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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/mapper__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seq/unit_test/mapper_unit_test.cpp Source File

34 #define NCBI_TEST_APPLICATION 57 #define CHECK_GI(id, gi) \ 58  BOOST_CHECK_EQUAL((id).Which(), CSeq_id::e_Gi); \ 59  BOOST_CHECK_EQUAL((id).GetGi(), gi); 61 #define CHECK_SEQ_INT(loc, gi, from, to, \ 62  have_strand, strand, \ 64  CHECK_GI((loc).GetId(), gi); \ 65  BOOST_CHECK_EQUAL((loc).GetFrom(), from); \ 66  BOOST_CHECK_EQUAL((loc).GetTo(), to); \ 67  BOOST_CHECK_EQUAL((loc).IsSetStrand(), have_strand); \ 69  BOOST_CHECK_EQUAL((loc).GetStrand(), strand); \ 71  if (fuzz_from != CInt_fuzz::eLim_unk) { \ 72  BOOST_CHECK((loc).IsSetFuzz_from()); \ 73  BOOST_CHECK_EQUAL((loc).GetFuzz_from().Which(), CInt_fuzz::e_Lim); \ 74  BOOST_CHECK_EQUAL((loc).GetFuzz_from().GetLim(), fuzz_from); \ 77  BOOST_CHECK(!(loc).IsSetFuzz_from()); \ 79  if (fuzz_to != CInt_fuzz::eLim_unk) { \ 80  BOOST_CHECK((loc).IsSetFuzz_to()); \ 81  BOOST_CHECK_EQUAL((loc).GetFuzz_to().Which(), CInt_fuzz::e_Lim); \ 82  BOOST_CHECK_EQUAL((loc).GetFuzz_to().GetLim(), fuzz_to); \ 85  BOOST_CHECK(!(loc).IsSetFuzz_to()); \ 90 #if NCBI_COMPILER_MSVC && (_MSC_VER < 1400) 91 # undef kInvalidSeqPos 92 # define kInvalidSeqPos -1 125  bool eq

= mapped->

Equals

(ref_mapped);

126

BOOST_CHECK(mapped->

Equals

(ref_mapped));

128

cout <<

"Expected mapped location:"

<< endl;

130

cout <<

"Actual mapped location:"

<< endl;

164  bool eq

= mapped->

Equals

(ref_mapped);

165

BOOST_CHECK(mapped->

Equals

(ref_mapped));

167

cout <<

"Expected mapped alignment:"

<< endl;

169

cout <<

"Actual mapped alignment:"

<< endl;

203  bool eq

= mapped->

Equals

(ref_mapped);

204

BOOST_CHECK(mapped->

Equals

(ref_mapped));

206

cout <<

"Expected mapped graph:"

<< endl;

208

cout <<

"Actual mapped graph:"

<< endl;

235

cout <<

"Basic mapping and truncaction test"

<< endl;

247

cout <<

" Simple interval"

<< endl;

249

cout <<

" Simple interval, reversed strand"

<< endl;

253

cout <<

" Truncated on the right"

<< endl;

255

cout <<

" Truncated on the right, reversed strand"

<< endl;

259

cout <<

" Truncated on the left"

<< endl;

261

cout <<

" Truncated on the left, reversed strand"

<< endl;

265

cout <<

" Truncated on both ends"

<< endl;

267

cout <<

" Truncated on both ends, reversed strand"

<< endl;

271

cout <<

" Minus strand interval"

<< endl;

273

cout <<

" Minus strand interval, reversed strand"

<< endl;

277

cout <<

" Minus strand interval, truncated on the right"

<< endl;

279

cout <<

" Minus strand interval, truncated on the right, reversed strand"

<< endl;

283

cout <<

" Minus strand interval, truncated on the left"

<< endl;

285

cout <<

" Minus strand interval, truncated on the left, reversed strand"

<< endl;

289

cout <<

" Minus strand interval, truncated on both ends"

<< endl;

291

cout <<

" Minus strand interval, truncated on both ends, reversed strand"

<< endl;

294

cout <<

" Null seq-loc"

<< endl;

297

cout <<

" Empty seq-loc"

<< endl;

301

cout <<

" Whole seq-loc"

<< endl;

303

cout <<

" Whole seq-loc, reversed strand"

<< endl;

