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

69

descrs->AddFlag(

"print_exp"

,

"Print expected values instead of testing"

);

70

descrs->AddFlag(

"verbose"

,

"Print detailed test progress"

);

108  size_t

num_aligns = 0;

109  while

( !

in

.eof() ) {

116  if

(limit > 0 && num_aligns >= limit)

break

;

129

unique_ptr<TScopeAlnIdMap>& aln_id_map)

135

aln_id_map->push_back(**aln_it);

165

cout << aln_idx <<

" "

<< anchor <<

" "

<<

row

<<

" "

<< pw.

GetFlags

() << endl;

177

cout <<

" aln="

<< aln_idx <<

", anchor="

<< anchor <<

", row="

<<

row

<< endl;

179  size_t

expected_aln_idx;

180  int

expected_row, expected_anchor;

181  int

first_width, second_width;

183

in_exp >> expected_aln_idx >> expected_anchor >> expected_row >>

flags

;

184

in_exp >> first_from >> first_to >> first_width;

186

in_exp >> second_from >> second_to >> second_width;

188

BOOST_CHECK(in_exp.good());

189

BOOST_CHECK(aln_idx == expected_aln_idx);

190

BOOST_CHECK(anchor == expected_anchor);

191

BOOST_CHECK(

row

== expected_row);

193

BOOST_CHECK(pw.

GetFirstId

()->GetSeqId().Equals(first_id));

194

BOOST_CHECK(pw.

GetSecondId

()->GetSeqId().Equals(second_id));

208

<< rg_it->GetSecondFrom() <<

" " 209

<< rg_it->GetLength() <<

" " 210

<< (rg.

IsDirect

() ? 1 : 0) << endl;

213

in_exp >> first_from >> second_from >>

len

>>

flags

;

214

BOOST_CHECK(in_exp.good());

215

BOOST_CHECK(rg_it->GetFirstFrom() == first_from);

216

BOOST_CHECK(rg_it->GetSecondFrom() == second_from);

217

BOOST_CHECK(rg_it->GetLength() ==

len

);

218

BOOST_CHECK(rg_it->IsDirect() == (

flags

!= 0));

228

BOOST_CHECK(in_exp.good());

235

cout <<

" "

<< gap->GetFirstFrom() <<

" " 236

<< gap->GetSecondFrom() <<

" " 237

<< gap->GetLength() <<

" " 238

<< (gap->IsDirect() ? 1 : 0) << endl;

241

in_exp >> first_from >> second_from >>

len

>>

flags

;

242

BOOST_CHECK(in_exp.good());

243

BOOST_CHECK(gap->GetFirstFrom() == first_from);

244

BOOST_CHECK(gap->GetSecondFrom() == second_from);

245

BOOST_CHECK(gap->GetLength() ==

len

);

246

BOOST_CHECK(gap->IsDirect() == (

flags

!= 0));

266  static const char

* kGap =

"<GAP>"

;

267  static const char

* kNoData =

"<NO SEQUENCE DATA>"

;

272

cout << sparse.

GetDim

() <<

" " 279  int

expected_dim, expected_numrows, expected_anchor;

280

in_exp >> expected_dim >> expected_numrows >> expected_anchor;

281

in_exp >> expected_aln_from >> expected_aln_to;

282

BOOST_CHECK(in_exp.good());

283

BOOST_CHECK(sparse.

GetDim

() == expected_dim);

284

BOOST_CHECK(sparse.

GetNumRows

() == expected_numrows);

285

BOOST_CHECK(sparse.

GetAnchor

() == expected_anchor);

297  int

expected_row, expected_width;

299

in_exp >> expected_row >> expected_width >>

MSerial_AsnText

>> expected_id;

300

BOOST_CHECK(in_exp.good());

301

BOOST_CHECK(

row

== expected_row);

303

BOOST_CHECK(sparse.

