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NCBI C++ ToolKit: include/algo/align/util/hit_filter.hpp Source File

<

THit>

box [] = { ph->GetQueryMin(), ph->GetQueryMax(),

ph->GetSubjMin(), ph->GetSubjMax() };

(box[

] > Finish0)?

<

THit>

THitRefs::const_iterator from,

THitRefs::const_iterator to)

THitRefs::const_iterator TCI;

THitRefs::iterator TI;

TI jj = hitrefs.begin();

THitComparator::ESortCriterion sort_type (

THitComparator::eQueryMin:

THitComparator::eSubjMin);

THitComparator sorter (sort_type);

stable_sort(hitrefs.begin(), hitrefs.end(), sorter);

accumulate(hitrefs.begin(), hitrefs.end(),

span[1] = span[3] = 0;

(

THitRefs::const_iterator ii = hitrefs.begin(),

ii_end = hitrefs.end(); ii != ii_end; ++ii) {

x = (*ii)->GetQueryMin();

x = (*ii)->GetSubjMin();

x = (*ii)->GetQueryMax();

x = (*ii)->GetSubjMax();

= minmax - maxmin + 1;

THitRefs::iterator hri_end,

min_hit_idty = .9,

retain_overlap = 0,

(unique_type) {

(hri_beg > hri_end) {

);

dim0 = hri_end - hri_beg;

dim_factor = 2;

restart =

;

(hri_beg, hri_end,

.begin());

.reserve(dim_factor * dim0);

THitRefs::iterator all_beg =

.begin();

THitRefs::iterator ii = all_beg;

(

= 0;

< dim0; ++

, ++ii) {

(

point = 0; point < 4; ++point) {

he.

= h->GetBox()[point];

where = ii->m_Point/2;

* hitrefptr = ii->m_Ptr;

((*hitrefptr)->GetId(where)->CompareOrdered(*

) != 0) {

open_hits.insert(hitrefptr);

= (*hitrefptr)->GetId(where);

iis = open_hits.find(hitrefptr);

(iis == open_hits.end()) {

open_hits.insert(hitrefptr);

open_hits.erase(iis);

curscore = (*hitrefptr)->GetScore();

(

& open_hit: open_hits) {

vector<bool> skip (dim0,

);

skip.reserve(dim_factor * dim0);

del.assign(dim0,

);

del.reserve(dim_factor * dim0);

* hitref_firstptr = &(*all_beg);

(restart ==

) {

score_best = 0;

THitRefs::iterator ii = all_beg, ii_best =

.end();

(

= 0;

< dim; ++

, ++ii) {

(skip[

] ==

) {

score = (*ii)->GetScore();

(score > score_best) {

(ii_best ==

.end()) {

(

where = min_idx; where < max_idx; ++where) {

cmin = hc->GetMin(where);

cmax = hc->GetMax(where);

(

ii_lcl=iters.first; ii_lcl != iters.second; ++ii_lcl) {

& he_lcl = *ii_lcl;

hitrefidx = he_lcl.

- hitref_firstptr;

alive = skip[hitrefidx] ==

;

= he_lcl.

== &hc;

(alive && !

) {

tie(newpos, newpoint)

cmin, cmax, min_hit_len,

min_hit_idty, & hit_new,

del[hitrefidx] = skip[hitrefidx] =

;

(++dim > 2 * dim0) {

.push_back(hit_new);

del.push_back(

);

skip.push_back(

);

box = hit_new->GetBox();

he2_lcl.

= ptr;

hit_ends.

(he2_lcl);

he3_lcl.

= ptr;

hit_ends.

(he3_lcl);

(*ptr, saved_box, margin, hit_ends, skip, hitref_firstptr);

skip[&hc - hitref_firstptr] =

;

THitRefs::iterator all_beg =

.begin(), ii = all_beg;

dim =

.size();

(

= 0;

< dim; ++

, ++ii) {

THitRefs::iterator idst = hri_beg, isrc = all_beg,

isrc_end =

.end();

(isrc != isrc_end && idst != hri_end) {

(isrc->NotEmpty()) {

(idst != hri_end) {

idst++ -> Reset(

);

phits_new->resize(0);

(isrc != isrc_end) {

(isrc->NotEmpty()) {

phits_new->push_back(*isrc);

THitRefs::iterator hri_end,

& maxlenfr,

(hri_beg > hri_end) {

);

dim0 = hri_end - hri_beg;

(

THitRefs::iterator hri = hri_beg; hri != hri_end; ++hri) {

((*hri)->GetQueryStrand() ==

) {

(*hri)->FlipStrands();

.push_back(*hri);

THitRefs::iterator ii1 =

.begin();

THitRefs::iterator ii2 =

.end(); --ii2;

(

point = 0; point < 4; ++point) {

he1.

