CBlastDB_BioseqFormatter Class Reference

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

Inheritance diagram for CBlastDB_BioseqFormatter:

Collaboration diagram for CBlastDB_BioseqFormatter:

Public Member Functions
	CBlastDB_BioseqFormatter (CSeqDB &blastdb, CNcbiOstream &out)
	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_BioseqFormatter (const CBlastDB_BioseqFormatter &rhs)
	Prohibit copy constructor. More...
CBlastDB_BioseqFormatter &	operator= (const CBlastDB_BioseqFormatter &rhs)
	Prohibit assignment operator. More...

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

Detailed Description

Definition at line 168 of file seq_formatter.hpp.

Constructor & Destructor Documentation

CBlastDB_BioseqFormatter() [1/2]

CBlastDB_BioseqFormatter::CBlastDB_BioseqFormatter	(	CSeqDB &	blastdb,
		CNcbiOstream &	out
	)

Constructor.

Parameters

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

Definition at line 509 of file seq_formatter.cpp.

CBlastDB_BioseqFormatter() [2/2]

CBlastDB_BioseqFormatter::CBlastDB_BioseqFormatter ( const CBlastDB_BioseqFormatter &  rhs )

private

Prohibit copy constructor.

Member Function Documentation

DumpAll()

void CBlastDB_BioseqFormatter::DumpAll ( const CBlastDB_FormatterConfig &  config )

virtual

Implements CBlastDB_Formatter.

Definition at line 543 of file seq_formatter.cpp.

References CSeqDB::CheckOrFindOID(), i, m_BlastDb, and Write().

operator=()

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

private

Prohibit assignment operator.

Write()

int CBlastDB_BioseqFormatter::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 514 of file seq_formatter.cpp.

References eGiId, CRef< C, Locker >::Empty(), CSeqDB::GetBioseq(), GI_FROM, kEmptyStr, m_BlastDb, m_Out, MSerial_AsnText, SeqDB_SimplifySeqid(), and ZERO_GI.

Referenced by DumpAll().

Member Data Documentation

m_BlastDb

CSeqDB& CBlastDB_BioseqFormatter::m_BlastDb

private

The BLAST database from which to extract data.

Definition at line 184 of file seq_formatter.hpp.

Referenced by DumpAll(), and Write().

m_Out

CNcbiOstream& CBlastDB_BioseqFormatter::m_Out

private

Definition at line 185 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