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Public Member Functions | Protected Member Functions | Private Attributes | List of all members
CSraRun Class Reference

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

+ Inheritance diagram for CSraRun:
+ Collaboration diagram for CSraRun:

Public Member Functions

 CSraRun (void)
 
 CSraRun (CSraMgr &mgr, const string &acc)
 
void Init (CSraMgr &mgr, const string &acc)
 
const stringGetAccession (void) const
 
CSeq_inst::TMol GetSequenceType (spotid_t spot_id, uint8_t read_id) const
 
TSeqPos GetSequenceLength (spotid_t spot_id, uint8_t read_id) const
 
CRef< CSeq_entryGetSpotEntry (spotid_t spot_id) const
 
- Public Member Functions inherited from CSraRef< const SRATable >
 CSraRef (void)
 
 CSraRef (const TSelf &ref)
 
 CSraRef (TSelf &&ref)
 Copy constructor from an existing CRef object,. More...
 
TSelfoperator= (const TSelf &ref)
 
TSelfoperator= (TSelf &&ref)
 
 ~CSraRef (void)
 
void Release (void)
 
TObjectGetPointer (void) const
 
 operator TObject * (void) const
 
TObjectoperator-> (void) const
 
TObjectoperator* (void) const
 

Protected Member Functions

void x_DoInit (CSraMgr &mgr, const string &acc)
 
- Protected Member Functions inherited from CSraRef< const SRATable >
 CSraRef (TPointer ptr)
 
TObject ** x_InitPtr (void)
 

Private Attributes

string m_Acc
 
bool m_Trim
 
CSraColumn m_Name
 
CSraColumn m_Read
 
CSraColumn m_Qual
 
CSraColumn m_SDesc
 
CSraColumn m_RDesc
 
CSraColumn m_TrimStart
 

Additional Inherited Members

- Public Types inherited from CSraRef< const SRATable >
typedef const SRATable TObject
 
typedef TObjectTPointer
 
- Protected Types inherited from CSraRef< const SRATable >
typedef CSraRef< const SRATable > TSelf
 
typedef CSraRefTraits< const SRATable > TTraits
 
- Static Protected Member Functions inherited from CSraRef< const SRATable >
static TObjects_AddRef (const TSelf &ref)
 

Detailed Description

Definition at line 155 of file sraread.hpp.

Constructor & Destructor Documentation

◆ CSraRun() [1/2]

CSraRun::CSraRun ( void  )
inline

Definition at line 159 of file sraread.hpp.

◆ CSraRun() [2/2]

CSraRun::CSraRun ( CSraMgr mgr,
const string acc 
)
inline

Definition at line 162 of file sraread.hpp.

References Init().

Member Function Documentation

◆ GetAccession()

const string& CSraRun::GetAccession ( void  ) const
inline

◆ GetSequenceLength()

TSeqPos CSraRun::GetSequenceLength ( spotid_t  spot_id,
uint8_t  read_id 
) const

◆ GetSequenceType()

CSeq_inst::TMol CSraRun::GetSequenceType ( spotid_t  spot_id,
uint8_t  read_id 
) const

◆ GetSpotEntry()

CRef< CSeq_entry > CSraRun::GetSpotEntry ( spotid_t  spot_id) const

◆ Init()

void CSraRun::Init ( CSraMgr mgr,
const string acc 
)

◆ x_DoInit()

void CSraRun::x_DoInit ( CSraMgr mgr,
const string acc 
)
protected

Member Data Documentation

◆ m_Acc

string CSraRun::m_Acc
private

Definition at line 182 of file sraread.hpp.

Referenced by GetAccession(), and Init().

◆ m_Name

CSraColumn CSraRun::m_Name
private

Definition at line 184 of file sraread.hpp.

Referenced by GetSpotEntry(), and x_DoInit().

◆ m_Qual

CSraColumn CSraRun::m_Qual
private

Definition at line 186 of file sraread.hpp.

Referenced by GetSpotEntry(), and x_DoInit().

◆ m_RDesc

CSraColumn CSraRun::m_RDesc
private

Definition at line 188 of file sraread.hpp.

Referenced by GetSequenceLength(), GetSpotEntry(), and x_DoInit().

◆ m_Read

CSraColumn CSraRun::m_Read
private

Definition at line 185 of file sraread.hpp.

Referenced by GetSpotEntry(), and x_DoInit().

◆ m_SDesc

CSraColumn CSraRun::m_SDesc
private

Definition at line 187 of file sraread.hpp.

Referenced by GetSequenceLength(), GetSequenceType(), GetSpotEntry(), and x_DoInit().

◆ m_Trim

bool CSraRun::m_Trim
private

Definition at line 183 of file sraread.hpp.

Referenced by GetSequenceLength(), GetSpotEntry(), and Init().

◆ m_TrimStart

CSraColumn CSraRun::m_TrimStart
private

Definition at line 189 of file sraread.hpp.

Referenced by GetSequenceLength(), GetSpotEntry(), and x_DoInit().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:03:36 2024 by modify_doxy.py rev. 669887