NCBI C++ ToolKit
Static Public Member Functions | List of all members

Search Toolkit Book for CSetupFactory

Auxiliary class to create the various C structures to set up the preliminary and/or traceback stages of the search. More...

#include <algo/blast/api/setup_factory.hpp>

Static Public Member Functions

static CRef< CBlastRPSInfoCreateRpsStructures (const string &rps_dbname, CRef< CBlastOptions > options)
 Initializes RPS-BLAST data structures. More...
 
static BlastScoreBlkCreateScoreBlock (const CBlastOptionsMemento *opts_memento, CRef< ILocalQueryData > query_data, BlastSeqLoc **lookup_segments, TSearchMessages &search_messages, TSeqLocInfoVector *masked_query_regions=NULL, const CBlastRPSInfo *rps_info=NULL)
 Initializes the BlastScoreBlk. More...
 
static LookupTableWrapCreateLookupTable (CRef< ILocalQueryData > query_data, const CBlastOptionsMemento *opts_memento, BlastScoreBlk *score_blk, CRef< CBlastSeqLocWrap > lookup_segments, const CBlastRPSInfo *rps_info=NULL, BlastSeqSrc *seqsrc=NULL, size_t num_threads=1)
 Initialize the lookup table. More...
 
static BlastDiagnosticsCreateDiagnosticsStructure ()
 Create and initialize the BlastDiagnostics structure for single-threaded applications. More...
 
static BlastDiagnosticsCreateDiagnosticsStructureMT ()
 Create and initialize the BlastDiagnostics structure for multi-threaded applications. More...
 
static BlastHSPStreamCreateHspStream (const CBlastOptionsMemento *opts_memento, size_t number_of_queries, BlastHSPWriter *writer)
 Create and initialize the BlastHSPStream structure. More...
 
static BlastHSPWriterCreateHspWriter (const CBlastOptionsMemento *opts_memento, BLAST_SequenceBlk *query, BlastQueryInfo *query_info)
 Create a writer to be registered for use by stream. More...
 
static BlastHSPPipeCreateHspPipe (const CBlastOptionsMemento *opts_memento, BlastQueryInfo *query_info)
 Create a pipe to be registered for use by stream. More...
 
static BlastSeqSrcCreateBlastSeqSrc (const CSearchDatabase &db)
 Create a BlastSeqSrc from a CSearchDatabase (uses CSeqDB) More...
 
static BlastSeqSrcCreateBlastSeqSrc (CSeqDB *db, int filt_algo=-1, ESubjectMaskingType mask_type=eNoSubjMasking)
 Create a BlastSeqSrc from an existing CSeqDB object. More...
 
static void InitializeMegablastDbIndex (CRef< CBlastOptions > options)
 Initialize a megablast BLAST database index. More...
 

Detailed Description

Auxiliary class to create the various C structures to set up the preliminary and/or traceback stages of the search.

Definition at line 192 of file setup_factory.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:26:38 2024 by modify_doxy.py rev. 669887