RetroSearch Browse

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/genomic__compart_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/align/util/genomic_compart.cpp Source File

49 bool

is_intersecting =

50 r1

.first.IntersectingWith(

.first);

56

": is_intersecting = " 57

<< (is_intersecting ?

"true"

"false"

)

61 return

is_intersecting;

65 const

pair<TSeqRange, TSeqRange>&

)

67 bool

is_intersecting =

68 r1

.second.IntersectingWith(

.second);

74

": is_intersecting = " 75

<< (is_intersecting ?

"true"

"false"

)

79 return

is_intersecting;

83 const

pair<TSeqRange, TSeqRange>&

86 bool

is_consistent =

false

;

88

is_consistent = (

.first <=

.first &&

.second <=

.second) ||

89

(

.first <=

.first &&

.second <=

.second);

92

is_consistent = (

.first <=

.first &&

.second <=

.second) ||

93

(

.first <=

.first &&

.second <=

.second);

107

": is_consistent = " 108

<< (is_consistent ?

"true"

"false"

)

109

" r1.first <= r2.first: " 110

<< (

.first <=

.first ?

"true"

"false"

)

111

" r1.second <= r2.second: " 112

<< (

.second <=

.second ?

"true"

"false"

)

116 return

is_consistent;

121 const

pair<TSeqRange, TSeqRange>&

126 if

(

.first.GetTo() <

.first.GetFrom()) {

127

diff +=

.first.GetFrom() -

.first.GetTo();

129 else if

(

.first.GetTo() <

.first.GetFrom()) {

130

diff +=

.first.GetFrom() -

.first.GetTo();

133 if

(

.second.GetTo() <

.second.GetFrom()) {

134

diff +=

.second.GetFrom() -

.second.GetTo();

136 else if

(

.second.GetTo() <

.second.GetFrom()) {

137

diff +=

.second.GetFrom() -

.second.GetTo();

161 #ifdef _VERBOSE_DEBUG 168

": diff = "

<< diff

176 typedef

pair<TSeqRange, TSeqRange>

TRange

;

186 if

(

.first.first !=

.first.first) {

187 return

(

.first.first <

.first.first);

189 if

(

.first.second !=

.first.second) {

190 return

(

.first.second <

.first.second);

208 r1

.first.second.GetLength());

210 r2

.first.second.GetLength());

227 return r1

.second->GetSeqRange(1) <

.second->GetSeqRange(1);

236 int

scores[2] = {0, 0};

240 if

(scores[0] > scores[1]) {

243 if

(scores[1] > scores[0]) {

256 return r1

.second->GetSeqRange(1) <

.second->GetSeqRange(1);

265 double

scores[2] = {0.0, 0.0};

268 if

(scores[0] == scores[1]) {

270 r1

.first.second.GetLength());

272 r2

.first.second.GetLength());

276 if

(scores[0] > scores[1]) {

279 if

(scores[1] > scores[0]) {

292 return r1

.second->GetSeqRange(1) <

.second->GetSeqRange(1);

303 if

(al1_len > al2_len) {

306 if

(al2_len > al1_len) {

328 int

scores[2] = {0, 0};

331 return

scores[0] > scores[1];

340 double

scores[2] = {0.0, 0.0};

343 if

(scores[0] == scores[1]) {

346 return

scores[0] > scores[1];

355 return

&*it1 < &*it2;

388 float

diff_len_filter)

393 typedef

pair<CSeq_id_Handle, ENa_strand> TIdStrand;

394 typedef

pair<TIdStrand, TIdStrand> TIdPair;

396

TAlignments alignments;

442

TIdPair p(TIdStrand(qid, q_strand), TIdStrand(sid, s_strand));

443

alignments[p].push_back(*it);

446 typedef

pair<SCompartScore, CRef<CSeq_align_set> > TCompartScore;

447

vector<TCompartScore> scored_compartments;

452 const

TIdPair& id_pair = align_it->first;

