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NCBI C++ ToolKit: src/algo/blast/api/seqinfosrc_seqdb.cpp Source File

SetFilteringAlgorithmId(-1);

vector<TSeqRange> targets;

targets.push_back(target);

(index, targets, retval);

vector<TSeqRange>& target,

(

it=0; it<target.size(); it++) {

target[it].IntersectingWith(*itr)) {

retval.push_back(sli);

(retval.empty() ?

:

);

Auxiliary functions for BLAST.

int GetNumOIDs() const

Returns the size of the (possibly sparse) OID range.

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.

const CSeqDBGiList * GetGiList() const

Get GI list attached to this database.

void GetMaskData(int oid, const vector< int > &algo_ids, TSequenceRanges &ranges)

Get masked ranges of a sequence.

Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and...

structure for seqloc info

Collection of masked regions for a single query sequence.

static const char si[8][64]

virtual size_t Size() const

Returns the size of the underlying container of sequences.

int m_FilteringAlgoId

Filtering algorithm ID used with these subjects, use -1 if not applicable.

virtual bool HasGiList() const

Returns true if the subject is restricted by a GI list.

virtual list< CRef< objects::CSeq_id > > GetId(Uint4 oid) const

Retrieve a sequence identifier given its ordinal number.

CRef< CSeqDB > m_iSeqDb

BLAST database object.

CSeqDbSeqInfoSrc(const string &dbname, bool is_protein)

Constructor: includes initializing the CSeqDB object.

void SetFilteringAlgorithmId(int algo_id)

Sets the filtering algorithm ID used in the search.

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(Uint4 oid) const

Method to retrieve the sequence location given its ordinal number.

virtual Uint4 GetLength(Uint4 oid) const

Retrieve sequence length given its ordinal number.

virtual ~CSeqDbSeqInfoSrc()

Our destructor.

virtual bool GetMasks(Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const

Retrieves the subject masks for the corresponding index.

CConstRef< objects::CSeq_loc > CreateWholeSeqLocFromIds(const list< CRef< objects::CSeq_id > > seqids)

Create a single CSeq_loc of type whole from the first id in the list.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

static TThisType GetEmpty(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval fro...

List of sequence offset ranges.

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