file table2asn_context.hpp.

Referenced by CForeignContaminationScreenReportReader::AnnotateOrRemove().

◆ m_ft_url

string CTable2AsnContext::m_ft_url

Definition at line 103 of file table2asn_context.hpp.

Referenced by ApplyFileTracks().

◆ m_ft_url_mod

string CTable2AsnContext::m_ft_url_mod

Definition at line 104 of file table2asn_context.hpp.

Referenced by ApplyFileTracks().

◆ m_gap_type

int CTable2AsnContext::m_gap_type { -1 }

Definition at line 140 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), CTbl2AsnApp::ProcessHugeFile(), CMultiReader::xReadASN1Text(), and CMultiReader::xReadFasta().

◆ m_gap_Unknown_length

TSeqPos CTable2AsnContext::m_gap_Unknown_length { 0 }

Definition at line 135 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), CTbl2AsnApp::ProcessHugeFile(), CMultiReader::xReadASN1Text(), and CMultiReader::xReadFasta().

◆ m_gapNmin

TSeqPos CTable2AsnContext::m_gapNmin { 0 }

Definition at line 134 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), CTbl2AsnApp::ProcessHugeFile(), CMultiReader::xReadASN1Text(), and CMultiReader::xReadFasta().

◆ m_GapsizeToEvidence

objects::CGapsEditor::TCountToEvidenceMap CTable2AsnContext::m_GapsizeToEvidence

Definition at line 138 of file table2asn_context.hpp.

Referenced by CHugeFastaReader::Open(), CTbl2AsnApp::ProcessHugeFile(), CMultiReader::xReadASN1Text(), and CMultiReader::xReadFasta().

◆ m_genome_center_id

string CTable2AsnContext::m_genome_center_id

Definition at line 108 of file table2asn_context.hpp.

Referenced by CMultiReader::GetIndexedAnnot(), CMultiReader::LoadIndexedAnnot(), and MakeGenomeCenterId().

◆ m_HandleAsSet

bool CTable2AsnContext::m_HandleAsSet { false }

Definition at line 130 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile(), CTbl2AsnApp::ProcessSingleEntry(), and CMultiReader::xReadFasta().

◆ m_HoldUntilPublish

CTime CTable2AsnContext::m_HoldUntilPublish

Definition at line 105 of file table2asn_context.hpp.

Referenced by UpdateSubmitObject().

◆ m_huge_files_mode

bool CTable2AsnContext::m_huge_files_mode { false }

Definition at line 167 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::Cleanup(), CTable2AsnValidator::CollectDiscrepancies(), CTbl2AsnApp::ProcessHugeFile(), CTbl2AsnApp::ProcessSecretFiles1Phase(), CTable2AsnValidator::ValCollect(), CTable2AsnValidator::Validate(), CTable2AsnValidator::ValReportErrors(), and CFeatureTableReader::xAddProteinToSeqEntry().

◆ m_locus_tag_prefix

string CTable2AsnContext::m_locus_tag_prefix

Definition at line 145 of file table2asn_context.hpp.

Referenced by CMultiReader::x_PostProcessAnnots().

◆ m_locus_tags_needed

bool CTable2AsnContext::m_locus_tags_needed

Definition at line 146 of file table2asn_context.hpp.

Referenced by CMultiReader::x_PostProcessAnnots().

◆ m_logger

objects::ILineErrorListener* CTable2AsnContext::m_logger { nullptr }

Definition at line 230 of file table2asn_context.hpp.

Referenced by CMultiReader::LoadGFF3Fasta(), CMultiReader::LoadIndexedAnnot(), CFeatureTableReader::MakeGap(), CTbl2AsnApp::ProcessHugeFile(), CMultiReader::ReadAlignment(), CFeatureTableReader::ReadProtein(), CFeatureTableReader::x_AddProteinFeatureToProtein(), CMultiReader::x_PostProcessAnnots(), CFeatureTableReader::xAddProteinToSeqEntry(), CMultiReader::xApplyTemplate(), CHugeFastaReader::xLoadNextSeq(), CMultiReader::xReadFasta(), CMultiReader::xReadFlatfile(), CMultiReader::xReadGFF3(), and CMultiReader::xReadGTF().

◆ m_make_flatfile

bool CTable2AsnContext::m_make_flatfile { false }

Definition at line 161 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile().

◆ m_master_genome_flag

string CTable2AsnContext::m_master_genome_flag

Definition at line 122 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::ValCollect(), CTable2AsnValidator::Validate(), and CTable2AsnValidator::x_ReportDiscrepancies().

◆ m_minimal_sequence_length

TSeqPos CTable2AsnContext::m_minimal_sequence_length { 0 }

Definition at line 136 of file table2asn_context.hpp.

