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NCBI C++ ToolKit: src/objtools/alnmgr/aln_generators.cpp Source File

);

);

);

);

<<

<< endl;

ncbi::CRangeCollection<CPairwiseAln::TPos>

;

cerr <<

<< endl;

cerr <<

<< *

;

cerr <<

<< *

<< endl;

( !addition.empty() ) {

cerr <<

<< addition << endl;

rr(add_it->GetFrom(), add_it->GetTo());

(it != TParent::m_vRanges.

() &&

rr.

() >= it->GetFrom()) {

it = TParent::m_vRanges.insert(it, rr);

cerr <<

<< endl << endl;

cerr <<

<< *

;

cerr <<

<< endl << endl;

TAnchorSegments anchor_segments;

anchor_segments.insert(

(rng_i->GetFirstFrom(), rng_i->GetFirstTo()));

(

anchor_segments_seg = anchor_segments.begin(); anchor_segments_seg != anchor_segments.end(); ++anchor_segments_seg ) {

diag->SetIds().resize(dim);

->Assign(anchored_aln.

(dim -

- 1)->GetSeqId());

diag->SetIds()[

] = id;

diag->SetStrands().resize(dim);

diag->SetLen(anchor_segments_seg->GetLength());

diags.push_back(diag);

CSeq_align::TSegs::TDendiag::iterator diag_it = diags.begin();

TAnchorSegments::const_iterator seg_i = anchor_segments.begin();

pairwises[dim -

- 1]->begin();

direct = aln_rng_i->IsDirect();

(seg_i != anchor_segments.end()) {

(aln_rng_i != pairwises[dim -

- 1]->end() &&

seg_i->GetFrom() >= aln_rng_i->GetFirstFrom()) {

(seg_i->GetToOpen() <= aln_rng_i->GetFirstToOpen());

(seg_i->GetToOpen() > aln_rng_i->GetFirstToOpen()) {

);

(right_delta >= seg_i->GetLength());

(right_delta < seg_i->

()) {

);

right_delta -= seg_i->GetLength();

(*diag_it)->SetStarts()[

] =

aln_rng_i->GetSecondFrom() + left_delta :

aln_rng_i->GetSecondFrom() + right_delta);

left_delta += seg_i->GetLength();

(right_delta == 0) {

(left_delta == aln_rng_i->GetLength());

(aln_rng_i != pairwises[dim -

- 1]->end()) {

direct = aln_rng_i->IsDirect();

right_delta = aln_rng_i->GetLength();

(*diag_it)->SetStrands()[

] =

(

< starts.size()) {

starts.erase(starts.begin() +

);

ids.erase(ids.begin() +

);

strands.erase(strands.begin() +

);

(diag.

().size() < 2)

;

dd.push_back(*diag_it);

TAnchorSegments anchor_segments;

anchor_segments.insert(

(rng_i->GetFirstFrom(), rng_i->GetFirstTo()));

dim = anchored_aln.

();

SerialAssign<CSeq_id>(*ids[

], anchored_aln.

(dim -

- 1)->GetSeqId());

TAnchorSegments::const_iterator seg_i = anchor_segments.begin();

(seg = 0; seg < numseg; ++seg, ++seg_i) {

lens[seg] = seg_i->GetLength();

matrix_size = dim * numseg;

starts.resize(matrix_size, -1);

matrix_row_pos =

;

seg_i = anchor_segments.begin();

direct = aln_rng_i->IsDirect();

(seg_i != anchor_segments.end()) {

(aln_rng_i != pairwises[dim -

- 1]->end() &&

seg_i->GetFrom() >= aln_rng_i->GetFirstFrom()) {

(seg_i->GetToOpen() <= aln_rng_i->GetFirstToOpen());

(seg_i->GetToOpen() > aln_rng_i->GetFirstToOpen()) {

);

(right_delta >= seg_i->GetLength());

