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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/snpread_8hpp_source.html below:

NCBI C++ ToolKit: include/sra/readers/sra/snpread.hpp Source File

1 #ifndef SRA__READER__SRA__SNPREAD__HPP 2 #define SRA__READER__SRA__SNPREAD__HPP 198 return

m_Seq_id_Handle;

206 return

m_SeqPos + m_PageCount*page_size;

209 return

m_RowId + m_PageCount;

214

m_PageSets.back().GetRowIdEnd());

241 return

m_SeqMapBySeq_id;

248 return

m_TrackMapByName;

251

TTrackInfoList::const_iterator FindTrack(

const string

& name)

const

;

252

TSeqInfoList::const_iterator FindSeq(

const string

& accession,

int version

);

253

TSeqInfoList::const_iterator FindSeq(

const CSeq_id_Handle

& seq_id);

255 TSeqPos

GetPageSize(

void

)

const

;

256 TSeqPos

GetOverviewZoom(

void

)

const

;

257 TSeqPos

GetCoverageZoom(

void

)

const

;

325 return

seq - GetSeqInfoList().begin();

328 return

track - GetTrackInfoList().begin();

331 return TVDBRowId

(x_GetSeqVDBIndex(seq) + 1);

334 return TVDBRowId

(x_GetTrackVDBIndex(track) + 1);

337 void

x_Update(TSeqInfoList::const_iterator seq);

339

x_GetPageVDBRowRange(TSeqInfoList::const_iterator seq);

340 TVDBRowId

x_GetGraphVDBRowId(TSeqInfoList::const_iterator seq,

341

TTrackInfoList::const_iterator track);

428 return

GetDb().x_GetTrackVDBRowId(m_Iter);

431 return

GetDb().x_GetTrackVDBIndex(m_Iter);

440 return

GetInfo().m_Name;

446 return

GetFilter().m_Filter;

449 return

GetFilter().m_FilterMask;

501 return

m_Iter->GetMainSeq_id();

504 return

m_Iter->GetMainSeq_id_Handle();

508 return

m_Iter->m_SeqLength;

511 bool

IsCircular(

void

)

const

;

514 return

GetDb().GetPageSize();

517 return

GetDb().GetOverviewZoom();

520 return

GetDb().GetCoverageZoom();

522 TSeqPos

GetMaxSNPLength(

void

)

const

;

527 Uint8

GetSNPCount(

void

)

const

;

531 return

GetDb().x_GetSeqVDBRowId(m_Iter);

534 return

GetDb().x_GetSeqVDBIndex(m_Iter);

537 return

GetDb().x_GetPageVDBRowRange(m_Iter);

540 return

GetDb().x_GetGraphVDBRowId(m_Iter, m_TrackIter);

547

fNoCoverageGraph = 1<<3,

548

fNoOverviewGraph = 1<<4,

549

fOnlySNPFeat = fNoCoverageGraph | fNoOverviewGraph,

552

fOverviewWithZoomAlways = 1<<5,

553

fOverviewWithZoomNever = 1<<6,

559

TFlags

flags

= fDefaultFlags)

const

;

562 const string

& annot_name,

563

TFlags

flags

= fDefaultFlags)

const

;

565

TFlags

flags

= fDefaultFlags)

const

;

570 const string

& annot_name,

571

TFlags

flags

= fDefaultFlags)

const

;

573

TFlags

flags

= fDefaultFlags)

const

;

577

TFlags

flags

= fDefaultFlags)

const

;

579

TFlags

flags

= fDefaultFlags)

const

;

582 const string

& annot_name,

584

TFlags

flags

= fDefaultFlags)

const

;

587

TFlags

flags

= fDefaultFlags)

const

;

589

TFlags

flags

= fDefaultFlags)

const

;

591 const string

& annot_name,

592

TFlags

flags

= fDefaultFlags)

const

;

596

TFlags

flags

= fDefaultFlags)

const

;

599

GetSplitInfoAndVersion(

const string

& base_name,

600

TFlags

flags

= fDefaultFlags)

const

;

602

GetChunkForVersion(

const string

& base_name,

607 return

m_Db.GetNCObject();

611 return

x_GetTrackIter()->

m_Filter

;

623 const

TInfo& GetInfo()

const

;

676 return

m_SearchRange;

683 return

GetRefIter().GetSeqId();

