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

num_threads = 1);

SetNumberOfThreads(

nthreads);

* user_data =

);

CheckInternalData();

max_num_hsps = 0,

* rm_hsps =

,

vector<bool> *rm_hsps_info =

)

;

{

m_MasksForAllQueries;}

num_threads = 1);

x_LaunchMultiThreadedSearch(

& internal_data);

User-defined methods of the data storage class.

SBlastProgress * SBlastProgressNew(void *user_data)

Allocates and initializes a new SBlastProgress structure.

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.

Search class to perform the preliminary stage of the BLAST search.

Wrapper class for SBlastProgress .

Class that supports setting the number of threads to use with a given algorithm.

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

CRef< CBlastOptions > m_Options

CBlastPrelimSearch(const CBlastPrelimSearch &rhs)

Prohibit copy constructor.

CRef< CLocalDbAdapter > m_DbAdapter

TSeqLocInfoVector m_MasksForAllQueries

Query masking information.

TSearchMessages m_Messages

Warnings and error messages.

CRef< SInternalData > m_InternalData

TInterruptFnPtr m_FnInterrupt

The interrupt callback.

CRef< CSBlastProgress > m_ProgressMonitor

The user data structure to aid in progress monitoring.

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...

TSeqLocInfoVector GetFilteredQueryRegions() const

Retrieve the filtered/masked query regions.

CRef< IQueryFactory > m_QueryFactory

Query factory is retained to ensure the lifetime of the data (queries) produced by it.

const CSearchDatabase * m_DbInfo

TSearchMessages GetSearchMessages() const

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

const TSeqLocInfoVector & GetQueryMasks(void) const

Return query masks.

CBlastPrelimSearch & operator=(const CBlastPrelimSearch &rhs)

Prohibit assignment operator.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

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...

vector< TMaskedQueryRegions > TSeqLocInfoVector

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

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

The structure to contain all BLAST results, for multiple queries.

Default implementation of BlastHSPStream.

Complete type definition of Blast Sequence Source ADT.

Lightweight wrapper to enclose C structures needed for running the preliminary and traceback stages o...

Uniform BLAST Search Interface.

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