NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | List of all members
CCSraDb Class Reference

Search Toolkit Book for CCSraDb

#include <sra/readers/sra/csraread.hpp>

+ Inheritance diagram for CCSraDb:
+ Collaboration diagram for CCSraDb:

Public Types

typedef CCSraDb_Impl::TSpotGroups TSpotGroups
 
- Public Types inherited from CRef< CCSraDb_Impl >
typedef CCSraDb_Impl element_type
 Define alias element_type. More...
 
typedef element_type TObjectType
 Define alias TObjectType. More...
 
typedef Locker locker_type
 Define alias for locking type. More...
 
typedef CRef< CCSraDb_Impl, Locker > TThisType
 Alias for this template type. More...
 
using enable_if_derived = typename std::enable_if< std::is_convertible< T *, TObjectType * >::value >
 Helper template to template enable methods only for derived types. More...
 
- Public Types inherited from SCSraDb_Defs
enum  ERefIdType { eRefId_SEQ_ID , eRefId_gnl_NAME }
 
enum  EPathInIdType { ePathInId_config , ePathInId_yes , ePathInId_no }
 
enum  EAlignType { fPrimaryAlign = 1<<0 , fSecondaryAlign = 1<<1 , fAnyAlign = fPrimaryAlign | fSecondaryAlign }
 
typedef EAlignType TAlignType
 

Public Member Functions

 CCSraDb (void)
 
 CCSraDb (CVDBMgr &mgr, const string &csra_path, IIdMapper *ref_id_mapper=NULL, ERefIdType ref_id_type=eRefId_SEQ_ID)
 
 CCSraDb (CVDBMgr &mgr, const string &csra_path, const string &sra_id_part, IIdMapper *ref_id_mapper=NULL, ERefIdType ref_id_type=eRefId_SEQ_ID)
 
TSeqPos GetRowSize (void) const
 
void GetSpotGroups (TSpotGroups &spot_groups)
 
- Public Member Functions inherited from CRef< CCSraDb_Impl >
 CRef (void) THROWS_NONE
 Constructor for null pointer. More...
 
 CRef (ENull) THROWS_NONE
 Constructor for ENull pointer. More...
 
 CRef (TObjectType *ptr)
 Constructor for explicit type conversion from pointer to object. More...
 
 CRef (TObjectType *ptr, const locker_type &locker_value)
 Constructor for explicit type conversion from pointer to object. More...
 
 CRef (const TThisType &ref)
 Copy constructor from an existing CRef object. More...
 
 CRef (const CRef< TDerived, Locker > &ref)
 Copy constructor from an existing CRef object of derived type. More...
 
 CRef (TThisType &&ref)
 Move constructor from an existing CRef object. More...
 
 CRef (CRef< TDerived, Locker > &&ref)
 Move constructor from an existing CRef object of derived type. More...
 
 ~CRef (void)
 Destructor. More...
 
const locker_typeGetLocker (void) const
 Get reference to locker object. More...
 
bool operator! (void) const THROWS_NONE
 Check if CRef is empty – not pointing to any object, which means having a null value. More...
 
bool Empty (void) const THROWS_NONE
 Check if CRef is empty – not pointing to any object, which means having a null value. More...
 
bool NotEmpty (void) const THROWS_NONE
 Check if CRef is not empty – pointing to an object and has a non-null value. More...
 
bool IsNull (void) const THROWS_NONE
 Check if pointer is null – same effect as Empty(). More...
 
bool NotNull (void) const THROWS_NONE
 Check if pointer is not null – same effect as NotEmpty(). More...
 
void Swap (TThisType &ref)
 Swaps the pointer with another reference. More...
 
void Reset (void)
 Reset reference object. More...
 
void Reset (TObjectType *newPtr)
 Reset reference object to new pointer. More...
 
TObjectTypeReleaseOrNull (void)
 Release a reference to the object and return a pointer to the object. More...
 
TObjectTypeRelease (void)
 Release a reference to the object and return a pointer to the object. More...
 
void AtomicResetFrom (const TThisType &ref)
 Reset reference object to new pointer. More...
 
void AtomicReleaseTo (TThisType &ref)
 Release referenced object to another CRef<> object. More...
 
