#include <objtools/data_loaders/genbank/seqref.hpp>

Inheritance diagram for CSeqref:

Collaboration diagram for CSeqref:

Public Types
enum	EBlobFlags { fPossible = 1 << 16 , fPrivate = 1 << 17 }

enum	ESat { eSat_ANNOT_CDD = 10 , eSat_ANNOT = 26 , eSat_TRACE = 28 , eSat_TRACE_ASSM = 29 , eSat_TR_ASSM_CH = 30 , eSat_TRACE_CHGR = 31 }

enum	ESubSat { eSubSat_main = 0 , eSubSat_SNP = 1<<0 , eSubSat_SNP_graph = 1<<2 , eSubSat_CDD = 1<<3 , eSubSat_MGC = 1<<4 , eSubSat_HPRD = 1<<5 , eSubSat_STS = 1<<6 , eSubSat_tRNA = 1<<7 , eSubSat_microRNA = 1<<8 , eSubSat_Exon = 1<<9 }

typedef TBlobContentsMask	TFlags

typedef Int4	TSat

typedef Int4	TSubSat

typedef Int4	TSatKey

typedef Int4	TVersion

typedef pair< pair< TSat, TSubSat >, TSatKey >	TKeyByTSE

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...

Public Member Functions
	CSeqref (void)

	CSeqref (TGi gi, TSat sat, TSatKey satkey)

	CSeqref (TGi gi, TSat sat, TSatKey satkey, TSubSat subsat, TFlags flags)

virtual	~CSeqref (void)

const string	print (void) const

const string	printTSE (void) const

TGi	GetGi () const

TSat	GetSat () const

TSubSat	GetSubSat () const

TSatKey	GetSatKey () const

TKeyByTSE	GetKeyByTSE (void) const

bool	SameTSE (const CSeqref &seqRef) const

bool	SameSeq (const CSeqref &seqRef) const

bool	LessByTSE (const CSeqref &seqRef) const

bool	LessBySeq (const CSeqref &seqRef) const

bool	operator< (const CSeqref &seqRef) const

TFlags	GetFlags (void) const

void	SetFlags (TFlags flags)

bool	IsEmpty (void) const

bool	IsMainBlob (void) const

TVersion	GetVersion (void) const

void	SetVersion (TVersion version)

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

Static Public Member Functions
static const string	printTSE (const TKeyByTSE &key)

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)

Protected Attributes
TFlags	m_Flags

TGi	m_Gi

TSat	m_Sat

TSubSat	m_SubSat

TSatKey	m_SatKey

TVersion	m_Version

Additional Inherited Members
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 42 of file seqref.hpp.

Member Typedef Documentation

◆ TFlags

typedef TBlobContentsMask CSeqref::TFlags

Definition at line 49 of file seqref.hpp.

◆ TKeyByTSE

typedef pair<pair<TSat, TSubSat>, TSatKey> CSeqref::TKeyByTSE

Definition at line 84 of file seqref.hpp.

◆ TSat

typedef Int4 CSeqref::TSat

Definition at line 72 of file seqref.hpp.

◆ TSatKey

typedef Int4 CSeqref::TSatKey

Definition at line 74 of file seqref.hpp.

◆ TSubSat

typedef Int4 CSeqref::TSubSat

Definition at line 73 of file seqref.hpp.

◆ TVersion

typedef Int4 CSeqref::TVersion

Definition at line 75 of file seqref.hpp.

Member Enumeration Documentation

◆ EBlobFlags

enum CSeqref::EBlobFlags

Enumerator
fPossible
fPrivate

Definition at line 45 of file seqref.hpp.

◆ ESat

enum CSeqref::ESat

Enumerator
eSat_ANNOT_CDD
eSat_ANNOT
eSat_TRACE
eSat_TRACE_ASSM
eSat_TR_ASSM_CH
eSat_TRACE_CHGR

Definition at line 51 of file seqref.hpp.

◆ ESubSat

enum CSeqref::ESubSat

Enumerator
eSubSat_main
eSubSat_SNP
eSubSat_SNP_graph
eSubSat_CDD
eSubSat_MGC
eSubSat_HPRD
eSubSat_STS
eSubSat_tRNA
eSubSat_microRNA
eSubSat_Exon

Definition at line 60 of file seqref.hpp.

Constructor & Destructor Documentation

◆ CSeqref() [1/3]

CSeqref::CSeqref ( void )

Definition at line 36 of file seqref.cpp.

◆ CSeqref() [2/3]

CSeqref::CSeqref	(	TGi	gi,
		TSat	sat,
		TSatKey	satkey
	)

Definition at line 44 of file seqref.cpp.

◆ CSeqref() [3/3]

CSeqref::CSeqref	(	TGi	gi,
		TSat	sat,
		TSatKey	satkey,
		TSubSat	subsat,
		TFlags	flags
	)

Definition at line 52 of file seqref.cpp.

◆ ~CSeqref()

CSeqref::~CSeqref ( void )

virtual

Definition at line 60 of file seqref.cpp.

Member Function Documentation

◆ GetFlags()

TFlags CSeqref::GetFlags ( void ) const

inline

Definition at line 146 of file seqref.hpp.

◆ GetGi()

TGi CSeqref::GetGi ( void ) const

inline

Definition at line 87 of file seqref.hpp.