GetSeqId

(

row

).Equals(expected_id));

309  TSeqPos

expected_seq_from, expected_seq_to,

310

expected_native_from, expected_native_to;

315

<< native_rg.

GetFrom

() <<

" "

<< native_rg.

GetTo

() << endl;

318

in_exp >> expected_aln_from >> expected_aln_to

319

>> expected_seq_from >> expected_seq_to

320

>> expected_native_from >> expected_native_to;

321

BOOST_CHECK(in_exp.good());

324

BOOST_CHECK(rg.

GetFrom

() == expected_seq_from);

325

BOOST_CHECK(rg.

GetTo

() == expected_seq_to);

326

BOOST_CHECK(native_rg.

GetFrom

() == expected_native_from);

327

BOOST_CHECK(native_rg.

GetTo

() == expected_native_to);

330  if

( check_sequence ) {

331  string

aln_sequence, row_sequence;

334  if

( aln_sequence.empty() ) {

335

aln_sequence = kNoData;

337  if

( row_sequence.empty() ) {

338

row_sequence = kNoData;

342

cout << aln_sequence << endl;

343

cout << row_sequence << endl;

347

cout <<

" whole row="

<<

row

<< endl;

349  string

expected_aln_sequence, expected_row_sequence;

351

getline(in_exp, expected_aln_sequence);

352

getline(in_exp, expected_row_sequence);

353

BOOST_CHECK(in_exp.good());

354

BOOST_CHECK(aln_sequence == expected_aln_sequence);

355

BOOST_CHECK(row_sequence == expected_row_sequence);

360  for

(; sparse_ci; ++sparse_ci) {

366

cout <<

" "

<< seg.

GetType

() <<

" " 368

<< seq_rg.

GetFrom

() <<

" "

<< seq_rg.

GetTo

() << endl;

372

cout <<

" segment: row="

<<

row

<<

", range="

<<

375  unsigned

expected_seg_type;

378

in_exp >> expected_seg_type

379

>> expected_aln_from >> expected_aln_to

380

>> expected_seq_from >> expected_seq_to;

381

BOOST_CHECK(in_exp.good());

382

BOOST_CHECK(seg.

GetType

() == expected_seg_type);

383

BOOST_CHECK(aln_rg.

GetFrom

() == expected_aln_from);

384

BOOST_CHECK(aln_rg.

GetTo

() == expected_aln_to);

385

BOOST_CHECK(seq_rg.

GetFrom

() == expected_seq_from);

386

BOOST_CHECK(seq_rg.

GetTo

() == expected_seq_to);

389  if

( check_sequence ) {

390  string

aln_sequence, row_sequence;

391  string

expected_aln_sequence, expected_row_sequence;

393  if

( !aln_rg.

Empty

() ) {

395  if

( aln_sequence.empty() ) {

396

aln_sequence = kNoData;

402  if

( !seq_rg.

Empty

() ) {

405  if

( row_sequence.empty() ) {

406

row_sequence = kNoData;

414

cout << aln_sequence << endl;

415

cout << row_sequence << endl;

419

getline(in_exp, expected_aln_sequence);

420

getline(in_exp, expected_row_sequence);

421

BOOST_CHECK(in_exp.good());

422

BOOST_CHECK(aln_sequence == expected_aln_sequence);

423

BOOST_CHECK(row_sequence == expected_row_sequence);

433

cout <<

"Test CAlnContainer and CAlnStats... (aligns1.asn / expected01.txt)"

<< endl;

443  size_t

num_aligns =

LoadAligns

(in_data, aligns);

446

cout << num_aligns << endl;

449  size_t

expected_num_aligns;

450

in_exp >> expected_num_aligns;

451

BOOST_CHECK(num_aligns == expected_num_aligns);

454

unique_ptr<TScopeAlnIdMap> aln_id_map;

458

BOOST_CHECK(aln_stats->GetAlnCount() == num_aligns);

459

BOOST_CHECK(aln_stats->CanBeAnchored());

464

cout << (*id_it)->GetBaseWidth() <<

" "

;

472

BOOST_CHECK(

id

.

