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CCSraRefSeqIterator Class Reference

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

+ Inheritance diagram for CCSraRefSeqIterator:
+ Collaboration diagram for CCSraRefSeqIterator:

Public Types

enum  EByName { eByName }
 
enum  ELoadData { eLoadData , eOmitData }
 
typedef list< CRef< CSeq_literal > > TLiterals
 
typedef CRange< TSeqPosTRange
 
- 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

 CCSraRefSeqIterator (void)
 
 CCSraRefSeqIterator (const CCSraDb &csra_db, CCSraDb_Impl::TRefInfoList::const_iterator iter)
 
 CCSraRefSeqIterator (const CCSraDb &csra_db)
 
 CCSraRefSeqIterator (const CCSraDb &csra_db, const string &seq_id)
 
 CCSraRefSeqIterator (const CCSraDb &csra_db, const string &name, EByName)
 
 CCSraRefSeqIterator (const CCSraDb &csra_db, const CSeq_id_Handle &seq_id)
 
bool operator! (void) const
 
 operator const void * (void) const
 
const CCSraDb_Impl::SRefInfoGetInfo (void) const
 
const CCSraDb_Impl::SRefInfooperator* (void) const
 
const CCSraDb_Impl::SRefInfooperator-> (void) const
 
CCSraRefSeqIteratoroperator++ (void)
 
const stringGetRefSeqId (void) const
 
CRef< CSeq_idGetRefSeq_id (void) const
 
const CSeq_id_HandleGetRefSeq_id_Handle (void) const
 
const CBioseq::TIdGetRefSeq_ids (void) const
 
bool IsCircular (void) const
 
TSeqPos GetSeqLength (void) const
 
size_t GetRowAlignCount (TVDBRowId row) const
 
size_t GetAlignCountAtPos (TSeqPos pos, TAlignType type=fAnyAlign) const
 
CRef< CSeq_graphGetCoverageGraph (void) const
 
CRef< CSeq_annotGetCoverageAnnot (void) const
 
CRef< CSeq_annotGetCoverageAnnot (const string &annot_name) const
 
CRef< CSeq_annotGetSeq_annot (void) const
 
CRef< CSeq_annotGetSeq_annot (const string &annot_name) const
 
CRef< CBioseqGetRefBioseq (ELoadData load=eLoadData) const
 
void GetRefLiterals (TLiterals &literals, TRange range, ELoadData load=eLoadData) const
 
const vector< TSeqPos > & GetAlnOverStarts (void) const
 
TSeqPos GetAlnOverToOpen (TRange range) const
 
Uint8 GetEstimatedNumberOfAlignments (void) const
 

Protected Member Functions

CRef< CSeq_annotx_GetSeq_annot (const string *annot_name) const
 
CCSraDb_ImplGetDb (void) const
 

Static Protected Member Functions

static CRef< CSeq_annotMakeSeq_annot (const string &annot_name)
 

Private Attributes

CCSraDb m_Db
 
CCSraDb_Impl::TRefInfoList::const_iterator m_Iter
 

Friends

class CCSraAlignIterator
 

Detailed Description

Definition at line 269 of file csraread.hpp.

Member Typedef Documentation

◆ TLiterals

Definition at line 345 of file csraread.hpp.

◆ TRange

Definition at line 346 of file csraread.hpp.

Member Enumeration Documentation

◆ EByName

Enumerator
eByName 

Definition at line 284 of file csraread.hpp.

◆ ELoadData

Enumerator
eLoadData 
eOmitData 

Definition at line 340 of file csraread.hpp.

Constructor & Destructor Documentation

◆ CCSraRefSeqIterator() [1/6]

CCSraRefSeqIterator::CCSraRefSeqIterator ( void  )
inline

Definition at line 272 of file csraread.hpp.

◆ CCSraRefSeqIterator() [2/6]

CCSraRefSeqIterator::CCSraRefSeqIterator ( const CCSraDb csra_db,
CCSraDb_Impl::TRefInfoList::const_iterator  iter 
)
inline

Definition at line 275 of file csraread.hpp.

◆ CCSraRefSeqIterator() [3/6]

CCSraRefSeqIterator::CCSraRefSeqIterator ( const CCSraDb csra_db)
explicit

Definition at line 607 of file csraread.cpp.

◆ CCSraRefSeqIterator() [4/6]

CCSraRefSeqIterator::CCSraRefSeqIterator ( const CCSraDb csra_db,
const string seq_id 
)

Definition at line 614 of file csraread.cpp.

References ERR_POST_X, CSeq_id_Handle::GetHandle(), m_Db, and m_Iter.

◆ CCSraRefSeqIterator() [5/6]

CCSraRefSeqIterator::CCSraRefSeqIterator ( const CCSraDb csra_db,
const string name,
EByName   
)

Definition at line 629 of file csraread.cpp.

References m_Db, and m_Iter.

◆ CCSraRefSeqIterator() [6/6]

CCSraRefSeqIterator::CCSraRefSeqIterator ( const CCSraDb csra_db,
const CSeq_id_Handle seq_id 
)

Definition at line 642 of file csraread.cpp.

References m_Db, and m_Iter.

Member Function Documentation

◆ GetAlignCountAtPos()

size_t CCSraRefSeqIterator::GetAlignCountAtPos ( TSeqPos  pos,
TAlignType  type = fAnyAlign 
) const

◆ GetAlnOverStarts()

const vector< TSeqPos > & CCSraRefSeqIterator::GetAlnOverStarts ( void  ) const

◆ GetAlnOverToOpen()

TSeqPos CCSraRefSeqIterator::GetAlnOverToOpen ( TRange  range) const

◆ GetCoverageAnnot() [1/2]

CRef< CSeq_annot > CCSraRefSeqIterator::GetCoverageAnnot ( const string annot_name) const

Definition at line 756 of file csraread.cpp.

