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.