#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>

Public Member Functions
	SSeqDBTaxInfo (TTaxId t=ZERO_TAX_ID)
	Default constructor. More...

Public Attributes
TTaxId	taxid
	An identifier for this species or taxonomic group. More...

string	scientific_name
	Scientific name, such as "Aotus vociferans". More...

string	common_name
	Common name, such as "noisy night monkey". More...

string	blast_name
	A simple category name, such as "birds". More...

string	s_kingdom
	A string of length 1 indicating the "Super Kingdom". More...

Friends
ostream &	operator<< (ostream &out, const SSeqDBTaxInfo &rhs)

Detailed Description

SSeqDBTaxInfo.

This structure contains the taxonomy information for a single given taxid.

Definition at line 1846 of file seqdbcommon.hpp.

Constructor & Destructor Documentation

◆ SSeqDBTaxInfo()

SSeqDBTaxInfo::SSeqDBTaxInfo ( TTaxId t = ZERO_TAX_ID )

inline

Default constructor.

Parameters

t	the taxonomy ID to set for this structure

Definition at line 1849 of file seqdbcommon.hpp.

Friends And Related Function Documentation

◆ operator<<

ostream& operator<<	(	ostream &	out,
		const SSeqDBTaxInfo &	rhs
	)

friend

Definition at line 1869 of file seqdbcommon.hpp.

Member Data Documentation

◆ blast_name

string SSeqDBTaxInfo::blast_name

A simple category name, such as "birds".

Definition at line 1864 of file seqdbcommon.hpp.

Referenced by CBlastDBExtractor::ExtractBlastName(), CShowBlastDefline::x_FormatDeflineTableLine(), CShowBlastDefline::x_GetTaxonomyInfoForTaxID(), CTaxFormat::x_InitBlastDBTaxInfo(), CBlastTabularInfo::x_SetTaxInfo(), and CBlastTabularInfo::x_SetTaxInfoAll().

◆ common_name

string SSeqDBTaxInfo::common_name

Common name, such as "noisy night monkey".

Definition at line 1861 of file seqdbcommon.hpp.

Referenced by CBlastDBExtractor::ExtractCommonTaxonomicName(), CBlastDBExtractor::ExtractLeafCommonTaxonomicNames(), CShowBlastDefline::x_FormatDeflineTableLine(), CShowBlastDefline::x_FormatDeflineTableLineCSV(), CShowBlastDefline::x_FormatDeflineTableLineText(), CSeqDBVol::x_GetTaxonomy(), CShowBlastDefline::x_GetTaxonomyInfoForTaxID(), CTaxFormat::x_InitBlastDBTaxInfo(), CBlastTabularInfo::x_SetTaxInfo(), and CBlastTabularInfo::x_SetTaxInfoAll().

◆ s_kingdom

string SSeqDBTaxInfo::s_kingdom

A string of length 1 indicating the "Super Kingdom".

Definition at line 1867 of file seqdbcommon.hpp.

Referenced by CBlastDBExtractor::ExtractSuperKingdom(), CBlastTabularInfo::x_SetTaxInfo(), and CBlastTabularInfo::x_SetTaxInfoAll().

◆ scientific_name

string SSeqDBTaxInfo::scientific_name

Scientific name, such as "Aotus vociferans".

Definition at line 1858 of file seqdbcommon.hpp.

Referenced by CMetaDataTest::DoTest(), CBlastDBExtractor::ExtractLeafScientificNames(), CBlastDBExtractor::ExtractScientificName(), s_SeqAlignToXMLHit(), CShowBlastDefline::x_FormatDeflineTableLine(), CShowBlastDefline::x_FormatDeflineTableLineCSV(), CShowBlastDefline::x_FormatDeflineTableLineText(), CGeneFileWriter::x_GetOrgnameForTaxId(), CSeqDBVol::x_GetTaxonomy(), CShowBlastDefline::x_GetTaxonomyInfoForTaxID(), CTaxFormat::x_InitBlastDBTaxInfo(), CBlastTabularInfo::x_SetTaxInfo(), and CBlastTabularInfo::x_SetTaxInfoAll().

◆ taxid

TTaxId SSeqDBTaxInfo::taxid

An identifier for this species or taxonomic group.

Definition at line 1855 of file seqdbcommon.hpp.

Referenced by CBlastDBExtractor::ExtractBlastName(), CBlastDBExtractor::ExtractCommonTaxonomicName(), CBlastDBExtractor::ExtractLeafCommonTaxonomicNames(), CBlastDBExtractor::ExtractLeafScientificNames(), CBlastDBExtractor::ExtractScientificName(), CBlastDBExtractor::ExtractSuperKingdom(), CShowBlastDefline::x_FormatDeflineTableLine(), CShowBlastDefline::x_FormatDeflineTableLineCSV(), CShowBlastDefline::x_FormatDeflineTableLineText(), and CShowBlastDefline::x_GetTaxonomyInfoForTaxID().

The documentation for this struct was generated from the following file:

include/objtools/blast/seqdb_reader/seqdbcommon.hpp

Public Member Functions

Public Attributes

Friends