src/algo/blast/api/blast_aux_priv.cpp File Reference

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Detailed Description

Implements various auxiliary (private) functions for BLAST.

Definition in file blast_aux_priv.cpp.

#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:

Go to the source code of this file.

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.
void	Blast_Message2TSearchMessages (const Blast_Message *blmsg, const BlastQueryInfo *query_info, TSearchMessages &messages)
	Converts the Blast_Message structure into a TSearchMessages object.
string	BlastErrorCode2String (Int2 error_code)
	Returns a string containing a human-readable interpretation of the error_code passed as this function's argument.
CRef< SBlastSetupData >	BlastSetupPreliminarySearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, bool is_multi_threaded=false)
	Set up internal data structures used by the BLAST CORE engine.
CRef< SBlastSetupData >	BlastSetupPreliminarySearchEx (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CConstRef< CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, bool is_multi_threaded)
	Extended interface to set up internal data structures used by the BLAST CORE engine.
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.
CRef< CSearchResultSet >	BlastBuildSearchResultSet (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.
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.
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.
Variables
static char const	rcsid []

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Variable Documentation

char const rcsid[] [static]

Initial value: "$Id: blast_aux_priv.cpp 163387 2009-06-15 18:32:16Z camacho $" Definition at line 2 of file blast_aux_priv.cpp.

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