References GetCoverageGraph(), GetSeq_annot(), and CSeq_annot_Base::SetData().

◆ GetCoverageAnnot() [2/2]

CRef< CSeq_annot > CCSraRefSeqIterator::GetCoverageAnnot ( void  ) const

Definition at line 748 of file csraread.cpp.

References GetCoverageGraph(), GetSeq_annot(), and CSeq_annot_Base::SetData().

Referenced by CCSRARefSeqInfo::LoadRanges().

◆ GetCoverageGraph()

CRef< CSeq_graph > CCSraRefSeqIterator::GetCoverageGraph ( void  ) const

◆ GetDb()

CCSraDb_Impl& CCSraRefSeqIterator::GetDb ( void  ) const
inlineprotected

◆ GetEstimatedNumberOfAlignments()

Uint8 CCSraRefSeqIterator::GetEstimatedNumberOfAlignments ( void  ) const

◆ GetInfo()

const CCSraDb_Impl::SRefInfo & CCSraRefSeqIterator::GetInfo ( void  ) const

◆ GetRefBioseq()

CRef< CBioseq > CCSraRefSeqIterator::GetRefBioseq ( ELoadData  load = eLoadData) const

◆ GetRefLiterals()

void CCSraRefSeqIterator::GetRefLiterals ( TLiterals literals,
TRange  range,
ELoadData  load = eLoadData 
) const

◆ GetRefSeq_id()

CRef<CSeq_id> CCSraRefSeqIterator::GetRefSeq_id ( void  ) const
inline

Definition at line 314 of file csraread.hpp.

References m_Iter.

Referenced by CCSraAlignIterator::GetMatchAlign().

◆ GetRefSeq_id_Handle()

const CSeq_id_Handle& CCSraRefSeqIterator::GetRefSeq_id_Handle ( void  ) const
inline

Definition at line 317 of file csraread.hpp.

References m_Iter.

Referenced by CCSRAFileInfo::IsValidReadId().

◆ GetRefSeq_ids()

const CBioseq::TId& CCSraRefSeqIterator::GetRefSeq_ids ( void  ) const
inline

Definition at line 320 of file csraread.hpp.

References m_Iter.

Referenced by GetRefBioseq().

◆ GetRefSeqId()

const string& CCSraRefSeqIterator::GetRefSeqId ( void  ) const
inline

Definition at line 311 of file csraread.hpp.

References m_Iter.

◆ GetRowAlignCount()

size_t CCSraRefSeqIterator::GetRowAlignCount ( TVDBRowId  row) const

Definition at line 680 of file csraread.cpp.

References SCSraDb_Defs::fPrimaryAlign, GetAlignCountAtPos(), GetDb(), and GetInfo().

◆ GetSeq_annot() [1/2]

CRef< CSeq_annot > CCSraRefSeqIterator::GetSeq_annot ( const string annot_name) const
inline

Definition at line 749 of file csraread.hpp.

References x_GetSeq_annot().

◆ GetSeq_annot() [2/2]

CRef< CSeq_annot > CCSraRefSeqIterator::GetSeq_annot ( void  ) const
inline

Definition at line 757 of file csraread.hpp.

References x_GetSeq_annot().

Referenced by GetCoverageAnnot().

◆ GetSeqLength()

TSeqPos CCSraRefSeqIterator::GetSeqLength ( void  ) const

◆ IsCircular()

bool CCSraRefSeqIterator::IsCircular ( void  ) const

Definition at line 664 of file csraread.cpp.

References GetInfo(), and CCSraDb_Impl::SRefInfo::m_Circular.

◆ MakeSeq_annot()

CRef< CSeq_annot > CCSraRefSeqIterator::MakeSeq_annot ( const string annot_name)
staticprotected

◆ operator const void *()

CCSraRefSeqIterator::operator const void * ( void  ) const
inline

Definition at line 294 of file csraread.hpp.

◆ operator!()

bool CCSraRefSeqIterator::operator! ( void  ) const
inline

Definition at line 291 of file csraread.hpp.

References m_Db, and m_Iter.

◆ operator*()

const CCSraDb_Impl::SRefInfo& CCSraRefSeqIterator::operator* ( void  ) const
inline

Definition at line 299 of file csraread.hpp.

References GetInfo().

◆ operator++()

CCSraRefSeqIterator& CCSraRefSeqIterator::operator++ ( void  )
inline

Definition at line 306 of file csraread.hpp.

References m_Iter.

◆ operator->()

const CCSraDb_Impl::SRefInfo* CCSraRefSeqIterator::operator-> ( void  ) const
inline

Definition at line 302 of file csraread.hpp.

References GetInfo().

◆ x_GetSeq_annot()

CRef< CSeq_annot > CCSraRefSeqIterator::x_GetSeq_annot ( const string annot_name) const
protected

Friends And Related Function Documentation

◆ CCSraAlignIterator

friend class CCSraAlignIterator
friend

Definition at line 362 of file csraread.hpp.

Member Data Documentation

◆ m_Db

CCSraDb CCSraRefSeqIterator::m_Db
private

◆ m_Iter

CCSraDb_Impl::TRefInfoList::const_iterator CCSraRefSeqIterator::m_Iter
private

The documentation for this class was generated from the following files:
Modified on Tue Feb 27 05:50:21 2024 by modify_doxy.py rev. 669887