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

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Detailed Description

Queueing and Polling code for Remote Blast API.

Definition in file remote_blast.cpp.

#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <serial/iterator.hpp>
#include <algo/blast/api/remote_blast.hpp>
#include <algo/blast/api/blast_options_builder.hpp>
#include <objects/blast/blastclient.hpp>
#include <objects/blast/blast__.hpp>
#include <objects/blast/names.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/scoremat/Pssm.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include "psiblast_aux_priv.hpp"
#include <util/format_guess.hpp>
#include <serial/objistrxml.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>

Include dependency graph for remote_blast.cpp:

Go to the source code of this file.

Typedefs
typedef list< CRef< objects::CBlast4_error > >	TErrorList
	Error value type used by Blast4 ASN.1 objects.
Functions
	USING_SCOPE (objects)
static bool	s_SearchPending (CRef< objects::CBlast4_reply > reply)
	Determine whether the search is still running.
static CRef< CBlast4_mask >	s_CreateBlastMask (const CPacked_seqint &packed_int, EBlastProgramType program)
	Creates a Blast4-mask which is supposed to contain all masked locations for a given query sequence and frame, all of which are in the packed_int argument.
static void	s_FlattenBioseqSet (const CBioseq_set &bss, list< CRef< CBioseq > > &seqs)
static const string	kNoRIDSpecified ("Cannot fetch query info: No RID was specified.")
EBlastProgramType	NetworkProgram2BlastProgramType (const string &program, const string &service)
	Function to convert from program and service name into the CORE BLAST program type This is based on the values set in the various CBlastOptionsHandle subclasses (look for SetRemoteProgramAndService_Blast3 in include tree).
objects::EBlast4_frame_type	FrameNumber2NetworkFrame (int frame, EBlastProgramType program)
	Converts the return value of CSeqLocInfo::GetFrame into the Blast4-frame-type field.
CSeqLocInfo::ETranslationFrame	NetworkFrame2FrameNumber (objects::EBlast4_frame_type frame, EBlastProgramType program)
	Converts Blast4-frame-type into CSeqLocInfo::ETranslationFrame.
static void	s_ExtractQueryIdsFromBioseqSet (const CBioseq_set &bss, CSearchResultSet::TQueryIdVector &query_ids)
	Extract the query IDs from a CBioseq_set.
CRef< objects::CBlast4_request >	ExtractBlast4Request (CNcbiIstream &in)
	Extract a Blast4-request (a.k.a.

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