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NCBI C++ ToolKit: src/algo/winmask/seq_masker.cpp Source File

arg_window_size,

arg_window_step,

arg_cutoff_score,

arg_set_max_score,

arg_set_min_score,

arg_merge_cutoff_score,

arg_abs_merge_cutoff_dist,

arg_mean_merge_cutoff_dist,

arg_merge_unit_step,

& arg_trigger,

( arg_window_size ), window_step( arg_window_step ),

unit_step( arg_unit_step ),

merge_pass( arg_merge_pass ),

merge_cutoff_score( arg_merge_cutoff_score ),

abs_merge_cutoff_dist( arg_abs_merge_cutoff_dist ),

mean_merge_cutoff_dist( arg_mean_merge_cutoff_dist ),

merge_unit_step( arg_merge_unit_step ),

trigger( arg_trigger ==

? eTrigger_Mean

discontig( arg_discontig ), pattern( arg_pattern )

( window_size < ustat->UnitSize() ) {

std::ostringstream os;

<<

( arg_merge_pass )

unique_ptr<CSeqMaskerWindow> window_ptr

start = 0, end = 0, cend = 0;

limit = textend;

ts = (*trigger_score)();

s = (*score)();

( window.

() > cend )

start = end = cend = 0;

( od != 0 && od->

!= 0 )

adv = window.

();

( !booster.

() )

( ts < cutoff_score )

( window.

() > cend + 1 )

start = end = cend = 0;

cend = window.

();

( window.

() > cend + 1 )

start = window.

();

start = window.

();

cend = end = window.

();

(

->size() < 2 )

.release();

TMaskList::iterator jtmp =

->end();

( TMaskList::iterator

=

->begin(), j = --jtmp;

masked.push_back(

(

->first,

->second, unit_size,

nstart = (

++)->second - unit_size + 2;

unmasked.push_back(

( nstart,

->first + unit_size - 2,

unit_size,

, *

) );

masked.push_back(

( (

->rbegin())->first,

(

->rbegin())->second,

unit_size,

, *

) );

TMList::iterator ii = masked.begin();

TMList::iterator j = unmasked.begin();

TMList::iterator k = ii,

= ii;

( ; ii != masked.end(); k =

= ii, --k, ++

)

ldist = (ii != masked.begin())

? ii->start - k->end - 1 : 0;

TMList::iterator tmpend = masked.end();

rdist = (ii != tmpend)

?

->start - ii->end - 1 : 0;

lavg = 0.0, ravg = 0.0;

can_go_left =

&& ldist

can_go_right = rdist

TMList::iterator

= j; --

;

ravg =

( ii, j, unit_size );

k->avg =

( k, --j, unit_size );

<< k->start <<

<< k->end

<< ii->start <<

<< ii->end );

( masked, k, unmasked, j );

( can_go_left )

k->avg =

( k, --j, unit_size );

<< k->start <<

<< k->end

<< ii->start <<

<< ii->end );

( masked, k, unmasked, j );

( ii = masked.begin(), j = unmasked.begin(), k = ii++;

ii != masked.end(); (k = ii++), j++ )

(

<< k->start <<

<< k->end

<< ii->start <<

<< ii->end );

k->avg =

( k, j, unit_size );

( masked, k, unmasked, j );

( ++ii == masked.end() )

;

( TMList::const_iterator iii = masked.begin(); iii != masked.end(); ++iii )

.release();

TMList::iterator & umi,

unit_size )

TMList::iterator

= mi++;

a1 =

->avg, a2 = umi->avg, a3 = mi->avg;

(a1*n1 + a2*n2 + a3*n3)/

;

& um, TMList::iterator & umi )

TMList::iterator

= mi++;

umi = um.erase( umi );

;

;

;

;

;

;

: start( arg_start ), end( arg_end ), avg( 0.0 )

( window->

() <

)

TMaskList::const_iterator

( src->begin() );

TMaskList::const_iterator send( src->end() );

TMaskList::iterator di( dest->begin() );

TMaskList::iterator dend( dest->end() );

( di != dend && di->first <

->first )

seg = *(

++);

(

->first < di->first ) {

next_seg = *(

++);

next_seg = *(

++);

}

( di != dend ) {

( seg.second + 1 < next_seg.first ) {

res.push_back( seg );

( seg.second < next_seg.second ) {

seg.second = next_seg.second;

res.push_back( seg );

ncbi::TMaskedQueryRegions mask

Interface to the bit array used to check if the score of a unit is below t_extend.

bool Check()

Check if the current state of the window and advance.

Factory class to generate an appropriate CSeqMaskerIstat derived class based on the format name.