686 return

GetRefIter().GetSeqIdHandle();

690 return

GetDb().GetPageSize();

693 return

m_CurrPagePos;

701 return

m_CurrPageRowId;

708 TVDBRowId

GetFirstFeatRowId(

void

)

const

;

712

m_SeqIter.SetTrack(track);

799 return

m_SearchRange;

803 return

GetDb().GetPageSize();

806 return

m_CurrPagePos;

814 return

m_CurrPageRowId;

817 Uint4

GetTotalValue(

void

)

const

;

822 return

m_Db.GetNCObject();

828 void

x_ReportInvalid(

const char

* method)

const

;

831

x_ReportInvalid(method);

887 static char

GetFeatSubtypeChar(EFeatSubtype subtype);

888 static CTempString

GetFeatSubtypeString(EFeatSubtype subtype);

898 return

GetPageIter().GetRefIter();

902 return

GetPageIter().GetSeqId();

905 return

GetPageIter().GetSeqIdHandle();

908 return

GetPageIter().GetSearchRange();

911 return

GetPageIter().GetSearchMode();

915 return

m_CurRange.GetFrom();

918 return

m_CurRange.GetLength();

922

eFeatIdPrefix_none = 0,

923

eFeatIdPrefix_rs = 1,

926 Uint4

GetFeatIdPrefix(

void

)

const

;

927 Uint8

GetFeatId(

void

)

const

;

929

TFilter GetBitfield(

void

)

const

;

930 void

GetBitfieldOS(vector<char>& octet_stream)

const

;

935 return

GetBitfield();

939

GetBitfieldOS(codes);

943

fIncludeAlleles = 1<<0,

945

fIncludeBitfield = 1<<2,

946

fIncludeQualityCodes = fIncludeBitfield,

947

fIncludeNeighbors = 1<<3,

948

fIncludeSubtype = 1<<4,

949

fUseSharedObjects = 1<<8,

950

fDefaultFlags = ( fIncludeAlleles |

963 return

GetPageIter().GetDb();

970 return

GetPageIter().GetPageRowId();

973 TSeqPos

x_GetFrom(

void

)

const

;

974 TSeqPos

x_GetLength(

void

)

const

;

978 void

x_ReportInvalid(

const char

* method)

const

;

981

x_ReportInvalid(method);

986 void

x_Settle(

void

);

992

EExcluded x_Excluded(

void

);

994 void

x_SetFilter(

const

SSelector& sel);

995 void

x_InitPage(

void

);

1000 return

GetPageIter().x_GetSeqIter();

AutoPtr< SCreateCache > m_CreateCache

TVDBRowId m_GraphBaseRowId

const CSNPDb_Impl::SFeatTableCursor & Cur(void) const

CSNPDbFeatIterator & operator++(void)

CSNPDb_Impl & GetDb(void) const

DECLARE_OPERATOR_BOOL(m_CurrFeatId< m_FirstBadFeatId)

TVDBRowId m_FirstBadFeatId

ESearchMode GetSearchMode(void) const

COpenRange< TSeqPos > m_CurRange

pair< TVDBRowId, size_t > TExtraRange

void x_Init(const CSNPDb &snp_db)

TSeqPos GetSNPLength(void) const

TVDBRowId GetPageRowId(void) const

const CSNPDbSeqIterator & GetRefIter(void) const

TSeqPos GetSNPPosition(void) const

CRef< CSNPDb_Impl::SGraphTableCursor > m_Graph

map< CTempString, CRef< CUser_field > > TUserFieldCache

CRef< CSNPDb_Impl::SExtraTableCursor > m_Extra

void x_CheckValid(const char *method) const

CSNPDb_Impl::TSeqInfoList::const_iterator x_GetSeqIter() const

const CRange< TSeqPos > & GetSearchRange(void) const

CSeq_id_Handle GetSeqIdHandle(void) const

CSNPDbPageIterator m_PageIter

CRef< CSNPDb_Impl::SFeatTableCursor > m_Feat

DECLARE_SAFE_FLAGS_TYPE(EFlags, TFlags)