307

cout <<

" Point"

<< endl;

309

cout <<

" Point, reversed strand"

<< endl;

313

cout <<

" Packed-points"

<< endl;

315

cout <<

" Packed-points, reversed strand"

<< endl;

318

cout <<

" Bond"

<< endl;

320

cout <<

" Bond, reversed strand"

<< endl;

328

cout <<

"Order of mapped intervals, direct"

<< endl;

330

cout <<

" Mapping plus to plus strand"

<< endl;

332

cout <<

" Mapping minus to minus strand"

<< endl;

335

cout <<

"Order of mapped intervals, plus to minus"

<< endl;

337

cout <<

" Mapping plus to minus strand (src on plus)"

<< endl;

339

cout <<

" Mapping minus to plus strand (src on plus)"

<< endl;

342

cout <<

"Order of mapped intervals, minus to plus"

<< endl;

344

cout <<

" Mapping plus to minus strand (src on minus)"

<< endl;

346

cout <<

" Mapping minus to plus strand (src on minus)"

<< endl;

349

cout <<

"Mapping through a mix, direct"

<< endl;

351

cout <<

" Mapping through a mix, plus to plus strand"

<< endl;

353

cout <<

" Mapping through a mix, plus to plus strand, with merge"

<< endl;

354

mapper->SetMergeAbutting();

356

mapper->SetMergeNone();

357

cout <<

" Mapping through a mix, minus to minus strand"

<< endl;

359

cout <<

" Mapping through a mix, minus to minus strand, with merge"

<< endl;

360

mapper->SetMergeAbutting();

362

mapper->SetMergeNone();

364

cout <<

"Mapping through a mix, plus to minus"

<< endl;

366

cout <<

" Mapping through a mix, plus to minus strand (src on plus)"

<< endl;

368

cout <<

" Mapping through a mix, plus to minus (src on plus), with merge"

<< endl;

369

mapper->SetMergeAbutting();

371

mapper->SetMergeNone();

372

cout <<

" Mapping through a mix, minus to plus strand (src on plus)"

<< endl;

374

cout <<

" Mapping through a mix, minus to plus (src on plus), with merge"

<< endl;

375

mapper->SetMergeAbutting();

377

mapper->SetMergeNone();

379

cout <<

"Mapping through a mix, minus to plus"

<< endl;

381

cout <<

" Mapping through a mix, plus to minus strand (src on minus)"

<< endl;

383

cout <<

" Mapping through a mix, plus to minus strand (src on minus), with merge"

<< endl;

384

mapper->SetMergeAbutting();

386

mapper->SetMergeNone();

387

cout <<

" Mapping through a mix, minus to plus strand (src on minus)"

<< endl;

389

cout <<

" Mapping through a mix, minus to plus strand (src on minus), with merge"

<< endl;

390

mapper->SetMergeAbutting();

392

mapper->SetMergeNone();

399

cout <<

"Merging of mapped intervals"

<< endl;

410

cout <<

" No merging"

<< endl;

413

cout <<

" No merging, reverse strand mapping"

<< endl;

416

cout <<

" Merge abutting"

<< endl;

419

cout <<

" Merge abutting, reverse strand mapping"

<< endl;

422

cout <<

" Merge contained"

<< endl;

425

cout <<

" Merge contained, reverse strand mapping"

<< endl;

428

cout <<

" Merge all"

<< endl;

431

cout <<

" Merge all, reverse strand mapping"

<< endl;

437

cout <<

" Minus strand original, no merging"

<< endl;

440

cout <<

" Minus strand original, no merging, reverse strand mapping"

<< endl;

443

cout <<

" Minus strand original, merge abutting"

<< endl;

446

cout <<

" Minus strand original, merge abutting, reverse strand mapping"

<< endl;

449

cout <<

" Minus strand original, merge contained"

<< endl;

452

cout <<

" Minus strand original, merge contained, reverse strand mapping"

<< endl;

455

cout <<

" Minus strand original, merge all"

<< endl;

458

cout <<

" Minus strand original, merge all, reverse strand mapping"

<< endl;

468

cout <<

"Mapping from protein to nucleotide"

<< endl;

476

cout <<

" Simple interval"

<< endl;

478

cout <<

" Partial on the right"

<< endl;

480

cout <<

" Original location on minus strand"

