Search Toolkit Book for SWGSCreateInfo

Inheritance diagram for SWGSCreateInfo:

Collaboration diagram for SWGSCreateInfo:

Public Member Functions
	SWGSCreateInfo (const CWGSDb &db)

	SWGSCreateInfo (const CWGSDb &db, EFromFlags, TFlags flags)

	SWGSCreateInfo (const CWGSDb &db, EFromSplitVersion, TSplitVersion split_version)

void	x_SetFlags (TFlags flags)

void	x_SetSplitVersion (TSplitVersion split_version)

template<class Iter >
void	x_SetId (Iter &it)

void	x_ResetId ()

template<class Iter >
void	x_SetSeq (Iter &it)

void	x_SetSeq (CWGSProteinIterator &it)

void	x_ResetSeq ()

void	x_AddDescr (CTempString bytes)

void	x_AddFeature (const CWGSFeatureIterator &it, CSeq_annot::TData::TFtable &dst)

void	x_AddFeaturesDirect (TVDBRowIdRange range, vector< TVDBRowId > &product_row_ids)

void	x_AddFeaturesSplit (TVDBRowIdRange range, vector< TVDBRowId > &product_row_ids)

void	x_AddFeatures (TVDBRowIdRange range, vector< TVDBRowId > &product_row_ids)

void	x_AddFeatures (TVDBRowIdRange range)

CBioseq_set &	x_GetProtSet (void)

void	x_CreateProtSet (TVDBRowIdRange range)

void	x_AddProducts (const vector< TVDBRowId > &product_row_ids)

Public Member Functions inherited from SWGSDb_Defs
	DECLARE_SAFE_FLAGS_TYPE (EFlags, TFlags)

Public Attributes
CWGSDb	db

TFlags	flags

bool	split_prod

bool	split_data

bool	split_feat

bool	split_qual

CRef< CSeq_id >	main_id

CRef< CSeq_id >	feat_id

CRef< CBioseq >	main_seq

CRef< CSeq_entry >	entry

CRef< CID2S_Split_Info >	split

TSplitVersion	split_version

CRef< CID2S_Chunk >	chunk

CRef< CWGSAsnBinData >	data

Additional Inherited Members
Public Types inherited from SWGSDb_Defs
enum	EFlags { fIds_gi = 1<<0 , fIds_acc = 1<<1 , fIds_gnl = 1<<2 , fMaskIds = fIds_gi\|fIds_acc\|fIds_gnl , fDefaultIds = fIds_gi\|fIds_acc\|fIds_gnl , fInst_ncbi4na = 0<<3 , fInst_delta = 1<<3 , fMaskInst = fInst_ncbi4na\|fInst_delta , fDefaultInst = fInst_delta , fSeqDescr = 1<<4 , fNucProtDescr = 1<<12 , fMasterDescr = 1<<5 , fMasterDescrMark = 1<<13 , fSeqDescrObj = 1<<14 , fMaskDescr = fSeqDescr\|fNucProtDescr\|fMasterDescr , fDefaultDescr = fSeqDescr\|fNucProtDescr\|fMasterDescr , fSeqAnnot = 1<<6 , fQualityGraph = 1<<7 , fMaskAnnot = fSeqAnnot\|fQualityGraph , fDefaultAnnot = fSeqAnnot\|fQualityGraph , fSplitQualityGraph = 1<<8 , fSplitSeqData = 1<<9 , fSplitProducts = 1<<10 , fSplitFeatures = 1<<11 , fSplitAll = fSplitQualityGraph \| fSplitSeqData \| fSplitProducts \| fSplitFeatures , fSplitMask = fSplitQualityGraph \| fSplitSeqData \| fSplitProducts \| fSplitFeatures , fDefaultSplit = fSplitAll , fDefaultFlags = fDefaultIds\|fDefaultDescr\|fDefaultAnnot\|fDefaultInst\|fDefaultSplit }

enum	EFeatLocIdType : Int1 { eFeatLocIdUninitialized = -1 , eFeatLocIdGi = 0 , eFeatLocIdAccVer , eFeatLocIdAccNoVer }

enum	EGBStateType { eGBStateZero = 0 , eGBStateRaw = 1 , eGBStateProject = 2 , eGBStateAll = 3 }

typedef int	TSplitVersion

typedef int	TChunkId

Static Public Attributes inherited from SWGSDb_Defs
static const TSplitVersion	kDefaultSplitVersion = 0

Detailed Description

Definition at line 3805 of file wgsread.cpp.

Constructor & Destructor Documentation

◆ SWGSCreateInfo() [1/3]

SWGSCreateInfo::SWGSCreateInfo ( const CWGSDb & db )

inlineexplicit

Definition at line 3808 of file wgsread.cpp.

