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

---

Detailed Description

Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.

Definition in file dust_filter.cpp.

#include <ncbi_pch.hpp>
#include "dust_filter.hpp"
#include <serial/iterator.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <objmgr/seq_vector.hpp>
#include <algo/dustmask/symdust.hpp>
#include <string.h>

Include dependency graph for dust_filter.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
void	Blast_FindDustFilterLoc (TSeqLocVector &query, const CBlastNucleotideOptionsHandle *nucl_handle)
	Finds dust locations for a given set of sequences by calling the the symmetric dust lib.
static CRef< CSeq_loc_Mapper >	s_CreateSeqLocMapper (CSeq_id &query_id, const CSeq_loc *target_seqloc, CScope *scope)
	Auxiliary function to create CSeq_loc_Mapper from a copy of the target Seq-loc.
void	s_CombineDustMasksWithUserProvidedMasks (CSeqVector &data, CConstRef< CSeq_loc > seqloc, CRef< CScope > scope, CRef< CSeq_id > query_id, CRef< CSeq_loc > &orig_query_mask, Uint4 level, Uint4 window, Uint4 linker)
void	Blast_FindDustFilterLoc (TSeqLocVector &query, Uint4 level=CSymDustMasker::DEFAULT_LEVEL, Uint4 window=CSymDustMasker::DEFAULT_WINDOW, Uint4 linker=CSymDustMasker::DEFAULT_LINKER)
	Overloaded version of the function above which takes the filtering implementation's arguments directly, TSeqLocVector version.
void	Blast_FindDustFilterLoc (CBlastQueryVector &query, Uint4 level=CSymDustMasker::DEFAULT_LEVEL, Uint4 window=CSymDustMasker::DEFAULT_WINDOW, Uint4 linker=CSymDustMasker::DEFAULT_LINKER)
	Overloaded version of the function above which takes the filtering implementation's arguments directly, CBlastQueryVector version.
Variables
static char const	rcsid [] = "$Id: dust_filter.cpp 161402 2009-05-27 17:35:47Z camacho $"

---

Variable Documentation

char const rcsid[] = "$Id: dust_filter.cpp 161402 2009-05-27 17:35:47Z camacho $" [static]

Definition at line 37 of file dust_filter.cpp.

---