CSeqFormatter Class Reference

Search Toolkit Book for CSeqFormatter

Customizable sequence writer interface. More...

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

Collaboration diagram for CSeqFormatter:

Public Member Functions
	CSeqFormatter (const string &fmt_spec, CSeqDB &blastdb, CNcbiOstream &out, CSeqFormatterConfig config=CSeqFormatterConfig())
	Constructor. More...
void	Write (CBlastDBSeqId &id)
	Write the sequence data associated with the requested ID in the format specified in the constructor. More...
void	DumpAll (CSeqDB &blastdb, CSeqFormatterConfig config=CSeqFormatterConfig())
	Full database FASTA dump This is an optimized version that does not support range and mask retrieval. More...
void	SetConfig (TSeqRange range, objects::ENa_strand strand, int filt_algo_id)
	Set range, strand and filter algo for each seq id. More...

Private Member Functions
void	x_Builder (vector< string > &data2write)
	Build data for write. More...
string	x_Replacer (const vector< string > &data2write) const
	Replace format specifiers for the data contained in data2write. More...
bool	x_RequireData () const
	Specifies whether or not data (e.g., Bioseq) is required. More...
	CSeqFormatter (const CSeqFormatter &rhs)
	Prohibit copy constructor. More...
CSeqFormatter &	operator= (const CSeqFormatter &rhs)
	Prohibit assignment operator. More...

Private Attributes
CNcbiOstream &	m_Out
	Stream to write output. More...
string	m_FmtSpec
	The output format specification. More...
CSeqDB &	m_BlastDb
	The BLAST database from which to extract data. More...
vector< SIZE_TYPE >	m_ReplOffsets
	Vector of offsets where the replacements will take place. More...
CBlastDBExtractor	m_DataExtractor
	Data extractor. More...
vector< char >	m_ReplTypes
	Vector of convertor objects. More...
bool	m_Fasta
	Fasta output? More...

Detailed Description

Customizable sequence writer interface.

Definition at line 77 of file seq_writer.hpp.

Constructor & Destructor Documentation

CSeqFormatter() [1/2]

CSeqFormatter::CSeqFormatter	(	const string &	fmt_spec,
		CSeqDB &	blastdb,
		CNcbiOstream &	out,
		CSeqFormatterConfig	config = CSeqFormatterConfig()
	)

Constructor.

Parameters

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

Definition at line 47 of file seq_writer.cpp.

References i, m_BlastDb, m_Fasta, m_FmtSpec, m_ReplOffsets, m_ReplTypes, NCBI_THROW, and CSeqDB::ValidateMaskAlgorithms().

CSeqFormatter() [2/2]

CSeqFormatter::CSeqFormatter ( const CSeqFormatter &  rhs )

private

Prohibit copy constructor.

Member Function Documentation

DumpAll()

void CSeqFormatter::DumpAll	(	CSeqDB &	blastdb,
		CSeqFormatterConfig	config = CSeqFormatterConfig()
	)

Full database FASTA dump This is an optimized version that does not support range and mask retrieval.

Exceptions

CExcpetion

derived classes on error

Definition at line 270 of file seq_writer.cpp.

References CScope::AddBioseq(), CSeqDB::CheckOrFindOID(), CRef< C, Locker >::Empty(), CFastaOstream::fEnableGI, CFastaOstream::fKeepGTSigns, CFastaOstream::fNoExpensiveOps, IRegistry::Get(), CSeqDB::GetBioseq(), CNcbiApplicationAPI::GetConfig(), CDbtag_Base::GetDb(), CSeq_id_Base::GetGeneral(), CBioseq_Base::GetId(), CObjectManager::GetInstance(), i, CNcbiApplication::Instance(), CSeq_id_Base::IsGeneral(), CSeq_id_Base::IsLocal(), m_Out, registry, CRef< C, Locker >::Reset(), s_GetTitle(), s_ReplaceCtrlAsInTitle(), CFastaOstream::SetAllFlags(), CFastaOstream::SetWidth(), CFastaOstream::Write(), and CFastaOstream::WriteSequence().

operator=()

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

private

Prohibit assignment operator.

SetConfig()

void CSeqFormatter::SetConfig	(	TSeqRange	range,
		objects::ENa_strand	strand,
		int	filt_algo_id
	)

Set range, strand and filter algo for each seq id.