◆ SWGSCreateInfo() [2/3]

SWGSCreateInfo::SWGSCreateInfo	(	const CWGSDb &	db,
		EFromFlags	,
		TFlags	flags
	)

inline

Definition at line 3819 of file wgsread.cpp.

References SWGSDb_Defs::fDefaultFlags, and flags.

◆ SWGSCreateInfo() [3/3]

SWGSCreateInfo::SWGSCreateInfo	(	const CWGSDb &	db,
		EFromSplitVersion	,
		TSplitVersion	split_version
	)

inline

Definition at line 3827 of file wgsread.cpp.

References SWGSDb_Defs::kDefaultSplitVersion.

Member Function Documentation

◆ x_AddDescr()

void SWGSCreateInfo::x_AddDescr ( CTempString bytes )

inline

Definition at line 5463 of file wgsread.cpp.

References CWGSAsnBinData::AddDescr(), data, CTempString::empty(), main_seq, CBioseq_Base::SetDescr(), and sx_AddDescrBytes().

◆ x_AddFeature()

void SWGSCreateInfo::x_AddFeature	(	const CWGSFeatureIterator &	it,
		CSeq_annot::TData::TFtable &	dst
	)

inline

Definition at line 5478 of file wgsread.cpp.

References CWGSAsnBinData::AddFeature(), data, CWGSFeatureIterator::GetSeq_feat(), and CWGSFeatureIterator::GetSeq_featBytes().

Referenced by x_AddFeaturesDirect().

◆ x_AddFeatures() [1/2]

void SWGSCreateInfo::x_AddFeatures ( TVDBRowIdRange range )

Definition at line 5813 of file wgsread.cpp.

References compile_time_bits::range(), and CSeq_annot_Base::SetData().

◆ x_AddFeatures() [2/2]

void SWGSCreateInfo::x_AddFeatures	(	TVDBRowIdRange	range,
		vector< TVDBRowId > &	product_row_ids
	)

inline

Definition at line 5801 of file wgsread.cpp.

References compile_time_bits::range().

◆ x_AddFeaturesDirect()

void SWGSCreateInfo::x_AddFeaturesDirect	(	TVDBRowIdRange	range,
		vector< TVDBRowId > &	product_row_ids
	)

Definition at line 5508 of file wgsread.cpp.

References db, main_seq, compile_time_bits::range(), CBioseq_Base::SetAnnot(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), x_AddFeature(), and x_GetProtSet().

◆ x_AddFeaturesSplit()

void SWGSCreateInfo::x_AddFeaturesSplit	(	TVDBRowIdRange	range,
		vector< TVDBRowId > &	product_row_ids
	)

Definition at line 5763 of file wgsread.cpp.

References SWGSFeatChunkInfo::AddFeature(), SWGSFeatChunkInfo::CreateChunkInfo(), SWGSFeatChunkInfo::feat_count, SWGSFeatChunkInfo::feat_id, kFeatPerChunk, SWGSFeatChunkInfo::main_id, compile_time_bits::range(), and split().

◆ x_AddProducts()

void SWGSCreateInfo::x_AddProducts ( const vector< TVDBRowId > & product_row_ids )

Definition at line 5929 of file wgsread.cpp.

References entries, ERR_POST_X, SWGSDb_Defs::fDefaultFlags, SWGSFeatChunkInfo::feat_id, flags, SWGSDb_Defs::fMasterDescr, ITERATE, kMainEntryId, SWGSFeatChunkInfo::main_id, CWGSProteinIterator::SelectRow(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CWGSProteinIterator::x_CreateBioseq().

◆ x_CreateProtSet()

void SWGSCreateInfo::x_CreateProtSet ( TVDBRowIdRange range )

Definition at line 5976 of file wgsread.cpp.

References _ASSERT, eChunk_prod, ERR_POST_X, flags, CWGSProteinIterator::GetIds(), ITERATE, kChunkIdStep, kMainEntryId, kProdPerChunk, PROFILE, compile_time_bits::range(), CWGSProteinIterator::SelectRow(), split(), and sx_AddSplitIds().

◆ x_GetProtSet()

CBioseq_set & SWGSCreateInfo::x_GetProtSet ( void )

Definition at line 5491 of file wgsread.cpp.

References CBioseq_set_Base::eClass_nuc_prot, entry, CSeq_entry_Base::IsSet(), kMainEntryId, main_seq, CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetId(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), split_feat, and split_prod.

Referenced by x_AddFeaturesDirect().

◆ x_ResetId()

void SWGSCreateInfo::x_ResetId ( )

inline

Definition at line 3867 of file wgsread.cpp.

◆ x_ResetSeq()

void SWGSCreateInfo::x_ResetSeq ( )

inline

Definition at line 3883 of file wgsread.cpp.

