NCBI C++ ToolKit
win_mask_sdust_masker.hpp
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1 /* $Id: win_mask_sdust_masker.hpp 78368 2017-06-13 18:26:55Z rackerst $
2  * ===========================================================================
3  *
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5  * National Center for Biotechnology Information
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24  * ===========================================================================
25  *
26  * Author: Aleksandr Morgulis
27  *
28  * File Description:
29  * CSDustMasker class definition.
30  *
31  */
32 
33 #ifndef C_SDUST_MASKER_H
34 #define C_SDUST_MASKER_H
35 
36 #include <string>
37 
38 #include <corelib/ncbitype.h>
39 
42 
44 
45 /**
46  **\brief This class encapsulates the dusting functionality of winmask.
47  **
48  **/
50 {
51 public:
52 
53  /**\brief Type representing a masked subsequence of a sequence. */
55 
56  /**\brief Type representing a list of masked segments. */
58 
59  /**
60  **\brief Object constructor.
61  **
62  **\param window dust window
63  **\param level dust level
64  **\param linker dust linker
65  **
66  **/
67  CSDustMasker( Uint4 window, Uint4 level, Uint4 linker );
68 
69  /**
70  **\brief Object destructor.
71  **
72  **/
73  ~CSDustMasker();
74 
75  /**
76  **\brief Function performing the actual dusting.
77  **
78  **\param data sequence data in IUPACNA format
79  **\return pointer to a list of dusted sequences
80  **
81  **/
82  TMaskList * operator()( const objects::CSeqVector & data,
83  const TMaskList & exclude_ranges );
84 
85 private:
86 
87  Uint4 window; /**<\internal dust window in base pairs */
88 
89  CSymDustMasker duster_; /**<\internal symmetric dust masker */
90 };
91 
93 
94 #endif
This class encapsulates the dusting functionality of winmask.
CSDustMasker(Uint4 window, Uint4 level, Uint4 linker)
Object constructor.
~CSDustMasker()
Object destructor.
CSeqMasker::TMaskList TMaskList
Type representing a list of masked segments.
CSeqMasker::TMaskedInterval TMaskedInterval
Type representing a masked subsequence of a sequence.
TMaskList * operator()(const objects::CSeqVector &data, const TMaskList &exclude_ranges)
Function performing the actual dusting.
CSymDustMasker duster_
pair< TSeqPos, TSeqPos > TMaskedInterval
Type representing a masked interval within a sequence.
Definition: seq_masker.hpp:67
vector< TMaskedInterval > TMaskList
A type representing the total of masking information about a sequence.
Definition: seq_masker.hpp:74
Looks for low complexity parts of sequences according to the symmetric version of DUST algorithm.
Definition: symdust.hpp:61
char data[12]
Definition: iconv.c:80
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 BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
Defines Limits for the types used in NCBI C/C++ toolkit.
Modified on Wed Apr 24 14:14:54 2024 by modify_doxy.py rev. 669887