NCBI C++ ToolKit
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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_FastaFormatteroperator= (const CBlastDB_FastaFormatter &rhs)
 Prohibit assignment operator. More...
 

Private Attributes

CSeqDBm_BlastDb
 The BLAST database from which to extract data. More...
 
CNcbiOstreamm_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
blastdbBLAST database from which to retrieve the data [in]
outoutput stream to write the data [in]
widthfasta 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

◆ 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

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().


The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:47:37 2024 by modify_doxy.py rev. 669887