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CCSraAlignIterator Class Reference

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

+ Inheritance diagram for CCSraAlignIterator:
+ Collaboration diagram for CCSraAlignIterator:

Classes

struct  SCreateCache
 

Public Types

enum  ESearchMode { eSearchByOverlap , eSearchByStart }
 
- 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

 CCSraAlignIterator (void)
 
 CCSraAlignIterator (const CCSraDb &csra_db, const string &ref_id, TSeqPos ref_pos, TSeqPos window=0, ESearchMode search_mode=eSearchByOverlap, TAlignType align_type=fAnyAlign)
 
 CCSraAlignIterator (const CCSraDb &csra_db, const CSeq_id_Handle &ref_id, TSeqPos ref_pos, TSeqPos window, ESearchMode search_mode, TAlignType align_type=fAnyAlign)
 
 CCSraAlignIterator (const CCSraDb &csra_db, const CSeq_id_Handle &ref_id, TSeqPos ref_pos, TSeqPos window=0, TAlignType align_type=fAnyAlign)
 
 ~CCSraAlignIterator (void)
 
void Reset (void)
 
 CCSraAlignIterator (const CCSraAlignIterator &iter)
 
CCSraAlignIteratoroperator= (const CCSraAlignIterator &iter)
 
void Select (TSeqPos ref_pos, TSeqPos window=0, ESearchMode search_mode=eSearchByOverlap, TAlignType align_type=fAnyAlign)
 
 operator const void * (void) const
 
bool operator! (void) const
 
CCSraAlignIteratoroperator++ (void)
 
TVDBRowId GetAlignmentId (void) const
 
bool IsSecondary (void) const
 
CTempString GetRefSeqId (void) const
 
TSeqPos GetRefSeqPos (void) const
 
TSeqPos GetRefSeqLen (void) const
 
bool GetRefMinusStrand (void) const
 
int GetMapQuality (void) const
 
TVDBRowId GetShortId1 (void) const
 
INSDC_coord_one GetShortId2 (void) const
 
TSeqPos GetShortPos (void) const
 
TSeqPos GetShortLen (void) const
 
CTempString GetSpotGroup (void) const
 
bool IsSetName (void) const
 
CTempString GetName (void) const
 
INSDC_read_filter GetReadFilter (void) const
 
CTempString GetCIGAR (void) const
 
CTempString GetCIGARLong (void) const
 
CTempString GetMismatchRead (void) const
 
CTempString GetMismatchRaw (void) const
 
void MakeFullMismatch (string &str, CTempString cigar, CTempString mismatch) const
 
CRef< CSeq_idGetRefSeq_id (void) const
 
CRef< CSeq_idGetShortSeq_id (void) const
 
CRef< CSeq_idGetMateShortSeq_id (void) const
 
CRef< CBioseqGetShortBioseq (void) const
 
CRef< CSeq_alignGetMatchAlign (void) const
 
CRef< CSeq_graphGetQualityGraph (void) const
 
CRef< CSeq_annotGetEmptyMatchAnnot (void) const
 
CRef< CSeq_annotGetEmptyMatchAnnot (const string &annot_name) const
 
CRef< CSeq_annotGetMatchAnnot (void) const
 
CRef< CSeq_annotGetMatchAnnot (const string &annot_name) const
 
CRef< CSeq_annotGetQualityGraphAnnot (void) const
 
CRef< CSeq_annotGetQualityGraphAnnot (const string &annot_name) const
 
CRef< CSeq_entryGetMatchEntry (void) const
 
CRef< CSeq_entryGetMatchEntry (const string &annot_name) const
 
CRef< CSeq_annotGetSeq_annot (void) const
 
CRef< CSeq_annotGetSeq_annot (const string &annot_name) const
 

Static Public Member Functions

static CRef< CSeq_annotMakeSeq_annot (const string &annot_name)
 
static CRef< CSeq_annotMakeEmptyMatchAnnot (const string &annot_name)
 
static CRef< CAnnotdescMakeMatchAnnotIndicator (void)
 

Protected Types

typedef CRef< CObject_idTObjectIdCache
 
typedef map< CTempString, CRef< CUser_field > > TUserFieldCache
 

Protected Member Functions

CCSraDb_ImplGetDb (void) const
 
 CCSraAlignIterator (const CCSraDb &csra_db, TAlignType align_type, TVDBRowId align_row)
 
void x_Settle (void)
 
void x_Next (void)
 
