CCSraAlignIterator Class Reference

Search Toolkit Book for CCSraAlignIterator

#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)
CCSraAlignIterator &	operator= (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
CCSraAlignIterator &	operator++ (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_id >	GetRefSeq_id (void) const
CRef< CSeq_id >	GetShortSeq_id (void) const
CRef< CSeq_id >	GetMateShortSeq_id (void) const
CRef< CBioseq >	GetShortBioseq (void) const
CRef< CSeq_align >	GetMatchAlign (void) const
CRef< CSeq_graph >	GetQualityGraph (void) const
CRef< CSeq_annot >	GetEmptyMatchAnnot (void) const
CRef< CSeq_annot >	GetEmptyMatchAnnot (const string &annot_name) const
CRef< CSeq_annot >	GetMatchAnnot (void) const
CRef< CSeq_annot >	GetMatchAnnot (const string &annot_name) const
CRef< CSeq_annot >	GetQualityGraphAnnot (void) const
CRef< CSeq_annot >	GetQualityGraphAnnot (const string &annot_name) const
CRef< CSeq_entry >	GetMatchEntry (void) const
CRef< CSeq_entry >	GetMatchEntry (const string &annot_name) const
CRef< CSeq_annot >	GetSeq_annot (void) const
CRef< CSeq_annot >	GetSeq_annot (const string &annot_name) const

Static Public Member Functions
static CRef< CSeq_annot >	MakeSeq_annot (const string &annot_name)
static CRef< CSeq_annot >	MakeEmptyMatchAnnot (const string &annot_name)
static CRef< CAnnotdesc >	MakeMatchAnnotIndicator (void)

Protected Types
typedef CRef< CObject_id >	TObjectIdCache
typedef map< CTempString, CRef< CUser_field > >	TUserFieldCache

Protected Member Functions
CCSraDb_Impl &	GetDb (void) const
	CCSraAlignIterator (const CCSraDb &csra_db, TAlignType align_type, TVDBRowId align_row)
void	x_Settle (void)
void	x_Next (void)
CRef< CSeq_entry >	x_GetMatchEntry (const string *annot_name) const
CRef< CSeq_annot >	x_GetEmptyMatchAnnot (const string *annot_name) const
CRef< CSeq_annot >	x_GetMatchAnnot (const string *annot_name) const
CRef< CSeq_annot >	x_GetQualityGraphAnnot (const string *annot_name) const
CRef< CSeq_annot >	x_GetSeq_annot (const string *annot_name) const
CRef< CUser_object >	x_GetSecondaryIndicator (void) const
CObject_id &	x_GetObject_id (const char *name, TObjectIdCache &cache) const
CUser_field &	x_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
SCreateCache &	x_GetCreateCache (void) const

Private Attributes
CCSraRefSeqIterator	m_RefIter
CRef< CCSraDb_Impl::SRefTableCursor >	m_Ref
CRef< CCSraDb_Impl::SAlnTableCursor >	m_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 TVDBRowId *	m_AlnRowCur
const TVDBRowId *	m_AlnRowEnd
AutoPtr< SCreateCache >	m_CreateCache

Friends
class	CCSraShortReadIterator

Detailed Description

Definition at line 378 of file csraread.hpp.

Member Typedef Documentation

TObjectIdCache

typedef CRef<CObject_id> CCSraAlignIterator::TObjectIdCache

protected

Definition at line 518 of file csraread.hpp.

TUserFieldCache

typedef map<CTempString, CRef<CUser_field> > CCSraAlignIterator::TUserFieldCache

protected

Definition at line 519 of file csraread.hpp.

Member Enumeration Documentation

ESearchMode

enum CCSraAlignIterator::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

Definition at line 1084 of file csraread.cpp.

References CCSraDb_Impl::Aln(), CCSraRefSeqIterator::eByName, eSearchByStart, SCSraDb_Defs::fPrimaryAlign, SCSraDb_Defs::fSecondaryAlign, CRef< C, Locker >::GetNCObject(), m_Aln, m_AlnRowCur, m_AlnRowEnd, m_AlnRowIsSecondary, m_ArgRefLast, m_ArgRefPos, m_CurRefLen, m_CurRefPos, m_Error, m_RefIter, m_RefRowLast, m_RefRowNext, m_SearchMode, and NCBI_THROW.

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

Definition at line 498 of file csraread.hpp.

References CCSraRefSeqIterator::GetDb(), and m_RefIter.

Referenced by GetMatchAlign(), GetMateShortSeq_id(), GetShortSeq_id(), Reset(), and Select().

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

Definition at line 1385 of file csraread.cpp.