Uint8 GetQualityCodes(void) const

CRef< CObject_id > TObjectIdCache

void x_ReportInvalid(const char *method) const

void GetQualityCodes(vector< char > &codes) const

CRef< CSeq_id > GetSeqId(void) const

const CSNPDbPageIterator & GetPageIter(void) const

TSeqPos GetPagePos(void) const

TVDBRowId GetGraphRowId(void) const

TVDBRowId m_CurrPageRowId

CSNPDb_Impl & GetDb(void) const

TSeqPos GetPageSize(void) const

const CRange< TSeqPos > & GetSearchRange(void) const

CRef< CSNPDb_Impl::SGraphTableCursor > m_Cur

DECLARE_OPERATOR_BOOL(m_CurrPagePos !=kInvalidSeqPos)

CSNPDbGraphIterator & operator++(void)

const CSNPDb_Impl::SGraphTableCursor & Cur(void) const

void x_CheckValid(const char *method) const

CRange< TSeqPos > m_SearchRange

CRange< TSeqPos > GetPageRange(void) const

TVDBRowId GetPageRowId(void) const

CSeq_id_Handle GetSeqIdHandle(void) const

TSeqPos GetPageSize(void) const

TSeqPos GetPagePos(void) const

CSNPDbPageIterator & operator++(void)

const CSNPDb_Impl::SPageTableCursor & Cur(void) const

ESearchMode GetSearchMode(void) const

TVDBRowId m_LastGraphRowId

CSNPDb_Impl::TSeqInfoList::const_iterator x_GetSeqIter() const

void SetTrack(const CSNPDbTrackIterator &track)

CRange< TVDBRowId > x_GetPageVDBRowRange() const

CSNPDbSeqIterator m_SeqIter

const CRange< TSeqPos > & GetSearchRange(void) const

CSNPDb_Impl::TTrackInfoList::const_iterator x_GetTrackIter() const

CRef< CSeq_id > GetSeqId(void) const

CSNPDb_Impl & GetDb(void) const

CRange< TSeqPos > GetPageRange(void) const

void x_CheckValid(const char *method) const

CRef< CSNPDb_Impl::SPageTableCursor > m_Cur

TVDBRowId m_CurrPageRowId

CRange< TSeqPos > m_SearchRange

const CSNPDbSeqIterator & GetRefIter(void) const

TVDBRowId x_GetSeqVDBRowId() const

TVDBRowId x_GetTrackVDBRowId() const

CRef< CSNPDb_Impl::SGraphTableCursor > m_GraphCur

DECLARE_OPERATOR_BOOL(m_CurrPagePos< m_SearchRange.GetToOpen())

TVDBRowId x_GetGraphVDBRowId() const

const SFilter & GetFilter() const

TList::const_iterator m_Iter

const TList & GetList() const

const TInfo * operator->(void) const

TSeqPos GetSeqLength(void) const

CSNPDb_Impl::TTrackInfoList::const_iterator m_TrackIter

CRef< CSeq_id > GetSeqId(void) const

vector< CRef< CSeq_annot > > TAnnotSet

TSeqPos GetCoverageZoom(void) const

TSeqPos GetOverviewZoom(void) const

const TInfo & operator*(void) const

TSeqPos GetPageSize(void) const

CSNPDb_Impl & GetDb(void) const

const CSeq_id_Handle & GetSeqIdHandle(void) const

TVDBRowId GetVDBRowId(void) const

const TInfo & GetInfo() const

TVDBRowId GetGraphVDBRowId() const

CSNPDb_Impl::TSeqInfoList TList

DECLARE_SAFE_FLAGS_TYPE(EFlags, TFlags)

CRange< TVDBRowId > GetPageVDBRowRange(void) const

DECLARE_OPERATOR_BOOL(m_Db &&m_Iter !=GetList().end())

TList::const_iterator x_GetSeqIter() const

size_t GetVDBSeqIndex(void) const

CSNPDb_Impl::TTrackInfoList::const_iterator x_GetTrackIter() const

CSNPDb_Impl & GetDb(void) const

const TInfo & operator*(void) const

TFilter GetFilterMask(void) const

CSNPDbTrackIterator & operator++(void)

TList::const_iterator m_Iter

TVDBRowId GetVDBRowId(void) const

const SFilter & GetFilter(void) const

size_t GetVDBTrackIndex(void) const

CSNPDbTrackIterator(void)

const string & GetName(void) const

TFilter GetFilterBits(void) const

const TInfo * operator->(void) const

CSNPDb_Impl::TTrackInfoList TList

const TList & GetList() const

DECLARE_OPERATOR_BOOL(m_Db &&m_Iter !=GetList().end())