(right_delta < seg_i->

()) {

);

right_delta -= seg_i->GetLength();

starts[matrix_row_pos] =

aln_rng_i->GetSecondFrom() + left_delta :

aln_rng_i->GetSecondFrom() + right_delta);

left_delta += seg_i->GetLength();

(right_delta == 0) {

(left_delta == aln_rng_i->GetLength());

(aln_rng_i != pairwises[dim -

- 1]->end()) {

direct = aln_rng_i->IsDirect();

right_delta = aln_rng_i->GetLength();

matrix_row_pos += dim;

matrix_size = 2 * numseg;

starts.resize(matrix_size, -1);

SerialAssign<CSeq_id>(*ids[0], pairwise_aln.

()->GetSeqId());

SerialAssign<CSeq_id>(*ids[1], pairwise_aln.

()->GetSeqId());

starts[matrix_pos++] = aln_rng_i->GetFirstFrom();

( !aln_rng_i->IsDirect() ) {

starts[matrix_pos++] = aln_rng_i->GetSecondFrom();

lens[seg++] = aln_rng_i->GetLength();

(matrix_pos == matrix_size);

TPos last_prod_end = 0;

TPos last_gen_end = 0;

gen_direct = rg_it == pairwise_aln.

() || rg_it->IsDirect();

prod_direct =

||

rg_it == pairwise_aln.

() || rg_it->IsFirstDirect();

( !prod_direct ) {

gen_direct = !gen_direct;

TPos prod_skip, gen_skip;

(rg_it == pairwise_aln.

()) {

gen_skip = gen_direct == prod_direct ?

(exon->IsSetProduct_start());

(exon->IsSetGenomic_start());

(exon->IsSetProduct_end());

(exon->IsSetGenomic_end());

exons.push_back(exon);

exons.push_front(exon);

ex_prod_rg = TRng::GetEmpty();

ex_gen_rg = TRng::GetEmpty();

(prod_skip > 0 || gen_skip > 0) {

chunk->SetMismatch(mismatch);

exon->SetParts().push_back(chunk);

exon->SetParts().push_front(chunk);

prod_skip -= mismatch;

gen_skip -= mismatch;

chunk->SetProduct_ins(prod_skip);

exon->SetParts().push_back(chunk);

exon->SetParts().push_front(chunk);

chunk->SetGenomic_ins(gen_skip);

exon->SetParts().push_back(chunk);

exon->SetParts().push_front(chunk);

exon->SetPartial(

);

exon->SetProduct_strand(prod_direct

exon->SetGenomic_strand(gen_direct

exon->SetParts().push_back(chunk);

exon->SetParts().push_front(chunk);

exon->SetProduct_start().SetProtpos().SetAmin(ex_prod_rg.GetFrom() / 3);

exon->SetProduct_start().SetProtpos().SetFrame(ex_prod_rg.GetFrom() % 3 + 1);

exon->SetProduct_end().SetProtpos().SetAmin(ex_prod_rg.GetTo() / 3);

exon->SetProduct_end().SetProtpos().SetFrame(ex_prod_rg.GetTo() % 3 + 1);

exon->SetProduct_start().SetNucpos(ex_prod_rg.GetFrom());

exon->SetProduct_end().SetNucpos(ex_prod_rg.GetTo());

exon->SetGenomic_start(ex_gen_rg.GetFrom());

exon->SetGenomic_end(ex_gen_rg.GetTo());

last_gen_end = gen_direct == prod_direct ?

