multisource_util.cpp File Reference

Utility functions and classes for multisource app. More...

#include <ncbi_pch.hpp>
#include <serial/typeinfo.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objtools/blast/seqdb_writer/multisource_util.hpp>

Include dependency graph for multisource_util.cpp:

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Functions
	USING_SCOPE (objects)
void	ReadTextFile (CNcbiIstream &f, vector< string > &lines)
void	MapToLMBits (const TLinkoutMap &gilist, TIdToBits &id2links)
	Read a set of GI lists, each a vector of strings, and combine the bits into the resulting linkbits map. More...
string	AccessionToKey (const string &acc)
bool	CheckAccession (const string &acc, TGi &gi, CRef< objects::CSeq_id > &seqid, bool &specific)
void	GetSeqIdKey (const objects::CSeq_id &id, string &key)
void	GetDeflineKeys (const objects::CBlast_def_line &defline, vector< string > &keys)
	Get all keys for a defline. More...

Detailed Description

Utility functions and classes for multisource app.

Definition in file multisource_util.cpp.

Function Documentation

AccessionToKey()

string AccessionToKey

(

const string &

acc

)

Definition at line 82 of file multisource_util.cpp.

References CheckAccession(), CRef< C, Locker >::Empty(), GetSeqIdKey(), NStr::NumericToString(), str(), and ZERO_GI.

Referenced by CTaxIdSet::AddTaxId(), MapToLMBits(), and CTaxIdSet::SetMappingFromFile().

CheckAccession()

bool CheckAccession	(	const string &	acc,
		TGi &	gi,
		CRef< objects::CSeq_id > &	seqid,
		bool &	specific
	)

Definition at line 108 of file multisource_util.cpp.

References i, isdigit(), CTextseq_id_Base::IsSetVersion(), NULL, CRef< C, Locker >::Reset(), and ZERO_GI.

Referenced by AccessionToKey(), and CBuildDatabase::x_ResolveGis().

GetDeflineKeys()

void GetDeflineKeys	(	const objects::CBlast_def_line &	defline,
		vector< string > &	keys
	)

Get all keys for a defline.

Definition at line 162 of file multisource_util.cpp.

References GetSeqIdKey(), ITERATE, and ncbi::grid::netcache::search::fields::key.

Referenced by CTaxIdSet::x_SelectBestTaxid(), and CBuildDatabase::x_SetLinkAndMbit().

GetSeqIdKey()

void GetSeqIdKey	(	const objects::CSeq_id &	id,
		string &	key
	)

Definition at line 157 of file multisource_util.cpp.

References CSeq_id::eContent, CSeq_id::fLabel_GeneralDbIsContent, and ncbi::grid::netcache::search::fields::key.

Referenced by AccessionToKey(), and GetDeflineKeys().

MapToLMBits()

void MapToLMBits	(	const TLinkoutMap &	gilist,
		TIdToBits &	id2links
	)

Read a set of GI lists, each a vector of strings, and combine the bits into the resulting linkbits map.

Definition at line 66 of file multisource_util.cpp.

References AccessionToKey(), ITERATE, and ncbi::grid::netcache::search::fields::key.

Referenced by CBuildDatabase::SetLinkouts(), and CBuildDatabase::SetMembBits().

ReadTextFile()

void ReadTextFile	(	CNcbiIstream &	f,
		vector< string > &	lines
	)

Definition at line 43 of file multisource_util.cpp.

References f, and NcbiGetlineEOL().

USING_SCOPE()

USING_SCOPE

(

objects

)