= h1->GetBox()[point];

he2.

= h2->GetBox()[point];

(

point = 0; point < 4; ++point) {

he.

= h->GetBox()[point];

THitComparator::ESortCriterion sort_type

(THitComparator::eQueryIdSubjIdSubjStrand);

THitComparator sorter (sort_type);

stable_sort(

.begin(),

.end(), sorter);

THitRefs::iterator ib =

.begin();

( ! (*ii)->GetQueryId()->Match(*(h0->GetQueryId())) ||

! (*ii)->GetSubjId()->Match(*(h0->GetSubjId())) ||

(*ii)->GetSubjStrand() != h0->GetSubjStrand() )

c < 0?

: (c > 0?

:

ostr <<

hd_score (((*(container_candidate))->GetScore() < curscore));

hd_xl (margin + (*(container_candidate))->GetMin(where)

< (*hit)->GetMin(where));

hd_xr (margin + (*hit)->GetMax(where)

< (*(container_candidate))->GetMax(where));

(hd_score && hd_xl && hd_xr) {

hm.

= container_candidate;

hm.

= ( (*hit)->GetStart(where)

+ (*hit)->GetStop(where) ) / 2;

is_constraint = hc->GetScore() > 1e20;

(

point = 0; point < 4; ++point) {

(is_constraint ==

) {

he[point].

= box[point];

is_start = (point & 1) == 0;

is_plus = hc->GetStrand(point / 2);

he[point].

= (is_start ^ is_plus)?

:

;

i1 = where << 1, i2 = i1 | 1;

(he[i1].m_X <= he[i2].m_X) {

prev_X = phe_lo->

;

(phe_lo->

>= margin +1) {

phe_lo->

-= margin +1;

phe_hi->

+= margin;

( ii0 != ii1 && ii0->m_X+margin < prev_X ) ++ii0;

(phe_lo->

== 0) {

hitref (*(ii0->m_Ptr));

& id_lcl (hitref->GetId(ii0->m_Point/2));

ii0 != ii_start; --ii0) {

& id2 (hr->GetId(ii0->m_Point/2));

(0 != id_lcl->CompareOrdered(*id2)) {

make_pair(ii0, ii1);

vector<bool>& skip,

* hitref_firstptr)

score = h->GetScore();

(

where: {0, 1}) {

(

it = iters.first; it != iters.second; ++it) {

hitrefidx = it->m_Ptr - hitref_firstptr;

alive = skip[hitrefidx] ==

;

= it->m_Ptr == &h;

(alive && !

) {

(it->m_Ptr, (*it->m_Ptr)->GetScore(), &h, where, margin, hit_mids);

min_hit_len,

& min_idty,

lmin = h->GetMin(where), lmax = h->GetMax(where);

(retain_overlap > 0) {

(overlap >= retain_overlap) {

make_pair(-1, 0);

(cmin <= lmin && lmax <= cmax) {

make_pair(-2, 0);

ldif = cmin - lmin, rdif = lmax - cmax;

reverse = h->GetStrand(where) ? 0 : 1;

(ldif >

(min_hit_len) && rdif >

(min_hit_len)) {

(*pnew_hit)->Modify(2*where, cmax + 1);

h->Modify(rp = 2*where + 1, lmax = cmin - 1);

((*pnew_hit)->GetIdentity() < min_idty) {

make_pair((h->GetIdentity() < min_idty)? -2: rv, rp ^ reverse);

(h->GetIdentity() < min_idty) {

make_pair(cmax + 1, (2*where) ^ reverse);

make_pair(0, rp ^ reverse);