(exon->IsSetProduct_start());

(exon->IsSetGenomic_start());

(exon->IsSetProduct_end());

(exon->IsSetGenomic_end());

exons.push_back(exon);

exons.push_front(exon);

( !exons.empty() ) {

exon = prod_direct ? exons.front() : exons.back();

( exon->GetProduct_end().IsNucpos() ) {

prod_end = exon->GetProduct_end().GetNucpos();

prod_end = exon->GetProduct_end().GetProtpos().GetAmin();

exon->SetPartial(

);

out_seqaligns.resize(pairwises.size() - 1);

(

= 0, sa_idx = 0;

< (

) pairwises.size();

(

== anchor)

;

sa->

().SetDenseg(*ds);

sa->

().SetDisc(*disc);

sa->

().SetPacked(*ps);

sa->

().SetSpliced(*ss);

);

);

out_seqaligns[sa_idx++].Reset(sa);

TAnchorSegments anchor_segments;

anchor_segments.insert(

(rng_i->GetFirstFrom(), rng_i->GetFirstTo()));

vector< CRef<CDense_seg> > dsegs;

dsegs.resize(numseg);

(

= 0;

< dsegs.size(); ++

) {

SerialAssign<CSeq_id>(*ids[

], anchored_aln.

(dim -

- 1)->GetSeqId());

TAnchorSegments::const_iterator seg_i = anchor_segments.begin();

direct = aln_rng_i->IsDirect();

(seg_i != anchor_segments.end()) {

dseg.

()[0] = seg_i->GetLength();

(aln_rng_i != pairwises[dim -

- 1]->end() &&

seg_i->GetFrom() >= aln_rng_i->GetFirstFrom()) {

(seg_i->GetToOpen() <= aln_rng_i->GetFirstToOpen());

(seg_i->GetToOpen() > aln_rng_i->GetFirstToOpen()) {

);

(right_delta >= seg_i->GetLength());

(right_delta < seg_i->

()) {

);

right_delta -= seg_i->GetLength();

aln_rng_i->GetSecondFrom() + left_delta :

aln_rng_i->GetSecondFrom() + right_delta);

left_delta += seg_i->GetLength();

(right_delta == 0) {

(left_delta == aln_rng_i->GetLength());

(aln_rng_i != pairwises[dim -

- 1]->end()) {

direct = aln_rng_i->IsDirect();

right_delta = aln_rng_i->GetLength();

(starts[0] >= 0 && starts[1] >= 0) {

disc->

().push_back(seg_aln);

seg_aln->

().SetDenseg(dseg);

vector< CRef<CDense_seg> > dsegs;

dsegs.resize(numseg);

(

= 0;

< dsegs.size(); ++

) {

disc->

().push_back(seg_aln);

dsegs[

].Reset(&dseg);

SerialAssign<CSeq_id>(*ids[0], pairwise_aln.

()->GetSeqId());

SerialAssign<CSeq_id>(*ids[1], pairwise_aln.

()->GetSeqId());

dseg.

()[0] = aln_rng_i->GetFirstFrom();

( !aln_rng_i->IsDirect() ) {

dseg.

()[1] = aln_rng_i->GetSecondFrom();

dseg.

()[0] = aln_rng_i->GetLength();

TAnchorSegments anchor_segments;

anchor_segments.insert(

(rng_i->GetFirstFrom(), rng_i->GetFirstTo()));

dim = anchored_aln.

();

SerialAssign<CSeq_id>(*ids[

], anchored_aln.

(dim -

- 1)->GetSeqId());

lens.resize(numseg);

TAnchorSegments::const_iterator seg_i = anchor_segments.begin();

(seg = 0; seg < numseg; ++seg, ++seg_i) {

lens[seg] = seg_i->GetLength();

matrix_size = dim * numseg;

present.resize(matrix_size);

starts.resize(matrix_size, 0);

matrix_row_pos =

;

seg_i = anchor_segments.begin();

direct = aln_rng_i->IsDirect();

(seg_i != anchor_segments.end()) {

(aln_rng_i != pairwises[dim -

- 1]->end() &&

seg_i->GetFrom() >= aln_rng_i->GetFirstFrom()) {

(seg_i->GetToOpen() <= aln_rng_i->GetFirstToOpen());

(seg_i->GetToOpen() > aln_rng_i->GetFirstToOpen()) {

);

(right_delta >= seg_i->GetLength());