Equals

((*id_it)->GetSeqId()));

473

BOOST_CHECK((*id_it)->GetBaseWidth() == width);

481

cout <<

"Test CPairwiseAln... (aligns1.asn / expected02.txt)"

<< endl;

491  size_t

num_aligns =

LoadAligns

(in_data, aligns);

494

cout << num_aligns << endl;

497  size_t

expected_num_aligns;

498

in_exp >> expected_num_aligns;

499

BOOST_CHECK(num_aligns == expected_num_aligns);

502

unique_ptr<TScopeAlnIdMap> aln_id_map;

508  for

(

size_t

aln_idx = 0; aln_idx < aln_vec.size(); ++aln_idx) {

513  for

(

int

anchor = 0; anchor < 2; anchor++) {

515  for

(

int row

= 0;

row

< aln_stats->GetDimForAln(aln_idx); ++

row

) {

516  if

(

row

== anchor)

continue

;

526

cout <<

" "

<< seg.GetFirstRange().GetFrom() <<

" " 527

<< seg.GetFirstRange().GetTo() <<

" " 528

<< seg.GetSecondRange().GetFrom() <<

" " 529

<< seg.GetSecondRange().GetTo() <<

" " 530

<< (seg.IsDirect() ? 1 : 0) <<

" " 531

<< (seg.IsFirstDirect() ? 1 : 0) <<

" " 535  int

direct, first_direct, aligned;

537

in_exp >> first_from >> first_to >> second_from >> second_to >>

538

direct >> first_direct >> aligned;

539

BOOST_CHECK(in_exp.good());

540

BOOST_CHECK(seg.GetFirstRange().GetFrom() == first_from);

541

BOOST_CHECK(seg.GetFirstRange().GetTo() == first_to);

542

BOOST_CHECK(seg.GetSecondRange().GetFrom() == second_from);

543

BOOST_CHECK(seg.GetSecondRange().GetTo() == second_to);

544

BOOST_CHECK(seg.IsDirect() == (direct != 0));

545

BOOST_CHECK(seg.IsFirstDirect() == (first_direct != 0));

558

cout <<

"Test ranged CPairwise_CI... (aligns1.asn / expected03.txt)"

<< endl;

580  size_t

num_aligns =

LoadAligns

(in_data, aligns);

583

cout << num_aligns << endl;

586  size_t

expected_num_aligns;

587

in_exp >> expected_num_aligns;

588

BOOST_CHECK(num_aligns == expected_num_aligns);

591

unique_ptr<TScopeAlnIdMap> aln_id_map;

597  for

(

size_t

aln_idx = 0; aln_idx < aln_vec.size(); ++aln_idx) {

602  for

(

int

anchor = 0; anchor < 2; anchor++) {

604  for

(

int row

= 0;

row

< aln_stats->GetDimForAln(aln_idx); ++

row

) {

605  if

(

row

== anchor)

continue

;

614

cout << aln_idx <<

" "

<< anchor <<

" "

<<

row

<<

" "

<< pw.

GetFlags

() << endl;

626

cout <<

" aln="

<< aln_idx <<

", anchor="

<< anchor <<

", row="

<<

row

<< endl;

628  size_t

expected_aln_idx;

629  int

expected_row, expected_anchor;

630  int

first_width, second_width,

flags

;

632

in_exp >> expected_aln_idx >> expected_anchor >> expected_row >>

flags

;

633

in_exp >> first_from >> first_to >> first_width;

635

in_exp >> second_from >> second_to >> second_width;

637

BOOST_CHECK(in_exp.good());

638

BOOST_CHECK(aln_idx == expected_aln_idx);

639

BOOST_CHECK(anchor == expected_anchor);

640

BOOST_CHECK(

row

== expected_row);

642

BOOST_CHECK(pw.

