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NCBI C++ ToolKit: include/algo/blast/api/local_db_adapter.hpp Source File

dbscan_mode=

);

ResetBlastSeqSrcIteration();

GetFilteringAlgorithm();

GetFilteringAlgorithmKey();

IsProtein()

;

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declaration of ADT to retrieve sequences for the BLAST engine.

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

Abstract base class to encapsulate retrieval of sequence identifiers.

string GetDatabaseName() const

Returns the database name if appropriate, else kEmptyStr for subject sequences.

CConstRef< CBlastOptionsHandle > m_OptsHandle

Options to be used when instantiating the subject sequences.

CRef< CSearchDatabase > m_DbInfo

Object containing BLAST database description.

int GetFilteringAlgorithm() const

Accessor for the filtering algorithm ID.

CRef< IBlastSeqInfoSrc > m_SeqInfoSrc

Pointer to the IBlastSeqInfoSrc.

bool IsBlastDb() const

Returns true if this object represents a BLAST database.

TSeqLocVector m_Subjects

This is initialized ONLY if the m_SubjectFactory is of type CObjMgr_QueryFactory, case in which it's ...

int GetFilteringAlgorithm()

Retrieve the database filtering algorithm.

CRef< IQueryFactory > m_SubjectFactory

IQueryFactory containing the subject sequences.

CLocalDbAdapter(const CLocalDbAdapter &)

Prohibit copy-constructor.

bool m_DbScanMode

Specifies that bl2seq search run in database scan mode (not pairwise)

CLocalDbAdapter & operator=(const CLocalDbAdapter &)

Prohibit assignment operator.

const string m_DbName

This is initialized ONLY if this object represents a BLAST database.

BlastSeqSrc * m_SeqSrc

Pointer to the BlastSeqSrc this object owns and manages.

CRef< CSearchDatabase > GetSearchDatabase()

bool IsDbScanMode() const

Returns true if this is not a database but is database scanning mode.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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.

Definition of SSeqLoc structure.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Complete type definition of Blast Sequence Source ADT.

Uniform BLAST Search Interface.

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