CRef< CSeq_entryx_GetMatchEntry (const string *annot_name) const
 
CRef< CSeq_annotx_GetEmptyMatchAnnot (const string *annot_name) const
 
CRef< CSeq_annotx_GetMatchAnnot (const string *annot_name) const
 
CRef< CSeq_annotx_GetQualityGraphAnnot (const string *annot_name) const
 
CRef< CSeq_annotx_GetSeq_annot (const string *annot_name) const
 
CRef< CUser_objectx_GetSecondaryIndicator (void) const
 
CObject_idx_GetObject_id (const char *name, TObjectIdCache &cache) const
 
CUser_fieldx_AddField (CUser_object &obj, const char *name, TObjectIdCache &cache) const
 
void x_AddField (CUser_object &obj, const char *name, CTempString value, TObjectIdCache &cache) const
 
void x_AddField (CUser_object &obj, const char *name, int value, TObjectIdCache &cache) const
 
void x_AddField (CUser_object &obj, const char *name, CTempString value, TObjectIdCache &id_cache, TUserFieldCache &cache, size_t max_value_length, size_t max_cache_size) const
 

Private Member Functions

SCreateCachex_GetCreateCache (void) const
 

Private Attributes

CCSraRefSeqIterator m_RefIter
 
CRef< CCSraDb_Impl::SRefTableCursorm_Ref
 
CRef< CCSraDb_Impl::SAlnTableCursorm_Aln
 
rc_t m_Error
 
TSeqPos m_ArgRefPos
 
TSeqPos m_ArgRefLast
 
TSeqPos m_CurRefPos
 
TSeqPos m_CurRefLen
 
TVDBRowId m_RefRowNext
 
TVDBRowId m_RefRowLast
 
bool m_AlnRowIsSecondary
 
ESearchMode m_SearchMode
 
TAlignType m_AlignType
 
const TVDBRowIdm_AlnRowCur
 
const TVDBRowIdm_AlnRowEnd
 
AutoPtr< SCreateCachem_CreateCache
 

Friends

class CCSraShortReadIterator
 

Detailed Description

Definition at line 378 of file csraread.hpp.

Member Typedef Documentation

◆ TObjectIdCache

Definition at line 518 of file csraread.hpp.

◆ TUserFieldCache

Definition at line 519 of file csraread.hpp.

Member Enumeration Documentation

◆ ESearchMode

Enumerator
eSearchByOverlap 
eSearchByStart 

Definition at line 383 of file csraread.hpp.

Constructor & Destructor Documentation

◆ CCSraAlignIterator() [1/6]

CCSraAlignIterator::CCSraAlignIterator ( void  )

Definition at line 1031 of file csraread.cpp.

◆ CCSraAlignIterator() [2/6]

CCSraAlignIterator::CCSraAlignIterator ( const CCSraDb csra_db,
const string ref_id,
TSeqPos  ref_pos,
TSeqPos  window = 0,
ESearchMode  search_mode = eSearchByOverlap,
TAlignType  align_type = fAnyAlign 
)

Definition at line 1037 of file csraread.cpp.

References Select().

◆ CCSraAlignIterator() [3/6]

CCSraAlignIterator::CCSraAlignIterator ( const CCSraDb csra_db,
const CSeq_id_Handle ref_id,
TSeqPos  ref_pos,
TSeqPos  window,
ESearchMode  search_mode,
TAlignType  align_type = fAnyAlign 
)

Definition at line 1053 of file csraread.cpp.

References Select().

◆ CCSraAlignIterator() [4/6]

CCSraAlignIterator::CCSraAlignIterator ( const CCSraDb csra_db,
const CSeq_id_Handle ref_id,
TSeqPos  ref_pos,
TSeqPos  window = 0,
TAlignType  align_type = fAnyAlign 
)

Definition at line 1069 of file csraread.cpp.

References eSearchByOverlap, and Select().

◆ ~CCSraAlignIterator()

CCSraAlignIterator::~CCSraAlignIterator ( void  )

Definition at line 1116 of file csraread.cpp.

References Reset().

◆ CCSraAlignIterator() [5/6]

CCSraAlignIterator::CCSraAlignIterator ( const CCSraAlignIterator iter)

Definition at line 995 of file csraread.cpp.