GetFirstId

()->GetSeqId().Equals(first_id));

643

BOOST_CHECK(pw.

GetSecondId

()->GetSeqId().Equals(second_id));

652  if

(pw.

size

() < 2)

continue

;

654

first_from = (pw.

begin

()+1)->GetFirstFrom() + 1;

655

first_to = pw.

rbegin

()->GetFirstFrom() - 2;

660

cout <<

" "

<< seg.GetFirstRange().GetFrom() <<

" " 661

<< seg.GetFirstRange().GetTo() <<

" " 662

<< seg.GetSecondRange().GetFrom() <<

" " 663

<< seg.GetSecondRange().GetTo() <<

" " 664

<< (seg.IsDirect() ? 1 : 0) <<

" " 665

<< (seg.IsFirstDirect() ? 1 : 0) <<

" " 669  int

direct, first_direct, aligned;

670

in_exp >> first_from >> first_to >> second_from >> second_to >>

671

direct >> first_direct >> aligned;

672

BOOST_CHECK(in_exp.good());

673

BOOST_CHECK(seg.GetFirstRange().GetFrom() == first_from);

674

BOOST_CHECK(seg.GetFirstRange().GetTo() == first_to);

675

BOOST_CHECK(seg.GetSecondRange().GetFrom() == second_from);

676

BOOST_CHECK(seg.GetSecondRange().GetTo() == second_to);

677

BOOST_CHECK(seg.IsDirect() == (direct != 0));

678

BOOST_CHECK(seg.IsFirstDirect() == (first_direct != 0));

690

cout <<

"Test CAnchoredAln... (aligns1.asn / expected04.txt)"

<< endl;

696  size_t

num_aligns =

LoadAligns

(in_data, aligns);

699

cout << num_aligns << endl;

702  size_t

expected_num_aligns;

703

in_exp >> expected_num_aligns;

704

BOOST_CHECK(num_aligns == expected_num_aligns);

707

unique_ptr<TScopeAlnIdMap> aln_id_map;

710  for

(

size_t

aln_idx = 0; aln_idx < aligns.

size

(); ++aln_idx) {

711  for

(

int

anchor = 0; anchor < aln_stats->GetDimForAln(aln_idx); ++anchor) {

714

aln_idx, user_options, anchor);

728  static const int

kMergeFlags[] = {

737

cout <<

"Test built CAnchoredAln... (aligns2.asn / expected05.txt)"

<< endl;

743  while

(!in_data.eof() && in_data.good()) {

746

in_data >> num_to_merge;

747  if

(num_to_merge == 0 || !in_data.good())

break

;

750  size_t

num_aligns =

LoadAligns

(in_data, aligns, num_to_merge);

753

cout << num_aligns << endl;

756  size_t

expected_num_aligns;

757

in_exp >> expected_num_aligns;

758

BOOST_CHECK(num_aligns == expected_num_aligns);

761

unique_ptr<TScopeAlnIdMap> aln_id_map;

765  for

(

size_t

anchor_idx = 0; anchor_idx < aln_ids.size(); anchor_idx++) {

770  for

(

size_t

flags_idx = 0; flags_idx <

sizeof

(kMergeFlags)/

sizeof

(kMergeFlags[0]); flags_idx++) {

774

cout << anchor_idx <<

" " 779

cout <<

" set="

<< setnum <<

", anchor="

<< anchor_idx <<

" ("

<<

780

anchor_id->GetSeqId().AsFastaString() <<

")"

<<

781  ", flags_idx="

<< flags_idx << endl;

783  size_t

expected_anchor_idx;

785

in_exp >> expected_anchor_idx >> expected_flags;

786

BOOST_CHECK(in_exp.good());

787

BOOST_CHECK(anchor_idx == expected_anchor_idx);

788

BOOST_CHECK(user_options.

m_MergeFlags

== expected_flags);

