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

cerr <<

<< endl << existing << endl;

cerr <<

<< endl << addition << endl;

cerr <<

<< endl << difference << endl;

existing.

(*rng_it);

cerr <<

<< endl << existing << endl;

(*it)->SortInsertions();

addition->GetSecondId(),

addition->GetPolicyFlags()));

cerr <<

<< endl << existing << endl;

cerr <<

<< endl << *addition << endl;

cerr <<

<< endl << *truncated << endl;

addition = truncated;

addition->AddInsertions(gaps_truncated);

addition = truncated;

CPairwiseAln::const_iterator it =

.find_insertion_point(

);

(it !=

.begin()) {

.IsDirect() ?

: left) ) {

(it !=

.end()) {

.IsDirect() ? right :

) ) {

TPairwiseAlnVector::iterator aln_it, aln_end;

CPairwiseAln::TInsertions::const_iterator gap_it = gaps.begin();

(rng_it->IsDirect()) {

(aln_it != aln_end) {

cerr << *rng_it << endl;

cerr << **aln_it << endl;

(aln_it == aln_end) {

(rng_it->IsDirect() &&

(*aln_it)->insert(*rng_it);

CPairwiseAln::const_iterator next_rng_it = rng_it;

(next_rng_it != addition.

()) {

next_rng_pos = next_rng_it->GetFirstFrom();

(gap_it != gaps.end() &&

(gap_it->GetFirstFrom() <= next_rng_pos || next_rng_pos < 0)) {

(*aln_it)->AddInsertion(*gap_it);

<<

<< endl;

total_number_of_rows = 0;

total_number_of_rows += (*merged_i)->GetPairwiseAlns().size();

(anchored_aln_vec.begin(),

anchored_aln_vec.end(),

( anchor_pw.

() )

;

aln_len += it->GetLength();

direct = anchor_pw.

()->IsFirstDirect();

out_anchor_pw.

(ar);

CPairwiseAln::TInsertions::const_iterator gap_it = gaps.begin();

(gap_it != gaps.end()) {

CPairwiseAln::const_iterator next_it = it;

(next_it != pw.

()) {

(gap_it != gaps.end() &&

gap_it->GetFirstFrom() <= next_it->GetFirstFrom()) {

(gap_it != gaps.end()) {

(new_gap_pos == -1) {

( !direct ) {

& anchor_pw = *pairwises[anchor_row];

direct = (new_anchor_pw->begin()->IsFirstDirect() == anchor_pw.

()->IsFirstDirect());

(

== anchor_row) {

pairwises[

].Reset(new_anchor_pw);

pairwises[

].Reset(new_pw);

have_direct =

;

have_reverse =

;

( !common_anchor_id ) {

( !common_anchor_id->GetSeqId().Equals(

( seg->IsFirstDirect() ) {

have_reverse =

;

(have_direct && have_reverse) {

(have_direct && have_reverse) {

(have_direct && have_reverse) {

(!have_direct || !have_reverse) {

out_alns->push_back(anchored_copy);

pw_copy->insert(seg_copy);

(anchored_it == adj_alns->begin()) {

}

(!anchor_first) {

( !adj_alns->empty() ) {

& first_anchored = *adj_alns->front();

merged_vec.resize(first_anchored.

());

errstr =

;

errstr =

;

(merged.

()) {

TIdMergedMap id_merged_map;

merged_vec.push_back(merged_anchor);

cerr << *merged_anchor << endl;

cerr <<

<< aln_idx <<

<< anchor_row <<

<< endl;

(anchored_it == adj_alns->begin()) {

id_merged_map[anchored_aln.

(anchor_row)].

(merged_anchor);

(

!= anchor_row) {

(merged.

()) {

merged_vec.push_back(merged);

cerr << *merged << endl;

cerr <<

<< aln_idx <<

<<

<< endl;

merged_vec.push_back(merged_anchor);

(*ma)->SortInsertions();

( !pseudo_seqid ) {

pseudo_seqid.

(aln_seq_id);

void MergePairwiseAlns(CPairwiseAln &existing, const CPairwiseAln &addition, const CAlnUserOptions::TMergeFlags &flags)

Merge two pariwise alignments.

void s_TranslateAnchorToAlnCoords(CPairwiseAln &out_anchor_pw, const CPairwiseAln &anchor_pw)

void SortAnchoredAlnVecByScore(TAnchoredAlnVec &anchored_aln_vec)

Sort anchored alignments by score.

