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NCBI C++ ToolKit: src/app/table2asn/table2asn_context.hpp Source File

CFixSuspectProductName;

<

_enum, _enum ... _options>

<

_enum, _enum ... _options>

objects::CBioseq_set::TClass

{ objects::CBioseq_set::eClass_genbank };

(objects::CSeq_descr&

,

genome_code,

& taxname,

taxid,

& strain)

;

(objects::CSeq_entry& entry)

;

(

objects::CSeqdesc& desc);

(

& name,

objects::CSeq_entry& entry);

(objects::CSeq_entry& dest,

objects::CSeq_descr& src,

only_set);

objects::CGapsEditor::TCountToEvidenceMap& gapsizeToEvidence,

objects::ILineErrorListener* pMessageListener);

@Seq_descr.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

string m_genome_center_id

void ApplyUpdateDate(objects::CSeq_entry &entry) const

CDiagnosticFileSet mDiagnosticWriters

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

CRef< objects::CObjectManager > m_ObjMgr

CDataFileSet::fileset_type mCurrentDataOutputs

void SetSeqId(objects::CSeq_entry &entry) const

void ApplyFileTracks(objects::CSeq_entry &entry) const

bool m_RemoteTaxonomyLookup

bool m_binary_asn1_output

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

unique_ptr< objects::edit::CRemoteUpdater > m_remote_updater

void SetOutputFilename(eFiles kind, const string &filename)

void ApplyAccession(objects::CSeq_entry &entry) const

bool m_disable_huge_files

objects::ILineErrorListener * m_logger

CRef< objects::CSeq_id > m_accession

string m_ProjectVersionNumber

bool m_can_use_huge_files

string m_single_structure_cmt

bool m_use_hypothetic_protein

CDataFileSet mDataWriters

TSeqPos m_gap_Unknown_length

SPrtAlnOptions prtAlnOptions

TSeqPos m_minimal_sequence_length

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

string m_master_genome_flag

objects::CGapsEditor::TEvidenceSet m_DefaultEvidence

void SetOutputFile(eFiles kind, ostream &ostr)

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

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

NDiscrepancy::EGroup m_discrepancy_group

CRef< objects::CSeq_entry > m_entry_template

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

void CorrectCollectionDates(objects::CSeq_entry &entry) const

CDiagnosticFileSet::fileset_type mCurrentDiagnosticOutputs

void SmartFeatureAnnotation(objects::CSeq_entry &entry) const

optional< size_t > m_use_threads

CRef< objects::CSeq_submit > m_submit_template

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

void MergeWithTemplate(objects::CSeq_entry &entry) const

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

string m_locus_tag_prefix

void OpenDiagnosticOutputs()

unique_ptr< CValidMessageHandler > pValMsgHandler

void RenameProteinIdsQuals(objects::CSeq_feat &feature) const

void CloseDiagnosticOutputs()

void ApplyComments(objects::CSeq_entry &entry) const

objects::CGapsEditor::TCountToEvidenceMap m_GapsizeToEvidence

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

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

std::ostream & GetOstream(eFiles suffix)

bool ApplyCreateUpdateDates(objects::CSeq_entry &entry) const

string m_ResultsDirectory

void RemoveProteinIdsQuals(objects::CSeq_feat &feature) const

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

string m_single_annot_file

objects::CBioseq_set::TClass m_ClassValue

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

unique_ptr< objects::CFixSuspectProductName > m_suspect_rules

static void UpdateTaxonFromTable(objects::CBioseq &bioseq)

void CopyFeatureIdsToComments(objects::CSeq_entry &entry) const

void MakeGenomeCenterId(objects::CSeq_entry &entry) const

string m_single_source_qual_file

void RemoveUnnecessaryXRef(objects::CSeq_entry &entry) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

typename fileset_type::enum_type enum_type

unsigned int TSeqPos

Type for sequence locations and lengths.

EDiagSev

Severity level for the posted diagnostics.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static const char label[]

The NCBI C++/STL use hints.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

void g_LogDiagMessage(objects::ILineErrorListener *, EDiagSev, const string &msg)

void g_LoadLinkageEvidence(const string &linkageEvidenceFilename, objects::CGapsEditor::TCountToEvidenceMap &gapsizeToEvidence, objects::ILineErrorListener *pMessageListener)

static CS_CONTEXT * context

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