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NCBI C++ ToolKit: include/algo/dustmask/symdust.hpp Source File

33 #ifndef C_SYM_DUST_MASKER_HPP 34 #define C_SYM_DUST_MASKER_HPP 82 case

78:

return

(m_Random.GetRand() & 0x3);

89 typedef

objects::CSeqVector

seq_t

;

103 static const Uint4

DEFAULT_LEVEL = 20;

104 static const Uint4

DEFAULT_WINDOW = 64;

105 static const Uint4

DEFAULT_LINKER = 1;

128

: bounds_( start, stop ), score_( score ), len_(

len

)

150

static_cast< size_type >

( DEFAULT_WINDOW ),

152

static_cast< size_type >

( DEFAULT_LINKER ) );

159

std::unique_ptr< TMaskList > operator()(

const sequence_type

& seq );

168

std::unique_ptr< TMaskList > operator()(

const sequence_type

& seq,

179

objects::CSeq_id & seq_id,

254 return count

< triplet_list_.size() &&

255

10*r_w > thresholds_[

count

];

277

{

+= c[

]; ++c[

]; }

289

{ --c[

];

-= c[

]; }

319 void

save_masked_regions(

void rem_triplet_info(Uint4 &r, counts_type &c, triplet_type t)

void add_triplet_info(Uint4 &r, counts_type &c, triplet_type t)

thres_table_type & thresholds_

std::deque< triplet_type > impl_type

bool needs_processing() const

impl_type::const_iterator impl_citer_type

Looks for low complexity parts of sequences according to the symmetric version of DUST algorithm.

Uint1 triplet_type

Type representing a triplet value.

objects::CSeqVector seq_t

std::list< perfect > perfect_list_type

Type representing a list of perfect intervals.

sequence_type::const_iterator seq_citer_type

std::pair< size_type, size_type > TMaskedInterval

Type respresenting an interval selected for masking.

std::vector< Uint4 > thres_table_type

Table type to store score sum thresholds for each window length.

CIupac2Ncbi2na_converter convert_t

thres_table_type thresholds_

seq_t sequence_type

Public sequence type.

sequence_type::size_type size_type

Integer size type corresponding to sequence_type.

std::vector< TMaskedInterval > TMaskList

Type representing a list of masked intervals.

The NCBI C++ standard methods for dealing with std::string.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALGODUSTMASK_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Defines Limits for the types used in NCBI C/C++ toolkit.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Uint1 operator()(Uint1 r)

perfect(size_type start, size_type stop, Uint4 score, size_type len)

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