◆ x_SetFlags()

void SWGSCreateInfo::x_SetFlags ( TFlags flags )

Definition at line 5438 of file wgsread.cpp.

References flags, kAssignedDefaultSplitVersion, and split_version.

◆ x_SetId()

template<class Iter >

void SWGSCreateInfo::x_SetId ( Iter & it )

inline

Definition at line 3854 of file wgsread.cpp.

References SWGSDb_Defs::eFeatLocIdGi, SWGSDb_Defs::fIds_gi, flags, and CSeq_id_Base::IsGi().

◆ x_SetSeq() [1/2]

void SWGSCreateInfo::x_SetSeq ( CWGSProteinIterator & it )

inline

Definition at line 3878 of file wgsread.cpp.

◆ x_SetSeq() [2/2]

template<class Iter >

void SWGSCreateInfo::x_SetSeq ( Iter & it )

inline

Definition at line 3873 of file wgsread.cpp.

◆ x_SetSplitVersion()

void SWGSCreateInfo::x_SetSplitVersion ( TSplitVersion split_version )

Definition at line 5445 of file wgsread.cpp.

References SWGSDb_Defs::fDefaultFlags, flags, kAssignedDefaultSplitVersion, SWGSDb_Defs::kDefaultSplitVersion, NCBI_THROW_FMT, and split_version.

Member Data Documentation

◆ chunk

CRef<CID2S_Chunk> SWGSCreateInfo::chunk

Definition at line 3850 of file wgsread.cpp.

◆ data

CRef<CWGSAsnBinData> SWGSCreateInfo::data

Definition at line 3851 of file wgsread.cpp.

Referenced by x_AddDescr(), and x_AddFeature().

◆ db

CWGSDb SWGSCreateInfo::db

Definition at line 3841 of file wgsread.cpp.

Referenced by x_AddFeaturesDirect().

◆ entry

CRef<CSeq_entry> SWGSCreateInfo::entry

Definition at line 3847 of file wgsread.cpp.

Referenced by x_GetProtSet().

◆ feat_id

CRef<CSeq_id> SWGSCreateInfo::feat_id

Definition at line 3845 of file wgsread.cpp.

◆ flags

TFlags SWGSCreateInfo::flags

Definition at line 3842 of file wgsread.cpp.

Referenced by x_SetFlags(), and x_SetSplitVersion().

◆ main_id

CRef<CSeq_id> SWGSCreateInfo::main_id

Definition at line 3844 of file wgsread.cpp.

◆ main_seq

CRef<CBioseq> SWGSCreateInfo::main_seq

Definition at line 3846 of file wgsread.cpp.

Referenced by x_AddDescr(), x_AddFeaturesDirect(), and x_GetProtSet().

◆ split

CRef<CID2S_Split_Info> SWGSCreateInfo::split

Definition at line 3848 of file wgsread.cpp.

◆ split_data

bool SWGSCreateInfo::split_data

Definition at line 3843 of file wgsread.cpp.

◆ split_feat

bool SWGSCreateInfo::split_feat

Definition at line 3843 of file wgsread.cpp.

Referenced by x_GetProtSet().

◆ split_prod

bool SWGSCreateInfo::split_prod

Definition at line 3843 of file wgsread.cpp.

Referenced by x_GetProtSet().

◆ split_qual

bool SWGSCreateInfo::split_qual

Definition at line 3843 of file wgsread.cpp.

◆ split_version

TSplitVersion SWGSCreateInfo::split_version

Definition at line 3849 of file wgsread.cpp.

Referenced by x_SetFlags(), and x_SetSplitVersion().

The documentation for this struct was generated from the following file:

src/sra/readers/sra/wgsread.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SWGSCreateInfo() [1/3]

◆ SWGSCreateInfo() [2/3]

◆ SWGSCreateInfo() [3/3]

Member Function Documentation

◆ x_AddDescr()

◆ x_AddFeature()

◆ x_AddFeatures() [1/2]

◆ x_AddFeatures() [2/2]

◆ x_AddFeaturesDirect()

◆ x_AddFeaturesSplit()

◆ x_AddProducts()

◆ x_CreateProtSet()

◆ x_GetProtSet()

◆ x_ResetId()

◆ x_ResetSeq()

◆ x_SetFlags()

◆ x_SetId()

◆ x_SetSeq() [1/2]

◆ x_SetSeq() [2/2]

◆ x_SetSplitVersion()

Member Data Documentation

◆ chunk

◆ data

◆ db

◆ entry

◆ feat_id

◆ flags

◆ main_id

◆ main_seq

◆ split

◆ split_data

◆ split_feat

◆ split_prod

◆ split_qual

◆ split_version