◆ CCSraAlignIterator() [6/6]

CCSraAlignIterator::CCSraAlignIterator ( const CCSraDb csra_db,
TAlignType  align_type,
TVDBRowId  align_row 
)
protected

Member Function Documentation

◆ GetAlignmentId()

TVDBRowId CCSraAlignIterator::GetAlignmentId ( void  ) const

Definition at line 1245 of file csraread.cpp.

References m_AlnRowCur.

◆ GetCIGAR()

CTempString CCSraAlignIterator::GetCIGAR ( void  ) const

Definition at line 1290 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign().

◆ GetCIGARLong()

CTempString CCSraAlignIterator::GetCIGARLong ( void  ) const

Definition at line 1296 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign(), and CCSRARefSeqInfo::LoadAnnotPileupChunk().

◆ GetDb()

CCSraDb_Impl& CCSraAlignIterator::GetDb ( void  ) const
inlineprotected

◆ GetEmptyMatchAnnot() [1/2]

CRef< CSeq_annot > CCSraAlignIterator::GetEmptyMatchAnnot ( const string annot_name) const
inline

Definition at line 784 of file csraread.hpp.

References x_GetEmptyMatchAnnot().

◆ GetEmptyMatchAnnot() [2/2]

CRef< CSeq_annot > CCSraAlignIterator::GetEmptyMatchAnnot ( void  ) const
inline

Definition at line 792 of file csraread.hpp.

References x_GetEmptyMatchAnnot().

◆ GetMapQuality()

int CCSraAlignIterator::GetMapQuality ( void  ) const

◆ GetMatchAlign()

CRef< CSeq_align > CCSraAlignIterator::GetMatchAlign ( void  ) const

Definition at line 1488 of file csraread.cpp.

References _ASSERT, CSeq_id::AsFastaString(), CTempString::data(), CCSraRefSeqIterator::eByName, CVDBValue::empty(), eNa_strand_minus, eNa_strand_plus, CTempString::end(), CSeq_align_Base::eType_diags, GetCIGAR(), GetCIGARLong(), GetDb(), GetMismatchRaw(), GetReadFilter(), GetRefMinusStrand(), CCSraRefSeqIterator::GetRefSeq_id(), GetRefSeq_id(), GetRefSeqPos(), GetShortLen(), GetShortPos(), GetShortSeq_id(), i, IsSecondary(), kInvalidSeqPos, len, m_Aln, m_AlnRowCur, CCSraRefSeqIterator::m_Db, CCSraDb_Impl::SRefInfo::m_Name, CCSraAlignIterator::SCreateCache::m_ObjectIdCIGAR, CCSraAlignIterator::SCreateCache::m_ObjectIdLcl, CCSraAlignIterator::SCreateCache::m_ObjectIdMateRead, CCSraAlignIterator::SCreateCache::m_ObjectIdMISMATCH, CCSraAlignIterator::SCreateCache::m_ObjectIdRefId, CCSraAlignIterator::SCreateCache::m_ObjectIdRefPos, CCSraAlignIterator::SCreateCache::m_ObjectIdTracebacks, CCSraAlignIterator::SCreateCache::m_ReadFilterIndicator, m_RefIter, CCSraAlignIterator::SCreateCache::m_UserFieldCacheCigar, CCSraAlignIterator::SCreateCache::m_UserFieldCacheMismatch, MakeFullMismatch(), NCBI_THROW_FMT, s_GetCigarInAlignExt(), s_GetExplicitMateInfoParam(), s_GetReadFilterInAlignExt(), CUser_field_Base::SetData(), CUser_object_Base::SetData(), CSeq_align_Base::SetExt(), CDense_seg_Base::SetIds(), CUser_field_Base::SetLabel(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CCSraDb_Impl::SetShortReadId(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CUser_object_Base::SetType(), CSeq_align_Base::SetType(), CVDBValue::size(), value, x_AddField(), x_GetCreateCache(), x_GetObject_id(), and x_GetSecondaryIndicator().

Referenced by CCSRARefSeqInfo::LoadAnnotAlignChunk(), and x_GetMatchAnnot().

◆ GetMatchAnnot() [1/2]

CRef< CSeq_annot > CCSraAlignIterator::GetMatchAnnot ( const string annot_name) const
inline

Definition at line 800 of file csraread.hpp.

References x_GetMatchAnnot().

◆ GetMatchAnnot() [2/2]

CRef< CSeq_annot > CCSraAlignIterator::GetMatchAnnot ( void  ) const
inline

Definition at line 808 of file csraread.hpp.

