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

TSegments::iterator seg_it =

.begin();

( ; seg_it !=

.end(); ) {

(seg_it->m_Rows.size() <=

) {

TSegments::iterator seg_it =

.begin();

( ; seg_it !=

.end(); ) {

(seg_it->m_Rows.size() <=

) {

TSegments::iterator old_it = seg_it;

aln_row.

;

aln_row.

;

aln_row.

;

TSegments::iterator ins_point = seg_it;

old_it->m_Rows.size(), src_reverse);

(

= 0;

< old_it->m_Rows.size(); ++

) {

lseg.

(

, old_it->m_Rows[

]);

old_it->m_Rows.size(),

(

= 0;

< old_it->m_Rows.size(); ++

) {

mseg.

(

, old_it->m_Rows[

]);

old_it->m_Rows.size(),

(

= 0;

< old_it->m_Rows.size(); ++

) {

rseg.

(

, old_it->m_Rows[

]);

TSegments::iterator old_it = seg_it;

aln_row.

;

(id_it == id_map.

()) {

aln_row.

;

( rmap.

() ) {

aln_row.

;

vector< CRef<CSeq_loc_Conversion> > TSortedConversions;

TSortedConversions cvts;

cvts.push_back(rg_it->second);

TSegments::iterator ins_point = seg_it;

mapped =

;

(

cvt_idx = 0; cvt_idx < cvts.size(); ++cvt_idx) {

dl, seg.

.size(), src_reverse);

(

= 0;

< seg.

.size(); ++

) {

(

= 0;

< seg.

.size(); ++

) {

left_shift += mseg.

;

seg.

[

].m_Id = rmap.

()->second->m_Dst_id_Handle;

(

= 0;

< seg.

.size(); ++

) {

sub->InitExon(spliced, exon);

sub.release();

bool IsReverse(ENa_strand s)

Class used to map seq-alignments.

CSeq_loc_Mapper_Base & GetLocMapper(void) const

void Convert(void)

Map the whole alignment through the linked seq-loc mapper.

void x_InvalidateScores(SAlignment_Segment *seg=NULL)

vector< CRef< CSeq_align_Mapper_Base > > TSubAligns

SAlignment_Segment & x_InsertSeg(TSegments::iterator &where, int len, size_t dim, bool reverse)

size_t GetMaxDim(void) const

Get max number of rows of all segments.

CRef< CSeq_align > m_DstAlign

void x_ConvertAlignCvt(CSeq_loc_Conversion_Set &cvts)

CSeq_id_Handle x_ConvertSegmentCvt(TSegments::iterator &seg_it, CSeq_loc_Conversion &cvt, size_t row)

virtual CSeq_align_Mapper_Base * CreateSubAlign(const CSeq_align &align)

CSeq_align_Mapper(const CSeq_align &align, CSeq_loc_Mapper_Base &loc_mapper)

void x_ConvertRowCvt(CSeq_loc_Conversion &cvt, size_t row)

unsigned int m_SingleIndex

TConvByIndex m_CvtByIndex

CRef< CSeq_loc_Conversion > m_SingleConv

CSeq_id_Handle m_Src_id_Handle

bool ConvertInterval(TSeqPos src_from, TSeqPos src_to, ENa_strand src_strand)

EMappedObjectType m_LastType

CSeq_id_Handle m_Dst_id_Handle

CSeq_loc_Mapper_Base –.

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

const_iterator begin(void) const

#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.

constexpr auto sort(_Init &&init)

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

#define row(bind, expected)

bool operator()(const CRef< CSeq_loc_Conversion > &x, const CRef< CSeq_loc_Conversion > &y) const

Single row of a single alignment segment.

ENa_strand m_Strand

Strand value.

TSeqPos m_Start

kInvalidSeqPos means gap

CSeq_id_Handle m_Id

Row's seq-id.

bool m_IsSetStrand

Is strand set for the row?

bool SameStrand(const SAlignment_Row &r) const

Check if the query row has the same strand orientation.

void SetMapped(void)

Mark the row as mapped.

Structure to hold information about a single alignment segment.

TRows m_Rows

Segment rows.

SAlignment_Row & CopyRow(size_t idx, const SAlignment_Row &src_row)

Create a copy of the given row, store is to this segment as row number 'idx'.

TScores m_Scores

Scores for this segment.

ssize_t m_ScoresGroupIdx

Group of scores.

bool m_HaveStrands

Do at least some rows have strand set?

int m_Len

Segment length.

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