<< endl;

482

cout <<

" Original location on minus strand, partial"

<< endl;

485

cout <<

" Simple interval, reversed strand"

<< endl;

487

cout <<

" Partial on the right, reversed strand"

<< endl;

489

cout <<

" Original location on minus strand, reversed strand"

<< endl;

491

cout <<

" Original location on minus strand, partial, reversed strand"

<< endl;

500

cout <<

"Mapping from nucleotide to protein"

<< endl;

508

cout <<

" Simple interval"

<< endl;

510

cout <<

" Partial on the right"

<< endl;

512

cout <<

" Original location on minus strand"

<< endl;

514

cout <<

" Original location on minus strand, partial"

<< endl;

516

cout <<

" Shifted nucleotide positions (incomplete codons)"

<< endl;

519

cout <<

" Simple interval, reversed strand"

<< endl;

521

cout <<

" Partial on the right, reversed strand"

<< endl;

523

cout <<

" Original location on minus strand, reversed strand"

<< endl;

525

cout <<

" Original location on minus strand, partial, reversed strand"

<< endl;

527

cout <<

" Shifted nucleotide positions (incomplete codons), reversed strand"

<< endl;

535

cout <<

"Mapping through mix"

<< endl;

537

mapper->SetMergeAbutting();

538

cout <<

" Single interval overlapping all source ranges"

<< endl;

540

cout <<

" Single interval on minus strand, partial overlapping"

<< endl;

543

cout <<

"Mapping through mix, reversed strand"

<< endl;

545

cout <<

" Original sec-loc is the same as mapping source"

<< endl;

547

cout <<

" Mapping a packed-int"

<< endl;

549

cout <<

" Mapping a multi-level seq-loc"

<< endl;

557

cout <<

"Mapping dense-diag alignment"

<< endl;

559

cout <<

" Single segment"

<< endl;

561

cout <<

" Unsupported mapped alignment - gaps in dense-diag"

<< endl;

564

cout <<

"Mapping dense-diag alignment, reverse"

<< endl;

566

cout <<

" Single segment, reversed strand"

<< endl;

574

cout <<

"Mapping dense-seg alignments"

<< endl;

576

cout <<

" Nuc to prot, converted to std-seg (mixed types)"

<< endl;

579

mapper->MixedAlignsAsSpliced(

true

);

580

cout <<

" Nuc to prot, converted to spliced-seg (mixed types)"

<< endl;

583

cout <<

" Unsupported alignment - dense-seg with mixed types"

<< endl;

587

cout <<

" Setting correct strands in gaps"

<< endl;

595

cout <<

"Mapping spliced-seg alignments"

<< endl;

597

cout <<

" Mapping spliced-seg product, nuc to nuc"

<< endl;

601

cout <<

" Mapping spliced-seg product, nuc to prot"

<< endl;

605

cout <<

" Mapping spliced-seg product, nuc to prot, reversed strand"

<< endl;

609

cout <<

" Mapping spliced-seg through multiple ranges"

<< endl;

615

cout <<

" Trimming indels"

<< endl;

617

cout <<

" Trimming indels - 2"

<< endl;

620

cout <<

" Trimming indels - 3"

<< endl;

623

cout <<

" Trimming indels, minus strand"

<< endl;

627

cout <<

" Trimming gen-ins - 1"

<< endl;

630

cout <<

" Trimming gen-ins - 2"

<< endl;

633

cout <<

" Trimming gen-ins - 3"

<< endl;

636

cout <<

" Trimming gen-ins - 4"

<< endl;

639

cout <<

" Trimming gen-ins - 5"

<< endl;

642

cout <<

" Trimming gen-ins - 6"

<< endl;

645

cout <<

" Trimming gen-ins - 7"

<< endl;

648

cout <<

" Trimming gen-ins - 8"

<< endl;

656

cout <<

"Mapping scores"

<< endl;

658

cout <<

" Dense-diag - scores are preserved"

<< endl;

662

cout <<

" Dense-seg, scores are preserved"

<< endl;

664

cout <<

" Dense-seg - partial mapping, scores are dropped"

<< endl;

666

cout <<

" Dense-seg - unmapped segment, scores are dropped"

<< endl;

668

cout <<

" Std-seg, scores are preserved"

<< endl;

