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NCBI C++ ToolKit: include/objtools/data_loaders/blastdb/blastdb_adapter.hpp Source File

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list< CRef<CSeq_id> >

(

oid) = 0;

@ kSequenceSliceSize

If sequence is shorter than this size but greater than kFastSequenceLoadSize, it will be "split" into...

@ kRmtSequenceSliceSize

Same as above, but used for fetching sequences from remote BLAST databases.

@ kFastSequenceLoadSize

If sequence is shorter than this size, it will not be split and it will be loaded full as soon as its...

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

Interface that provides a common interface to retrieve sequence data from local vs.

virtual ~IBlastDbAdapter()

Virtual destructor.

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

Get all or part of the sequence data as a Seq-data object.

virtual TTaxId GetTaxId(const CSeq_id_Handle &)

Retrieve the taxonomy ID for the requested sequence identifier.

virtual CRef< CBioseq > GetBioseqNoData(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_id=NULL)=0

Get a CBioseq for the requested oid, but without sequence data.

virtual bool SeqidToOid(const CSeq_id &id, int &oid)=0

Find a Seq-id in the database and get an OID if found.

virtual list< CRef< CSeq_id > > GetSeqIDs(int oid)=0

Get the list of Seq-ids for the given OID.

list< CRef< CSeq_id > > TSeqIdList

Convenience typedef for a list of CSeq_id-s.

virtual CSeqDB::ESeqType GetSequenceType()=0

Get the molecule type of this object (protein or nucleotide)

virtual int GetSeqLength(int oid)=0

Get the length of the sequence.

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

SStrictId_Tax::TId TTaxId

Taxon id type.

#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.

Defines BLAST database access classes.

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