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

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Detailed Description

C++ version of repeats filtering.

Definition in file repeats_filter_cxx.cpp.

#include <ncbi_pch.hpp>
#include <serial/iterator.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objmgr/util/sequence.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/seqsrc_seqdb.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/repeats_filter.hpp>
#include "blast_setup.hpp"
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_filter.h>
#include <algo/blast/api/blast_aux.hpp>

Include dependency graph for repeats_filter_cxx.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
static CSeq_loc *	s_BlastSeqLoc2CSeqloc (const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list)
	Convert a list of mask locations to a CSeq_loc object.
static CSeq_loc *	s_BlastSeqLoc2CSeqloc (SSeqLoc &query, BlastSeqLoc *loc_list)
	Convert a list of mask locations to a CSeq_loc object.
TMaskedQueryRegions	s_BlastSeqLoc2MaskedRegions (const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list, EBlastProgramType program)
	Convert a list of mask locations to TMaskedQueryRegions.
static void	s_SeqAlignToBlastSeqLoc (const CSeq_align_set &alignment, BlastSeqLoc **locs)
	Build a list of BlastSeqLoc's from a set of Dense-seg contained in a Seq-align-set.
static void	s_FillMaskLocFromBlastResults (TSeqLocVector &query, const CSearchResultSet &results)
	Fills the mask locations in the query SSeqLoc structures, as if it was a lower case mask, given the results of a BLAST search against a database of repeats.
static void	s_FillMaskLocFromBlastResults (CBlastQueryVector &query, const CSearchResultSet &results, EBlastProgramType program)
	Fills the mask locations in the BlastSearchQuery structures, as if it was a lower case mask, given the results of a BLAST search against a database of repeats.
static CRef< CBlastOptionsHandle >	s_CreateRepeatsSearchOptions ()
	Create an options handle with the defaults set for a search for repeats.
void	Blast_FindRepeatFilterLoc (TSeqLocVector &query_loc, const CBlastOptionsHandle *opts_handle)
	Finds repeats locations for a given set of sequences.
void	Blast_FindRepeatFilterLoc (TSeqLocVector &query, const char *filter_db)
	Overloaded version of the function above which takes the name of the repeats filtering database to use, and a TSeqLocVector.
void	Blast_FindRepeatFilterLoc (CBlastQueryVector &query, const char *filter_db)
	Overloaded version of the function above which takes the name of the repeats filtering database to use, and a CBlastQueryVector.
Variables
static char const	rcsid [] = "$Id: repeats_filter_cxx.cpp 125908 2008-04-28 17:54:36Z camacho $"

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Variable Documentation

char const rcsid[] = "$Id: repeats_filter_cxx.cpp 125908 2008-04-28 17:54:36Z camacho $" [static]

Definition at line 40 of file repeats_filter_cxx.cpp.

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