CSeqMaskerWindow::TUnit AmbigUnit() const

Get the value of the unit used to represent an ambuguity.

Uint4 get_textend() const

Get the value of T_extend.

virtual Uint1 UnitSize() const =0

Get the unit size.

const optimization_data * get_optimization_data() const

Get the data structure optimization parameters.

Uint4 get_threshold() const

Get the value of T_threshold.

Average unit score form the start of the sequence to the end of current window.

Score function object computing mean of unit in a window.

The score function object that computes maxmin of k consecutive units in a window.

Abstract base class for score function objects.

virtual void PreAdvance(Uint4 step)=0

Window advancement notification.

void SetWindow(const CSeqMaskerWindow &new_window)

Set the window object that should be used for score computation.

virtual void PostAdvance(Uint4 step)=0

Window advancement notification.

static Uint1 BitCount(Uint4 mask, Uint1 bit_value=1)

Count the bits with given value in a given bit pattern.

Windows with units that may contain ambiguities.

Window iterator for discontiguous units used for the merging pass.

Window iterator used for discontiguous units.

Sliding window skipping over the ambiguities.

Uint4 Step() const

Get the current value of the window step.

Uint4 End() const

Get the current ending position of the window.

Uint4 Start() const

Get the current starting position of the window.

Uint4 TUnit

Integer type used to represent units within a window.

Represents different error situations that can occur in the masking process.

@ eValidation

Insconsistent internal parameters.

@ eLstatSyntax

Error parsing the length statistics file.

@ eLstatParam

Error deducing parameters from lstat or command line.

@ eScoreAllocFail

Error allocating the score function object.

@ eLstatStreamIpenFail

Error opening the length statistics file.

@ eScoreP3AllocFail

Error allocating the score function object for merging pass.

virtual const char * GetErrCodeString() const override

Get the exception description string.

Main interface to window based masker functionality.

void Merge(TMList &m, TMList::iterator mi, TMList &um, TMList::iterator &umi) const

~CSeqMasker()

Object destructor.

static void MergeMaskInfo(TMaskList *dest, const TMaskList *src)

Merge together two result lists.

@ eTrigger_Min

Using min score of k unit in the window.

CSeqMaskerScore * trigger_score

Uint4 abs_merge_cutoff_dist

CSeqMaskerScore * score_p3

pair< TSeqPos, TSeqPos > TMaskedInterval

Type representing a masked interval within a sequence.

Uint4 mean_merge_cutoff_dist

TMaskList * DoMask(const objects::CSeqVector &data, TSeqPos start, TSeqPos end) const

vector< TMaskedInterval > TMaskList

A type representing the total of masking information about a sequence.

TMaskList * operator()(const objects::CSeqVector &data) const

Sequence masking operator.

double MergeAvg(TMList::iterator mi, const TMList::iterator &umi, Uint4 unit_size) const

enum CSeqMasker::@32 trigger

static CSeqMaskerVersion AlgoVersion

Version of window masking algorithm.

CRef< CSeqMaskerIstat > ustat

CSeqMasker(const string &lstat_name, Uint1 arg_window_size, Uint4 arg_window_step, Uint1 arg_unit_step, Uint4 arg_textend, Uint4 arg_cutoff_score, Uint4 arg_max_score, Uint4 arg_min_score, Uint4 arg_set_max_score, Uint4 arg_set_min_score, bool arg_merge_pass, Uint4 arg_merge_cutoff_score, Uint4 arg_abs_merge_cutoff_dist, Uint4 arg_mean_merge_cutoff_dist, Uint1 arg_merge_unit_step, const string &arg_trigger, Uint1 tmin_count, bool arg_discontig, Uint4 arg_pattern, bool arg_use_ba, double min_pct=-1.0, double extend_pct=-1.0, double thres_pct=-1.0, double max_pct=-1.0)

Object constructor.

static const char si[8][64]

unsigned int TSeqPos

Type for sequence locations and lengths.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed 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.

unsigned int

A callback function used to compare two keys in a database.

#define WIN_MASK_ALGO_VER_MAJOR

#define WIN_MASK_ALGO_NAME

#define WIN_MASK_ALGO_VER_PATCH

#define WIN_MASK_ALGO_VER_MINOR

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Structure containing information about optimization parameters used.

Uint4 * cba_

Bit array with zeroes where all corresponding units have counts below t_extend.

Uint4 start

Start of the interval.

Uint4 end

End of the interval.

mitem(Uint4 start, Uint4 end, Uint1 unit_size, const objects::CSeqVector &data, const CSeqMasker &owner)

Object constructor.

double avg

Average score of the units in the interval.

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