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NCBI C++ ToolKit: src/algo/blast/api/bl2seq.cpp Source File

: m_DbScanMode(

), m_InterruptFnx(0), m_InterruptUserData(0)

queries.push_back(

);

x_Init(queries, subjects);

: m_DbScanMode(

), m_InterruptFnx(0), m_InterruptUserData(0)

queries.push_back(

);

(queries, subjects);

: m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)

queries.push_back(

);

(queries, subjects);

: m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)

queries.push_back(

);

(queries, subjects);

: m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)

(queries, subjects);

: m_DbScanMode(dbscan_mode), m_InterruptFnx(0), m_InterruptUserData(0)

(queries, subjects);

((*r)->HasAlignments()) {

retval.push_back(sa);

(*res)->GetSubjectMasks(subj_masks);

retval.push_back(subj_masks);

Declares the CBl2Seq (BLAST 2 Sequences) class.

BlastDiagnostics * Blast_DiagnosticsFree(BlastDiagnostics *diagnostics)

Free the BlastDiagnostics structure and all substructures.

BlastDiagnostics * Blast_DiagnosticsCopy(const BlastDiagnostics *diagnostics)

Free the BlastDiagnostics structure and all substructures.

Definitions which are dependant on the NCBI C++ Object Manager.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

Runs the BLAST algorithm between 2 sequences.

Handle to the options to the BLAST algorithm.

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...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Search Results for All Queries.

void x_InitCLocalBlast()

Common initialization of the CLocalBlast object.

void x_Init(const TSeqLocVector &queries, const TSeqLocVector &subjs)

Common initialization code for all c-tors.

TSearchMessages m_Messages

Stores any warnings emitted during query setup.

TInterruptFnPtr m_InterruptFnx

Interrupt callback.

void x_ResetInternalDs()

Clean up structures and results from any previous search.

CRef< CBlastOptionsHandle > m_OptsHandle

Blast options.

virtual ~CBl2Seq()

Destructor.

CRef< SInternalData > m_InternalData

Internal core data structures which are used in the preliminary and traceback stages of the search.

BlastDiagnostics * mi_pDiagnostics

Return search statistics data.

bool m_DbScanMode

Scan like a databsase (as opposed to pairwise)

void x_BuildAncillaryData()

Populate the internal m_AncillaryData member.

void GetFilteredSubjectRegions(vector< TSeqLocInfoVector > &retval) const

Retrieves regions filtered on the subject sequence(s)

void * m_InterruptUserData

Interrupt user datacallback.

CSearchResultSet::TAncillaryVector m_AncillaryData

Ancillary BLAST data.

CRef< CSearchResultSet > Run()

Executes the search.

TSeqLocInfoVector GetFilteredQueryRegions() const

Retrieves the filtered query regions.

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

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

TInterruptFnPtr SetInterruptCallback(TInterruptFnPtr fnptr, void *user_data=NULL)

Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in pr...

TSearchMessages GetSearchMessages() const

Retrieve any error/warning messages that occurred during the search.

void SetHitlistSize(int s)

Sets HitlistSize.

virtual TSeqAlignVector Run()

Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as fo...

size_type size() const

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

CRef< CSearchResultSet > m_Results

CLocalBlast results.

CRef< CSearchResultSet > RunEx()

Performs the same functionality as Run(), but it returns a different data type.

static TSeqAlignVector CSearchResultSet2TSeqAlignVector(CRef< CSearchResultSet > res)

Converts m_Results data member to a TSeqAlignVector.

TSeqLocVector m_tQueries

query sequence(s)

TSeqLocVector m_tSubjects

sequence(s) to BLAST against

CRef< CSeq_align_set > CreateEmptySeq_align_set()

Constructs an empty Seq-align-set containing an empty discontinuous seq-align, and appends it to a pr...

bool empty() const

Returns whether this container is empty or not.

CRef< TBlastDiagnostics > m_Diagnostics

Diagnostic output from preliminary and traceback stages.

CBl2Seq(const SSeqLoc &query, const SSeqLoc &subject, EProgram p)

Constructor to compare 2 sequences with default options.

TSeqLocInfoVector GetFilteredQueryRegions() const

Retrieves regions filtered on the query/queries.

CRef< CLocalBlast > m_Blast

The actual BLAST instance.

size_type GetNumResults() const

Return the number of results contained by this object.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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.

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.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to represent a single sequence to be fed to BLAST.

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