NCBI C++ ToolKit
Classes | Functions
blast_objmgr_priv.hpp File Reference

Definitions which are dependant on the NCBI C++ Object Manager. More...

#include "blast_setup.hpp"
#include <algo/blast/api/sseqloc.hpp>
#include <algo/blast/api/blast_seqinfosrc.hpp>
#include <algo/blast/api/blast_types.hpp>
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Classes

class  CBlastQuerySourceOM
 Implements the object manager dependant version of the IBlastQuerySource. More...
 

Functions

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 SetupQueryInfo (const CBlastQueryVector &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...
 
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...
 

Detailed Description

Definitions which are dependant on the NCBI C++ Object Manager.

Definition in file blast_objmgr_priv.hpp.

Modified on Thu Feb 29 12:18:26 2024 by modify_doxy.py rev. 669887