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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/idmapper_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/readers/idmapper.hpp Source File

1 #ifndef OBJTOOLS_IDMAPPER___IDMAPPER_IMPL__HPP 2 #define OBJTOOLS_IDMAPPER___IDMAPPER_IMPL__HPP 71 bool

bInvert =

false

84 virtual void

AddMapping(

const CSeq_loc

& loc_from,

134

kPriority_Default = 0

143

TPriority priority = kPriority_Default,

162

: m_Mapper(mapper, ownership),

165

m_Order = sm_Counter.

Add

(1);

173 return

m_Order < node.

m_Order

;

244 bool

bInvert =

false

248 bool

bInvert =

false

266

list<SMappingContext>& contexts);

279 bool

m_LocalOnly =

true

;

305 bool

bInvert =

false

343 bool

bInvert =

false

345

CIdMapper

(strContext, bInvert, pErrors),

346

m_strServer(strServer),

347

m_strDatabase(strDatabase)

409

EAliasMapping mapping,

410 const string

& alias_scope =

kEmptyStr

);

415

EAliasMapping mapping,

416 const string

& alias_scope =

kEmptyStr

);

424 void

x_AddUnversionedMapping(

const CSeq_id

& src_id,

426 void

x_AddAccessionMapping(

const CSeq_id

id

);

428

EAliasMapping mapping,

429 const string

& alias_scope);

431

EAliasMapping mapping,

432 const string

& alias_scope);

434

EAliasMapping mapping,

435 const string

& alias_scope);

448 virtual const char

* GetErrCodeString(

void

)

const override

;

User-defined methods of the data storage class.

IdMapper implementation using hardcoded values.

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

IdMapper implementation combining multiple id mappers with the selected priorities.

EPriority

Sub-mapper priority.

CAtomicCounter::TValue TOrder

IdMapper implementation using an external configuration file.

IdMapper implementation using an external database.

const std::string m_strDatabase

const std::string m_strServer

CIdMapperDatabase(const std::string &strServer, const std::string &strDatabase, const std::string &strContext, bool bInvert=false, ILineErrorListener *pErrors=0)

Constructor specifying a database containing the actual mapping, the mapping context,...

NCBI_EXCEPTION_DEFAULT(CIdMapperException, CException)

IdMapper implementation using a GC-Assembly.

EAliasMapping

Mapping destination type.

@ eUCSC

External UCSC id.

@ eGenBankAcc

GenBank accession.

@ eRefSeqAcc

RefSeq accession.

IdMapper implementaion using CScope.

IdMapper base class implementation.

ILineErrorListener * m_pErrors

std::map< CSeq_id_Handle, SMapper > TMapperCache

const std::string m_strContext

Base class for all serializable objects.

General IdMapper interface.

virtual void MapObject(CSerialObject &)=0

Map all embedded IDs in a given object at once.

virtual CSeq_id_Handle Map(const CSeq_id_Handle &id)=0

Map a single given CSeq_id_Handle to another.

Include a standard set of the NCBI C++ Toolkit most basic headers.

CRange< Position > Map(const CRange< Position > &target, const CRange< Position > &range)

@ eTakeOwnership

An object can take ownership of another.

TNCBIAtomicValue TValue

Alias TValue for TNCBIAtomicValue.

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

EErrCode

Error types that an application can generate.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

enum ENcbiOwnership EOwnership

Ownership relations between objects.

#define NCBI_XOBJREAD_EXPORT

bool operator<(const SNode &node) const

SNode(IIdMapper *mapper, TPriority priority, EOwnership ownership)

CIdMapperComposite::TPriority TPriority

static CAtomicCounter sm_Counter

CIdMapperComposite::TOrder TOrder

AutoPtr< IIdMapper > m_Mapper

CRef< CSeq_loc_Mapper > dest_mapper

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