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NCBI C++ ToolKit: src/objmgr/seq_map_switch.cpp Source File

60 enum

ESeqMapSegmentEdge

66

SSeqPos(

const CSeqMap_CI

& iter, ESeqMapSegmentEdge edge)

67

: id(iter.GetRefSeqid()),

68

minus_strand(iter.GetRefMinusStrand())

71 if

( !minus_strand ) {

79 if

( !minus_strand ) {

90

pos += minus_strand? -diff: diff;

95

pos += minus_strand? diff: -diff;

102

minus_strand = !minus_strand;

106 struct

SSeq_align_Info

128

m_SegmentIds.

insert

(seg_it.GetRefSeqid());

136 match

.align.Reset(&align);

144

m_SegmentIds.

find

(

->m_Id) == m_SegmentIds.

end

() ) {

148 match

.range1.SetFrom(

->m_Start);

155

m_SegmentIds.

find

(

->m_Id)==m_SegmentIds.

end

() ){

159 match

.range2.SetFrom(

->m_Start);

160 match

.range2.SetLength(s->m_Len);

161 match

.same_strand =

->SameStrand(*

);

179 return

pos >= range.

GetFrom

() && pos <= range.

GetTo

();

184 if

( pos.minus_strand ) {

185 return

pos.pos - range.

GetFrom

() + 1;

188 return

range.

GetTo

() - pos.pos + 1;

201 bool

operator!(

void

)

const 206 bool operator<

(

const

SMatchInfo& m)

const 208 if

( skip != m.skip )

210 return

m1+m2 < m.m1+m.m2;

214 typedef

SMatchInfo TMatch;

221 if

( pos.minus_strand ) {

230

TMatch GetMatchOrdered(

const

SSeqPos& pos1,

const

SSeqPos& pos2)

const 233 if

( same_strand != (pos1.minus_strand==pos2.minus_strand) ) {

249

ret.m1 = ret.m2 = m1.

GetTo

()+1;

258

TMatch GetMatch(

const

SSeqPos& pos1,

const

SSeqPos& pos2)

const 260 if

( pos1.id == id1 && pos2.id == id2 ) {

261 return

GetMatchOrdered(pos1, pos2);

263 if

( pos2.id == id1 && pos1.id == id2 ) {

264

TMatch ret = GetMatchOrdered(pos2, pos1);

265 swap

(ret.m1, ret.m2);

271 typedef

vector<SMatch> TMatches;

272 typedef

pair<CSeq_id_Handle, CSeq_id_Handle> TKey;

290 return

match_map[GetKey(id1, id2)];

297

pair<TSeqPos, TSeqPos>

298

x_FindAlignMatch(SSeqPos pos1,

305

pair<TSeqPos, TSeqPos>

306

SSeq_align_Info::x_FindAlignMatch(SSeqPos pos1,

312

pair<TSeqPos, TSeqPos> ret(0, 0);

317

TMatchMap::const_iterator miter =

318

match_map.find(GetKey(pos1.id, pos2.id));

319 if

( miter != match_map.end() ) {

320 const

TMatches& matches = miter->second;

321 ITERATE

( TMatches, it, matches ) {

322

SMatch::TMatch m = it->GetMatch(pos1, pos2);

331 if

( !first_align ) {

332

first_align = add.align;

348 if

( skip1 || skip2 ) {

349

diff[skip_pos].second += skip1;

350

diff[skip_pos].first += skip2;

360

ret.second = ret.first;

372

SSeq_align_Info&

info

383

SSeqPos pos1(iter1, SSeqPos::eEnd);

384

SSeqPos pos2(iter2, SSeqPos::eStart);

394

pair<TSeqPos, TSeqPos> ext2 =

399

pair<TSeqPos, TSeqPos> ext1 =

415 while

( iter != diff.

end

() &&

offset

>= iter->first ) {

416 if

(

offset

- iter->first <= iter->second.second ) {

424

ret.first += iter->second.first;

425

ret.second += iter->second.second;

454 "switch point is not initialized"

);

458 "switch point is not in valid range"

);

474 return

iter == diff->

end

()? 0: iter->second.first;

502 "switch point is not initialized"

);

506 "switch point is not in valid range"

);

508 if

( add > 0 && add >

GetInsert

(pos) ) {

510 "adding more bases than available"

