NCBI C++ ToolKit
Functions
winmask_filter.cpp File Reference

Blast wrappers for WindowMasker filtering. More...

#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/windowmask_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.

Go to the SVN repository for this file.

Functions

 USING_SCOPE (objects)
 
static string s_WINDOW_MASKER_STAT_FILE_NAME ("wmasker.obinary")
 
static string s_WINDOW_MASKER_PATH (kEmptyStr)
 
 DEFINE_STATIC_MUTEX (InitMutex)
 
int WindowMaskerPathInit (const string &window_masker_path)
 Initialize the path to the windowmasker data files. More...
 
void WindowMaskerPathReset ()
 Resets the path to the windowmasker data files. More...
 
string WindowMaskerPathGet ()
 Retrieves the path to the windowmasker data files. More...
 
CSeqMaskers_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. More...
 
void Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptions *opts)
 Find Window Masker filtered locations using BlastOptions. More...
 
void Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptionsHandle *opts_handle)
 Find Window Masker filtered locations using a BlastOptionsHandle. More...
 
void Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptionsHandle *opts_handle)
 Find Window Masker filtered locations using a BlastOptionsHandle. More...
 
void Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const string &lstat)
 Find Window Masker filtered locations by database name. More...
 
void Blast_FindWindowMaskerLoc (TSeqLocVector &query, const string &lstat)
 Find Window Masker filtered locations on TSeqLocVector by database name. More...
 
static string s_FindPathToWM (void)
 Find the path to the window masker files, first checking the (optionally set) value passed to the WindowMaskerPathInit function, then the environment variable WINDOW_MASKER_PATH, then the section WINDOW_MASKER, label WINDOW_MASKER_PATH in the NCBI configuration file. More...
 
string WindowMaskerTaxidToDb (const string &window_masker_path, int taxid)
 Get the windowmasker file path for a given taxid and base path. More...
 
string WindowMaskerTaxidToDb (int taxid)
 Get the windowmasker file path for a given taxid. More...
 
void Blast_FindWindowMaskerLocTaxId (CBlastQueryVector &query, int taxid)
 Find Window Masker filtered locations by taxonomic ID. More...
 
void Blast_FindWindowMaskerLocTaxId (TSeqLocVector &query, int taxid)
 Find Window Masker filtered locations on a TSeqLocVector by Taxid. More...
 
static void s_OldGetTaxIdWithWindowMaskerSupport (set< int > &supported_taxids)
 
void GetTaxIdWithWindowMaskerSupport (set< int > &supported_taxids)
 This function returns a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support organism specific filtering. More...
 

Detailed Description

Blast wrappers for WindowMasker filtering.

Definition in file winmask_filter.cpp.

Modified on Wed Jul 24 17:19:25 2024 by modify_doxy.py rev. 669887