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NCBI C++ ToolKit: include/objtools/data_loaders/asn_cache/asn_index.hpp Source File

TVersion GetVersion()

;

TTimestamp GetTimestamp()

;

TSize GetSize()

;

SetSeqId(TSeqId

);

SetVersion(TVersion

);

SetTimestamp(TTimestamp

);

SetSize(TSize

);

, timestamp(index.GetTimestamp())

, chunk(index.GetChunkId())

, offs(index.GetOffset())

,

(index.GetSize())

size_t IndexABioseq(const objects::CBioseq &bioseq, CAsnIndex &index, CAsnIndex::TTimestamp timestamp, CAsnIndex::TChunkId chunk_id, CAsnIndex::TOffset offset, CAsnIndex::TSize size)

void BioseqIndexData(const objects::CBioseq &bioseq, CAsnIndex::TGi &gi, CAsnIndex::TSeqLength &seq_length, CAsnIndex::TTaxId &taxid)

int TOffset

Basic data type for offsets into a sequence.

This is a simple BDB structure holding information about a given accession and its indexed location.

SBDB_TypeTraits< TGi >::TFieldType m_Gi

associated gi

SBDB_TypeTraits< TChunkId >::TFieldType m_ChunkId

file chunk and offset

E_index_type m_type

Flag indicating which type of index this is.

E_index_type GetIndexType() const

SBDB_TypeTraits< TSeqId >::TFieldType m_SeqId

flattened, normalized seq-id representation

SBDB_TypeTraits< TVersion >::TFieldType m_Version

version (or 0 if not applicable)

SBDB_TypeTraits< TOffset >::TFieldType m_Offset

SBDB_TypeTraits< TSize >::TFieldType m_Size

SBDB_TypeTraits< TTimestamp >::TFieldType m_Timestamp

timestamp of update; this permist multiple gis and query by date

string CurrentLocationAsString() const

SBDB_TypeTraits< TSeqLength >::TFieldType m_SeqLength

sequence-specific data

SBDB_TypeTraits< TTaxId >::TFieldType m_TaxId

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

int GetSeqLength(const CBioseq &bioseq)

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

SStrictId_Tax::TId TTaxId

Taxon id type.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

const string version

version string

const struct ncbi::grid::netcache::search::fields::SIZE size

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

SIndexInfo(const CAsnIndex &index)

TSeqLength sequence_length

Type trait classes for finding the correct BDB field type automagically.

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