References x_GetMatchAnnot().

◆ GetMatchEntry() [1/2]

CRef< CSeq_entry > CCSraAlignIterator::GetMatchEntry ( const string annot_name) const
inline

Definition at line 768 of file csraread.hpp.

References x_GetMatchEntry().

◆ GetMatchEntry() [2/2]

CRef< CSeq_entry > CCSraAlignIterator::GetMatchEntry ( void  ) const
inline

Definition at line 776 of file csraread.hpp.

References x_GetMatchEntry().

◆ GetMateShortSeq_id()

CRef< CSeq_id > CCSraAlignIterator::GetMateShortSeq_id ( void  ) const

Definition at line 1353 of file csraread.cpp.

References GetDb(), m_Aln, m_AlnRowCur, CCSraDb_Impl::MakeShortReadId(), and value.

◆ GetMismatchRaw()

CTempString CCSraAlignIterator::GetMismatchRaw ( void  ) const

Definition at line 1308 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign().

◆ GetMismatchRead()

CTempString CCSraAlignIterator::GetMismatchRead ( void  ) const

Definition at line 1302 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by CCSRARefSeqInfo::LoadAnnotPileupChunk().

◆ GetName()

CTempString CCSraAlignIterator::GetName ( void  ) const

Definition at line 1275 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetShortBioseq(), and IsSetName().

◆ GetQualityGraph()

CRef< CSeq_graph > CCSraAlignIterator::GetQualityGraph ( void  ) const

◆ GetQualityGraphAnnot() [1/2]

CRef< CSeq_annot > CCSraAlignIterator::GetQualityGraphAnnot ( const string annot_name) const
inline

Definition at line 816 of file csraread.hpp.

References x_GetQualityGraphAnnot().

◆ GetQualityGraphAnnot() [2/2]

CRef< CSeq_annot > CCSraAlignIterator::GetQualityGraphAnnot ( void  ) const
inline

Definition at line 824 of file csraread.hpp.

References x_GetQualityGraphAnnot().

◆ GetReadFilter()

INSDC_read_filter CCSraAlignIterator::GetReadFilter ( void  ) const

Definition at line 1281 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign().

◆ GetRefMinusStrand()

bool CCSraAlignIterator::GetRefMinusStrand ( void  ) const

Definition at line 1257 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign(), and GetQualityGraph().

◆ GetRefSeq_id()

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

◆ GetRefSeqId()

CTempString CCSraAlignIterator::GetRefSeqId ( void  ) const

Definition at line 1251 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

◆ GetRefSeqLen()

TSeqPos CCSraAlignIterator::GetRefSeqLen ( void  ) const
inline

Definition at line 439 of file csraread.hpp.

References m_CurRefLen.

◆ GetRefSeqPos()

TSeqPos CCSraAlignIterator::GetRefSeqPos ( void  ) const
inline

◆ GetSeq_annot() [1/2]

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

Definition at line 840 of file csraread.hpp.

References x_GetSeq_annot().

◆ GetSeq_annot() [2/2]

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

Definition at line 848 of file csraread.hpp.

References x_GetSeq_annot().

◆ GetShortBioseq()

CRef< CBioseq > CCSraAlignIterator::GetShortBioseq ( void  ) const

◆ GetShortId1()

TVDBRowId CCSraAlignIterator::GetShortId1 ( void  ) const

Definition at line 1314 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetShortSeq_id().

◆ GetShortId2()

INSDC_coord_one CCSraAlignIterator::GetShortId2 ( void  ) const

Definition at line 1320 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetShortSeq_id().

◆ GetShortLen()

TSeqPos CCSraAlignIterator::GetShortLen ( void  ) const

Definition at line 1379 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign(), and GetQualityGraph().

◆ GetShortPos()

TSeqPos CCSraAlignIterator::GetShortPos ( void  ) const

Definition at line 1365 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by GetMatchAlign(), and CCSRARefSeqInfo::LoadAnnotPileupChunk().

◆ GetShortSeq_id()

CRef< CSeq_id > CCSraAlignIterator::GetShortSeq_id ( void  ) const

◆ GetSpotGroup()

CTempString CCSraAlignIterator::GetSpotGroup ( void  ) const

Definition at line 1263 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

Referenced by SChunkAnnots::Select().