Referenced by CForeignContaminationScreenReportReader::AnnotateOrRemove(), and CForeignContaminationScreenReportReader::xCheckLen().

◆ m_mutex

std::mutex CTable2AsnContext::m_mutex

mutable

Definition at line 241 of file table2asn_context.hpp.

◆ m_ObjMgr

CRef<objects::CObjectManager> CTable2AsnContext::m_ObjMgr

Definition at line 233 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ m_OrganismName

string CTable2AsnContext::m_OrganismName

Definition at line 99 of file table2asn_context.hpp.

◆ m_output

CNcbiOstream* CTable2AsnContext::m_output { nullptr }

Definition at line 95 of file table2asn_context.hpp.

◆ m_output_filename

string CTable2AsnContext::m_output_filename

Definition at line 96 of file table2asn_context.hpp.

Referenced by GenerateOutputFilename().

◆ m_postprocess_pubs

bool CTable2AsnContext::m_postprocess_pubs { false }

Definition at line 143 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ m_ProjectVersionNumber

string CTable2AsnContext::m_ProjectVersionNumber

Definition at line 126 of file table2asn_context.hpp.

◆ m_remote_updater

unique_ptr<objects::edit::CRemoteUpdater> CTable2AsnContext::m_remote_updater

Definition at line 174 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::CTable2AsnValidator(), and CTbl2AsnApp::ProcessSingleEntry().

◆ m_RemotePubLookup

bool CTable2AsnContext::m_RemotePubLookup { false }

Definition at line 129 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ m_RemoteTaxonomyLookup

bool CTable2AsnContext::m_RemoteTaxonomyLookup { false }

Definition at line 128 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ m_ResultsDirectory

string CTable2AsnContext::m_ResultsDirectory

Definition at line 94 of file table2asn_context.hpp.

Referenced by GenerateOutputFilename().

◆ m_run_discrepancy

bool CTable2AsnContext::m_run_discrepancy { false }

Definition at line 162 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::CollectDiscrepancies().

◆ m_save_bioseq_set

bool CTable2AsnContext::m_save_bioseq_set { false }

Definition at line 118 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile().

◆ m_SetIDFromFile

bool CTable2AsnContext::m_SetIDFromFile { false }

Definition at line 132 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSingleEntry().

◆ m_single_annot_file

string CTable2AsnContext::m_single_annot_file

Definition at line 102 of file table2asn_context.hpp.

◆ m_single_source_qual_file

string CTable2AsnContext::m_single_source_qual_file

Definition at line 100 of file table2asn_context.hpp.

◆ m_single_structure_cmt

string CTable2AsnContext::m_single_structure_cmt

Definition at line 125 of file table2asn_context.hpp.

◆ m_split_discrepancy

bool CTable2AsnContext::m_split_discrepancy { false }

Definition at line 163 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::CollectDiscrepancies().

◆ m_split_log_files

bool CTable2AsnContext::m_split_log_files { false }

Definition at line 142 of file table2asn_context.hpp.

◆ m_submit_template

CRef<objects::CSeq_submit> CTable2AsnContext::m_submit_template

Definition at line 228 of file table2asn_context.hpp.

Referenced by CreateSeqEntryFromTemplate(), CreateSubmitFromTemplate(), and CMultiReader::LoadTemplate().

◆ m_suspect_rules

unique_ptr<objects::CFixSuspectProductName> CTable2AsnContext::m_suspect_rules

Definition at line 176 of file table2asn_context.hpp.

Referenced by CTable2AsnValidator::Cleanup().

◆ m_t

bool CTable2AsnContext::m_t { false }

Definition at line 117 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile(), and CMultiReader::xApplyTemplate().

◆ m_use_hypothetic_protein

bool CTable2AsnContext::m_use_hypothetic_protein { false }

Definition at line 147 of file table2asn_context.hpp.

Referenced by CFeatureTableReader::xAddProteinToSeqEntry(), and CFeatureTableReader::xTranslateProtein().

◆ m_use_threads

optional<size_t> CTable2AsnContext::m_use_threads {}

Definition at line 169 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile().

◆ m_validate

string CTable2AsnContext::m_validate

Definition at line 109 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile(), and CTbl2AsnApp::ProcessSingleEntry().

◆ m_verbose

bool CTable2AsnContext::m_verbose { false }

Definition at line 152 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSecretFiles1Phase().

◆ mCommandLineMods

string CTable2AsnContext::mCommandLineMods

Definition at line 234 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessSecretFiles1Phase().

◆ mCurrentDataOutputs

CDataFileSet::fileset_type CTable2AsnContext::mCurrentDataOutputs

private

Definition at line 249 of file table2asn_context.hpp.