);

516 "invalid CSeqMapSwitchPoint"

);

521

SSeqPos(right, SSeqPos::eStart).pos !=

m_RightPos

) {

523 "invalid CSeqMapSwitchPoint"

);

529

SSeqPos(left, SSeqPos::eEnd).pos !=

m_LeftPos

) {

531 "invalid CSeqMapSwitchPoint"

);

574 "switch point is not initialized"

);

579 "adding more bases than available"

);

588

SSeq_align_Info

info

(seq, align);

589 if

(

info

.match_map.size() != 1 ) {

591 "Seq-align dimension is not 2"

);

599 "Sequence is not segmented"

);

604 for

( ; iter2; ++iter1, ++iter2 ) {

609 return

x_GetSwitchPoint(seq,

info

, iter1, iter2);

615 "Seq-align doesn't refer to segments"

);

627 "Sequence is not segmented"

);

632

SSeq_align_Info

info

(seq);

637 for

( ; iter2; ++iter1, ++iter2 ) {

640

pp.push_back(x_GetSwitchPoint(seq,

info

, iter1, iter2));

ENa_strand Reverse(ENa_strand s)

User-defined methods of the data storage class.

Storage for multiple mapping ranges.

Base class for all object manager exceptions.

SeqMap related exceptions.

list< SAlignment_Segment > TSegments

container_type::const_iterator const_iterator

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

bool operator<(const CEquivRange &A, const CEquivRange &B)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

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

#define NCBI_THROW(exception_class, err_code, message)

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

const TInst_Hist & GetInst_Hist(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

TSeqPos GetRefPosition(void) const

bool GetRefMinusStrand(void) const

CSeqMap::ESegmentType GetType(void) const

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

TSeqPos GetRefEndPosition(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

void SetSegmentRef(const CSeqMap_CI &seg, TSeqPos length, const CSeq_id_Handle &ref_id, TSeqPos ref_pos, bool ref_minus_strand)

vector< CRef< CSeqMapSwitchPoint > > TSeqMapSwitchPoints

CRange< TSeqPos > m_MasterRange

pair< TSeqPos, TSeqPos > TInsertDelete

const_iterator begin(CScope *scope) const

STL style methods.

TSeqPos GetInsert(TSeqPos pos) const

CConstRef< CSeq_align > m_FirstAlign

TInsertDelete GetDifferences(TSeqPos new_pos, TSeqPos add=0) const

TSeqMapSwitchPoints GetAllSwitchPoints(const CBioseq_Handle &seq, const TSeqMapSwitchAligns &aligns)

TDifferences m_RightDifferences

TSeqPos GetLeftInPlaceInsert(void) const

TSeqPos GetRightInPlaceInsert(void) const

void InsertInPlace(TSeqPos add_left, TSeqPos add_right)

CSeqMap_CI FindSegment(TSeqPos pos, CScope *scope) const

Find segment containing the position.

list< CRef< CSeq_align > > TSeqMapSwitchAligns

TDifferences m_LeftDifferences

CRef< CSeqMapSwitchPoint > GetSwitchPoint(const CBioseq_Handle &seq, const CSeq_align &align)

CRange< TSeqPos > m_ExactMasterRange

void ChangeSwitchPoint(TSeqPos pos, TSeqPos add)

int GetLengthDifference(TSeqPos new_pos, TSeqPos add=0) const

@ eSeqRef

reference to Bioseq

position_type GetLength(void) const

TThisType & SetLength(position_type length)

#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.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TAssembly & GetAssembly(void) const

Get the Assembly member data.

CNcbiMatrix< T > & operator+=(CNcbiMatrix< T > &, const CNcbiMatrix< U > &)

global addition: matrix += matrix

CNcbiMatrix< T > & operator-=(CNcbiMatrix< T > &, const CNcbiMatrix< U > &)

global subtraction: matrix -= matrix

const struct ncbi::grid::netcache::search::fields::KEY key

static bool Contains(const CSeq_loc &a, const CSeq_loc &b, CScope *scope)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static const sljit_gpr r1

static const sljit_gpr r2

vector< SAlignment_Row > TRows

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NCBI C++ ToolKit: src/objmgr/seq_map_switch.cpp Source File

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