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

96

dbtag->

SetTag

().SetId(

id

);

97

src.SetOrg().SetDb().push_back(dbtag);

104

COrg_ref::TDb::iterator it = src.

SetOrg

().SetDb().begin();

105  while

(it != src.

SetOrg

().SetDb().end()) {

107

&& (

id

== 0 || ((*it)->IsSetTag() && (*it)->GetTag().IsId() && (*it)->GetTag().GetId() ==

id

))) {

108

it = src.

SetOrg

().SetDb().erase(it);

132

entry->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set(

"AATTGGCCAAAATTGGCCAAAATTGGCCAAAATTGGCCAAAATTGGCCAAAATTGGCCAA"

);

136  id

->SetLocal().SetStr (

"good"

);

165  if

(entry->

IsSeq

()) {

167

}

else if

(entry->

IsSet

()) {

173  if

(entry->

IsSeq

()) {

175

}

else if

(entry->

IsSet

()) {

186

odesc->

SetSource

().

SetOrg

().SetOrgname().SetLineage(

"some lineage"

);

193  if

(entry->

IsSeq

()) {

195

}

else if

(entry->

IsSet

()) {

205

dbtag->

SetTag

().SetStr(

id

);

206

src.

SetOrg

().SetDb().push_back(dbtag);

215  if

(entry->

IsSeq

()) {

217  if

((*it)->IsSource()) {

221

}

else if

(entry->

IsSet

()) {

223  if

((*it)->IsSource()) {

236  if

(entry->

IsSeq

()) {

238  if

((*it)->IsSource()) {

242

}

else if

(entry->

IsSet

()) {

244  if

((*it)->IsSource()) {

259

dbtag->

SetTag

().SetId(

id

);

271

dbtag->

SetTag

().SetStr(

id

);

282  if

(entry->

IsSeq

()) {

284  if

((*it)->IsSource()) {

288

}

else if

(entry->

IsSet

()) {

290  if

((*it)->IsSource()) {

304

CSeq_feat::TDbxref::iterator it = feat->

SetDbxref

().begin();

305  while

(it != feat->

SetDbxref

().end()) {

307

&& (

id

== 0 || ((*it)->IsSetTag() && (*it)->GetTag().IsId() && (*it)->GetTag().GetId() ==

id

))) {

322  if

(entry->

IsSeq

()) {

324  if

((*it)->IsSource()) {

325  SetTaxon

((*it)->SetSource(), taxon);

328

}

else if

(entry->

IsSet

()) {

330  if

((*it)->IsSource()) {

331  SetTaxon

((*it)->SetSource(), taxon);

340  if

(!entry || !annot) {

343  if

(entry->

IsSeq

()) {

345

}

else if

(entry->

IsSet

()) {

357  if

(entry->

IsSeq

()) {

366

}

else if

(entry->

IsSet

()) {

376

annot->

SetData

().SetFtable().push_back(feat);

383

feat->

SetData

().SetProt().SetName().push_back(

"fake protein name"

);

395

feat->

SetData

().SetBiosrc().SetOrg().SetTaxname(

"Trichechus manatus"

);

397

feat->

SetData

().SetBiosrc().SetOrg().SetOrgname().SetLineage(

"some lineage"

);

398

feat->

SetLocation

().SetInt().SetId().SetLocal().SetStr(

"good"

);

402

annot->

SetData

().SetFtable().push_back(feat);

411

feat->

SetLocation

().SetInt().SetId().Assign(*

id

);

414

feat->

SetData

().SetImp().SetKey(

"misc_feature"

);

422

feat->

SetLocation

().SetInt().SetId().SetLocal().SetStr(

"good"

);

425

feat->

SetData

().SetImp().SetKey(

"misc_feature"

);

433  if

(entry->

IsSeq

()) {

435

}

else if

(entry->

IsSet

()) {

447

feat->

SetComment

(

"misc_feature needs a comment"

);

464  if

(entry->

IsSeq

()) {

466  if

((*it)->IsSource()) {

468

(*it)->SetSource().SetOrg().ResetTaxname();

470

(*it)->SetSource().SetOrg().SetTaxname(taxname);