795  id

->SetLocal().SetStr(

"pseudo-id"

);

798  BuildAln

(anchored_aln_vec, built_aln, user_options, pseudo_id);

813

cout <<

"Test CSparseAln coordinates... (aligns2.asn / expected06.txt)"

<< endl;

819  while

(!in_data.eof() && in_data.good()) {

822

in_data >> num_to_merge;

823  if

(num_to_merge == 0 || !in_data.good())

break

;

826  size_t

num_aligns =

LoadAligns

(in_data, aligns, num_to_merge);

829

cout << num_aligns << endl;

832  size_t

expected_num_aligns;

833

in_exp >> expected_num_aligns;

834

BOOST_CHECK(num_aligns == expected_num_aligns);

837

unique_ptr<TScopeAlnIdMap> aln_id_map;

841  for

(

size_t

anchor_idx = 0; anchor_idx < aln_ids.size(); anchor_idx++) {

848

cout << anchor_idx <<

" " 853

cout <<

" set="

<< setnum <<

", anchor="

<< anchor_idx <<

" ("

<<

854

anchor_id->GetSeqId().AsFastaString() <<

")"

<< endl;

856  size_t

expected_anchor_idx;

857

in_exp >> expected_anchor_idx;

860

BOOST_CHECK(in_exp.good());

861

BOOST_CHECK(anchor_idx == expected_anchor_idx);

862

BOOST_CHECK(anchor_id->GetSeqId().Equals(expected_anchor_id));

869  id

->SetLocal().SetStr(

"pseudo-id"

);

872  BuildAln

(anchored_aln_vec, built_aln, user_options, pseudo_id);

884

cout <<

"Test CSparseAln sequence... (aligns3.asn / expected07.txt)"

<< endl;

890  while

(!in_data.eof() && in_data.good()) {

893

in_data >> num_to_merge;

894  if

(num_to_merge == 0 || !in_data.good())

break

;

897  size_t

num_aligns =

LoadAligns

(in_data, aligns, num_to_merge);

900

cout << num_aligns << endl;

903  size_t

expected_num_aligns;

904

in_exp >> expected_num_aligns;

905

BOOST_CHECK(num_aligns == expected_num_aligns);

908

unique_ptr<TScopeAlnIdMap> aln_id_map;

912  for

(

size_t

anchor_idx = 0; anchor_idx < aln_ids.size(); anchor_idx++) {

919

cout << anchor_idx <<

" " 924

cout <<

" set="

<< setnum <<

", anchor="

<< anchor_idx <<

" ("

<<

925

anchor_id->GetSeqId().AsFastaString() <<

")"

<< endl;

927  size_t

expected_anchor_idx;

928

in_exp >> expected_anchor_idx;

931

BOOST_CHECK(in_exp.good());

932

BOOST_CHECK(anchor_idx == expected_anchor_idx);

933

BOOST_CHECK(anchor_id->GetSeqId().Equals(expected_anchor_id));

940  id

->SetLocal().SetStr(

"pseudo-id"

);

943  BuildAln

(anchored_aln_vec, built_aln, user_options, pseudo_id);

958

BOOST_CHECK(aln->

Equals

(expected_aln));

966

cout <<

"Test seq-align types... (aligns4.asn / expected08.txt)"

<< endl;

972  size_t

num_aligns =

LoadAligns

(in_data, aligns);

975

cout << num_aligns << endl;

978  size_t

expected_num_aligns;

979

in_exp >> expected_num_aligns;

980

BOOST_CHECK(num_aligns == expected_num_aligns);

983

unique_ptr<TScopeAlnIdMap> aln_id_map;

986  for

(

size_t

aln_idx = 0; aln_idx < aligns.

size

(); ++aln_idx) {

987  for

(

int

anchor = 0; anchor < aln_stats->GetDimForAln(aln_idx); ++anchor) {

990  if

(aln_stats->GetAlnVec()[aln_idx]->GetSegs().IsSparse() && anchor > 0) {

996

aln_idx, user_options, anchor);

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

void ConvertSeqAlignToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSeq_align &sa, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a seq-align.

void CreateAnchoredAlnVec(_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)

Create anchored alignment from each seq-align in the stats.