456

vector< CRef<CSeq_align> >& aligns = align_it->second;

467 #ifdef _VERBOSE_DEBUG 469

cerr <<

"ids: "

<< id_pair.first.first <<

" x " 470

<< id_pair.second.first << endl;

472

cerr <<

" sort by score"

<< endl;

475

cerr <<

" sort by percent identity"

<< endl;

478

cerr <<

" sort by size"

<< endl;

483

<< (*it)->GetSeqRange(0) <<

", " 486

<< (*it)->GetSeqRange(1) <<

", " 498

vector<TAlignRange> align_ranges;

501 TSeqRange

q_range = (*iter)->GetSeqRange(0);

502 TSeqRange

s_range = (*iter)->GetSeqRange(1);

507 #ifdef _VERBOSE_DEBUG 510

<< id_pair.first.first <<

"/"

<< q_strand

512

<< id_pair.second.first <<

"/"

<< s_strand

514

vector<TAlignRange>::const_iterator prev_it = align_ranges.end();

515 ITERATE

(vector<TAlignRange>, it, align_ranges) {

517

<< it->first.first <<

", " 518

<< it->first.second <<

")" 519

" ["

<< it->first.first.GetLength()

520

", "

<< it->first.second.GetLength() <<

"]"

;

521 if

(prev_it != align_ranges.end()) {

522

cerr <<

" consistent=" 524

q_strand, s_strand) ?

"true"

"false"

);

541 std::sort

(align_ranges.begin(), align_ranges.end(),

545 std::sort

(align_ranges.begin(), align_ranges.end(),

549 std::sort

(align_ranges.begin(), align_ranges.end(),

553

list< TAlignRangeMultiSet > compartments;

562

list<TAlignRangeMultiSet>::iterator best_compart =

567

compart_it, compartments) {

570

compart_it->lower_bound(*it);

573 bool

is_consistent =

false

;

574 bool

is_intersecting_query =

false

;

575 bool

is_intersecting_subject =

false

;

576 if

(place == compart_it->end()) {

580

is_intersecting_query =

582

is_intersecting_subject =

592 if

(place == compart_it->begin()) {

595

is_intersecting_query =

597

is_intersecting_subject =

609

is_intersecting_query =

611

is_intersecting_subject =

622

is_intersecting_query |=

624

is_intersecting_subject |=

633

q_strand, s_strand));

637 #ifdef _VERBOSE_DEBUG 638 float

diff_len_ratio = double(diff) / it->second->GetAlignLength(

false

);

639

cerr <<

" comp_id="

<< comp_id

640

" is_consistent="

<< (is_consistent ?

"true"

"false"

)

641

" is_intersecting_query="

<< (is_intersecting_query ?

"true"

"false"

)

642

" is_intersecting_subject="

<< (is_intersecting_subject ?

"true"

"false"

)

643

" allow intersect_query=" 645

" allow intersect_subject=" 647

" allow intersect_both=" 650

" best_diff="

<< best_diff

651

" align_len="

<< it->second->GetAlignLength(

false

)

652

" diff_len_ratio="

<< diff_len_ratio

653

" filter="

<< (diff_len_ratio <= diff_len_filter ?

"pass"

"fail"

)

657 if

( ((is_consistent && !is_intersecting_query && !is_intersecting_subject) ||

660

is_intersecting_query ) ||

662

is_intersecting_subject ) ||

664

is_intersecting_query && is_intersecting_subject )))) &&

666

best_compart = compart_it;

672 if

( !found || best_compart == compartments.end() ) {

674

compartments.back().insert(*it);

677

best_compart->insert(*it);

680 #ifdef _VERBOSE_DEBUG 682

cerr <<

"compartments: found "

<< compartments.size() << endl;

684 ITERATE

(list<TAlignRangeMultiSet>, it, compartments) {

686

cerr <<

" compartment "

count

<< endl;

689

->first.first <<

", " 690

->first.second <<

")" 691

" ["

->first.first.GetLength()