◆ IsSecondary()

bool CCSraAlignIterator::IsSecondary ( void  ) const
inline

Definition at line 431 of file csraread.hpp.

References m_AlnRowIsSecondary.

Referenced by GetMatchAlign().

◆ IsSetName()

bool CCSraAlignIterator::IsSetName ( void  ) const

Definition at line 1269 of file csraread.cpp.

References CTempString::empty(), GetName(), and m_Aln.

Referenced by GetShortBioseq().

◆ MakeEmptyMatchAnnot()

CRef< CSeq_annot > CCSraAlignIterator::MakeEmptyMatchAnnot ( const string annot_name)
static

◆ MakeFullMismatch()

void CCSraAlignIterator::MakeFullMismatch ( string str,
CTempString  cigar,
CTempString  mismatch 
) const

◆ MakeMatchAnnotIndicator()

CRef< CAnnotdesc > CCSraAlignIterator::MakeMatchAnnotIndicator ( void  )
static

◆ MakeSeq_annot()

CRef< CSeq_annot > CCSraAlignIterator::MakeSeq_annot ( const string annot_name)
inlinestatic

Definition at line 856 of file csraread.hpp.

References CCSraRefSeqIterator::MakeSeq_annot().

Referenced by SChunkAnnots::Create(), and MakeEmptyMatchAnnot().

◆ operator const void *()

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

Definition at line 417 of file csraread.hpp.

References m_Error.

◆ operator!()

bool CCSraAlignIterator::operator! ( void  ) const
inline

Definition at line 420 of file csraread.hpp.

References m_Error.

◆ operator++()

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

Definition at line 424 of file csraread.hpp.

References x_Next().

◆ operator=()

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

◆ Reset()

void CCSraAlignIterator::Reset ( void  )

◆ Select()

void CCSraAlignIterator::Select ( TSeqPos  ref_pos,
TSeqPos  window = 0,
ESearchMode  search_mode = eSearchByOverlap,
TAlignType  align_type = fAnyAlign 
)

◆ x_AddField() [1/4]

void CCSraAlignIterator::x_AddField ( CUser_object obj,
const char *  name,
CTempString  value,
TObjectIdCache cache 
) const
protected

Definition at line 1851 of file csraread.cpp.

References CUser_field_Base::SetData(), value, and x_AddField().

◆ x_AddField() [2/4]

void CCSraAlignIterator::x_AddField ( CUser_object obj,
const char *  name,
CTempString  value,
TObjectIdCache id_cache,
TUserFieldCache cache,
size_t  max_value_length,
size_t  max_cache_size 
) const
protected

◆ x_AddField() [3/4]

void CCSraAlignIterator::x_AddField ( CUser_object obj,
const char *  name,
int  value,
TObjectIdCache cache 
) const
protected

Definition at line 1860 of file csraread.cpp.

References CUser_field_Base::SetData(), value, and x_AddField().

◆ x_AddField() [4/4]

CUser_field & CCSraAlignIterator::x_AddField ( CUser_object obj,
const char *  name,
TObjectIdCache cache 
) const
protected

◆ x_GetCreateCache()

CCSraAlignIterator::SCreateCache & CCSraAlignIterator::x_GetCreateCache ( void  ) const
private

Definition at line 1479 of file csraread.cpp.

References m_CreateCache.

Referenced by GetMatchAlign(), x_GetEmptyMatchAnnot(), and x_GetSecondaryIndicator().

◆ x_GetEmptyMatchAnnot()

CRef< CSeq_annot > CCSraAlignIterator::x_GetEmptyMatchAnnot ( const string annot_name) const
protected

◆ x_GetMatchAnnot()

CRef< CSeq_annot > CCSraAlignIterator::x_GetMatchAnnot ( const string annot_name) const
protected

Definition at line 1789 of file csraread.cpp.

References GetMatchAlign(), CSeq_annot_Base::SetData(), and x_GetEmptyMatchAnnot().

Referenced by GetMatchAnnot(), and x_GetMatchEntry().

◆ x_GetMatchEntry()

CRef< CSeq_entry > CCSraAlignIterator::x_GetMatchEntry ( const string annot_name) const
protected

◆ x_GetObject_id()

CObject_id & CCSraAlignIterator::x_GetObject_id ( const char *  name,
TObjectIdCache cache 
) const
protected

Definition at line 1829 of file csraread.cpp.

References CObject_id_Base::SetStr().

