Search Toolkit Book for CBlastDB_SeqFormatter

Customizable sequence formatter interface. More...

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

Inheritance diagram for CBlastDB_SeqFormatter:

Collaboration diagram for CBlastDB_SeqFormatter:

Public Member Functions
	CBlastDB_SeqFormatter (const string &fmt_spec, CSeqDB &blastdb, CNcbiOstream &out)
	Constructor. More...

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

void	DumpAll (const CBlastDB_FormatterConfig &config)

Public Member Functions inherited from CBlastDB_Formatter
	CBlastDB_Formatter ()

virtual	~CBlastDB_Formatter ()

Private Types
enum	EOtherFields { e_seq = 0 , e_mask , e_hash , e_max_other_fields }
	Fields not in defline. More...

Private Member Functions
void	x_Print (CSeqDB::TOID oid, vector< string > &defline_data, vector< string > &other_fields)
	Build data for write. More...

void	x_DataRequired ()

void	x_GetSeq (CSeqDB::TOID oid, const CBlastDB_FormatterConfig &config, string &seq)

string	x_GetSeqHash (CSeqDB::TOID oid)

string	x_GetSeqMask (CSeqDB::TOID oid, int algo_id)

	CBlastDB_SeqFormatter (const CBlastDB_SeqFormatter &rhs)
	Prohibit copy constructor. More...

CBlastDB_SeqFormatter &	operator= (const CBlastDB_SeqFormatter &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< string >	m_Seperators
	Vector of offsets where the replacements will take place. More...

vector< char >	m_ReplTypes
	Vector of convertor objects. More...

bool	m_GetDefline

CBlastDeflineUtil::BlastDeflineFields	m_DeflineFields

unsigned int	m_OtherFields
	Bit Mask for other fields. More...

Detailed Description

Customizable sequence formatter interface.

Definition at line 88 of file seq_formatter.hpp.

Member Enumeration Documentation

◆ EOtherFields

enum CBlastDB_SeqFormatter::EOtherFields

private

Fields not in defline.

Enumerator
e_seq
e_mask
e_hash
e_max_other_fields

Definition at line 102 of file seq_formatter.hpp.

Constructor & Destructor Documentation

◆ CBlastDB_SeqFormatter() [1/2]

CBlastDB_SeqFormatter::CBlastDB_SeqFormatter	(	const string &	fmt_spec,
		CSeqDB &	blastdb,
		CNcbiOstream &	out
	)

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 59 of file seq_formatter.cpp.

References i, kEmptyStr, m_DeflineFields, m_FmtSpec, m_ReplTypes, m_Seperators, NCBI_THROW, and x_DataRequired().

◆ CBlastDB_SeqFormatter() [2/2]

CBlastDB_SeqFormatter::CBlastDB_SeqFormatter ( const CBlastDB_SeqFormatter & rhs )

private

Prohibit copy constructor.

Member Function Documentation

◆ DumpAll()

void CBlastDB_SeqFormatter::DumpAll ( const CBlastDB_FormatterConfig & config )

virtual

Implements CBlastDB_Formatter.

Definition at line 372 of file seq_formatter.cpp.

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

◆ operator=()

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

private

Prohibit assignment operator.

◆ Write()

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

virtual

Implements CBlastDB_Formatter.

Definition at line 315 of file seq_formatter.cpp.

References CBlastDeflineUtil::BlastDeflineFields::asn_defline, e_hash, e_mask, e_max_other_fields, e_seq, CRef< C, Locker >::Empty(), CBlastDeflineUtil::ExtractDataFromBlastDefline(), CBlastDeflineUtil::ExtractDataFromBlastDeflineSet(), CBlast_def_line_set_Base::Get(), CSeqDB::GetHdr(), ITERATE, kEmptyStr, m_BlastDb, m_DeflineFields, m_GetDefline, m_OtherFields, m_Out, mask, CBlastDeflineUtil::max_index, MSerial_AsnText, x_GetSeq(), x_GetSeqHash(), x_GetSeqMask(), and x_Print().

Referenced by DumpAll().