670

cout <<

" Std-seg - partial mapping, scores are dropped"

<< endl;

672

cout <<

" Std-seg - unmapped segment, scores are dropped"

<< endl;

674

cout <<

" Packed-seg, scores are preserved"

<< endl;

676

cout <<

" Packed-seg - partial mapping, scores are dropped"

<< endl;

678

cout <<

" Packed-seg - unmapped segment, scores are dropped"

<< endl;

680

cout <<

" Spliced-seg, scores are preserved"

<< endl;

682

cout <<

" Spliced-seg, partial mapping, scores are dropped"

<< endl;

684

cout <<

" Spliced-seg, unmapped segment, scores are dropped"

<< endl;

692

cout <<

"Mapping graphs"

<< endl;

694

cout <<

" Mapping whole graph"

<< endl;

696

cout <<

" Partial - skip a range in the middle"

<< endl;

698

cout <<

" Mapping a graph on minus strand"

<< endl;

701

cout <<

"Graph mapping, nuc to prot"

<< endl;

703

cout <<

" Simple graph, using comp=3 to allow mapping"

<< endl;

706

cout <<

" Unsupported: different original and mapped location lengths"

<< endl;

708

cout <<

" Unsupported: unknown destination sequence type"

<< endl;

716

cout <<

"Test mapping alignments to bioseq segments"

<< endl;

723

cout <<

" Alignment #1, mapping row 1"

<< endl;

726

cout <<

" Alignment #1, mapping row 2"

<< endl;

731

cout <<

" Alignment #2, mapping row 1"

<< endl;

734

cout <<

" Alignment #2, mapping row 2"

<< endl;

739

cout <<

" Alignment #3, mapping row 1"

<< endl;

742

cout <<

" Alignment #3, mapping row 2"

<< endl;

747

cout <<

" Alignment #4, mapping row 1"

<< endl;

750

cout <<

" Alignment #4, mapping row 2"

<< endl;

759

cout <<

"Test mapping through alignments"

<< endl;

762  const char

* titles[] = {

763  " Mapping through dense-diag"

,

764  " Mapping through dense-seg (with some gaps)"

,

765  " Mapping through packed-seg (with some gaps)"

,

766  " Mapping through std-seg"

,

767  " Mapping through disc"

,

768  " Mapping through spliced-seg"

,

769  " Mapping through spliced-seg, reversed strand"

,

770  " Mapping through sparse-seg" 773  for

(

size_t i

= 0;

i

<

sizeof

(titles)/

sizeof

(titles[0]);

i

++) {

774

cout << titles[

i

] << endl;

777

cout <<

" Whole sequence"

<< endl;

779

cout <<

" Interval, complete"

<< endl;

781

cout <<

" Interval, split"

<< endl;

830

cout <<

"Test mapping with sequence info provider"

<< endl;

839

unique_ptr<CSeq_loc_Mapper_Base> mapper(

842

cout <<

" Test mapping whole, nuc to prot"

<< endl;

844

cout <<

" Test mapping interval, nuc to prot"

<< endl;

852

cout <<

"Mapping fuzzes"

<< endl;

865

cout <<

" Fuzz-from lim lt"

<< endl;

867

cout <<

" Fuzz-from lim lt, reversed strand"

<< endl;

871

cout <<

" Fuzz-from lim gt"

<< endl;

873

cout <<

" Fuzz-from lim gt, reversed strand"

<< endl;

877

cout <<

" Fuzz-from lim tl"

<< endl;

879

cout <<

" Fuzz-from lim tl, reversed strand"

<< endl;

883

cout <<

" Fuzz-from lim tr"

<< endl;

885

cout <<

" Fuzz-from lim tr, reversed strand"

<< endl;

889

cout <<

" Fuzz-from alt #1"

<< endl;

891

cout <<

" Fuzz-from alt #1, reversed strand"

<< endl;

895

cout <<

" Fuzz-from alt #2"

<< endl;

897

cout <<

" Fuzz-from alt #2, reversed strand"

<< endl;

901

cout <<

" Fuzz-from range #1"

<< endl;

903

cout <<

" Fuzz-from range #1, reversed strand"

<< endl;

907

cout <<

" Fuzz-from range #2"

<< endl;

909

cout <<

" Fuzz-from range #2, reversed strand"

<< endl;

