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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asn__index_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/asn_cache/asn_index.cpp Source File

ostr <<

.seq_id <<

<<

.version <<

<<

.timestamp <<

<<

.chunk <<

<<

.sequence_length <<

<<

.taxonomy_id;

seqid_count = 0;

(objects::CBioseq::TId, id_iter, bioseq.GetId()) {

error_string =

;

error_string +=

+ index.

();

(bioseq.CanGetInst() && bioseq.GetInst().CanGetLength())

seq_length = bioseq.GetInst().GetLength();

ancestor_set && !taxid;

ancestor_set = ancestor_set->GetParentSet())

(ancestor_set->IsSetDescr()) {

(objects::CBioseq_set::TDescr::Tdata, it,

ancestor_set->GetDescr().Get())

objects::CSeqdesc& desc = **it;

taxid_from_org = desc.GetOrg().GetTaxId();

}

(desc.IsSource() && desc.GetSource().IsSetOrg()) {

(objects::CBioseq::TId, id_iter, bioseq.GetId()) {

((*id_iter)->IsGi()) {

void GetNormalizedSeqId(const objects::CSeq_id_Handle &id, string &id_str, Uint4 &version)

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)

CNcbiOstream & operator<<(CNcbiOstream &ostr, const CAsnIndex::SIndexInfo &info)

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

TChunkId GetChunkId() const

SBDB_TypeTraits< TGi >::TFieldType m_Gi

associated gi

SBDB_TypeTraits< TChunkId >::TFieldType m_ChunkId

file chunk and offset

TOffset GetOffset() const

E_index_type m_type

Flag indicating which type of index this is.

void SetSeqId(TSeqId val)

E_index_type GetIndexType() const

CAsnIndex(E_index_type type)

void SetVersion(TVersion val)

SBDB_TypeTraits< TSeqId >::TFieldType m_SeqId

flattened, normalized seq-id representation

SBDB_TypeTraits< TVersion >::TFieldType m_Version

version (or 0 if not applicable)

void SetTaxId(TTaxId val)

void SetChunkId(TChunkId val)

SBDB_TypeTraits< TOffset >::TFieldType m_Offset

TTimestamp GetTimestamp() const

SBDB_TypeTraits< TSize >::TFieldType m_Size

SBDB_TypeTraits< TTimestamp >::TFieldType m_Timestamp

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

void SetOffset(TOffset val)

TVersion GetVersion() const

void SetSeqLength(TSeqLength val)

TSeqLength GetSeqLength() const

void SetTimestamp(TTimestamp val)

SBDB_TypeTraits< TSeqLength >::TFieldType m_SeqLength

sequence-specific data

SBDB_TypeTraits< TTaxId >::TFieldType m_TaxId

TSeqId GetSeqId() const

accessors

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define TAX_ID_TO(T, tax_id)

SStrictId_Tax::TId TTaxId

Taxon id type.

EBDB_ErrCode UpdateInsert(EAfterWrite write_flag=eDiscardData)

Update record corresponding to the current key value.

const string & GetFileName() const

Return file name.

void BindKey(const char *field_name, CBDB_Field *key_field, size_t buf_size=0)

void BindData(const char *field_name, CBDB_Field *data_field, size_t buf_size=0, ENullable is_null=eNullable)

void SetPageSize(unsigned int page_size)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

const string version

version string

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

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