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CIdMapperBuiltin Class Reference

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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_locMap (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, SMapperTMapperCache
 
- 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
 
ILineErrorListenerm_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
strContextthe mapping context or genome source IDs will belong to. Something like "mm6" or "hg18".
bInvertMapping direction. "true" will map in reverse direction.
pErrorsOptional 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:
Modified on Sun Apr 14 05:25:36 2024 by modify_doxy.py rev. 669887