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

---

Detailed Description

Blast wrappers for WindowMasker filtering.

Definition in file winmask_filter.cpp.

#include <ncbi_pch.hpp>
#include "winmask_filter.hpp"
#include <sstream>
#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 <algo/winmask/seq_masker.hpp>
#include <corelib/env_reg.hpp>

Include dependency graph for winmask_filter.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
CSeqMasker *	s_BuildSeqMasker (const string &lstat)
void	s_BuildMaskedRanges (CSeqMasker::TMaskList &masks, const CSeq_loc &seqloc, CSeq_id &query_id, TMaskedQueryRegions *mqr, CRef< CSeq_loc > *psl)
template<class TQueries>
void	Blast_FindWindowMaskerLoc_Fwd (TQueries &query, const CBlastOptions *opts)
template<class TQueries>
void	Blast_FindWindowMaskerLoc_Fwd (TQueries &query, const CBlastOptionsHandle *opts_handle)
void	Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptions *opts_handle)
	Find Window Masker filtered locations using a BlastOptions.
void	Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptions *opts)
	Find Window Masker filtered locations using BlastOptions.
void	Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptionsHandle *opts_handle)
	Find Window Masker filtered locations using a BlastOptionsHandle.
void	Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptionsHandle *opts_handle)
	Find Window Masker filtered locations using a BlastOptionsHandle.
void	Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const string &lstat)
	Find Window Masker filtered locations by database name.
void	Blast_FindWindowMaskerLoc (TSeqLocVector &query, const string &lstat)
	Find Window Masker filtered locations on TSeqLocVector by database name.
static void	s_VersionNumberTransform (const string &a, vector< int > &b)
static bool	s_VersionNumberLess (const string &a, const string &b)
static string	s_FindPathToWM (void)
	Find the path to the window masker files, first checking the environment variable WINDOW_MASKER_PATH, then the section WINDOW_MASKER, label WINDOW_MASKER_PATH in the NCBI configuration file.
static string	s_WindowMaskerTaxidToDb (int taxid)
void	Blast_FindWindowMaskerLocTaxId (CBlastQueryVector &query, int taxid)
	Find Window Masker filtered locations by taxonomic ID.
void	Blast_FindWindowMaskerLocTaxId (TSeqLocVector &query, int taxid)
	Find Window Masker filtered locations on a TSeqLocVector by Taxid.
Variables
static char const	rcsid [] = "$Id: winmask_filter.cpp 141260 2008-09-24 19:30:13Z camacho $"

---

Variable Documentation

char const rcsid[] = "$Id: winmask_filter.cpp 141260 2008-09-24 19:30:13Z camacho $" [static]

Definition at line 39 of file winmask_filter.cpp.

---