NCBI C++ ToolKit
Classes | Functions | Variables
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.

Modified on Sun Feb 25 03:00:34 2024 by modify_doxy.py rev. 669887