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

: m_SeqSrc(0), m_SeqInfoSrc(0), m_DbName(dbinfo.GetDatabaseName()), m_DbScanMode(

)

: m_SeqSrc(0), m_SeqInfoSrc(0), m_SubjectFactory(subject_sequences),

m_OptsHandle(opts_handle), m_DbName(

), m_DbScanMode(dbscan_mode)

(subject_sequences.

()) {

);

(opts_handle.

()) {

: m_SeqSrc(seqSrc), m_SeqInfoSrc(seqInfoSrc), m_DbName(

), m_DbScanMode(

)

(error_str);

retval =

;

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Boolean Blast_SubjectIsProtein(EBlastProgramType p)

Returns true if the subject is protein.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Boolean BlastSeqSrcGetIsProt(const BlastSeqSrc *seq_src)

Find if the Blast Sequence Source contains protein or nucleotide sequences.

char * BlastSeqSrcGetInitError(const BlastSeqSrc *seq_src)

Function to retrieve NULL terminated string containing the description of an initialization error or ...

BlastSeqSrc * BlastSeqSrcFree(BlastSeqSrc *seq_src)

Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined construct...

void BlastSeqSrcResetChunkIterator(BlastSeqSrc *seq_src)

Reset the internal "bookmark" of the last chunk for iteration provided by this object.

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

Defines BLAST error codes (user errors included)

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

NCBI C++ Object Manager dependant implementation of IQueryFactory.

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

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

Abstract base class to encapsulate retrieval of sequence identifiers.

static void QueryFactory(CRef< IQueryFactory > query_factory, const CBlastOptionsHandle &opts_handle, EQueryFactoryType query_factory_type=eQFT_Query)

Function to perform sanity checks on the query factory.

bool IsProtein() const

Returns true if this object represents protein or nucleotide sequences.

CConstRef< CBlastOptionsHandle > m_OptsHandle

Options to be used when instantiating the subject sequences.

CRef< CSearchDatabase > m_DbInfo

Object containing BLAST database description.

BlastSeqSrc * QueryFactoryBlastSeqSrcInit(CRef< IQueryFactory > query_factory, EBlastProgramType program)

Initialize the sequence source structure from a query factory.

int GetFilteringAlgorithm() const

Accessor for the filtering algorithm ID.

static void s_CheckForBlastSeqSrcErrors(const BlastSeqSrc *seqsrc)

Checks if the BlastSeqSrc initialization succeeded.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

TSeqLocVector GetTSeqLocVector()

Retrieves the TSeqLocVector used to construct this object or a conversion of the CBlastQueryVector pr...

string GetFilteringAlgorithmKey()

Retrieve the database filtering id from key.

CRef< IBlastSeqInfoSrc > m_SeqInfoSrc

Pointer to the IBlastSeqInfoSrc.

string GetFilteringAlgorithmKey() const

Accessor for the filtering algorithm key.

BlastSeqSrc * MakeSeqSrc()

Retrieves or constructs the BlastSeqSrc.

bool IsProtein() const

Determine whether this database contains protein sequences or not.

virtual ~CLocalDbAdapter()

Destructor.

TSeqLocVector m_Subjects

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

BlastSeqSrc * MultiSeqBlastSeqSrcInit(TSeqLocVector &seq_vector, EBlastProgramType program, bool dbscan_mode=false)

Initialize the sequence source structure.

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

static BlastSeqSrc * CreateBlastSeqSrc(const CSearchDatabase &db)

Create a BlastSeqSrc from a CSearchDatabase (uses CSeqDB)

CRef< IQueryFactory > m_SubjectFactory

IQueryFactory containing the subject sequences.

EProgram GetProgram() const

Accessors/Mutators for individual options.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

virtual CRef< objects::CBioseq_set > GetBioseqSet()=0

Accessor for the CBioseq_set.

IBlastSeqInfoSrc * MakeSeqInfoSrc()

Retrieves or constructs the IBlastSeqInfoSrc.

void ResetBlastSeqSrcIteration()

This method should be called so that if the implementation has an internal "bookmark" of the chunks o...

CRef< IRemoteQueryData > MakeRemoteQueryData()

Creates and caches an IRemoteQueryData.

bool m_DbScanMode

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

CLocalDbAdapter(const CSearchDatabase &dbinfo)

Constructor.

BlastSeqSrc * m_SeqSrc

Pointer to the BlastSeqSrc this object owns and manages.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

bool Empty(void) const THROWS_NONE

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

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

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.

Declares class which provides internal BLAST database representations to the internal BLAST APIs.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Declarations of auxiliary functions/classes for PSI-BLAST.

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

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

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

Implementation of the BlastSeqSrc interface for a vector of sequence locations.

Implementation of the BlastSeqSrc interface for a query factory.

Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Complete type definition of Blast Sequence Source ADT.

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