(ldif > rdif) {

(lmin <= cmin && cmin <= lmax) {

(cmin == 0)

make_pair(-2, 0);

h->Modify(rp = 2*where + 1, lmax = cmin - 1);

(lmin <= cmax && cmax <= lmax) {

h->Modify(rp = 2*where, lmin = cmax + 1);

(lmin <= cmax && cmax <= lmax) {

h->Modify(rp = 2*where, lmin = cmax + 1);

(lmin <= cmin && cmin <= lmax) {

(cmin == 0)

make_pair(-2, 0);

h->Modify(rp = 2*where + 1, lmax = cmin - 1);

(1 + lmax - lmin < min_hit_len || h->GetIdentity() < min_idty) {

make_pair(-2, 0);

make_pair(rv, rp ^ reverse);

sstrand (lhs->GetSubjStrand());

(sstrand != rhs->GetSubjStrand()) {

);

qgap ((!sstrand && where == 1)?

(

(lhs->GetQueryMin()) -

(rhs->GetQueryMax())):

(

(rhs->GetQueryMin()) -

(lhs->GetQueryMax())));

sgap ((!sstrand && where == 0)?

(

(lhs->GetSubjMin()) -

(rhs->GetSubjMax())):

(

(rhs->GetSubjMin()) -

(lhs->GetSubjMax())));

bv1 (

(qgap) == 1 &&

(sgap) > 0);

bv2 (

(sgap) == 1 &&

(qgap) > 0);

(x_lhs.size() && x_rhs.size()) {

x_gap.assign(

(sgap) - 1,

);

x_gap.assign(

(qgap) - 1,

);

(where == 0 || sstrand) {

xcript = x_lhs + x_gap + x_rhs;

xcript = x_rhs + x_gap + x_lhs;

rv.

(

(h->GetId(0), h->GetStart(0), h->GetStrand(0),

h->GetId(1), h->GetStart(1), h->GetStrand(1),

rv->SetId(0, lhs->GetId(0));

rv->SetId(1, lhs->GetId(1));

lhs->GetQueryStart(), rhs->GetQueryStop(),

lhs->GetSubjStart(), rhs->GetSubjStop()

(

, ii, xcript) {

:

: q0 = q; q += qinc; s0 = s; s += sinc;

;

: s0 = s; s += sinc;

;

: q0 = q; q += qinc;

;

);

THitRefs::iterator ii_beg,

THitRefs::iterator ii_end,

& maxlenfr,

THitComparator::ESortCriterion sort_type (

THitComparator::eQueryMinScore:

THitComparator::eSubjMinScore);

THitComparator sorter (sort_type);

stable_sort(ii_beg, ii_end, sorter);

THitRefs::iterator TIter;

(TIter ii = ii_beg; ii != ii_end; ++ii) {

cmax = (*ii)->GetMax(where);

(++jj; jj != ii_end && cmax >= cmin; ++jj) {

cmin = (*jj)->GetMin(where);

(cmax + 1 == cmin) {

can_merge =

;

where2 (where ^ 1);

subj_strand ((*ii)->GetSubjStrand());

can_merge = (*ii)->GetMax(where2) < (*jj)->GetMin(where2);

can_merge = (*jj)->GetMax(where2) < (*ii)->GetMin(where2);

he_ii.

= &(*ii);

he_ii.

= (*ii)->GetStop(where2) + 1;

he_jj.

= &(*jj);

he_jj.

= (*jj)->GetStart(where2) - 1;

he_jj.

= &(*ii);

he_jj.

= (*ii)->GetStop(where2) - 1;

he_ii.

= &(*jj);

he_ii.

= (*jj)->GetStart(where2) + 1;

= size_t(maxlenfr *

((*ii)->GetLength(),

(

ii_lcl = ii0; ii_lcl != ii1; ++ii_lcl) {

& h = *(ii_lcl->m_Ptr);

cmin_lcl (h->GetMin(where2));

(cmin_lcl < he_ii.

) cmin_lcl = he_ii.

;

cmax_lcl (h->GetMax(where2));

(cmax_lcl < he_jj.

) cmax_lcl = he_jj.

;

(cmax_lcl - cmin_lcl + 1 > max_len) {

TIterMap::iterator imi = m.

