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NCBI C++ ToolKit: src/algo/dustmask/symdust.cpp Source File

: start_( 0 ), stop_( 0 ), max_size_( window - 2 ), low_k_( low_k ),

L( 0 ),

( perfect_list ), thresholds_( thresholds ),

r_w( 0 ), r_v( 0 ), num_diff( 0 )

std::fill(

,

+ 64, 0 );

std::fill(

,

+ 64, 0 );

triplet_list_.pop_back();

rem_triplet_info( r_w, c_w, s );

( c_w[s] == 0 ) --num_diff;

triplet_list_.push_front(

);

( c_w[

] == 0 ) ++num_diff;

add_triplet_info( r_w, c_w,

);

( num_diff <= 1 ) {

.insert(

.begin(),

( start_, stop_ + 1, 0, 0 ) );

( triplet_list_.size() >= max_size_ ) {

( num_diff <= 1 ) {

shift_high(

);

triplet_list_.pop_back();

rem_triplet_info( r_w, c_w, s );

( c_w[s] == 0 ) --num_diff;

rem_triplet_info( r_v, c_v, s );

triplet_list_.push_front(

);

( c_w[

] == 0 ) ++num_diff;

add_triplet_info( r_w, c_w,

);

add_triplet_info( r_v, c_v,

);

off = triplet_list_.size() - (L - start_) - 1;

rem_triplet_info( r_v, c_v, triplet_list_[off] );

}

( triplet_list_[off--] !=

);

( triplet_list_.size() >= max_size_ && num_diff <= 1 ) {

.insert(

.begin(),

( start_, stop_ + 1, 0, 0 ) );

perfect_list_type::iterator perfect_iter_type;

perfect_iter_type perfect_iter =

.begin();

max_perfect_score = 0;

( ; it != iend; ++it, ++

, --pos ) {

add_triplet_info( score, counts, *it );

( perfect_iter !=

.end()

&& pos <= perfect_iter->bounds_.first ) {

( max_perfect_score == 0

|| max_len*perfect_iter->score_

> max_perfect_score*perfect_iter->len_ ) {

max_perfect_score = perfect_iter->score_;

max_len = perfect_iter->len_;

( max_perfect_score == 0

|| score*max_len >= max_perfect_score*

) {

max_perfect_score = score;

perfect_iter =

.insert(

perfect_iter,

( pos, stop_ + 1,

max_perfect_score,

) );

( !

.empty() ) {

(

.first < wstart ) {

( !res.empty() ) {

( s +

>= b1.first ) {

res.back().second =

( s, b1.second );

( !

.empty() &&

.back().bounds_.first < wstart ) {

std::unique_ptr< CSymDustMasker::TMaskList >

std::unique_ptr< TMaskList > res(

);

( stop >= seq.size() )

stop = seq.size() - 1;

( stop > 2 + start )

c1 = *it, c2 = *++it;

it.SetPos(start + w.

() + 2);

( !

&& it.GetPos() <= stop )

( it.GetPos() <= stop ) {

( !

.empty() ) {

std::unique_ptr< CSymDustMasker::TMaskList >

{

(*

)( seq, 0, seq.size() - 1 ); }

objects::CSeq_id & seq_id,

std::unique_ptr< TMaskList > res = (*this)( seq );

locs.reserve( res->size() );

( TMaskList::const_iterator it = res->begin(); it != res->end(); ++it )

objects::CSeq_loc( seq_id, it->first, it->second ) ) );

std::unique_ptr< TMaskList > res = (*this)( seq );

( TMaskList::const_iterator it = res->begin(); it != res->end(); ++it )

->AddInterval( seq_id, it->first, it->second );

bool shift_high(triplet_type t)

bool shift_window(triplet_type t)

bool needs_processing() const

triplets(size_type window, Uint1 low_k, perfect_list_type &perfect_list, thres_table_type &thresholds)

impl_type::const_iterator impl_citer_type

CSymDustMasker(Uint4 level=DEFAULT_LEVEL, size_type window=static_cast< size_type >(DEFAULT_WINDOW), size_type linker=static_cast< size_type >(DEFAULT_LINKER))

Object constructor.

Uint1 triplet_type

Type representing a triplet value.

std::list< perfect > perfect_list_type

Type representing a list of perfect intervals.

static const Uint4 DEFAULT_LEVEL

Default value of score threshold.

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.

static const triplet_type TRIPLET_MASK

Selects the significant bits in triplet_type.

CRef< objects::CPacked_seqint > GetMaskedInts(objects::CSeq_id &seq_id, const sequence_type &seq)

Mask a sequence and return result as a CPacked_seqint instance.

std::unique_ptr< TMaskList > operator()(const sequence_type &seq)

Mask a sequence.

void GetMaskedLocs(objects::CSeq_id &seq_id, const sequence_type &seq, std::vector< CConstRef< objects::CSeq_loc > > &locs)

Mask a sequence and return result as a sequence of CSeq_loc objects.

static const Uint4 DEFAULT_LINKER

Default value of the longest distance between consequtive masked intervals at which they should be me...

static const Uint4 DEFAULT_WINDOW

Default window size.

void save_masked_regions(TMaskList &res, size_type w, size_type start)

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.

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.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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