CVDBObjectCache< SGraphTableCursor > m_Graph

map< CSeq_id_Handle, size_t > TSeqInfoMapBySeq_id

const CVDBTable & ExtraTable(void)

TTrackInfoMapByName m_TrackMapByName

const TTrackInfoMapByName & GetTrackInfoMapByName(void) const

map< TVDBRowId, TVDBRowId > TSeq2PageMap

const CVDBTable & PageTable(void)

const string & GetDbPath(void) const

const TTrackInfoList & GetTrackInfoList(void) const

TVDBRowId x_GetSeqVDBRowId(TSeqInfoList::const_iterator seq) const

vector< SSeqInfo > TSeqInfoList

const CVDBTable & FeatTable(void)

const TSeqInfoList & GetSeqInfoList(void) const

TTrackInfoList m_TrackList

TSeqPos GetOverviewZoom(void) const

const CVDBTable & SeqTable(void)

TSeqPos GetCoverageZoom(void) const

size_t x_GetTrackVDBIndex(TTrackInfoList::const_iterator track) const

map< string, size_t > TTrackInfoMapByName

CVDBObjectCache< SExtraTableCursor > m_Extra

CVDBObjectCache< SFeatTableCursor > m_Feat

CVDBTableIndex m_SeqAccIndex

CVDBObjectCache< SSeqTableCursor > m_Seq

size_t x_GetSeqVDBIndex(TSeqInfoList::const_iterator seq) const

TSeq2PageMap m_Seq2PageMap

TVDBRowId x_GetTrackVDBRowId(TTrackInfoList::const_iterator track) const

const TSeqInfoMapBySeq_id & GetSeqInfoMapBySeq_id(void) const

CVDBObjectCache< SPageTableCursor > m_Page

vector< STrackInfo > TTrackInfoList

const CVDBTable & GraphTable(void)

TSeqInfoMapBySeq_id m_SeqMapBySeq_id

size_t GetTrackCount() const

CSNPDb(CSNPDb_Impl *impl)

CSNPDb(CVDBMgr &mgr, CTempString path_or_acc)

TSeqPos GetCoverageZoom() const

TSeqPos GetOverviewZoom() const

namespace ncbi::objects::

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

objects::CSeqFeatData::ESubtype GetFeatSubtype(const string &feat_type)

CObject & operator=(const CObject &src) THROWS_NONE

Assignment operator.

TObjectType & GetObject(void)

Get object.

TObjectType & GetNCObject(void) const

Get object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define NCBI_SRAREAD_EXPORT

const string version

version string

double value_type

The numeric datatype used by the parser.

Multi-threading â mutexes; rw-locks; semaphore.

DECLARE_SAFE_FLAGS(CSNPDbSeqIterator::EFlags)

#define row(bind, expected)

TSeqPos GetSeqPosEnd(TSeqPos page_size) const

TVDBRowId GetRowIdEnd(void) const

vector< SPageSet > TPageSets

CRange< TVDBRowId > GetPageVDBRowRange() const

const CSeq_id_Handle & GetMainSeq_id_Handle(void) const

const CRef< CSeq_id > & GetMainSeq_id(void) const

CSeq_id_Handle m_Seq_id_Handle

SFilter(TFilter filter, TFilter filter_mask=TFilter(-1))

bool Matches(TFilter bits) const

void SetFilter(TFilter filter, TFilter filter_mask=TFilter(-1))

SSelector(ESearchMode search_mode, const SFilter &filter=SFilter())

SSelector & SetFilter(const SFilter &filter)

SSelector & SetNoFilter(void)

SSelector(const SFilter &filter=SFilter())

SSelector & SetFilter(TFilter filter, TFilter filter_mask=TFilter(-1))

@ eFeatSubtypeChar_insertion

@ eFeatSubtypeChar_identity

@ eFeatSubtypeChar_unknown

@ eFeatSubtypeChar_multi_nucleotide_variation

@ eFeatSubtypeChar_deletion

@ eFeatSubtypeChar_single_nucleotide_variation

@ eFeatSubtypeChar_inversion

@ eFeatSubtypeChar_deletion_insertion

@ eFeatSubtype_deletion_insertion

@ eFeatSubtype_multi_nucleotide_variation

@ eFeatSubtype_single_nucleotide_variation

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