474

}

else if

(entry->

IsSet

()) {

476  if

((*it)->IsSource()) {

478

(*it)->SetSource().SetOrg().ResetTaxname();

480

(*it)->SetSource().SetOrg().SetTaxname(taxname);

506  SetTaxname

(entry,

"Drosophila melanogaster"

);

516  if

(entry->

IsSeq

()) {

518  if

((*it)->IsSource()) {

520

(*it)->SetSource().SetOrg().ResetCommon();

522

(*it)->SetSource().SetOrg().SetCommon(common);

526

}

else if

(entry->

IsSet

()) {

528  if

((*it)->IsSource()) {

530

(*it)->SetSource().SetOrg().ResetCommon();

532

(*it)->SetSource().SetOrg().SetCommon(common);

545  if

(entry->

IsSeq

()) {

547  if

((*it)->IsSource()) {

549

(*it)->SetSource().SetOrg().SetOrgname().ResetLineage();

551

(*it)->SetSource().SetOrg().SetOrgname().SetLineage(lineage);

555

}

else if

(entry->

IsSet

()) {

557  if

((*it)->IsSource()) {

559

(*it)->SetSource().SetOrg().SetOrgname().ResetLineage();

561

(*it)->SetSource().SetOrg().SetOrgname().SetLineage(lineage);

574  if

(entry->

IsSeq

()) {

576  if

((*it)->IsSource()) {

578

(*it)->SetSource().SetOrg().SetOrgname().ResetDiv();

580

(*it)->SetSource().SetOrg().SetOrgname().SetDiv(div);

584

}

else if

(entry->

IsSet

()) {

586  if

((*it)->IsSource()) {

588

(*it)->SetSource().SetOrg().SetOrgname().ResetDiv();

590

(*it)->SetSource().SetOrg().SetOrgname().SetDiv(div);

603  if

(entry->

IsSeq

()) {

605  if

((*it)->IsSource()) {

606

(*it)->SetSource().SetOrigin(

origin

);

609

}

else if

(entry->

IsSet

()) {

611  if

((*it)->IsSource()) {

612

(*it)->SetSource().SetOrigin(

origin

);

624  if

(entry->

IsSeq

()) {

626  if

((*it)->IsSource()) {

627

(*it)->SetSource().SetOrg().SetOrgname().SetGcode(gcode);

630

}

else if

(entry->

IsSet

()) {

632  if

((*it)->IsSource()) {

633

(*it)->SetSource().SetOrg().SetOrgname().SetGcode(gcode);

645  if

(entry->

IsSeq

()) {

647  if

((*it)->IsSource()) {

648

(*it)->SetSource().SetOrg().SetOrgname().SetMgcode(mgcode);

651

}

else if

(entry->

IsSet

()) {

653  if

((*it)->IsSource()) {

654

(*it)->SetSource().SetOrg().SetOrgname().SetMgcode(mgcode);

666  if

(entry->

IsSeq

()) {

668  if

((*it)->IsSource()) {

669

(*it)->SetSource().SetOrg().SetOrgname().SetPgcode(pgcode);

672

}

else if

(entry->

IsSet

()) {

674  if

((*it)->IsSource()) {

675

(*it)->SetSource().SetOrg().SetOrgname().SetPgcode(pgcode);

687  if

(entry->

IsSeq

()) {

689  if

((*it)->IsSource()) {

690

(*it)->SetSource().SetOrg().ResetOrgname();

693

}

else if

(entry->

IsSet

()) {

695  if

((*it)->IsSource()) {

696

(*it)->SetSource().SetOrg().ResetOrgname();

708  if

(entry->

IsSeq

()) {

710  if

((*it)->IsSource()) {

711

(*it)->SetSource().SetIs_focus();

714

}

else if

(entry->

IsSet

()) {

716  if

((*it)->IsSource()) {

717

(*it)->SetSource().SetIs_focus();

729  if

(entry->

IsSeq

()) {

731  if

((*it)->IsSource()) {

732

(*it)->SetSource().ResetIs_focus();

735

}

else if

(entry->

IsSet

()) {

737  if

((*it)->IsSource()) {

738

(*it)->SetSource().ResetIs_focus();

750  if

(entry->

IsSeq

()) {

752  if

((*it)->IsSource()) {

753

(*it)->SetSource().SetGenome(genome);

756

}

else if

(entry->

IsSet

()) {

758  if

((*it)->IsSource()) {

759

(*it)->SetSource().SetGenome(genome);

770

CBioSource::TSubtype::iterator it = src.

