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CBamRefSeqIterator Class Reference

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#include <sra/readers/bam/bamread.hpp>

+ Collaboration diagram for CBamRefSeqIterator:

Classes

struct  SAADBImpl
 

Public Member Functions

 CBamRefSeqIterator ()
 
 CBamRefSeqIterator (const CBamDb &bam_db)
 
 CBamRefSeqIterator (const CBamRefSeqIterator &iter)
 
CBamRefSeqIteratoroperator= (const CBamRefSeqIterator &iter)
 
 DECLARE_OPERATOR_BOOL (m_AADBImpl||m_RawDB)
 
IIdMapperGetIdMapper (void) const
 
CBamRefSeqIteratoroperator++ (void)
 
CTempString GetRefSeqId (void) const
 
CRef< CSeq_idGetRefSeq_id (void) const
 
TSeqPos GetLength (void) const
 

Private Types

typedef rc_t(* TGetString) (const AlignAccessRefSeqEnumerator *self, char *buffer, size_t bsize, size_t *size)
 

Private Member Functions

void x_AllocBuffers (void)
 
void x_InvalidateBuffers (void)
 
void x_CheckValid (void) const
 
bool x_CheckRC (CBamString &buf, rc_t rc, size_t size, const char *msg) const
 
void x_GetString (CBamString &buf, const char *msg, TGetString func) const
 

Private Attributes

const CBamDbm_DB
 
CRef< SAADBImplm_AADBImpl
 
CRef< CObjectFor< CBamRawDb > > m_RawDB
 
size_t m_RefIndex
 
CRef< CSeq_idm_CachedRefSeq_id
 

Detailed Description

Definition at line 615 of file bamread.hpp.

Member Typedef Documentation

◆ TGetString

typedef rc_t(* CBamRefSeqIterator::TGetString) (const AlignAccessRefSeqEnumerator *self, char *buffer, size_t bsize, size_t *size)
private

Definition at line 639 of file bamread.hpp.

Constructor & Destructor Documentation

◆ CBamRefSeqIterator() [1/3]

CBamRefSeqIterator::CBamRefSeqIterator ( )

Definition at line 1656 of file bamread.cpp.

◆ CBamRefSeqIterator() [2/3]

CBamRefSeqIterator::CBamRefSeqIterator ( const CBamDb bam_db)
explicit

◆ CBamRefSeqIterator() [3/3]

CBamRefSeqIterator::CBamRefSeqIterator ( const CBamRefSeqIterator iter)

Definition at line 1706 of file bamread.cpp.

Member Function Documentation

◆ DECLARE_OPERATOR_BOOL()

CBamRefSeqIterator::DECLARE_OPERATOR_BOOL ( m_AADBImpl||  m_RawDB)

◆ GetIdMapper()

IIdMapper* CBamRefSeqIterator::GetIdMapper ( void  ) const
inline

Definition at line 626 of file bamread.hpp.

References CBamDb::GetIdMapper(), and m_DB.

◆ GetLength()

TSeqPos CBamRefSeqIterator::GetLength ( void  ) const

◆ GetRefSeq_id()

CRef< CSeq_id > CBamRefSeqIterator::GetRefSeq_id ( void  ) const

Definition at line 1820 of file bamread.cpp.

References CBamDb::GetRefSeq_id(), GetRefSeqId(), m_CachedRefSeq_id, and m_DB.

◆ GetRefSeqId()

CTempString CBamRefSeqIterator::GetRefSeqId ( void  ) const

Definition at line 1807 of file bamread.cpp.

References CObjectFor< T >::GetData(), m_AADBImpl, m_RawDB, m_RefIndex, and x_GetString().

Referenced by GetRefSeq_id().

◆ operator++()

CBamRefSeqIterator & CBamRefSeqIterator::operator++ ( void  )

◆ operator=()

CBamRefSeqIterator & CBamRefSeqIterator::operator= ( const CBamRefSeqIterator iter)

◆ x_AllocBuffers()

void CBamRefSeqIterator::x_AllocBuffers ( void  )
private

Definition at line 1694 of file bamread.cpp.

References m_AADBImpl.

Referenced by CBamRefSeqIterator().

◆ x_CheckRC()

bool CBamRefSeqIterator::x_CheckRC ( CBamString buf,
rc_t  rc,
size_t  size,
const char *  msg 
) const
private

Definition at line 1760 of file bamread.cpp.

References _ASSERT, buf, ERR_POST, NCBI_THROW3, and ncbi::grid::netcache::search::fields::size.

Referenced by x_GetString().

◆ x_CheckValid()

void CBamRefSeqIterator::x_CheckValid ( void  ) const
private

Definition at line 1725 of file bamread.cpp.

References NCBI_THROW.

Referenced by x_GetString().

◆ x_GetString()

void CBamRefSeqIterator::x_GetString ( CBamString buf,
const char *  msg,
TGetString  func 
) const
private

Definition at line 1793 of file bamread.cpp.

References buf, m_AADBImpl, ncbi::grid::netcache::search::fields::size, x_CheckRC(), and x_CheckValid().

Referenced by GetRefSeqId().

◆ x_InvalidateBuffers()

void CBamRefSeqIterator::x_InvalidateBuffers ( void  )
private

Definition at line 1700 of file bamread.cpp.

References m_AADBImpl.

Referenced by operator++().

Member Data Documentation

◆ m_AADBImpl

CRef<SAADBImpl> CBamRefSeqIterator::m_AADBImpl
private

◆ m_CachedRefSeq_id

CRef<CSeq_id> CBamRefSeqIterator::m_CachedRefSeq_id
mutableprivate

Definition at line 661 of file bamread.hpp.

Referenced by GetRefSeq_id(), operator++(), and operator=().

◆ m_DB

const CBamDb* CBamRefSeqIterator::m_DB
private

Definition at line 657 of file bamread.hpp.

Referenced by GetIdMapper(), GetRefSeq_id(), and operator=().

◆ m_RawDB

CRef< CObjectFor<CBamRawDb> > CBamRefSeqIterator::m_RawDB
private

Definition at line 659 of file bamread.hpp.

Referenced by CBamRefSeqIterator(), GetLength(), GetRefSeqId(), operator++(), and operator=().

◆ m_RefIndex

size_t CBamRefSeqIterator::m_RefIndex
private

Definition at line 660 of file bamread.hpp.

Referenced by CBamRefSeqIterator(), GetLength(), GetRefSeqId(), operator++(), and operator=().


The documentation for this class was generated from the following files:
Modified on Tue Apr 16 20:14:38 2024 by modify_doxy.py rev. 669887