References m_Aln, and m_AlnRowCur.

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

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(), rapidjson::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 rapidjson::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

Definition at line 1694 of file csraread.cpp.

References eNa_strand_minus, GetRefMinusStrand(), GetShortLen(), GetShortSeq_id(), i, m_Aln, m_AlnRowCur, max(), CByte_graph_Base::SetAxis(), CSeq_interval_Base::SetFrom(), CSeq_graph_Base::SetGraph(), CSeq_interval_Base::SetId(), CSeq_graph_Base::SetLoc(), CByte_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CSeq_interval_Base::SetStrand(), CSeq_graph_Base::SetTitle(), CSeq_interval_Base::SetTo(), CByte_graph_Base::SetValues(), and ncbi::grid::netcache::search::fields::size.

Referenced by x_GetQualityGraphAnnot().

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

Definition at line 472 of file csraread.hpp.

References CCSraDb_Impl::SRefInfo::GetMainSeq_id(), and m_RefIter.

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

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

Definition at line 436 of file csraread.hpp.

References m_CurRefPos.

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

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

Definition at line 1732 of file csraread.cpp.

References data, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eRepr_raw, GetName(), GetShortSeq_id(), IsSetName(), m_Aln, m_AlnRowCur, CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetMol(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), and CSeqdesc_Base::SetTitle().

Referenced by x_GetMatchEntry().

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

Definition at line 1347 of file csraread.cpp.

References GetDb(), GetShortId1(), GetShortId2(), and CCSraDb_Impl::MakeShortReadId().

Referenced by GetMatchAlign(), GetQualityGraph(), and GetShortBioseq().

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

Definition at line 1780 of file csraread.cpp.

References MakeMatchAnnotIndicator(), MakeSeq_annot(), and CSeq_annot_Base::SetDesc().

Referenced by SChunkAnnots::Create().

MakeFullMismatch()

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

Definition at line 1391 of file csraread.cpp.

References CTempString::data(), CTempString::end(), i, m_Aln, m_AlnRowCur, NCBI_THROW_FMT, CTempString::size(), and CVDBValue::size().

Referenced by GetMatchAlign().

MakeMatchAnnotIndicator()

CRef< CAnnotdesc > CCSraAlignIterator::MakeMatchAnnotIndicator ( void  )

static

Definition at line 1754 of file csraread.cpp.

References CUser_object::AddField(), CUser_object_Base::SetType(), and CAnnotdesc_Base::SetUser().

Referenced by MakeEmptyMatchAnnot(), and x_GetEmptyMatchAnnot().

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

)

Definition at line 1001 of file csraread.cpp.

References m_AlignType, m_Aln, m_AlnRowCur, m_AlnRowEnd, m_AlnRowIsSecondary, m_ArgRefLast, m_ArgRefPos, m_CurRefLen, m_CurRefPos, m_Error, m_Ref, m_RefIter, m_RefRowLast, m_RefRowNext, m_SearchMode, and Reset().

Reset()

void CCSraAlignIterator::Reset

(

void

)

Definition at line 975 of file csraread.cpp.

References eSearchByOverlap, SCSraDb_Defs::fAnyAlign, GetDb(), m_AlignType, m_Aln, m_AlnRowCur, m_AlnRowEnd, m_AlnRowIsSecondary, m_ArgRefLast, m_ArgRefPos, m_CurRefLen, m_CurRefPos, m_Error, m_Ref, m_RefIter, m_RefRowLast, m_RefRowNext, m_SearchMode, CCSraDb_Impl::Put(), and RC_NO_MORE_ALIGNMENTS.

Referenced by operator=(), and ~CCSraAlignIterator().

Select()

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

Definition at line 1122 of file csraread.cpp.

References eSearchByOverlap, CCSraRefSeqIterator::GetAlnOverStarts(), GetDb(), CCSraDb_Impl::GetRowSize(), info, kInvalidSeqPos, m_AlignType, m_AlnRowCur, m_AlnRowEnd, m_AlnRowIsSecondary, m_ArgRefLast, m_ArgRefPos, m_Error, m_Ref, m_RefIter, m_RefRowLast, m_RefRowNext, m_SearchMode, max(), min(), RC_NO_MORE_ALIGNMENTS, and x_Settle().

Referenced by CCSraAlignIterator().

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(), rapidjson::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

Definition at line 1869 of file csraread.cpp.