(right_delta < seg_i->

()) {

);

right_delta -= seg_i->GetLength();

aln_rng_i->GetSecondFrom() + left_delta

: aln_rng_i->GetSecondFrom() + right_delta);

starts[matrix_row_pos] = start;

left_delta += seg_i->GetLength();

(right_delta == 0) {

(left_delta == aln_rng_i->GetLength());

(aln_rng_i != pairwises[dim -

- 1]->end()) {

direct = aln_rng_i->IsDirect();

right_delta = aln_rng_i->GetLength();

matrix_row_pos += dim;

matrix_size = 2 * numseg;

lens.resize(numseg);

starts.resize(matrix_size, 0);

present.resize(matrix_size, 0);

SerialAssign<CSeq_id>(*ids[0], pairwise_aln.

()->GetSeqId());

SerialAssign<CSeq_id>(*ids[1], pairwise_aln.

()->GetSeqId());

starts[matrix_pos++] = start;

( !aln_rng_i->IsDirect() ) {

( !ps->IsSetStrands() ) {

start = aln_rng_i->GetSecondFrom();

starts[matrix_pos++] = start;

lens[seg++] = aln_rng_i->GetLength();

(matrix_pos == matrix_size);

id_extract(src, ids);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CRef< CAnchoredAln > CreateAnchoredAlnFromAln(const _TAlnStats &aln_stats, size_t aln_idx, const CAlnUserOptions &options, objects::CSeq_align::TDim explicit_anchor_row=-1)

Create an anchored alignment from Seq-align using hints.

vector< TAlnSeqIdIRef > TAlnSeqIdVec

void InitSplicedsegFromPairwiseAln(CSpliced_seg &spliced_seg, const CPairwiseAln &pairwise_aln, CScope *scope)

CRef< CSeq_align > CreateSeqAlignFromPairwiseAln(const CPairwiseAln &pairwise_aln, CSeq_align::TSegs::E_Choice choice, CScope *scope)

Convert CPairwiseAln to seq-align of the selected type.

CRef< CDense_seg > CreateDensegFromAnchoredAln(const CAnchoredAln &anchored_aln, CScope *scope)

CRef< CSpliced_seg > CreateSplicedsegFromPairwiseAln(const CPairwiseAln &pairwise_aln, CScope *scope)

CRef< CSeq_align > ConvertSeq_align(const CSeq_align &src, CSeq_align::TSegs::E_Choice dst_choice, CSeq_align::TDim anchor_row, CScope *scope)

Convert source alignment to a new type.

CRef< CPacked_seg > CreatePackedsegFromPairwiseAln(const CPairwiseAln &pairwise_aln, CScope *scope)

CRef< CPacked_seg > CreatePackedsegFromAnchoredAln(const CAnchoredAln &anchored_aln, CScope *scope)

void CreateDense_diagFromAnchoredAln(CSeq_align::TSegs::TDendiag &dd, const CAnchoredAln &anchored_aln, CScope *scope)

void s_TranslatePairwise(CPairwiseAln &out_pw, const CPairwiseAln &pw, const CPairwiseAln &tr)

CRef< CSpliced_seg > CreateSplicedsegFromAnchoredAln(const CAnchoredAln &anchored_aln, CScope *scope)

CRef< CSeq_align > CreateSeqAlignFromAnchoredAln(const CAnchoredAln &anchored_aln, CSeq_align::TSegs::E_Choice choice, CScope *scope)

Convert CAnchoredAln to seq-align of the selected type.

CRef< CSeq_align_set > CreateAlignSetFromPairwiseAln(const CPairwiseAln &pairwise_aln, CScope *scope)

void CreateSeqAlignFromEachPairwiseAln(const CAnchoredAln::TPairwiseAlnVector pairwises, TDim anchor, vector< CRef< CSeq_align > > &out_seqaligns, CSeq_align::TSegs::E_Choice choice, CScope *scope)

Create seq-align from each of the pairwise alignments vs the selected anchor row.