692

", "

->first.second.GetLength() <<

"]" 693

" (0x"

std::hex

<< ((

intptr_t

)

->second.GetPointer()) << std::dec <<

")" 701 #ifdef DEBUG_VERBOSE_OUTPUT 703

cerr <<

"found "

<< compartments.size() << endl;

705 ITERATE

(list<TAlignRangeMultiSet>, it, compartments) {

707

cerr <<

" compartment "

count

<< endl;

710

->first.first <<

", " 711

->first.second <<

")" 712

" ["

->first.first.GetLength()

713

", "

->first.second.GetLength() <<

"]" 721 #ifdef DEBUG_VERBOSE_OUTPUT 722 size_t

compart_count = 0;

724 ITERATE

(list<TAlignRangeMultiSet>, it, compartments) {

725 #ifdef DEBUG_VERBOSE_OUTPUT 742 for

(; second_subject_range != it->end()

743

&& second_subject_range->first.second

744

== it->begin()->first.second; ++second_subject_range);

745 bool

reverse_subject = second_subject_range != it->end() &&

746

second_subject_range->first.second

747

< it->begin()->first.second;

748 TSeqPos

subject_end = (reverse_subject

750

: it->rbegin()->first) . second.GetTo();

752

forward_breaks, backward_breaks;

755 #ifdef _VERBOSE_DEBUG 760 #ifdef _VERBOSE_DEBUG 762

->first.first <<

", " 763

->first.second <<

")" 764

" ["

->first.first.GetLength()

765

", "

->first.second.GetLength() <<

"]" 769

(reverse_subject ? subject_end -

->first.second.GetTo()

770

->first.second.GetFrom());

772

(reverse_subject ? subject_end -

->first.second.GetFrom()

773

->first.second.GetTo());

774 #ifdef _VERBOSE_DEBUG 775 if

(

!= it->begin()) {

776

cerr <<

"At "

<< ++

count

" Gap "

int

(start_point - current_end_point) <<

" on length "

<< (current_potential_break - current_end_point) << endl;

779 if

(

!= it->begin() &&

780

start_point > current_potential_break)

785 #ifdef _VERBOSE_DEBUG 786

cerr <<

"Break! "

<< (

count

- last_break) <<

" members start_point "

<< start_point <<

" current break "

<< current_potential_break << endl;

790

current_end_point =

max

(current_potential_break, end_point);

791

current_potential_break = current_end_point +

792

diff_len_filter *

->second->GetAlignLength(

false

);

794

current_potential_break = current_end_point = INT_MAX;

795 #ifdef _VERBOSE_DEBUG 801 #ifdef _VERBOSE_DEBUG 803

->first.first <<

", " 804

->first.second <<

")" 805

" ["

->first.first.GetLength()

806

", "

->first.second.GetLength() <<

"]" 810

(reverse_subject ? subject_end -

->first.second.GetTo()

811

->first.second.GetFrom());

813

(reverse_subject ? subject_end -

->first.second.GetFrom()

814

->first.second.GetTo());

815 #ifdef _VERBOSE_DEBUG 816 if

(

!= it->rbegin()) {

817

cerr <<

"At "

<< ++

count

" Gap "

int

(current_end_point - end_point) <<

" on length "

<< (current_end_point - current_potential_break) << endl;

820 if

(

!= it->rbegin() &&

821

end_point < current_potential_break)

826

backward_breaks.

insert

(breakpoint);

827 #ifdef _VERBOSE_DEBUG 828 if

(forward_breaks.count(breakpoint)) {

829

cerr <<

"Double after "

<< (

count

- last_double_break) <<

' '

;

830

last_double_break =

count

;

832

cerr <<

"Break! "

<< (

count

- last_break) <<

" members end_point "

<< end_point <<

" current break "

<< current_potential_break << endl;

836

current_end_point =

min

(current_potential_break, start_point);

837

current_potential_break = current_end_point -

838

diff_len_filter *

->second->GetAlignLength(

false

);

840

set_intersection(forward_breaks.

begin

(), forward_breaks.

end

(),

841

backward_breaks.

begin

(), backward_breaks.

end

(),

842

inserter(break_positions, break_positions.

end

()),

846 if

(break_positions.count(

)) {

847 #ifdef DEBUG_VERBOSE_OUTPUT 848

cerr <<

"compartment "

<< compart_count <<

" break at "

->first.first.GetFrom() <<

".."