References map_checker< Container >::end(), CUser_field_Base::GetData(), CUser_field_Base::C_Data::GetStr(), map_checker< Container >::insert(), ncbi::grid::netcache::search::fields::key, map_checker< Container >::lower_bound(), CUser_field_Base::SetData(), CUser_object_Base::SetData(), CUser_field_Base::SetLabel(), map_checker< Container >::size(), rapidjson::value, x_AddField(), and x_GetObject_id().

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(), rapidjson::value, and x_AddField().

x_AddField() [4/4]

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

protected

Definition at line 1840 of file csraread.cpp.

References CUser_object_Base::SetData(), CUser_field_Base::SetLabel(), and x_GetObject_id().

Referenced by GetMatchAlign(), and x_AddField().

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

Definition at line 1765 of file csraread.cpp.

References CCSraAlignIterator::SCreateCache::m_MatchAnnotIndicator, MakeMatchAnnotIndicator(), s_GetExplicitMateInfoParam(), CSeq_annot_Base::SetDesc(), x_GetCreateCache(), and x_GetSeq_annot().

Referenced by GetEmptyMatchAnnot(), and x_GetMatchAnnot().

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

Definition at line 1807 of file csraread.cpp.

References GetShortBioseq(), CBioseq_Base::SetAnnot(), CSeq_entry_Base::SetSeq(), and x_GetMatchAnnot().

Referenced by GetMatchEntry().

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

Definition at line 1817 of file csraread.cpp.

References CCSraAlignIterator::SCreateCache::m_SecondaryIndicator, CUser_object_Base::SetData(), CUser_object_Base::SetType(), and x_GetCreateCache().

Referenced by GetMatchAlign().

x_GetSeq_annot()

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

inlineprotected

Definition at line 832 of file csraread.hpp.

References m_RefIter, and CCSraRefSeqIterator::x_GetSeq_annot().

Referenced by GetSeq_annot(), x_GetEmptyMatchAnnot(), and x_GetQualityGraphAnnot().

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

Definition at line 1169 of file csraread.cpp.

References CCSraDb_Impl::Aln(), CVDBValueFor< V >::data(), eSearchByStart, SCSraDb_Defs::fPrimaryAlign, SCSraDb_Defs::fSecondaryAlign, CCSraRefSeqIterator::GetDb(), len, m_AlignType, m_Aln, m_AlnRowCur, m_AlnRowEnd, m_AlnRowIsSecondary, m_ArgRefLast, m_ArgRefPos, m_CurRefLen, m_CurRefPos, m_Error, CCSraDb_Impl::SAlnTableCursor::m_IsSecondary, m_Ref, m_RefIter, m_RefRowLast, m_RefRowNext, m_SearchMode, CCSraDb_Impl::Put(), RC_NO_MORE_ALIGNMENTS, row, and CVDBValue::size().

Referenced by Select(), and x_Next().

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

Definition at line 536 of file csraread.hpp.

Referenced by CCSraAlignIterator(), GetCIGAR(), GetCIGARLong(), GetMapQuality(), GetMatchAlign(), GetMateShortSeq_id(), GetMismatchRaw(), GetMismatchRead(), GetName(), GetQualityGraph(), GetReadFilter(), GetRefMinusStrand(), GetRefSeqId(), GetShortBioseq(), GetShortId1(), GetShortId2(), GetShortLen(), GetShortPos(), GetSpotGroup(), IsSetName(), MakeFullMismatch(), operator=(), Reset(), and x_Settle().

m_AlnRowCur

const TVDBRowId* CCSraAlignIterator::m_AlnRowCur

private

Definition at line 547 of file csraread.hpp.

Referenced by CCSraAlignIterator(), GetAlignmentId(), GetCIGAR(), GetCIGARLong(), GetMapQuality(), GetMatchAlign(), GetMateShortSeq_id(), GetMismatchRaw(), GetMismatchRead(), GetName(), GetQualityGraph(), GetReadFilter(), GetRefMinusStrand(), GetRefSeqId(), GetShortBioseq(), GetShortId1(), GetShortId2(), GetShortLen(), GetShortPos(), GetSpotGroup(), MakeFullMismatch(), operator=(), Reset(), Select(), x_Next(), and x_Settle().

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

Definition at line 538 of file csraread.hpp.

Referenced by CCSraAlignIterator(), operator const void *(), operator!(), operator=(), Reset(), Select(), and x_Settle().

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

Definition at line 534 of file csraread.hpp.

Referenced by CCSraAlignIterator(), GetDb(), GetMatchAlign(), GetRefSeq_id(), operator=(), Reset(), Select(), x_GetSeq_annot(), and x_Settle().

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().

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The documentation for this class was generated from the following files:

• include/sra/readers/sra/csraread.hpp
• src/sra/readers/sra/csraread.cpp