Search Toolkit Book for CIdMapperBuiltin

IdMapper implementation using hardcoded values. More...

#include <objtools/readers/idmapper.hpp>

Inheritance diagram for CIdMapperBuiltin:

Collaboration diagram for CIdMapperBuiltin:

Public Member Functions
	CIdMapperBuiltin (const std::string &strContext, bool bInvert=false, ILineErrorListener *pErrors=0)
	Constructor specifying the mapping context, direction, and error handling. More...

void	Initialize ()

Public Member Functions inherited from CIdMapperConfig
	CIdMapperConfig (CNcbiIstream &istr, const std::string &strContext="", bool bInvert=false, ILineErrorListener *pErrors=0)
	Constructor specifying the content of the mapping table, mapping context, direction, and error handling. More...

	CIdMapperConfig (const std::string &strContext="", bool bInvert=false, ILineErrorListener *pErrors=0)

void	Initialize (CNcbiIstream &istr)

Public Member Functions inherited from CIdMapper
	CIdMapper (const std::string &strContext="", bool bInvert=false, ILineErrorListener *pErrors=0)
	Constructor specifying the mapping context, direction, and error handling. More...

virtual	~CIdMapper ()

virtual void	AddMapping (const CSeq_id_Handle &from, const CSeq_id_Handle &to)
	Add a mapping to the internal mapping table. More...

virtual void	AddMapping (const CSeq_loc &loc_from, const CSeq_loc &loc_to)

virtual CSeq_id_Handle	Map (const CSeq_id_Handle &)
	Map a single given CSeq_id_Handle to another. More...

virtual CRef< CSeq_loc >	Map (const CSeq_loc &loc)

virtual void	MapObject (CSerialObject &)
	Map all embedded IDs in a given object at once. More...

Public Member Functions inherited from IIdMapper
virtual	~IIdMapper ()

Protected Member Functions
void	AddMapEntry (const std::string &, int)

Protected Member Functions inherited from CIdMapperConfig
void	AddMapEntry (const std::string &)

void	SetCurrentContext (const std::string &, std::string &)

CSeq_id_Handle	SourceHandle (const std::string &)

CSeq_id_Handle	TargetHandle (const std::string &)

Additional Inherited Members
Static Public Member Functions inherited from CIdMapperConfig
static void	DescribeContexts (CNcbiIstream &istr, list< SMappingContext > &contexts)

Protected Types inherited from CIdMapper
typedef std::map< CSeq_id_Handle, SMapper >	TMapperCache

Static Protected Member Functions inherited from CIdMapper
static std::string	MapErrorString (const CSeq_id_Handle &)

static std::string	MapErrorString (const CSeq_loc &)

Protected Attributes inherited from CIdMapper
const std::string	m_strContext

const bool	m_bInvert

TMapperCache	m_Cache

ILineErrorListener *	m_pErrors

Detailed Description

IdMapper implementation using hardcoded values.

Mapping targets are fixed at compile time and cannot be modified later. Useful for self contained applications that should work without external configuration files or databases.

Definition at line 274 of file idmapper.hpp.

Constructor & Destructor Documentation

◆ CIdMapperBuiltin()

CIdMapperBuiltin::CIdMapperBuiltin	(	const std::string &	strContext,
		bool	bInvert = `false`,
		ILineErrorListener *	pErrors = `0`
	)

Constructor specifying the mapping context, direction, and error handling.

Parameters

strContext	the mapping context or genome source IDs will belong to. Something like "mm6" or "hg18".
bInvert	Mapping direction. "true" will map in reverse direction.
pErrors	Optional error container. If specified, mapping errors will be passed to the error container for further processing. If not specified, mapping errors result in exceptions that need to be handled.

Definition at line 51 of file idmapper_builtin.cpp.

References Initialize().

Member Function Documentation

◆ AddMapEntry()

void CIdMapperBuiltin::AddMapEntry	(	const std::string &	,
		int
	)

protected

◆ Initialize()

void CIdMapperBuiltin::Initialize ( void )

Definition at line 60 of file idmapper_builtin.cpp.

References CIdMapperConfig::Initialize(), and sc_BuiltinConfig.

Referenced by CIdMapperBuiltin().

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

include/objtools/readers/idmapper.hpp
src/objtools/readers/idmapper_builtin.cpp

Public Member Functions