TThisTypeoperator= (const TThisType &ref)
 Assignment operator for references. More...
 
TThisTypeoperator= (const CRef< TDerived, Locker > &ref)
 Assignment operator for references of derived types. More...
 
TThisTypeoperator= (TThisType &&ref)
 Move assignment operator for references. More...
 
TThisTypeoperator= (CRef< TDerived, Locker > &&ref)
 Move assignment operator for references of derived types. More...
 
TThisTypeoperator= (TObjectType *ptr)
 Assignment operator for references with right hand side set to a pointer. More...
 
TThisTypeoperator= (ENull)
 Assignment operator with right hand side set to ENull. More...
 
TObjectTypeGetNonNullPointer (void)
 Get pointer value and throw a null pointer exception if pointer is null. More...
 
const TObjectTypeGetNonNullPointer (void) const
 Get pointer value and throw a null pointer exception if pointer is null – constant version. More...
 
TObjectTypeGetPointerOrNull (void) THROWS_NONE
 Get pointer value. More...
 
const TObjectTypeGetPointerOrNull (void) const THROWS_NONE
 Get pointer value – constant version. More...
 
TObjectTypeGetPointer (void) THROWS_NONE
 Get pointer,. More...
 
const TObjectTypeGetPointer (void) const THROWS_NONE
 Get pointer – constant version,. More...
 
TObjectTypeGetObject (void)
 Get object. More...
 
const TObjectTypeGetObject (void) const
 Get object – constant version. More...
 
TObjectTypeoperator* (void)
 Dereference operator returning object. More...
 
const TObjectTypeoperator* (void) const
 Dereference operator returning object – constant version. More...
 
TObjectTypeoperator-> (void)
 Reference operator. More...
 
const TObjectTypeoperator-> (void) const
 Reference operator – constant version. More...
 
 operator TObjectType * (void)
 Dereference operator returning pointer. More...
 
 operator const TObjectType * (void) const
 Dereference operator returning pointer – constant version. More...
 
TObjectTypeGetNonNullNCPointer (void) const
 Get pointer value and throw a null pointer exception if pointer is null. More...
 
TObjectTypeGetNCPointerOrNull (void) const THROWS_NONE
 Get pointer value. More...
 
TObjectTypeGetNCPointer (void) const THROWS_NONE
 Get pointer,. More...
 
TObjectTypeGetNCObject (void) const
 Get object. More...
 

Static Public Member Functions

static string MakeSraIdPart (EPathInIdType path_in_id_type, const string &dir_path, const string &csra_file)
 
- Static Public Member Functions inherited from CRef< CCSraDb_Impl >
static void ThrowNullPointerException (void)
 

Detailed Description

Definition at line 233 of file csraread.hpp.

Member Typedef Documentation

◆ TSpotGroups

Definition at line 261 of file csraread.hpp.

Constructor & Destructor Documentation

◆ CCSraDb() [1/3]

CCSraDb::CCSraDb ( void  )
inline

Definition at line 236 of file csraread.hpp.

◆ CCSraDb() [2/3]

CCSraDb::CCSraDb ( CVDBMgr mgr,
const string csra_path,
IIdMapper ref_id_mapper = NULL,
ERefIdType  ref_id_type = eRefId_SEQ_ID 
)

Definition at line 406 of file csraread.cpp.

◆ CCSraDb() [3/3]

CCSraDb::CCSraDb ( CVDBMgr mgr,
const string csra_path,
const string sra_id_part,
IIdMapper ref_id_mapper = NULL,
ERefIdType  ref_id_type = eRefId_SEQ_ID 
)

Definition at line 418 of file csraread.cpp.

Member Function Documentation

◆ GetRowSize()

TSeqPos CCSraDb::GetRowSize ( void  ) const
inline

◆ GetSpotGroups()

void CCSraDb::GetSpotGroups ( TSpotGroups spot_groups)
inline

◆ MakeSraIdPart()

string CCSraDb::MakeSraIdPart ( EPathInIdType  path_in_id_type,
const string dir_path,
const string csra_file 
)
static

The documentation for this class was generated from the following files:
Modified on Sat Mar 02 10:54:02 2024 by modify_doxy.py rev. 669887