Referenced by CloseDataOutputs(), GetOstream(), and OpenDataOutputs().

◆ mCurrentDiagnosticOutputs

CDiagnosticFileSet::fileset_type CTable2AsnContext::mCurrentDiagnosticOutputs

private

Definition at line 248 of file table2asn_context.hpp.

Referenced by CloseDiagnosticOutputs(), GetOstream(), and OpenDiagnosticOutputs().

◆ mDataWriters

CDataFileSet CTable2AsnContext::mDataWriters

private

Definition at line 246 of file table2asn_context.hpp.

Referenced by CloseDataOutputs(), CTable2AsnContext(), DeleteOutputs(), OpenDataOutputs(), SetOutputFile(), and SetOutputFilename().

◆ mDiagnosticWriters

CDiagnosticFileSet CTable2AsnContext::mDiagnosticWriters

private

Definition at line 245 of file table2asn_context.hpp.

Referenced by CloseDiagnosticOutputs(), CTable2AsnContext(), DeleteOutputs(), OpenDiagnosticOutputs(), SetOutputFile(), and SetOutputFilename().

◆ prtAlnOptions

SPrtAlnOptions CTable2AsnContext::prtAlnOptions

Definition at line 159 of file table2asn_context.hpp.

Referenced by CFeatureTableReader::xAddProteinToSeqEntry().

◆ pValMsgHandler

unique_ptr<CValidMessageHandler> CTable2AsnContext::pValMsgHandler

Definition at line 231 of file table2asn_context.hpp.

Referenced by CTbl2AsnApp::ProcessHugeFile(), and CTbl2AsnApp::ProcessSingleEntry().

◆ Q

string CTable2AsnContext::Q

Definition at line 114 of file table2asn_context.hpp.

◆ R

bool CTable2AsnContext::R { false }

Definition at line 112 of file table2asn_context.hpp.

◆ S

bool CTable2AsnContext::S { false }

Definition at line 113 of file table2asn_context.hpp.

◆ W

bool CTable2AsnContext::W { false }

Definition at line 116 of file table2asn_context.hpp.

◆ X

string CTable2AsnContext::X

Definition at line 121 of file table2asn_context.hpp.

◆ zOufFile

string CTable2AsnContext::zOufFile

Definition at line 120 of file table2asn_context.hpp.

The documentation for this class was generated from the following files:

src/app/table2asn/table2asn_context.hpp
src/app/table2asn/table2asn_context.cpp

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CTable2AsnContext()

◆ ~CTable2AsnContext()

Member Function Documentation

◆ AddUserTrack()

◆ ApplyAccession()

◆ ApplyComments()

◆ ApplyCreateUpdateDates()

◆ ApplyFileTracks()

◆ ApplyUpdateDate()

◆ CloseDataOutputs()

◆ CloseDiagnosticOutputs()

◆ CopyFeatureIdsToComments()

◆ CorrectCollectionDates()

◆ CreateSeqEntryFromTemplate()

◆ CreateSubmitFromTemplate()

◆ DeleteOutputs()

◆ GenerateOutputFilename()

◆ GetOrgName()

◆ GetOrgRef()

◆ GetOstream()

◆ IsDBLink()

◆ MakeGenomeCenterId()

◆ MergeSeqDescr()

◆ MergeWithTemplate()

◆ OpenDataOutputs()

◆ OpenDiagnosticOutputs()

◆ RemoveProteinIdsQuals()

◆ RemoveUnnecessaryXRef()

◆ RenameProteinIdsQuals()

◆ SetOrganismData()

◆ SetOutputFile()

◆ SetOutputFilename()

◆ SetSeqId()

◆ SetUserObject()

◆ SmartFeatureAnnotation()

◆ UpdateSubmitObject()

◆ UpdateTaxonFromTable()

◆ x_ApplyAccession()

Member Data Documentation

◆ A

◆ c

◆ F

◆ G

◆ L

◆ m

◆ m_accession

◆ m_accumulate_mods

◆ m_allow_accession

◆ m_asn1_suffix

◆ m_base_name

◆ m_binary_asn1_output

◆ m_can_use_huge_files

◆ m_ClassValue

◆ m_cleanup

◆ m_Comment

◆ m_current_file

◆ m_d_fasta

◆ m_DefaultEvidence

◆ m_delay_genprodset

◆ m_di_fasta

◆ m_disable_huge_files

◆ m_disc_lineage

◆ m_discrepancy_group

◆ m_entry_template

◆ m_eukaryote

◆ m_fcs_trim

◆ m_ft_url

◆ m_ft_url_mod

◆ m_gap_type

◆ m_gap_Unknown_length

◆ m_gapNmin

◆ m_GapsizeToEvidence