913

cout <<

" Fuzz-from range #3"

<< endl;

915

cout <<

" Fuzz-from range #3, reversed strand"

<< endl;

919

cout <<

" Fuzz-from range #4"

<< endl;

921

cout <<

" Fuzz-from range #4, reversed strand"

<< endl;

926

cout <<

" Fuzz-to lim lt"

<< endl;

928

cout <<

" Fuzz-to lim lt, reversed strand"

<< endl;

932

cout <<

" Fuzz-to lim gt"

<< endl;

934

cout <<

" Fuzz-to lim gt, reversed strand"

<< endl;

938

cout <<

" Fuzz-to lim tl"

<< endl;

940

cout <<

" Fuzz-to lim tl, reversed strand"

<< endl;

944

cout <<

" Fuzz-to lim tr"

<< endl;

946

cout <<

" Fuzz-to lim tr, reversed strand"

<< endl;

950

cout <<

" Fuzz-to alt #1"

<< endl;

952

cout <<

" Fuzz-to alt #1, reversed strand"

<< endl;

956

cout <<

" Fuzz-to alt #2"

<< endl;

958

cout <<

" Fuzz-to alt #2, reversed strand"

<< endl;

962

cout <<

" Fuzz-to range #1"

<< endl;

964

cout <<

" Fuzz-to range #1, reversed strand"

<< endl;

968

cout <<

" Fuzz-to range #2"

<< endl;

970

cout <<

" Fuzz-to range #2, reversed strand"

<< endl;

974

cout <<

" Fuzz-to range #3"

<< endl;

976

cout <<

" Fuzz-to range #3, reversed strand"

<< endl;

980

cout <<

" Fuzz-to range #4"

<< endl;

982

cout <<

" Fuzz-to range #4, reversed strand"

<< endl;

990

cout <<

"Testing sort order of mapped exons"

<< endl;

1002

cout <<

" Both rows on plus, map genomic to plus, no trim"

<< endl;

1005

cout <<

" Both rows on plus, map genomic to plus, trim"

<< endl;

1008

cout <<

" Both rows on plus, map genomic to minus, no trim"

<< endl;

1011

cout <<

" Both rows on plus, map genomic to minus, trim"

<< endl;

1016

cout <<

" Both rows on plus, map product to plus, no trim"

<< endl;

1019

cout <<

" Both rows on plus, map product to plus, trim"

<< endl;

1022

cout <<

" Both rows on plus, map product to minus, no trim"

<< endl;

1025

cout <<

" Both rows on plus, map product to minus, trim"

<< endl;

1030

cout <<

" Genomic on minus, map genomic to minus, no trim"

<< endl;

1033

cout <<

" Genomic on minus, map genomic to minus, trim"

<< endl;

1036

cout <<

" Genomic on minus, map genomic to plus, no trim"

<< endl;

1039

cout <<

" Genomic on minus, map genomic to plus, trim"

<< endl;

1044

cout <<

" Genomic on minus, map product to plus, no trim"

<< endl;

1047

cout <<

" Genomic on minus, map product to plus, trim"

<< endl;

1050

cout <<

" Genomic on minus, map product to minus, no trim"

<< endl;

1053

cout <<

" Genomic on minus, map product to minus, trim"

<< endl;

1058

cout <<

" Product on minus, map genomic to plus, no trim"

<< endl;

1061

cout <<

" Product on minus, map genomic to plus, trim"

<< endl;

1064

cout <<

" Product on minus, map genomic to minus, no trim"

<< endl;

1067

cout <<

" Product on minus, map genomic to minus, trim"

<< endl;

1072

cout <<

" Product on minus, map product to minus, no trim"

<< endl;

1075

cout <<

" Product on minus, map product to minus, trim"

<< endl;

1078

cout <<

" Product on minus, map product to plus, no trim"

<< endl;

1081

cout <<

" Product on minus, map product to plus, trim"

<< endl;

1087

cout <<

"Testing sort order of mapped exons, local strands"

<< endl;

1092

cout <<

" Both rows on plus, map genomic to plus"

<< endl;

1094

cout <<

" Both rows on plus, map genomic to minus"

<< endl;

1098

cout <<

" Both rows on plus, map product to plus"

<< endl;

1100

cout <<

" Both rows on plus, map product to minus"

<< endl;