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.

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

Convert CAnchoredAln to seq-align of the selected type.

CAlnStats< TScopeAlnIdMap > TScopeAlnStats

CAlnIdMap< vector< const CSeq_align * >, TScopeIdExtract > TScopeAlnIdMap

const_iterator begin() const

const_reverse_iterator rbegin() const

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

position_type GetFirstFrom() const

@ fDefaultPolicy

do not store insertions

const TInsertions & GetInsertions() const

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

vector< TAlignRange > TInsertions

position_type GetFirstTo() const

CAlignRange Represents an element of pairwise alignment of two sequences.

const_iterator insert(const CSeq_align &seq_align)

Insert new CSeq_align into the list.

size_type size(void) const

Default IAlnSeqId implementation based on CSeq_id_Handle.

_TAlnIdVec::TAlnVec TAlnVec

Vector of original seq-aligns.

_TAlnIdVec::TIdVec TIdVec

Vector of ids used in all alignments.

Options for different alignment manager operations.

void SetAnchorId(const TAlnSeqIdIRef &anchor_id)

Set anchor id.

@ eBothDirections

No filtering: use both direct and reverse sequences.

@ fUseAnchorAsAlnSeq

Use the anchor sequence as the alignment sequence.

@ fAllowTranslocation

Allow translocations on the same row.

@ 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).

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

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

TDim GetAnchorRow(void) const

Which is the anchor row?

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static CNcbiApplication * Instance(void)

Singleton method.

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.

CPairwiseAln iterator. Iterates over aligned ranges and gaps.

@ eAligned

Aligned range.

Scope-aware seq-id converter.

void Validate(bool full_test=false) const

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TRng GetAlnRange(void) const

Get whole alignment range.

TNumrow GetNumRows(void) const

Synonym of the above.

int GetBaseWidth(TNumrow row) const

Get base width for the sequence (1 for nucleotides, 3 for proteins).

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

TRange GetSeqRange(TNumrow row) const

Get sequence range in sequence coords.

CAnchoredAln::TDim TDim

Synonym of TNumrow.

_TRange AlnRangeToNativeSeqRange(TNumrow row, _TRange aln_range) const

Convert alignment range (genomic coordinates) on the selected row to real sequence range.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

TDim GetDim(void) const

Alignment dimension (number of sequence rows in the alignment)

TNumrow GetAnchor(void) const

Get anchor row index.

string & GetSeqString(TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const

Fetch sequence data for the given row and range.

const objects::CSeq_id & GetSeqId(TNumrow row) const

Get seq-id for the row.

Implementation of IAlnSegmentIterator for CSparseAln.

@ eAllSegments

Iterate all segments.

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define MSerial_AsnText

I/O stream manipulators –.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

position_type GetFirstFrom(void) const

static TThisType GetWhole(void)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

static bool Equals(const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

#define row(bind, expected)

Utility stuff for more convenient using of Boost.Test library.

CRef< TScopeAlnStats > InitAlnStats(const CAlnContainer &aligns, unique_ptr< TScopeAlnIdMap > &aln_id_map)

size_t LoadAligns(CNcbiIstream &in, CAlnContainer &aligns, size_t limit=0)

void CheckSparseAln(CNcbiIstream &in_exp, const CSparseAln &sparse, bool check_sequence)

NCBITEST_INIT_CMDLINE(descrs)

void CheckPairwiseAln(CNcbiIstream &in_exp, const CPairwiseAln &pw, size_t aln_idx, int anchor, int row)

BOOST_AUTO_TEST_CASE(s_TestLoadAlign)

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