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NCBI C++ ToolKit: include/algo/blast/api/bl2seq.hpp Source File

dbscan_mode=

);

p,

dbscan_mode=

);

& GetQuery()

;

& GetSubject()

;

GetFilteredSubjectRegions(vector<TSeqLocInfoVector>& retval)

;

* user_data =

);

x_BuildAncillaryData();

x_InitCLocalBlast();

x_ResetInternalDs();

class ::CBlastFilterTest;

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

Boolean(* TInterruptFnPtr)(SBlastProgress *progress_info)

Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted...

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definition of classes which constitute the results of running a BLAST search.

Definitions of special type used in BLAST.

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.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

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.

const SSeqLoc & GetSubject() const

Retrieve the subject sequence.

const CBlastOptionsHandle & GetOptionsHandle() const

Retrieve the options handle.

void SetSubject(const SSeqLoc &subject)

Set the subject sequence.

BlastDiagnostics * mi_pDiagnostics

Return search statistics data.

void GetMessages(TSearchMessages &messages) const

Returns error messages/warnings.

bool m_DbScanMode

Scan like a databsase (as opposed to pairwise)

void SetSubjects(const TSeqLocVector &subjects)

Set a vector of subject sequences.

void * m_InterruptUserData

Interrupt user datacallback.

const SSeqLoc & GetQuery() const

Retrieve the query sequence.

CSearchResultSet::TAncillaryVector m_AncillaryData

Ancillary BLAST data.

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...

void SetQueries(const TSeqLocVector &queries)

Set a vector of query sequences for a concatenated search.

CRef< CSearchResultSet > m_Results

CLocalBlast results.

void GetAncillaryResults(CSearchResultSet::TAncillaryVector &retval) const

Get the ancillary results for a BLAST search (to be used with the Run() method)

TSeqLocVector m_tQueries

query sequence(s)

const TSeqLocVector & GetQueries() const

Retrieve a vector of query sequences.

TSeqLocVector m_tSubjects

sequence(s) to BLAST against

CBlastOptionsHandle & SetOptionsHandle()

Set the options handle.

CBl2Seq(const CBl2Seq &rhs)

Prohibit copy constructor.

CBl2Seq & operator=(const CBl2Seq &rhs)

Prohibit assignment operator.

vector< CRef< CBlastAncillaryData > > TAncillaryVector

typedef for a vector of CRef<CBlastAncillaryData>

void SetQuery(const SSeqLoc &query)

Set the query.

CRef< CLocalBlast > m_Blast

The actual BLAST instance.

const TSeqLocVector & GetSubjects() const

Retrieve a vector of subject sequences.

BlastDiagnostics * GetDiagnostics() const

Retrieves the diagnostics information returned from the engine.

#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.

void Run(void)

Enter the main loop.

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

vector< TMaskedQueryRegions > TSeqLocInfoVector

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

Definition of SSeqLoc structure.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Return statistics from the BLAST search.

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

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