NCBI C++ ToolKit
Functions
blast_aux_priv.cpp File Reference

Implements various auxiliary (private) functions for BLAST. More...

#include <ncbi_pch.hpp>
#include "blast_aux_priv.hpp"
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_hspstream.h>
#include <algo/blast/api/blast_mtlock.hpp>
#include <algo/blast/api/seqinfosrc_seqdb.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include "psiblast_aux_priv.hpp"
#include "blast_memento_priv.hpp"
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
+ Include dependency graph for blast_aux_priv.cpp:

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Functions

 USING_SCOPE (objects)
 
CConstRef< objects::CSeq_loc > CreateWholeSeqLocFromIds (const list< CRef< objects::CSeq_id > > seqids)
 Create a single CSeq_loc of type whole from the first id in the list. More...
 
void Blast_Message2TSearchMessages (const Blast_Message *blmsg, const BlastQueryInfo *query_info, TSearchMessages &messages)
 Converts the Blast_Message structure into a TSearchMessages object. More...
 
string BlastErrorCode2String (Int2 error_code)
 Returns a string containing a human-readable interpretation of the error_code passed as this function's argument. More...
 
CRef< SBlastSetupDataBlastSetupPreliminarySearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, size_t num_threads=1)
 Set up internal data structures used by the BLAST CORE engine. More...
 
CRef< SBlastSetupDataBlastSetupPreliminarySearchEx (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CConstRef< CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, size_t num_threads)
 Extended interface to set up internal data structures used by the BLAST CORE engine. More...
 
void BuildBlastAncillaryData (EBlastProgramType program, const vector< CConstRef< CSeq_id > > &query_ids, const BlastScoreBlk *sbp, const BlastQueryInfo *qinfo, const TSeqAlignVector &alignments, const EResultType result_type, CSearchResultSet::TAncillaryVector &retval)
 Builds an CSearchResultSet::TAncillaryVector. More...
 
CRef< CSearchResultSetBlastBuildSearchResultSet (const vector< CConstRef< CSeq_id > > &query_ids, const BlastScoreBlk *sbp, const BlastQueryInfo *qinfo, EBlastProgramType program, const TSeqAlignVector &alignments, TSearchMessages &messages, const vector< TSeqLocInfoVector > &subj_masks, const TSeqLocInfoVector *query_masks=NULL, const EResultType result_type=ncbi::blast::eDatabaseSearch)
 Build a CSearchResultSet from internal BLAST data structures. More...
 
TMaskedQueryRegions PackedSeqLocToMaskedQueryRegions (CConstRef< objects::CSeq_loc > sloc, EBlastProgramType program, bool assume_both_strands=false)
 Auxiliary function to convert a Seq-loc describing masked query regions to a TMaskedQueryRegions object. More...
 
CRef< objects::CSeq_loc > MaskedQueryRegionsToPackedSeqLoc (const TMaskedQueryRegions &sloc)
 Interface to build a CSeq-loc from a TMaskedQueryRegion; note that conversion conversion in this direction can be lossy. More...
 

Detailed Description

Implements various auxiliary (private) functions for BLAST.

Definition in file blast_aux_priv.cpp.

Modified on Wed Apr 24 14:18:44 2024 by modify_doxy.py rev. 669887