Referenced by GetMatchAlign(), and x_AddField().

◆ x_GetQualityGraphAnnot()

CRef< CSeq_annot > CCSraAlignIterator::x_GetQualityGraphAnnot ( const string annot_name) const
protected

Definition at line 1798 of file csraread.cpp.

References GetQualityGraph(), CSeq_annot_Base::SetData(), and x_GetSeq_annot().

Referenced by GetQualityGraphAnnot().

◆ x_GetSecondaryIndicator()

CRef< CUser_object > CCSraAlignIterator::x_GetSecondaryIndicator ( void  ) const
protected

◆ x_GetSeq_annot()

CRef< CSeq_annot > CCSraAlignIterator::x_GetSeq_annot ( const string annot_name) const
inlineprotected

◆ x_Next()

void CCSraAlignIterator::x_Next ( void  )
inlineprotected

Definition at line 507 of file csraread.hpp.

References m_AlnRowCur, and x_Settle().

Referenced by operator++().

◆ x_Settle()

void CCSraAlignIterator::x_Settle ( void  )
protected

Friends And Related Function Documentation

◆ CCSraShortReadIterator

friend class CCSraShortReadIterator
friend

Definition at line 496 of file csraread.hpp.

Member Data Documentation

◆ m_AlignType

TAlignType CCSraAlignIterator::m_AlignType
private

Definition at line 546 of file csraread.hpp.

Referenced by operator=(), Reset(), Select(), and x_Settle().

◆ m_Aln

CRef<CCSraDb_Impl::SAlnTableCursor> CCSraAlignIterator::m_Aln
private

◆ m_AlnRowCur

const TVDBRowId* CCSraAlignIterator::m_AlnRowCur
private

◆ m_AlnRowEnd

const TVDBRowId* CCSraAlignIterator::m_AlnRowEnd
private

Definition at line 548 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator=(), Reset(), Select(), and x_Settle().

◆ m_AlnRowIsSecondary

bool CCSraAlignIterator::m_AlnRowIsSecondary
private

Definition at line 544 of file csraread.hpp.

Referenced by CCSraAlignIterator(), IsSecondary(), operator=(), Reset(), Select(), and x_Settle().

◆ m_ArgRefLast

TSeqPos CCSraAlignIterator::m_ArgRefLast
private

Definition at line 539 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator=(), Reset(), Select(), and x_Settle().

◆ m_ArgRefPos

TSeqPos CCSraAlignIterator::m_ArgRefPos
private

Definition at line 539 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator=(), Reset(), Select(), and x_Settle().

◆ m_CreateCache

AutoPtr<SCreateCache> CCSraAlignIterator::m_CreateCache
mutableprivate

Definition at line 565 of file csraread.hpp.

Referenced by x_GetCreateCache().

◆ m_CurRefLen

TSeqPos CCSraAlignIterator::m_CurRefLen
private

Definition at line 540 of file csraread.hpp.

Referenced by CCSraAlignIterator(), GetRefSeqLen(), operator=(), Reset(), and x_Settle().

◆ m_CurRefPos

TSeqPos CCSraAlignIterator::m_CurRefPos
private

Definition at line 540 of file csraread.hpp.

Referenced by CCSraAlignIterator(), GetRefSeqPos(), operator=(), Reset(), and x_Settle().

◆ m_Error

rc_t CCSraAlignIterator::m_Error
private

◆ m_Ref

CRef<CCSraDb_Impl::SRefTableCursor> CCSraAlignIterator::m_Ref
private

Definition at line 535 of file csraread.hpp.

Referenced by operator=(), Reset(), Select(), and x_Settle().

◆ m_RefIter

CCSraRefSeqIterator CCSraAlignIterator::m_RefIter
private

◆ m_RefRowLast

TVDBRowId CCSraAlignIterator::m_RefRowLast
private

Definition at line 543 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator=(), Reset(), Select(), and x_Settle().

◆ m_RefRowNext

TVDBRowId CCSraAlignIterator::m_RefRowNext
private

Definition at line 542 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator=(), Reset(), Select(), and x_Settle().

◆ m_SearchMode

ESearchMode CCSraAlignIterator::m_SearchMode
private

Definition at line 545 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator=(), Reset(), Select(), and x_Settle().


The documentation for this class was generated from the following files:
Modified on Mon Mar 04 05:13:45 2024 by modify_doxy.py rev. 669887