->first.first.GetTo() << endl;

850

TCompartScore sc(score, sas);

851

scored_compartments.push_back(sc);

855

sas->

Set

().push_back(

->second);

861

TCompartScore sc(score, sas);

862

scored_compartments.push_back(sc);

869 std::sort

(scored_compartments.begin(), scored_compartments.end());

870 ITERATE

(vector<TCompartScore>, it, scored_compartments) {

871

align_sets.push_back(it->second);

881 typedef const

list <CRef<CSeq_align> > TConstSeqAlignList;

882

TConstSeqAlignList& alignments = compartment->

Get

();

884 ITERATE

(TConstSeqAlignList, al_it, alignments) {

885 len

+= (*al_it)->GetAlignLength(

false

);

888 ITERATE

(TConstSeqAlignList, al_it, alignments) {

889

TConstSeqAlignList::const_iterator al_it_next = al_it;

892

disc_align_set->

Set

().push_back(*al_it);

893 if

(al_it_next == alignments.end() ||

894

(*al_it)->GetSeqStop(0) + max_gap_len < (*al_it_next)->GetSeqStart(0) ||

895

(*al_it)->GetSeqStop(1) + max_gap_len < (*al_it_next)->GetSeqStart(1))

900

comp_align->

SetSegs

().SetDisc(*disc_align_set);

901

aligns.push_back(comp_align);

902

disc_align_set.

Reset

(0);

bool SameOrientation(ENa_strand a, ENa_strand b)

@ eScore_PercentIdentity_Ungapped

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

bool GetNamedScore(const string &id, int &score) const

Get score.

TSeqPos GetAlignLength(bool include_gaps=true) const

Get the length of this alignment.

parent_type::iterator iterator

parent_type::const_iterator const_iterator

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

pair< TSeqRange, TSeqRange > TRange

bool IsConsistent(const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)

void JoinCompartment(const CRef< CSeq_align_set > &compartment, float gap_ratio, list< CRef< CSeq_align > > &aligns)

bool IsIntersectingQuery(const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)

multiset< TAlignRange, SRangesByStart > TAlignRangeMultiSet

pair< TRange, CRef< CSeq_align > > TAlignRange

TSeqPos Difference(const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)

void FindCompartments(const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options, float diff_len_filter)

bool IsIntersectingSubject(const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)

@ fCompart_AllowIntersectionsSubject

@ fCompart_SortByPctIdent

@ fCompart_FilterByDiffLen

@ fCompart_AllowIntersectionsBoth

@ fCompart_AllowIntersectionsQuery

@ fCompart_AllowInconsistentIntersection

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define REVERSE_ITERATE(Type, Var, Cont)

ITERATE macro to reverse sequence through container elements.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

Tdata & Set(void)

Assign a value to data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetType(TType value)

Assign a value to Type data member.

const Tdata & Get(void) const

Get the member data.

@ eType_disc

discontinuous alignment

ENa_strand

strand of nucleic acid

unsigned int

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

static void hex(unsigned char c)

constexpr auto sort(_Init &&init)

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

static const sljit_gpr r1

static const sljit_gpr r2

bool operator<(const SCompartScore &o) const

bool operator()(TAlignRangeMultiSet::const_iterator it1, TAlignRangeMultiSet::const_iterator it2) const

bool operator()(const TAlignRange &r1, const TAlignRange &r2) const

bool operator()(const CRef< CSeq_align > &al_ref1, const CRef< CSeq_align > &al_ref2) const

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4