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NCBI C++ ToolKit: src/objtools/data_loaders/blastdb/local_blastdb_adapter.cpp Source File

(

.NotEmpty()) {

retval = gi_to_taxid[idh.

()];

retval = gi_to_taxid.

()->second;

v4.reserve((length+1)/2);

length_whole = length & ~1;

(

= 0;

< length_whole;

+= 2) {

(length_whole != length) {

((length_whole) == (length-1));

v4.push_back(

[length_whole] << 4);

(begin == end && begin == 0) {

((end-begin) <= (

)length);

((end-begin) == (

)length);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

virtual CSeqDB::ESeqType GetSequenceType()

@inheritDoc

virtual CRef< CBioseq > GetBioseqNoData(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_id=NULL)

@inheritDoc

CRef< CSeqDB > m_SeqDB

The BLAST database handle.

virtual TSeqIdList GetSeqIDs(int oid)

@inheritDoc

virtual TTaxId GetTaxId(const CSeq_id_Handle &id)

@inheritDoc

virtual int GetSeqLength(int oid)

@inheritDoc

virtual bool SeqidToOid(const CSeq_id &id, int &oid)

@inheritDoc

virtual CRef< CSeq_data > GetSequence(int oid, int begin=0, int end=0)

@inheritDoc

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Gets a list of sequence identifiers.

int GetSeqLength(int oid) const

Returns the sequence length in base pairs or residues.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

void RetAmbigSeq(const char **buffer) const

Returns any resources associated with the sequence.

CRef< CBioseq > GetBioseqNoData(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence without sequence data.

void GetTaxIDs(int oid, map< TGi, TTaxId > &gi_to_taxid, bool persist=false) const

Get taxid for an OID.

void RetSequence(const char **buffer) const

Returns any resources associated with the sequence.

int GetSequence(int oid, const char **buffer) const

Get a pointer to raw sequence data.

int GetAmbigSeq(int oid, const char **buffer, int nucl_code) const

Get a pointer to sequence data with ambiguities.

list< CRef< CSeq_id > > TSeqIdList

Convenience typedef for a list of CSeq_id-s.

const_iterator begin() const

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

CConstRef< CSeq_id > GetSeqId(void) const

#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.

TNcbistdaa & SetNcbistdaa(void)

Select the variant.

TNcbi4na & SetNcbi4na(void)

Select the variant.

static void s_AssignBufferToSeqData(const char *buffer, CSeq_data &seq_data, TSeqPos length)

Assigns a buffer of nucleotide sequence data as retrieved from CSeqDB into the CSeq_data object.

Declaration of the CLocalBlastDbAdapter class.

const int kSeqDBNuclNcbiNA8

Used to request ambiguities in Ncbi/NA8 format.

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