62 retval = gi_to_taxid[idh.
GetGi()];
64 retval = gi_to_taxid.
begin()->second;
106 v4.reserve((length+1)/2);
108 const TSeqPos length_whole = length & ~1;
110 for(
TSeqPos i = 0;
i < length_whole;
i += 2) {
113 if (length_whole != length) {
114 _ASSERT((length_whole) == (length-1));
115 v4.push_back(
buffer[length_whole] << 4);
130 if (begin == end && begin == 0) {
145 _ASSERT((end-begin) <= (
int)length);
152 _ASSERT((end-begin) == (
int)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.