blast_objmgr_tools.cpp File Reference

Functions in xblast API code that interact with object manager. More...

#include <ncbi_pch.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/create_defline.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <algo/blast/api/blast_options.hpp>
#include "blast_setup.hpp"
#include "blast_objmgr_priv.hpp"
#include <algo/blast/core/blast_encoding.h>
#include <algo/blast/api/blast_seqinfosrc.hpp>
#include <algo/blast/api/blast_seqinfosrc_aux.hpp>
#include <serial/iterator.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include "blast_seqalign.hpp"
#include "dust_filter.hpp"
#include <algo/blast/api/repeats_filter.hpp>
#include "winmask_filter.hpp"

Include dependency graph for blast_objmgr_tools.cpp:

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Classes
class	CBlastSeqVectorOM
	Implementation of the IBlastSeqVector interface which obtains data from a CSeq_loc and a CScope relying on the CSeqVector class. More...

Functions
	USING_SCOPE (objects)
void	SetupQueryInfo (TSeqLocVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)
	Allocates the query information structure and fills the context offsets, in case of multiple queries, frames or strands. More...
void	SetupQueries (TSeqLocVector &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)
	Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST. More...
void	SetupSubjects (TSeqLocVector &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)
	Sets up internal subject data structure for the BLAST search. More...
void	s_Ncbi4naToNcbi2na (const string &ncbi4na, int base_length, unsigned char *ncbi2na)
SBlastSequence	GetSequence (const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)
	Retrieves a sequence using the object manager. More...
CRef< objects::CPacked_seqint >	TSeqLocVector2Packed_seqint (const TSeqLocVector &sequences)
	Converts a TSeqLocVector into a CPacked_seqint. More...

Variables
static unsigned char	ctable [16]

Detailed Description

Functions in xblast API code that interact with object manager.

Definition in file blast_objmgr_tools.cpp.