#include <objtools/import/id_resolver.hpp>

Inheritance diagram for CIdResolver:

Collaboration diagram for CIdResolver:

Public Member Functions
	CIdResolver ()

virtual	~CIdResolver ()

virtual CRef< CSeq_id >	operator() (const string &) const

	CIdResolver (CScope &scope)

CSeq_id_Handle	GetAccessionVersion (const string &identifier) const

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Private Member Functions
bool	x_TryProcessLRG (const string &identifier, CSeq_id_Handle &idh) const

bool	x_TryProcessGenomicLRG (const string &identifier, CSeq_id_Handle &idh) const

bool	x_LooksLikeLRG (const string &identifier) const

bool	x_LooksLikeCCDS (const string &identifier) const

Private Attributes
CScope &	m_Scope

unique_ptr< CRegexp >	m_LRGregex

unique_ptr< CRegexp >	m_CCDSregex

unique_ptr< CEntrez2Client >	m_E2Client

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 43 of file id_resolver.hpp.

Constructor & Destructor Documentation

◆ CIdResolver() [1/2]

CIdResolver::CIdResolver ( )

Definition at line 43 of file id_resolver.cpp.

◆ ~CIdResolver()

CIdResolver::~CIdResolver ( )

virtual

Definition at line 49 of file id_resolver.cpp.

◆ CIdResolver() [2/2]

CIdResolver::CIdResolver ( CScope & scope )

Definition at line 11 of file id_resolver.cpp.

Member Function Documentation

◆ GetAccessionVersion()

CSeq_id_Handle CIdResolver::GetAccessionVersion ( const string & identifier ) const

Definition at line 18 of file id_resolver.cpp.

References eGetId_ForceAcc, eGetId_ThrowOnError, CSeq_id_Handle::GetHandle(), GetId(), NStr::IsBlank(), m_Scope, NCBI_THROW, and x_TryProcessLRG().

Referenced by CHgvsNaIrepReader::CreateSeqfeat(), CHgvsProtIrepReader::CreateSeqfeat(), CHgvsNaIrepReader::x_CreateConversionVarref(), CHgvsNaIrepReader::x_CreateSimpleVariantFeat(), and CHgvsProtIrepReader::x_CreateSimpleVariantFeat().

◆ operator()()

CRef< CSeq_id > CIdResolver::operator() ( const string & rawId ) const

virtual

Reimplemented in CIdResolverPrefix, and CIdResolverCanonical.

Definition at line 56 of file id_resolver.cpp.

◆ x_LooksLikeCCDS()

bool CIdResolver::x_LooksLikeCCDS ( const string & identifier ) const

private

Definition at line 201 of file id_resolver.cpp.

References m_CCDSregex.

◆ x_LooksLikeLRG()

bool CIdResolver::x_LooksLikeLRG ( const string & identifier ) const

private

Definition at line 195 of file id_resolver.cpp.

References m_LRGregex.

Referenced by x_TryProcessGenomicLRG().

◆ x_TryProcessGenomicLRG()

bool CIdResolver::x_TryProcessGenomicLRG	(	const string &	identifier,
		CSeq_id_Handle &	idh
	)		const

private

Definition at line 57 of file id_resolver.cpp.

References eGetId_ForceAcc, eGetId_ThrowOnError, GetId(), NStr::IsBlank(), m_Scope, Ref(), and x_LooksLikeLRG().

Referenced by x_TryProcessLRG().

◆ x_TryProcessLRG()

bool CIdResolver::x_TryProcessLRG	(	const string &	identifier,
		CSeq_id_Handle &	idh
	)		const

private

Definition at line 87 of file id_resolver.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, eGetId_ForceAcc, NStr::Equal(), CScope::GetBioseqHandle(), GetId(), SAnnotSelector::IncludeFeatType(), NStr::IsBlank(), ITERATE, m_LRGregex, m_Scope, NCBI_THROW, SAnnotSelector::SetResolveTSE(), and x_TryProcessGenomicLRG().

Referenced by GetAccessionVersion().

Member Data Documentation

◆ m_CCDSregex

unique_ptr<CRegexp> CIdResolver::m_CCDSregex

private

Definition at line 26 of file id_resolver.hpp.

Referenced by x_LooksLikeCCDS().

◆ m_E2Client

unique_ptr<CEntrez2Client> CIdResolver::m_E2Client

private

Definition at line 27 of file id_resolver.hpp.

◆ m_LRGregex

unique_ptr<CRegexp> CIdResolver::m_LRGregex

private

Definition at line 25 of file id_resolver.hpp.

Referenced by x_LooksLikeLRG(), and x_TryProcessLRG().

◆ m_Scope

CScope& CIdResolver::m_Scope

private

Definition at line 24 of file id_resolver.hpp.

Referenced by GetAccessionVersion(), x_TryProcessGenomicLRG(), and x_TryProcessLRG().

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

include/objtools/import/id_resolver.hpp
src/objtools/import/id_resolver.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CIdResolver() [1/2]

◆ ~CIdResolver()

◆ CIdResolver() [2/2]

Member Function Documentation

◆ GetAccessionVersion()

◆ operator()()

◆ x_LooksLikeCCDS()

◆ x_LooksLikeLRG()

◆ x_TryProcessGenomicLRG()

◆ x_TryProcessLRG()

Member Data Documentation

◆ m_CCDSregex

◆ m_E2Client

◆ m_LRGregex

◆ m_Scope