CBlastDB_FastaFormatter Class Reference

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Fasta formatter interface. More...

#include <objtools/blast/blastdb_format/seq_formatter.hpp>

Inheritance diagram for CBlastDB_FastaFormatter:

Collaboration diagram for CBlastDB_FastaFormatter:

Public Member Functions
	CBlastDB_FastaFormatter (CSeqDB &blastdb, CNcbiOstream &out, TSeqPos width=80, bool useLongSeqId=false)
	Constructor. More...
void	DumpAll (const CBlastDB_FormatterConfig &config)
int	Write (CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string target_id=kEmptyStr)
	Retun 0 if Sucess otherwise -1. More...
Public Member Functions inherited from CBlastDB_Formatter
	CBlastDB_Formatter ()
virtual	~CBlastDB_Formatter ()

Private Member Functions
	CBlastDB_FastaFormatter (const CBlastDB_FastaFormatter &rhs)
	Prohibit copy constructor. More...
CBlastDB_FastaFormatter &	operator= (const CBlastDB_FastaFormatter &rhs)
	Prohibit assignment operator. More...

Private Attributes
CSeqDB &	m_BlastDb
	The BLAST database from which to extract data. More...
CNcbiOstream &	m_Out
CFastaOstream	m_fasta
bool	m_UseLongSeqIds

Detailed Description

Fasta formatter interface.

Definition at line 140 of file seq_formatter.hpp.

Constructor & Destructor Documentation

CBlastDB_FastaFormatter() [1/2]

CBlastDB_FastaFormatter::CBlastDB_FastaFormatter	(	CSeqDB &	blastdb,
		CNcbiOstream &	out,
		TSeqPos	width = 80,
		bool	useLongSeqId = false
	)

Constructor.

Parameters

blastdb	BLAST database from which to retrieve the data [in]
out	output stream to write the data [in]
width	fasta line width [in]

Definition at line 379 of file seq_formatter.cpp.

References CFastaOstream::fEnableGI, CFastaOstream::fKeepGTSigns, CFastaOstream::fNoExpensiveOps, m_fasta, CFastaOstream::SetAllFlags(), and CFastaOstream::SetWidth().

CBlastDB_FastaFormatter() [2/2]

CBlastDB_FastaFormatter::CBlastDB_FastaFormatter ( const CBlastDB_FastaFormatter &  rhs )

private

Prohibit copy constructor.

Member Function Documentation

DumpAll()

void CBlastDB_FastaFormatter::DumpAll ( const CBlastDB_FormatterConfig &  config )

virtual

Implements CBlastDB_Formatter.

Definition at line 495 of file seq_formatter.cpp.

References CSeqDB::CheckOrFindOID(), eNa_strand_minus, CFastaOstream::fEnableGI, CFastaOstream::fKeepGTSigns, CFastaOstream::fNoExpensiveOps, CFastaOstream::fReverseStrand, i, m_BlastDb, m_fasta, CFastaOstream::SetAllFlags(), and Write().

operator=()

CBlastDB_FastaFormatter& CBlastDB_FastaFormatter::operator= ( const CBlastDB_FastaFormatter &  rhs )

private

Prohibit assignment operator.

Write()

int CBlastDB_FastaFormatter::Write ( CSeqDB::TOID  oid, const CBlastDB_FormatterConfig &  config, string  target_id = kEmptyStr  )

virtual

Retun 0 if Sucess otherwise -1.

Implements CBlastDB_Formatter.

Definition at line 397 of file seq_formatter.cpp.

References CScope::AddBioseq(), CSeq_id::BestRank(), CSeqDB::TSequenceRanges::empty(), ctll::empty(), CRef< C, Locker >::Empty(), eNa_strand_minus, CFastaOstream::eSoftMask, NStr::fConvErr_NoThrow, FindBestChoice(), CSeq_id::fParse_Default, CSeq_id::fParse_PartialOK, CFastaOstream::fReverseStrand, CSeqDB::GetBioseq(), CBioseq_Base::GetId(), CObjectManager::GetInstance(), CSeqDB::GetMaskData(), CSeqDB::GetSeqLength(), GI_FROM, kEmptyStr, m_BlastDb, m_fasta, m_Out, m_UseLongSeqIds, CBlastDeflineUtil::ProcessFastaDeflines(), r(), compile_time_bits::range(), CFastaOstream::ResetFlag(), s_GetMaskSeqLoc(), s_GetSeqMask(), s_ReplaceCtrlAsInTitle(), CFastaOstream::SetFlag(), CSeq_loc::SetId(), CFastaOstream::SetMask(), CFastaOstream::Write(), CFastaOstream::WriteSequence(), and ZERO_GI.

Referenced by DumpAll().

Member Data Documentation

m_BlastDb

CSeqDB& CBlastDB_FastaFormatter::m_BlastDb

private

The BLAST database from which to extract data.

Definition at line 157 of file seq_formatter.hpp.

Referenced by DumpAll(), and Write().

m_fasta

CFastaOstream CBlastDB_FastaFormatter::m_fasta

private

Definition at line 159 of file seq_formatter.hpp.

Referenced by CBlastDB_FastaFormatter(), DumpAll(), and Write().

m_Out

CNcbiOstream& CBlastDB_FastaFormatter::m_Out

private

Definition at line 158 of file seq_formatter.hpp.

Referenced by Write().

m_UseLongSeqIds

bool CBlastDB_FastaFormatter::m_UseLongSeqIds

private

Definition at line 160 of file seq_formatter.hpp.

Referenced by Write().

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

• include/objtools/blast/blastdb_format/seq_formatter.hpp
• src/objtools/blast/blastdb_format/seq_formatter.cpp