NCBI C++ ToolKit
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CSeqref Class Reference

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#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 >, TSatKeyTKeyByTSE
 
- 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< Uint8TCounter
 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...
 
CObjectoperator= (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

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

Definition at line 72 of file seqref.hpp.

◆ TSatKey

Definition at line 74 of file seqref.hpp.

◆ TSubSat

Definition at line 73 of file seqref.hpp.

◆ TVersion

Definition at line 75 of file seqref.hpp.

Member Enumeration Documentation

◆ EBlobFlags

Enumerator
fPossible 
fPrivate 

Definition at line 45 of file seqref.hpp.

◆ 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

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:
Modified on Mon Apr 22 04:06:14 2024 by modify_doxy.py rev. 669887