SetSubtype

().begin();

772  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

794  if

(entry->

IsSeq

()) {

796  if

((*it)->IsSource()) {

800

}

else if

(entry->

IsSet

()) {

802  if

((*it)->IsSource()) {

814

CBioSource::TSubtype::iterator it = src.

SetSubtype

().begin();

835  if

(entry->

IsSeq

()) {

837  if

((*it)->IsSource()) {

841

}

else if

(entry->

IsSet

()) {

843  if

((*it)->IsSource()) {

857

CBioSource::TSubtype::iterator it = src.

SetSubtype

().begin();

874  if

(entry->

IsSeq

()) {

876  if

((*it)->IsSource()) {

880

}

else if

(entry->

IsSet

()) {

882  if

((*it)->IsSource()) {

894

COrgName::TMod::iterator it = src.

SetOrg

().SetOrgname().SetMod().begin();

895  while

(it != src.

SetOrg

().SetOrgname().SetMod().end()) {

896  if

((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {

897

it = src.

SetOrg

().SetOrgname().SetMod().erase(it);

905

src.

SetOrg

().SetOrgname().SetMod().push_back(sub);

915  if

(entry->

IsSeq

()) {

917  if

((*it)->IsSource()) {

921

}

else if

(entry->

IsSet

()) {

923  if

((*it)->IsSource()) {

934

author->

SetName

().SetName().SetLast(

"Darwin"

);

935

author->

SetName

().SetName().SetFirst(

"Charles"

);

936

author->

SetName

().SetName().SetMiddle(

"R"

);

946

art_title->SetName(

"article title"

);

949

journal_title->SetName(

"journal_title"

);

950

pub->

SetArticle

().

SetFrom

().SetJournal().SetTitle().Set().push_back(journal_title);

952

iso_jta->SetIso_jta(

"abbr"

);

953

pub->

SetArticle

().

SetFrom

().SetJournal().SetTitle().Set().push_back(iso_jta);

957

pub->

SetArticle

().

SetFrom

().SetJournal().SetImp().SetDate().SetStd().SetYear(2009);

971  if

(serial_number > -1) {

983

pub->

SetSub

().

SetAuthors

().SetAffil().SetStd().SetAffil(

"A Major University"

);

993  if

(seq.

SetInst

().IsSetSeq_data()) {

995

seq.

SetInst

().SetSeq_data().SetIupacna().Set().clear();

996  for

(

int i

= 0;

i

< 100;

i

++) {

997

seq.

SetInst

().SetSeq_data().SetIupacna().Set().append(

998  "AAAAATTTTTGGGGGCCCCCTTTTTAAAAATTTTTGGGGGCCCCCTTTTTAAAAATTTTTGGGGGCCCCCTTTTTAAAAATTTTTGGGGGCCCCCTTTTT"

);

1000

seq.

SetInst

().SetLength(10000);

1002

seq.

SetInst

().SetSeq_data().SetIupacaa().Set().clear();

1003  for

(

int i

= 0;

i

< 100;

i

++) {

1004

seq.

SetInst

().SetSeq_data().SetIupacaa().Set().append(

1005  "MPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSLMPRKTEINSL"

);

1007

seq.

SetInst

().SetLength(10000);

1015  bool

found =

false

;

1018  if

((*it)->IsMolinfo()) {

1019

(*it)->SetMolinfo().SetBiomol(biomol);

1033  bool

found =

false

;

1036  if

((*it)->IsMolinfo()) {

1037

(*it)->SetMolinfo().SetTech(tech);

1051  if

(entry->

IsSeq

()) {

1052  bool

found =

false

;

1054  if

((*it)->IsMolinfo()) {

1055

(*it)->SetMolinfo().SetCompleteness (completeness);

1078

entry->

SetSeq

().

