NCBI C++ ToolKit
dust_filter.hpp
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1 /* $Id: dust_filter.hpp 33815 2007-05-04 17:18:18Z kazimird $
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26  * Author: Tom Madden
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28  * Initial Version Creation Date: June 20, 2005
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30  * */
31 
32 /// @file dust_filter.hpp
33 /// Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.
34 
35 #ifndef ALGO_BLAST_API__DUST_FILTER_HPP
36 #define ALGO_BLAST_API__DUST_FILTER_HPP
37 
42 
43 /** @addtogroup AlgoBlast
44  *
45  * @{
46  */
47 
49 BEGIN_SCOPE(blast)
50 
51 /** Finds dust locations for a given set of sequences by calling the the symmetric dust lib.
52  * The locations are saved in the respective fields of the SSeqLoc structures. If previous masks
53  * exist, they are combined with the new masks.
54  *
55  * @param query Vector of sequence locations. [in] [out]
56  * @param nucl_handle options handle for blast search [in]
57  */
59 void
61  const CBlastNucleotideOptionsHandle* nucl_handle);
62 
63 /** Overloaded version of the function above which takes the filtering
64  * implementation's arguments directly, TSeqLocVector version.
65  * @param query Vector of sequence locations. [in] [out]
66  * @param level Dust filtering level argument [in]
67  * @param window Dust filtering window argument [in]
68  * @param linker Dust filtering linker argument [in]
69  */
71 void
76 
77 /** Overloaded version of the function above which takes the filtering
78  * implementation's arguments directly, CBlastQueryVector version.
79  * @param query Vector of sequence locations. [in] [out]
80  * @param level Dust filtering level argument [in]
81  * @param window Dust filtering window argument [in]
82  * @param linker Dust filtering linker argument [in]
83  */
85 void
90 
91 END_SCOPE(blast)
93 
94 /* @} */
95 
96 #endif /* ALGO_BLAST_API__DUST_FILTER_HPP */
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
Declares the CBlastNucleotideOptionsHandle class.
Handle to the nucleotide-nucleotide options to the BLAST algorithm.
Query Vector.
Definition: sseqloc.hpp:276
static const Uint4 DEFAULT_LEVEL
Default value of score threshold.
Definition: symdust.hpp:103
static const Uint4 DEFAULT_LINKER
Default value of the longest distance between consequtive masked intervals at which they should be me...
Definition: symdust.hpp:105
static const Uint4 DEFAULT_WINDOW
Default window size.
Definition: symdust.hpp:104
void Blast_FindDustFilterLoc(TSeqLocVector &queries, const CBlastNucleotideOptionsHandle *nucl_handle)
Finds dust locations for a given set of sequences by calling the the symmetric dust lib.
Definition: dust_filter.cpp:60
uint32_t Uint4
4-byte (32-bit) unsigned integer
Definition: ncbitype.h:103
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
Definition of SSeqLoc structure.
vector< SSeqLoc > TSeqLocVector
Vector of sequence locations.
Definition: sseqloc.hpp:129
static string query
Modified on Wed Apr 17 13:10:17 2024 by modify_doxy.py rev. 669887