Referenced by print().

◆ GetKeyByTSE()

TKeyByTSE CSeqref::GetKeyByTSE ( void ) const

inline

Definition at line 104 of file seqref.hpp.

◆ GetSat()

TSat CSeqref::GetSat ( void ) const

inline

Definition at line 91 of file seqref.hpp.

Referenced by operator<(), print(), and printTSE().

◆ GetSatKey()

TSatKey CSeqref::GetSatKey ( void ) const

inline

Definition at line 99 of file seqref.hpp.

Referenced by operator<(), print(), and printTSE().

◆ GetSubSat()

TSubSat CSeqref::GetSubSat ( void ) const

inline

Definition at line 95 of file seqref.hpp.

Referenced by print(), and printTSE().

◆ GetVersion()

TVersion CSeqref::GetVersion ( void ) const

inline

Definition at line 165 of file seqref.hpp.

Referenced by operator<().

◆ IsEmpty()

bool CSeqref::IsEmpty ( void ) const

inline

Definition at line 155 of file seqref.hpp.

◆ IsMainBlob()

bool CSeqref::IsMainBlob ( void ) const

inline

Definition at line 160 of file seqref.hpp.

References fBlobHasCore.

◆ LessBySeq()

bool CSeqref::LessBySeq ( const CSeqref & seqRef ) const

inline

Definition at line 130 of file seqref.hpp.

References m_Gi.

◆ LessByTSE()

bool CSeqref::LessByTSE ( const CSeqref & seqRef ) const

inline

Definition at line 120 of file seqref.hpp.

References m_Sat, m_SatKey, and m_SubSat.

◆ operator<()

bool CSeqref::operator< ( const CSeqref & seqRef ) const

inline

Definition at line 137 of file seqref.hpp.

References GetSat(), GetSatKey(), and GetVersion().

◆ print()

const string CSeqref::print ( void ) const

Definition at line 65 of file seqref.cpp.

References eSubSat_main, GetGi(), GetSat(), GetSatKey(), and GetSubSat().

◆ printTSE() [1/2]

const string CSeqref::printTSE ( const TKeyByTSE & key )

static

Definition at line 87 of file seqref.cpp.

References eSubSat_main, and ncbi::grid::netcache::search::fields::key.

◆ printTSE() [2/2]

const string CSeqref::printTSE ( void ) const

Definition at line 76 of file seqref.cpp.

References eSubSat_main, GetSat(), GetSatKey(), and GetSubSat().

◆ SameSeq()

bool CSeqref::SameSeq ( const CSeqref & seqRef ) const

inline

Definition at line 116 of file seqref.hpp.

References m_Gi.

◆ SameTSE()

bool CSeqref::SameTSE ( const CSeqref & seqRef ) const

inline

Definition at line 109 of file seqref.hpp.

References m_Sat, m_SatKey, and m_SubSat.

◆ SetFlags()

void CSeqref::SetFlags ( TFlags flags )

inline

Definition at line 150 of file seqref.hpp.

References flags.

◆ SetVersion()

void CSeqref::SetVersion ( TVersion version )

inline

Definition at line 169 of file seqref.hpp.

References version.

Member Data Documentation

◆ m_Flags

TFlags CSeqref::m_Flags

protected

Definition at line 175 of file seqref.hpp.

◆ m_Gi

TGi CSeqref::m_Gi

protected

Definition at line 177 of file seqref.hpp.

Referenced by LessBySeq(), and SameSeq().

◆ m_Sat

TSat CSeqref::m_Sat

protected

Definition at line 178 of file seqref.hpp.

Referenced by LessByTSE(), and SameTSE().

◆ m_SatKey

TSatKey CSeqref::m_SatKey

protected

Definition at line 180 of file seqref.hpp.

Referenced by LessByTSE(), and SameTSE().

◆ m_SubSat

TSubSat CSeqref::m_SubSat

protected

Definition at line 179 of file seqref.hpp.

Referenced by LessByTSE(), and SameTSE().

◆ m_Version

TVersion CSeqref::m_Version

protected

Definition at line 181 of file seqref.hpp.

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

include/objtools/data_loaders/genbank/seqref.hpp
src/objtools/data_loaders/genbank/seqref.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TFlags

◆ TKeyByTSE

◆ TSat

◆ TSatKey

◆ TSubSat

◆ TVersion

Member Enumeration Documentation

◆ EBlobFlags

◆ ESat

◆ ESubSat

Constructor & Destructor Documentation

◆ CSeqref() [1/3]

◆ CSeqref() [2/3]

◆ CSeqref() [3/3]

◆ ~CSeqref()

Member Function Documentation

◆ GetFlags()

◆ GetGi()

◆ GetKeyByTSE()

◆ GetSat()

◆ GetSatKey()

◆ GetSubSat()

◆ GetVersion()

◆ IsEmpty()

◆ IsMainBlob()

◆ LessBySeq()

◆ LessByTSE()

◆ operator<()

◆ print()

◆ printTSE() [1/2]

◆ printTSE() [2/2]

◆ SameSeq()

◆ SameTSE()

◆ SetFlags()

◆ SetVersion()

Member Data Documentation

◆ m_Flags

◆ m_Gi

◆ m_Sat

◆ m_SatKey

◆ m_SubSat

◆ m_Version