1104

cout <<

" Genomic on minus, map genomic to minus"

<< endl;

1106

cout <<

" Genomic on minus, map genomic to plus"

<< endl;

1110

cout <<

" Genomic on minus, map product to plus"

<< endl;

1112

cout <<

" Genomic on minus, map product to minus"

<< endl;

1116

cout <<

" Product on minus, map genomic to plus"

<< endl;

1118

cout <<

" Product on minus, map genomic to minus"

<< endl;

1122

cout <<

" Product on minus, map product to minus"

<< endl;

1124

cout <<

" Product on minus, map product to plus"

<< endl;

1132

cout <<

"Testing truncation of mix parts"

<< endl;

1144

cout <<

" Plus, direct, unmapped ranges on the left"

<< endl;

1146

cout <<

" Plus, reversed, unmapped ranges on the left"

<< endl;

1150

cout <<

" Plus, direct, unmapped ranges on the right"

<< endl;

1152

cout <<

" Plus, reversed, unmapped ranges on the right"

<< endl;

1156

cout <<

" Plus, direct, range truncated on the left"

<< endl;

1158

cout <<

" Plus, reversed, range truncated on the left"

<< endl;

1162

cout <<

" Plus, direct, range truncated on the right"

<< endl;

1164

cout <<

" Plus, reversed, range truncated on the right"

<< endl;

1168

cout <<

" Minus, direct, unmapped ranges on the left"

<< endl;

1170

cout <<

" Minus, reversed, unmapped ranges on the left"

<< endl;

1174

cout <<

" Minus, direct, unmapped ranges on the right"

<< endl;

1176

cout <<

" Minus, reversed, unmapped ranges on the right"

<< endl;

1180

cout <<

" Minus, direct, range truncated on the left"

<< endl;

1182

cout <<

" Minus, reversed, range truncated on the left"

<< endl;

1186

cout <<

" Minus, direct, range truncated on the right"

<< endl;

1188

cout <<

" Minus, reversed, range truncated on the right"

<< endl;

1196

cout <<

"Testing trimming of mapped locations"

<< endl;

1211

cout <<

" Test stop codon mapping: trimming=off"

<< endl;

1212

unique_ptr<CSeq_loc_Mapper_Base> mapper(

1218

cout <<

" Test stop codon mapping: trimming=on"

<< endl;

1227

cout <<

" Test stop codon mapping, prot->nuc: trimming=off"

<< endl;

1234

cout <<

" Test stop codon mapping, prot->nuc: trimming=on"

<< endl;

1242

cout <<

" Test stop codon trimming on minus strand, nuc->prot"

<< endl;

1250

cout <<

" Test stop codon trimming on minus strand, prot->nuc"

<< endl;

1258

cout <<

" Test stop codon non-extension, multi-id destionation"

<< endl;

1267

cout <<

" Test stop codon non-extension, multi-id source"

<< endl;

1271

mapper->SetMergeAbutting();

1275

cout <<

" Test trimming while mapping to minus strand, nuc->nuc, #1"

<< endl;

1284

cout <<

" Test trimming while mapping to minus strand, nuc->nuc, #2"

<< endl;

1287

cout <<

" Test trimming while mapping to minus strand, nuc->nuc, #3"

<< endl;

1291

cout <<

" Test trimming while mapping to minus strand, prot->nuc, #1"

<< endl;

1300

cout <<

" Test trimming while mapping to minus strand, prot->nuc, #2"

<< endl;

1303

cout <<

" Test trimming while mapping to minus strand, prot->nuc, #3"

<< endl;

1307

cout <<

" Test trimming while mapping from minus strand, nuc->nuc, #1"

<< endl;

1316

cout <<

" Test trimming while mapping from minus strand, nuc->nuc, #2"

<< endl;

1319

cout <<

" Test trimming while mapping from minus strand, nuc->nuc, #3"

<< endl;

1323

cout <<

" Test trimming while mapping from minus strand, nuc->prot, #1"

<< endl;

1332

cout <<

" Test trimming while mapping from minus strand, nuc->prot, #2"

<< endl;

1335

cout <<

" Test trimming while mapping from minus strand, nuc->prot, #3"

<< endl;

1343

cout <<

"Testing frame and incomplete codon trimming"

<< endl;

1345  CSeq_loc

nuc_orig_long, nuc_orig_short, prot_orig_long, prot_orig_short;

1352

feat.