void s_TranslatePairwiseToAlnCoords(CPairwiseAln &out_pw, const CPairwiseAln &pw, const CPairwiseAln &tr, bool direct)

vector< CRef< CMergedPairwiseAln > > TMergedVec

void x_AdjustAnchorDirection(TAnchoredAlnVec &in_alns, AutoPtr< TAnchoredAlnVec > &out_alns)

ostream & operator<<(ostream &out, const CMergedPairwiseAln &merged)

void BuildAln(const TMergedVec &merged_vec, CAnchoredAln &out_aln)

void s_TranslateToAlnCoords(CAnchoredAln &anchored_aln, const TAlnSeqIdIRef &pseudo_seqid)

void SubtractAlnRngCollections(const CAlignRangeCollectionList< TAlnRng > &minuend, const CAlignRangeCollectionList< TAlnRng > &subtrahend, CAlignRangeCollectionList< TAlnRng > &difference)

Subtract one range collection from another.

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

int GetPolicyFlags() const

const_iterator begin() const

const_iterator insert(const TAlignRange &r)

@ fAllowOverlap

allow segments with different orientation

@ fAllowAbutting

allow segments overlapping on the first sequence

@ fAllowMixedDir

enforce all policies after any modification

@ fReversed

contains at least one direct range

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

const TInsertions & GetInsertions() const

Each insertion shows where the 'first' sequence has a gap while the 'second' sequence has the inserti...

vector< TAlignRange > TInsertions

const_iterator end() const

void AddInsertion(const TAlignRange &r)

void AddInsertions(const TInsertions &insertions)

CAlignRange Represents an element of pairwise alignment of two sequences.

Default IAlnSeqId implementation based on CSeq_id_Handle.

Options for different alignment manager operations.

@ eMergeAllSeqs

Merge all sequences (greedy algo).

@ ePreserveRows

Preserve all rows as they were in the input (e.g.

@ eQuerySeqMergeOnly

Only put the query seq on same row (input order is not significant).

@ fUseAnchorAsAlnSeq

Use the anchor sequence as the alignment sequence.

@ fAllowTranslocation

Allow translocations on the same row.

@ fSkipSortByScore

In greedy algos, skip sorting input alignments by score thus allowing for user-defined sort order.

@ fAnchorRowFirst

Store anchor row in the first pairwise alignment (by default it's stored in the last one).

@ fTruncateOverlaps

Truncate overlapping ranges.

@ fIgnoreInsertions

Do not collect and store insertions (gaps on the anchor).

@ fAllowMixedStrand

Allow mixed strands on the same row.

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.

void SetAnchorRow(TDim anchor_row)

Modify anchor row (never do this unless you are creating a new alignment and know what you're doing).

TPairwiseAlnVector & SetPairwiseAlns(void)

Modify pairwise alns.

void SetScore(int score)

Set the total score.

TDim GetAnchorRow(void) const

Which is the anchor row?

int GetScore(void) const

What is the total score?

const TAlnSeqIdIRef & GetAnchorId(void) const

What is the seq id of the anchor?

void SetDim(TDim dim)

Modify the number of rows.

bool x_ValidNeighboursOnSecondDim(const CPairwiseAln::TAlnRng &left, const CPairwiseAln::TAlnRng &right)

const TPairwiseAlnVector & GetPairwiseAlns() const

bool x_CanInsertRng(CPairwiseAln &a, const CPairwiseAln::TAlnRng &r)

void x_TruncateOverlaps(CRef< CPairwiseAln > &addition)

size_t m_NumberOfDirectAlns

bool x_ValidNeighboursOnFirstDim(const CPairwiseAln::TAlnRng &left, const CPairwiseAln::TAlnRng &right)

const CAlnUserOptions::TMergeFlags m_MergeFlags

void SortInsertions(void)

const CAlnUserOptions::TMergeFlags & GetMergedFlags() const

CMergedPairwiseAln(const CAlnUserOptions::TMergeFlags &merge_flags)

void x_AddPairwise(const CPairwiseAln &addition)

void insert(const CRef< CPairwiseAln > &pairwise)

CAnchoredAln::TPairwiseAlnVector TPairwiseAlnVector

TPairwiseAlnVector m_PairwiseAlns

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

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

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

main entry point for tests

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

@ eTakeOwnership

An object can take ownership of another.

@ eNoOwnership

No ownership is assumed.

#define NCBI_THROW(exception_class, err_code, message)

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

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

position_type GetFirstToOpen(void) const

position_type GetFirstTo(void) const

position_type GetSecondFrom(void) const

void SetDirect(bool direct=true)

TThisType & SetFirstFrom(position_type from)

void SetFirstDirect(bool direct=true)

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.

@ eCurrent

Use current time. See also CCurrentTime.

constexpr auto sort(_Init &&init)

Defines: CTimeFormat - storage class for time format.

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

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

#define row(bind, expected)

Compare alignments by score.

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