CRef< CSeq_align_set > CreateAlignSetFromAnchoredAln(const CAnchoredAln &anchored_aln, CScope *scope)

CRef< CDense_seg > CreateDensegFromPairwiseAln(const CPairwiseAln &pairwise_aln, CScope *scope)

static const TSignedSeqPos kMaxSplicedExonIndelLength

class CAlignRangeCollectionList<TAlignRange> represent a sorted collection of TAlignRange.

const_iterator begin() const

const_iterator insert(const TAlignRange &r)

TSignedSeqPos GetSecondPosByFirstPos(position_type pos, ESearchDirection dir=eNone) const

@ fMixedDir

contains at least one reversed range

const_iterator end() const

CAlignRange Represents an element of pairwise alignment of two sequences.

Container mapping seq-aligns to vectors of participating seq-ids.

void push_back(const CSeq_align &aln)

Adding an alignment.

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

Options for different alignment manager operations.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

vector< CRef< CPairwiseAln > > TPairwiseAlnVector

const TAlnSeqIdIRef & GetId(TDim row) const

Seq ids of the rows.

TDim GetDim(void) const

How many rows.

TDim GetAnchorRow(void) const

Which is the anchor row?

void Validate(bool full_test=false) const

A pairwise aln is a collection of ranges for a pair of rows.

int GetSecondBaseWidth(void) const

Base width of the second row.

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

int GetFirstBaseWidth(void) const

Base width of the first row.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

const_iterator end() const

iterator find_nc(position_type pos)

TRanges::iterator iterator

CPairwiseAln::TPos position_type

TThisType & CombineWithAndKeepAbutting(const TThisType &c)

TThisType & DivideAfter(const position_type &p)

If position is in middle of range, divide into two consecutive ranges after this position.

Scope-aware seq-id converter.

void insert(const TRange &r)

void CutAtPosition(position_type pos)

ncbi::CRangeSet< CPairwiseAln::TPos > TParent

void Validate(bool full_test=false) const

Validators.

CNcbiOstream & operator<<(CNcbiOstream &out, const CEquivRange &range)

std::ofstream out("events_result.xml")

main entry point for tests

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

void Reset(void)

Reset reference object.

position_type GetFirstToOpen(void) const

position_type GetFirstTo(void) const

position_type GetSecondFrom(void) const

TThisType & SetFirstFrom(position_type from)

position_type GetSecondTo(void) const

position_type GetFirstFrom(void) const

position_type GetSecondToOpen(void) const

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TFrom GetFrom(void) const

Get the From member data.

vector< CRef< CSeq_id > > TIds

vector< TSeqPos > TStarts

Tdata & Set(void)

Assign a value to data member.

vector< ENa_strand > TStrands

TLens & SetLens(void)

Assign a value to Lens data member.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

void SetProduct_id(TProduct_id &value)

Assign a value to Product_id data member.

E_Choice

Choice variants.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< ENa_strand > TStrands

TExons & SetExons(void)

Assign a value to Exons data member.

void SetDim(TDim value)

Assign a value to Dim data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

void SetDim(TDim value)

Assign a value to Dim data member.

vector< TSignedSeqPos > TStarts

void SetDim(TDim value)

Assign a value to Dim data member.

vector< TSeqPos > TStarts

void SetType(TType value)

Assign a value to Type data member.

vector< CRef< CSeq_id > > TIds

vector< CRef< CSeq_id > > TIds

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetProduct_type(TProduct_type value)

Assign a value to Product_type data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

list< CRef< CSpliced_exon > > TExons

vector< ENa_strand > TStrands

void SetGenomic_id(TGenomic_id &value)

Assign a value to Genomic_id data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

TIds & SetIds(void)

Assign a value to Ids data member.

list< CRef< CDense_diag > > TDendiag

TIds & SetIds(void)

Assign a value to Ids data member.

@ e_not_set

No variant selected.

@ eType_partial

mapping pieces together

@ eProduct_type_transcript

double value_type

The numeric datatype used by the parser.

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

#define row(bind, expected)

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