Definition at line 390 of file seq_writer.cpp.

Write()

void CSeqFormatter::Write

(

CBlastDBSeqId &

id

)

Write the sequence data associated with the requested ID in the format specified in the constructor.

Parameters

id	identifier for a sequence in the BLAST database

Exceptions

CException

derived classes on error

Definition at line 220 of file seq_writer.cpp.

References CBlastDBExtractor::ExtractFasta(), m_DataExtractor, m_Fasta, m_Out, CBlastDBExtractor::SetSeqId(), x_Builder(), x_Replacer(), and x_RequireData().

x_Builder()

void CSeqFormatter::x_Builder ( vector< string > &  data2write )

private

Build data for write.

Parameters

data2write

data to replace in the output string [in]

Definition at line 116 of file seq_writer.cpp.

References CBlastDBExtractor::ExtractAccession(), CBlastDBExtractor::ExtractAsn1Bioseq(), CBlastDBExtractor::ExtractAsn1Defline(), CBlastDBExtractor::ExtractBlastName(), CBlastDBExtractor::ExtractCommonTaxonomicName(), CBlastDBExtractor::ExtractGi(), CBlastDBExtractor::ExtractHash(), CBlastDBExtractor::ExtractLeafCommonTaxonomicNames(), CBlastDBExtractor::ExtractLeafScientificNames(), CBlastDBExtractor::ExtractLeafTaxIds(), CBlastDBExtractor::ExtractLinksInteger(), CBlastDBExtractor::ExtractMaskingData(), CBlastDBExtractor::ExtractMembershipInteger(), CBlastDBExtractor::ExtractOid(), CBlastDBExtractor::ExtractPig(), CBlastDBExtractor::ExtractScientificName(), CBlastDBExtractor::ExtractSeqData(), CBlastDBExtractor::ExtractSeqId(), CBlastDBExtractor::ExtractSeqLen(), CBlastDBExtractor::ExtractSuperKingdom(), CBlastDBExtractor::ExtractTaxId(), CBlastDBExtractor::ExtractTitle(), ITERATE, m_DataExtractor, m_ReplTypes, and NCBI_THROW.

Referenced by Write().

x_Replacer()

string CSeqFormatter::x_Replacer ( const vector< string > &  data2write ) const

private

Replace format specifiers for the data contained in data2write.

Parameters

data2write

data to replace in the output string [in]

Definition at line 368 of file seq_writer.cpp.

Referenced by Write().

x_RequireData()

bool CSeqFormatter::x_RequireData ( ) const

private

Specifies whether or not data (e.g., Bioseq) is required.

Definition at line 97 of file seq_writer.cpp.

References ITERATE, and m_ReplTypes.

Referenced by Write().

Member Data Documentation

m_BlastDb

CSeqDB& CSeqFormatter::m_BlastDb

private

The BLAST database from which to extract data.

Definition at line 106 of file seq_writer.hpp.

Referenced by CSeqFormatter().

m_DataExtractor

CBlastDBExtractor CSeqFormatter::m_DataExtractor

private

Data extractor.

Definition at line 110 of file seq_writer.hpp.

Referenced by Write(), and x_Builder().

m_Fasta

bool CSeqFormatter::m_Fasta

private

Fasta output?

Definition at line 114 of file seq_writer.hpp.

Referenced by CSeqFormatter(), and Write().

m_FmtSpec

string CSeqFormatter::m_FmtSpec

private

The output format specification.

Definition at line 104 of file seq_writer.hpp.

Referenced by CSeqFormatter().

m_Out

CNcbiOstream& CSeqFormatter::m_Out

private

Stream to write output.

Definition at line 102 of file seq_writer.hpp.

Referenced by DumpAll(), and Write().

m_ReplOffsets

vector<SIZE_TYPE> CSeqFormatter::m_ReplOffsets

private

Vector of offsets where the replacements will take place.

Definition at line 108 of file seq_writer.hpp.

Referenced by CSeqFormatter().

m_ReplTypes

vector<char> CSeqFormatter::m_ReplTypes

private

Vector of convertor objects.

Definition at line 112 of file seq_writer.hpp.

Referenced by CSeqFormatter(), x_Builder(), and x_RequireData().

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

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