Assign

(feat_base);

1355  for

(

int

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

1367  for

(

TSeqPos

extra_bases = 0; extra_bases < 3; ++extra_bases) {

1368

cout <<

" nuc->prot, boundaries, "

<<

1369

(str_idx ?

"minus"

:

"plus"

) <<

1370  ", frame="

<< frame <<

1371  ", " " extra bases="

<< extra_bases << endl;

1377

cout <<

" nuc->prot, position, "

<<

1378

(str_idx ?

"minus"

:

"plus"

) <<

1379  ", frame="

<< frame <<

1380  ", " " extra bases="

<< extra_bases << endl;

1383

cout <<

" prot->nuc, boundaries, "

<<

1384

(str_idx ?

"minus"

:

"plus"

) <<

1385  ", frame="

<< frame <<

1386  ", " " extra bases="

<< extra_bases << endl;

1392

cout <<

" prot->nuc, position, "

<<

1393

(str_idx ?

"minus"

:

"plus"

) <<

1394  ", frame="

<< frame <<

1395  ", " " extra bases="

<< extra_bases << endl;

User-defined methods of the data storage class.

Seq-loc and seq-align mapper exceptions.

namespace ncbi::objects::

CSeq_loc_Mapper_Base –.

CSeq_loc_Mapper_Options –.

virtual TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

Get sequence length or kInvalidSeqPos.

void AddSeq(TGi gi, TSeqType seqtype, TSeqPos len)

virtual TSeqType GetSequenceType(const CSeq_id_Handle &idh)

Get information about sequence type (nuc or prot).

map< TGi, TSeqPos > TLenMap

map< TGi, TSeqType > TTypeMap

virtual void CollectSynonyms(const CSeq_id_Handle &id, TSynonyms &synonyms)

Collect all synonyms for the id including the id itself.

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

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

Set object to copy of another one.

#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.

void ResetStrand(void)

Reset the strand on this location.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CSeq_loc_Mapper_Options & SetTrimMappedLocation(bool value=true)

CSeq_loc_Mapper_Base & SetMergeNone(void)

Intervals' merging mode MergeNone and MergeAbutting do not change the order of ranges in the destinat...

CSeq_loc_Mapper_Base & SetTrimSplicedSeg(bool trim)

For mapping spliced-segs only: preserve or trim starting/ending indels.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

CSeq_loc_Mapper_Base & SetMergeContained(void)

Merge intervals only if one is completely covered by another.

CSeq_loc_Mapper_Base & SetMergeAll(void)

Merge any abutting or overlapping intervals.

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetFrame(TFrame value)

Assign a value to Frame data member.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

void TestMapping_ThroughMix()

void TestMapping_Spliced()

void TestMapping_NucToProt()

void TestMapper_Sequence_Info()

void TestMapping_Scores()

void TestMapping_ProtToNuc()

void TestMappingSeq_align(CSeq_loc_Mapper_Base &mapper, const CSeq_align &orig, CNcbiIstream &in)

void TestMapping_Dendiag()

void TestMappingSeq_graph_Exception(CSeq_loc_Mapper_Base &mapper, CNcbiIstream &in)

BOOST_AUTO_TEST_CASE(s_TestMapping)

void TestMapping_Merging()

void TestMapper_TruncatedMix()

void TestMapper_ExonPartsOrder()

void TestMapping_Denseg()

void TestMapping_AlignmentsToParts()

void TestMappingSeq_loc_Exception(CSeq_loc_Mapper_Base &mapper, CNcbiIstream &in)

void TestMappingSeq_loc(CSeq_loc_Mapper_Base &mapper, const CSeq_loc &orig, CNcbiIstream &in)

void TestMapping_ThroughAlignments()

CSeq_loc_Mapper_Base * CreateMapperFromSeq_locs(CNcbiIstream &in)

void TestMapper_Trimming()

void TestMapping_Simple()

void TestMappingSeq_graph(CSeq_loc_Mapper_Base &mapper, const CSeq_graph &orig, CNcbiIstream &in)

void TestMappingSeq_align_Exception(CSeq_loc_Mapper_Base &mapper, CNcbiIstream &in)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

bool eq(T x_, T y_, T round_)

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

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

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