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

: m_Queries(query_factory),

m_DomainDb(domain_db),

: m_Queries(query_factory),

m_DomainDb(domain_db),

m_RpsOptions(rps_options)

(query_lens[

]),

.push_back(pssm_engine->Run());

(!

.back()->GetPssm().GetQuery().GetSeq().GetFirstId()) {

.back()->SetPssm().SetQuery().SetSeq().SetId().push_back(

(index >= (

)

.size()) {

(index >= (

)

.size()) {

blaster.

();

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Int2 PSIBlastOptionsNew(PSIBlastOptions **psi_options)

Initialize default options for PSI BLAST.

PSIDiagnosticsRequest * PSIDiagnosticsRequestNewEx(Boolean save_ascii_pssm)

Allocates a PSIDiagnosticsRequest structure, setting fields to their default values for their use in ...

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

Defines BLAST error codes (user errors included)

Handle to the options to the BLAST algorithm.

Strategy for pre-processing RPS-BLAST matches for PSSM computation.

Handle to the protein-protein options to the BLAST algorithm.

A simple realization of the DELTA-BLAST algorithm: seacrch domain database, compute PSSM,...

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

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

Wrapper class for PSIBlastOptions .

Wrapper class for PSIDiagnosticsRequest .

Runs a single iteration of the PSI-BLAST algorithm between 2 sequences.

Runs a single iteration of the PSI-BLAST algorithm on a BLAST database.

Computes a PSSM as specified in PSI-BLAST.

Search Results for All Queries.

Source of query sequence data for BLAST Provides an interface for search classes to retrieve sequence...

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

CRef< CSearchResultSet > Run()

Run the PSI-BLAST engine for one iteration.

virtual CConstRef< objects::CSeq_loc > GetSeq_loc(size_t index)=0

Get the Seq_loc for the sequence indicated by index.

string GetDatabaseName() const

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

size_t GetNumberOfThreads(void) const

Accessor for the number of threads to use.

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

CRef< CSearchResultSet > m_Results

Pssm-protein search results.

CConstRef< objects::CPssmWithParameters > GetPssm(int index=0) const

Accessor for PSSM computd from CDD hits and used in protein search.

CRef< IQueryFactory > m_Queries

Queries.

CRef< CLocalDbAdapter > m_Subject

Reference to a BLAST subject/database object.

CRef< CSearchResultSet > Run()

Executes the search.

virtual BLAST_SequenceBlk * GetSequenceBlk()=0

Accessor for the BLAST_SequenceBlk structure.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested program,...

bool IsBlastDb() const

Returns true if this object represents a BLAST database.

CRef< CSearchResultSet > Run()

Run the DELTA-BLAST engine with one iteration.

PSIBlastOptions * Get() const

vector< CRef< CPssmWithParameters > > m_Pssm

PSSMs computed for each query.

size_type size() const

Identical to GetNumResults, provided to facilitate STL-style iteration.

void Reset(PSIDiagnosticsRequest *p=NULL)

const char * GetMatrixName() const

Returns MatrixName.

int GetGapExtensionCost() const

Returns GapExtensionCost.

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

CDeltaBlast(CRef< IQueryFactory > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CLocalDbAdapter > domaindb, CConstRef< CDeltaBlastOptionsHandle > options)

Constructor to compare a single sequence against a database of protein sequences, and use RPS-BLAST t...

CConstRef< CDeltaBlastOptionsHandle > m_Options

Delta Blast options.

CRef< CBlastRPSOptionsHandle > m_RpsOptions

RPS Blast options.

CRef< CSearchResultSet > Run()

Run the PSI-BLAST 2 Sequences engine.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

virtual size_t GetNumQueries()=0

Get the number of queries.

void x_Validate(void)

Perform sanity checks on input parameters.

CRef< CSearchResultSet > x_FindDomainHits(void)

Search domain database.

void push_back(value_type &element)

Add a value to the back of this container.

void SetFilterString(const char *f, bool clear=true)

Sets FilterString.

double GetDomainInclusionThreshold(void) const

Get e-value threshold for including domains in Pssm calculation.

CRef< CLocalDbAdapter > m_DomainDb

Reference to a BLAST conserved domain database object.

int GetGapOpeningCost() const

Returns GapOpeningCost.

CRef< CSearchResultSet > m_DomainResults

Conseved domain search (intermediate) results.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

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

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

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 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.

Main class to perform a BLAST search on the local machine.

Declares CPsiBl2Seq, the C++ API for the PSI-BLAST 2 Sequences engine.

Declares CPsiBlast, the C++ API for the PSI-BLAST engine.

C++ API for the PSI-BLAST PSSM engine.

Structure to hold a sequence.

Uint1 * sequence_start

Start of sequence, usually one byte before sequence as that byte is a NULL sentinel byte.

Int4 query_length

Length of this query, strand or frame.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

The query related information.

BlastContextInfo * contexts

Information per context.

double inclusion_ethresh

Minimum evalue for inclusion in PSSM calculation.

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