(ii);

lhs (imi == m.

()? *ii: imi->second);

THitRefs::iterator ii_end,

& maxlenfr,

THitRefs::iterator TIter;

(0, ii_beg, ii_end, hit_ends, maxlenfr, m);

(1, ii_beg, ii_end, hit_ends, maxlenfr, m);

(TIter ii = ii_beg; ii != ii_end; ++ii) {

TIterMap::iterator imi = m.find(ii);

hr (imi == m.end()? *ii: imi->second);

pout->push_back(hr);

bool GetQueryStrand(void) const

TCoord GetQueryStart(void) const

TCoord GetSubjStop(void) const

static string s_RunLengthDecode(const string &in)

TCoord GetSubjStart(void) const

bool GetSubjStrand(void) const

const TId & GetId(Uint1 where) const

TCoord GetQueryStop(void) const

const TTranscript & GetTranscript(void) const

float GetScore(void) const

const_iterator end() const

const_iterator find(const key_type &key) const

const_iterator begin() const

const_iterator upper_bound(const key_type &key) const

iterator insert(const value_type &val)

const_iterator end() const

parent_type::iterator iterator

const_iterator lower_bound(const key_type &key) const

TCoord operator()(TCoord iVal, const THitRef &ph)

Overloaded function call operator to be used with std::accumulate()

static void s_RunGreedy(typename THitRefs::iterator hri_beg, typename THitRefs::iterator hri_end, THitRefs *phits_new, TCoord min_hit_len=100, double min_hit_idty=.9, TCoord margin=1, TCoord retain_overlap=0, EUnique_type unique_type=e_Strict)

EUnique_type

Multiple-sequences greedy alignment uniquification algorithm.

static TCoord s_GetOverlap(TCoord L1, TCoord R1, TCoord L2, TCoord R2)

static pair< int, Uint1 > sx_Cleave(THitRef &h, Uint1 where, TCoord cmin, TCoord cmax, TCoord min_hit_len, double &min_idty, THitRef *pnew_hit, TCoord retain_overlap)

bool operator<(const SHitEnd &rhs) const

friend ostream & operator<<(ostream &ostr, const SHitEnd &he)

static void sx_AddMidIfNeeded(THitRef *hit, const float curscore, THitRef *container_candidate, const Uint1 where, TCoord margin, THitEnds &hit_mids)

static void sx_AddMidPoints(THitRef &h, const TCoord *outer_box, TCoord margin, THitEnds &hit_ends, vector< bool > &skip, const THitRef *hitref_firstptr)

THitEnds::iterator THitEndsIter

static void s_GetSpan(const THitRefs &hitrefs, TCoord span[4])

Get sequence span for a set of alignments (hits).

static TCoord s_GetCoverage(Uint1 where, typename THitRefs::const_iterator from, typename THitRefs::const_iterator to)

Collect coverage for the range of hits on the specified source sequence.

CHitCoverageAccumulator(Uint1 where)

Create the object; specify the accumulation sequence.

multiset< THitEnd > THitEnds

static bool s_TrackHit(const THit &h)

static void sx_TestAndMerge(typename THitRefs::iterator ii_beg, typename THitRefs::iterator ii_end, const THitEnds &hit_ends, const double &maxlenfr, THitRefs *pout)

static pair< THitEndsIter, THitEndsIter > sx_GetEndsInRange(const THitRef &hc, const TCoord *box, Uint1 where, TCoord margin, THitEnds &hit_ends)

static void s_MergeAbutting(typename THitRefs::iterator hri_beg, typename THitRefs::iterator hri_end, const double &maxlenfr, THitRefs *pout)

static void sx_TM(Uint1 where, typename THitRefs::iterator ii_beg, typename THitRefs::iterator ii_end, const THitEnds &hit_ends, const double &maxlenfr, map< typename THitRefs::iterator, THitRef > &m)

vector< THitRef > THitRefs

static THitRef sx_Merge(const THitRef &lhs, const THitRef &rhs, Uint1 where)

static bool s_PNullRef(const THitRef &hr)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

objects::CSeq_id element_type

Define alias element_type.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

uint8_t Uint1

1-byte (8-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.

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

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