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NCBI C++ ToolKit: src/algo/blast/api/prelim_search_runner.hpp Source File

: m_InternalData(internal_data), m_OptsMemento(opts_memento)

(m_InternalData.m_Queries);

(m_InternalData.m_QueryInfo);

(m_InternalData.m_SeqSrc);

(m_InternalData.m_ScoreBlk);

(m_InternalData.m_LookupTable);

(m_InternalData.m_HspStream);

m_InternalData.m_Queries,

m_InternalData.m_QueryInfo,

m_InternalData.m_SeqSrc->GetPointer(),

m_OptsMemento->m_ScoringOpts,

m_InternalData.m_ScoreBlk->GetPointer(),

m_InternalData.m_LookupTable->GetPointer(),

m_OptsMemento->m_InitWordOpts,

m_OptsMemento->m_ExtnOpts,

m_OptsMemento->m_HitSaveOpts,

m_OptsMemento->m_EffLenOpts,

m_OptsMemento->m_PSIBlastOpts,

m_OptsMemento->m_DbOpts,

m_InternalData.m_HspStream->GetPointer(),

m_InternalData.m_Diagnostics->GetPointer(),

m_InternalData.m_FnInterrupt,

m_InternalData.m_ProgressMonitor->Get());

(retval);

void SBlastProgressReset(SBlastProgress *progress_info)

Resets the progress structure to its original state (as if newly allocated) for a fresh start without...

SBlastProgress * SBlastProgressNew(void *user_data)

Allocates and initializes a new SBlastProgress structure.

Function calls to actually perform a BLAST search (high level).

Int2 Blast_RunPreliminarySearchWithInterrupt(EBlastProgramType program, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, const BlastSeqSrc *seq_src, const BlastScoringOptions *score_options, BlastScoreBlk *sbp, LookupTableWrap *lookup_wrap, const BlastInitialWordOptions *word_options, const BlastExtensionOptions *ext_options, const BlastHitSavingOptions *hit_options, const BlastEffectiveLengthsOptions *eff_len_options, const PSIBlastOptions *psi_options, const BlastDatabaseOptions *db_options, BlastHSPStream *hsp_stream, BlastDiagnostics *diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress *progress_info)

Same as above, with support for user interrupt function.

Classes that capture the state of the BLAST options (or subsets of options) and restore them later (u...

#define BLASTERR_DB_MEMORY_MAP

Database file error.

#define BLASTERR_DB_TOO_MANY_OPEN_FILES

BlastQueryInfo * BlastQueryInfoDup(const BlastQueryInfo *query_info)

Duplicates the query information structure.

BlastQueryInfo * BlastQueryInfoFree(BlastQueryInfo *query_info)

Deallocate memory for query information structure.

BlastSeqSrc * BlastSeqSrcCopy(const BlastSeqSrc *seq_src)

Copy function: needed to guarantee thread safety.

BlastSeqSrc * BlastSeqSrcFree(BlastSeqSrc *seq_src)

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

Class that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLA...

Functor to run the preliminary stage of the BLAST search.

Thread class to run the preliminary stage of the BLAST search.

Wrapper class for SBlastProgress .

@ eTooManyOpenFiles

Too many open files.

SInternalData m_InternalData

CPrelimSearchRunner(SInternalData &internal_data, const CBlastOptionsMemento *opts_memento)

CPrelimSearchThread(SInternalData &internal_data, const CBlastOptionsMemento *opts_memento)

CRef< TBlastSeqSrc > m_SeqSrc

The source of subject sequence data.

virtual ~CPrelimSearchThread(void)

SBlastProgress * Get() const

CStructWrapper< BlastSeqSrc > TBlastSeqSrc

CRef< CSBlastProgress > m_ProgressMonitor

The user data structure to aid in progress monitoring.

const CBlastOptionsMemento * m_OptsMemento

Pointer to memento which this class doesn't own.

BlastQueryInfo * m_QueryInfo

The query information structure.

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CPrelimSearchRunner & operator=(const CPrelimSearchRunner &rhs)

Prohibit assignment operator.

SInternalData & m_InternalData

Data structure containing all the needed C structures for the preliminary stage of the BLAST search.

CPrelimSearchRunner(const CPrelimSearchRunner &rhs)

Prohibit copy constructor.

const CBlastOptionsMemento * m_OptsMemento

TErrCode GetErrCode(void) const

Get error code.

void Reset(void)

Reset reference object.

int16_t Int2

2-byte (16-bit) signed 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.

Multi-threading – classes, functions, and features.

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

The query related information.

Complete type definition of Blast Sequence Source ADT.

Progress monitoring structure.

void * user_data

Pointer to user-provided data.

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

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