SetInst

().SetSeq_data().SetIupacaa().Set(

"PRKTEIN"

);

1081  if

((*it)->IsMolinfo()) {

1098

pseq->

SetInst

().SetSeq_data().SetIupacaa().Set(

"MPRKTEIN"

);

1099

pseq->

SetInst

().SetLength(8);

1103

pseq->

SetId

().push_back(pid);

1108

pseq->

SetDescr

().Set().push_back(mpdesc);

1114

feat->

SetData

().SetProt().SetName().push_back(

"fake protein name"

);

1115

feat->

SetLocation

().SetInt().SetId().SetLocal().SetStr(

id

);

1127

cds->

SetData

().SetCdregion();

1128

cds->

SetProduct

().SetWhole().SetLocal().SetStr(prot_id);

1129

cds->

SetLocation

().SetInt().SetId().SetLocal().SetStr(nuc_id);

1145

nseq->

SetInst

().SetSeq_data().SetIupacna().Set(

"ATGCCCAGAAAAACAGAGATAAACTAAGGGATGCCCAGAAAAACAGAGATAAACTAAGGG"

);

1146

nseq->

SetInst

().SetLength(60);

1149  id

->SetLocal().SetStr (

"nuc"

);

1150

nseq->

SetId

().push_back(

id

);

1154

nseq->

SetDescr

().Set().push_back(mdesc);

1159  set

->SetSeq_set().push_back(nentry);

1164  set

->SetSeq_set().push_back(pentry);

1186  if

(entry->

IsSeq

()) {

1189

}

else if

(entry->

IsSet

()) {

1193  if

(

prot

&& prot_seq) {

1194  prot

->SetLocation().SetInt().SetTo(prot_seq->

SetSeq

().

SetInst

().SetLength() - 1);

1207  if

(entry->

IsSeq

()) {

1210

}

else if

(entry->

IsSet

()) {

1215  if

(

prot

->SetData().SetProt().SetName().size() > 0) {

1216  prot

->SetData().SetProt().SetName().pop_front();

1218  prot

->SetData().SetProt().SetName().push_front(new_name);

1225  return

entry->

SetSet

().

SetAnnot

().front()->SetData().SetFtable().front();

1244  return

pentry->

SetSeq

().

SetAnnot

().front()->SetData().SetFtable().front();

1261  prot

->SetPartial(partial5 || partial3);

1266  if

(partial5 && partial3) {

1268

}

else if

(partial5) {

1270

}

else if

(partial3) {

1294

pseq->

SetSeq

().

SetId

().front()->Assign(*

id

);

1297

pfeat->

SetLocation

().SetInt().SetId().Assign(*

id

);

1300

cds->

SetProduct

().SetWhole().Assign(*

id

);

1307

nseq->

SetSeq

().

SetId

().front()->Assign(*

id

);

1311

cds->

SetLocation

().SetInt().SetId().Assign(*

id

);

1313

cds->

SetLocation

().SetMix().Set().front()->SetInt().SetId().Assign(*

id

);

1314

cds->

SetLocation

().SetMix().Set().back()->SetInt().SetId().Assign(*

id

);

1326

nuc_seq->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set(

"ATGCCCAGAAAAACAGAGATAAACAAAGGGATGCCCAGAAAAACAGAGATAAACAAAGGG"

);

1328

prot_seq->

SetSeq

().

SetInst

().SetSeq_data().SetIupacaa().Set(

"MPRKTEINKGMPRKTEINKG"

);

1332  prot

->SetLocation().SetInt().SetTo(19);

1334  prot

->SetPartial(

true

);

1340  if

(annot && annot->

IsFtable

()) {

1341

CSeq_annot::C_Data::TFtable::iterator it = annot->

SetData

().SetFtable().begin();

1342  while

(it != annot->

SetData

().SetFtable().end()) {

1343

(*it)->SetLocation().SetInt().SetId().Assign(*

id

);

1352  if

(annot && annot->

IsFtable

()) {

1353

CSeq_annot::C_Data::TFtable::iterator it = annot->

SetData

().SetFtable().begin();

1354  while

(it != annot->

SetData

().SetFtable().end()) {

1355  if

((*it)->IsSetProduct()) {

1356

(*it)->SetProduct().SetWhole().Assign(*

id

);

1366  if

(!np_set || !np_set->

IsSet

()) {

1372

nuc_entry->

SetSeq

().