◆ x_DataRequired()

void CBlastDB_SeqFormatter::x_DataRequired ( )

private

◆ x_GetSeq()

void CBlastDB_SeqFormatter::x_GetSeq	(	CSeqDB::TOID	oid,
		const CBlastDB_FormatterConfig &	config,
		string &	seq
	)

private

Definition at line 282 of file seq_formatter.cpp.

References CBlastSeqUtil::ApplySeqMask(), CSeqDB::TSequenceRanges::empty(), eNa_strand_minus, CBlastSeqUtil::GetReverseStrandSeq(), CSeqDB::GetSeqLength(), CSeqDB::GetSequenceAsString(), m_BlastDb, r(), and s_GetSeqMask().

Referenced by Write().

◆ x_GetSeqHash()

string CBlastDB_SeqFormatter::x_GetSeqHash ( CSeqDB::TOID oid )

private

Definition at line 265 of file seq_formatter.cpp.

References CBlastSeqUtil::GetSeqHash(), CSeqDB::GetSequenceAsString(), hex(), and m_BlastDb.

Referenced by Write().

◆ x_GetSeqMask()

string CBlastDB_SeqFormatter::x_GetSeqMask	(	CSeqDB::TOID	oid,
		int	algo_id
	)

private

Definition at line 275 of file seq_formatter.cpp.

References CBlastSeqUtil::GetMasksString(), m_BlastDb, and s_GetSeqMask().

Referenced by Write().

◆ x_Print()

void CBlastDB_SeqFormatter::x_Print	(	CSeqDB::TOID	oid,
		vector< string > &	defline_data,
		vector< string > &	other_fields
	)

private

Member Data Documentation

◆ m_BlastDb

CSeqDB& CBlastDB_SeqFormatter::m_BlastDb

private

The BLAST database from which to extract data.

Definition at line 114 of file seq_formatter.hpp.

Referenced by DumpAll(), Write(), x_GetSeq(), x_GetSeqHash(), x_GetSeqMask(), and x_Print().

◆ m_DeflineFields

CBlastDeflineUtil::BlastDeflineFields CBlastDB_SeqFormatter::m_DeflineFields

private

Definition at line 120 of file seq_formatter.hpp.

Referenced by CBlastDB_SeqFormatter(), Write(), and x_DataRequired().

◆ m_FmtSpec

string CBlastDB_SeqFormatter::m_FmtSpec

private

The output format specification.

Definition at line 112 of file seq_formatter.hpp.

Referenced by CBlastDB_SeqFormatter().

◆ m_GetDefline

bool CBlastDB_SeqFormatter::m_GetDefline

private

Definition at line 119 of file seq_formatter.hpp.

Referenced by Write(), and x_DataRequired().

◆ m_OtherFields

unsigned int CBlastDB_SeqFormatter::m_OtherFields

private

Bit Mask for other fields.

Definition at line 122 of file seq_formatter.hpp.

Referenced by Write(), and x_DataRequired().

◆ m_Out

CNcbiOstream& CBlastDB_SeqFormatter::m_Out

private

Stream to write output.

Definition at line 110 of file seq_formatter.hpp.

Referenced by Write(), and x_Print().

◆ m_ReplTypes

vector<char> CBlastDB_SeqFormatter::m_ReplTypes

private

Vector of convertor objects.

Definition at line 118 of file seq_formatter.hpp.

Referenced by CBlastDB_SeqFormatter(), x_DataRequired(), and x_Print().

◆ m_Seperators

vector<string> CBlastDB_SeqFormatter::m_Seperators

private

Vector of offsets where the replacements will take place.

Definition at line 116 of file seq_formatter.hpp.

Referenced by CBlastDB_SeqFormatter(), and x_Print().

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

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ EOtherFields

Constructor & Destructor Documentation

◆ CBlastDB_SeqFormatter() [1/2]

◆ CBlastDB_SeqFormatter() [2/2]

Member Function Documentation

◆ DumpAll()

◆ operator=()

◆ Write()

◆ x_DataRequired()

◆ x_GetSeq()

◆ x_GetSeqHash()

◆ x_GetSeqMask()

◆ x_Print()

Member Data Documentation

◆ m_BlastDb

◆ m_DeflineFields

◆ m_FmtSpec

◆ m_GetDefline

◆ m_OtherFields

◆ m_Out

◆ m_ReplTypes

◆ m_Seperators