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

Auxiliary functions for BLAST. More...

#include <corelib/ncbiobj.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/blast_results.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <algo/blast/api/query_data.hpp>
#include <algo/blast/api/blast_options.hpp>
#include <algo/blast/api/setup_factory.hpp>
#include "split_query.hpp"
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Classes

struct  TQueryMessagesLessComparator
 
struct  TQueryMessagesEqualComparator
 
struct  SBlastSetupData
 Return type of BlastSetupPreliminarySearch. More...
 

Functions

CConstRef< objects::CSeq_loc > CreateWholeSeqLocFromIds (const list< CRef< objects::CSeq_id > > seqids)
 Create a single CSeq_loc of type whole from the first id in the list. More...
 
void Blast_Message2TSearchMessages (const Blast_Message *blmsg, const BlastQueryInfo *query_info, TSearchMessages &messages)
 Converts the Blast_Message structure into a TSearchMessages object. More...
 
string BlastErrorCode2String (Int2 error_code)
 Returns a string containing a human-readable interpretation of the error_code passed as this function's argument. More...
 
CRef< SBlastSetupDataBlastSetupPreliminarySearch (CRef< IQueryFactory > query_factory, CRef< CBlastOptions > options, size_t num_threads=1)
 Set up internal data structures used by the BLAST CORE engine. More...
 
CRef< SBlastSetupDataBlastSetupPreliminarySearchEx (CRef< IQueryFactory > qf, CRef< CBlastOptions > options, CConstRef< CPssmWithParameters > pssm, BlastSeqSrc *seqsrc, size_t num_threads)
 Extended interface to set up internal data structures used by the BLAST CORE engine. More...
 
void BuildBlastAncillaryData (EBlastProgramType program, const vector< CConstRef< CSeq_id > > &query_ids, const BlastScoreBlk *sbp, const BlastQueryInfo *qinfo, const TSeqAlignVector &alignments, const EResultType result_type, CSearchResultSet::TAncillaryVector &retval)
 Builds an CSearchResultSet::TAncillaryVector. More...
 
CRef< CSearchResultSetBlastBuildSearchResultSet (const vector< CConstRef< CSeq_id > > &query_ids, const BlastScoreBlk *sbp, const BlastQueryInfo *qinfo, EBlastProgramType program, const TSeqAlignVector &alignments, TSearchMessages &messages, const vector< TSeqLocInfoVector > &subj_masks, const TSeqLocInfoVector *query_masks=NULL, const EResultType result_type=ncbi::blast::eDatabaseSearch)
 Build a CSearchResultSet from internal BLAST data structures. More...
 

Detailed Description

Auxiliary functions for BLAST.

Definition in file blast_aux_priv.hpp.

Modified on Sun Jul 14 04:56:02 2024 by modify_doxy.py rev. 669887