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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fasta__ex_8cpp_source.html below:

NCBI C++ ToolKit: src/app/table2asn/fasta_ex.cpp Source File

(

::EType)m_context.m_gap_type,

m_context.m_DefaultEvidence,

m_context.m_GapsizeToEvidence,

m_context.m_gap_Unknown_length)

(entry.

()) {

(create_date_desc.

())

, 0);

->SetGapLinkageEvidence(

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CSeqdesc & Set(bool skip_lookup=false)

Modification of the CFastaReader class that allows for reading a single sequence as a degenarate mult...

objects::CGapsEditor m_gap_editor

virtual CRef< objects::CSeq_entry > ReadDeltaFasta(objects::ILineErrorListener *pMessageListener)

void AssembleSeq(objects::ILineErrorListener *pMessageListener) override

CFastaReaderEx(ILineReader &reader, CFastaReader::TFlags flags=0)

Constructor.

void AssignMolType(objects::ILineErrorListener *pMessageListener) override

Base class for reading FASTA sequences.

void Open(objects::edit::CHugeFile *file, objects::ILineErrorListener *pMessageListener) override

CConstRef< objects::CSubmit_block > GetSubmitBlock() const override

deque< CRef< objects::CSeq_entry > > m_seqs

CRef< objects::CSeq_entry > GetNextSeqEntry() override

CHugeFastaReader(CTable2AsnContext &context)

unique_ptr< CFastaReaderEx > m_fasta

CRef< objects::CSeq_entry > xLoadNextSeq()

CTable2AsnContext & m_context

bool GetNextBlob() override

objects::ILineErrorListener * m_logger

TSeqPos m_gap_Unknown_length

objects::CGapsEditor::TEvidenceSet m_DefaultEvidence

objects::CGapsEditor::TCountToEvidenceMap m_GapsizeToEvidence

objects::CBioseq_set::TClass m_ClassValue

void MakeGenomeCenterId(objects::CSeq_entry &entry) const

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

long TFlags

binary OR of EFlags

CBioseq & SetCurrentSeq(void)

virtual void AssembleSeq(ILineErrorListener *pMessageListener)

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

virtual void AssignMolType(ILineErrorListener *pMessageListener)

ILineReader & GetLineReader(void)

@ fHyphensIgnoreAndWarn

When a hyphen is encountered in seq data, ignore it but warn.

@ fLetterGaps

Parse runs of Ns when splitting data.

@ fIgnoreMods

Ignore mods entirely. Incompatible with fAddMods.

@ fNoUserObjs

Don't save raw deflines in User-objects.

@ fForceType

Force specified type regardless of accession.

@ fParseRawID

Try to identify raw accessions.

@ fNoSplit

Don't split out ambiguous sequence regions.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fParseGaps

Make a delta sequence if gaps found.

@ fValidate

Check (alphabetic) residue validity.

@ fDisableParseRange

No ranges in seq-ids. Ranges part of seq-id instead.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TErrCode GetErrCode(void) const

Get error code.

@ eCurrent

Use current time. See also CCurrentTime.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetMol(void) const

Check if a value has been assigned to Mol data member.

bool IsSetBiomol(void) const

Check if a value has been assigned to Biomol data member.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TMol GetMol(void) const

Get the Mol member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

TMolinfo & SetMolinfo(void)

Select the variant.

TCreate_date & SetCreate_date(void)

Select the variant.

void SetMol(TMol value)

Assign a value to Mol data member.

@ e_Molinfo

info on the molecule and techniques

@ e_Create_date

date entry first created/released

@ eMol_na

just a nucleic acid

static CS_CONTEXT * context

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