SetId

().front()->Assign(*

id

);

1388  if

(!np_set || !np_set->

IsSet

()) {

1395

prot_entry->

SetSeq

().

SetId

().front()->Assign(*

id

);

1409  id

->SetOther().SetAccession(

"NC_123456"

);

1416  if

(entry->

IsSeq

()) {

1417

entry->

SetSeq

().

SetId

().front()->Assign(*

id

);

1419

CBioseq::TAnnot::iterator annot_it = entry->

SetSeq

().

SetAnnot

().begin();

1421  if

((*annot_it)->IsFtable()) {

1422

CSeq_annot::C_Data::TFtable::iterator it = (*annot_it)->SetData().SetFtable().begin();

1423  while

(it != (*annot_it)->SetData().SetFtable().end()) {

1424

(*it)->SetLocation().SetId(*

id

);

1437  if

(annot && annot->

IsFtable

()) {

1438

CSeq_annot::C_Data::TFtable::iterator it = annot->

SetData

().SetFtable().begin();

1439  while

(it != annot->

SetData

().SetFtable().end()) {

1440

(*it)->SetLocation().SetInt().SetId().SetLocal().SetStr().append(suffix);

1441  if

((*it)->IsSetProduct()) {

1442

(*it)->SetProduct().SetWhole().SetLocal().SetStr().append(suffix);

1452  if

(entry->

IsSeq

()) {

1453

entry->

SetSeq

().

SetId

().front()->SetLocal().SetStr().append(suffix);

1455

CBioseq::TAnnot::iterator annot_it = entry->

SetSeq

().

SetAnnot

().begin();

1461

}

else if

(entry->

IsSet

()) {

1462

CBioseq_set::TSeq_set::iterator it = entry->

SetSet

().

SetSeq_set

().begin();

1468

CBioseq_set::TAnnot::iterator annot_it = entry->

SetSet

().

SetAnnot

().begin();

1482  nuc

->SetSeq().SetInst().SetSeq_data().SetIupacna().Set(

"ATGCCCAGAAAAACAGAGATAAACTAA"

);

1483  nuc

->SetSeq().SetInst().SetLength(27);

1510

contig->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set(

"ATGCCCAGAAAAACAGAGATAAACTAAGGGATGCCCAGAAAAACAGAGATAAACTAAGGG"

);

1522

cds->

SetLocation

().SetInt().SetId().SetLocal().SetStr(

"good"

);

1525

mrna->

SetProduct

().SetWhole().Assign(*nuc_id);

1568  string

new_seq =

""

;

1569

string::iterator sit = seq.end();

1570  while

(sit != seq.begin()) {

1572  string

new_ch =

""

;

1583

new_seq.append(new_ch);

1586

bioseq.

SetInst

().SetSeq_data().SetIupacna().Set(new_seq);

1590  TSeqPos

new_from =

len

- (*feat_it)->GetLocation().GetInt().GetTo() - 1;

1591  TSeqPos

new_to =

len

- (*feat_it)->GetLocation().GetInt().GetFrom() - 1;

1592

(*feat_it)->SetLocation().SetInt().SetFrom(new_from);

1593

(*feat_it)->SetLocation().SetInt().SetTo(new_to);

1594  if

((*feat_it)->GetLocation().GetInt().IsSetStrand()

1607  if

(loc.

IsInt

()) {

1610

loc.

SetInt

().SetFrom(new_from);

1611

loc.

SetInt

().SetTo(new_to);

1618

}

else if

(loc.

IsMix

()) {

1628  if

(entry->

IsSeq

()) {

1630

}

else if

(entry->

IsSet

()) {

1651

gap_seg->SetLiteral().SetSeq_data().SetGap();

1652

gap_seg->SetLiteral().SetLength(10);

1653

entry->

SetSeq

().

SetInst

().SetExt().SetDelta().Set().push_back(gap_seg);

1663

CDelta_ext::Tdata::iterator seg_it = entry->

SetSeq

().

SetInst

().SetExt().SetDelta().Set().begin();

1664  while

(seg_it != entry->

SetSeq

().

SetInst

().SetExt().SetDelta().Set().end()) {

1665  if

((*seg_it)->IsLiteral()

1666

&& (!(*seg_it)->GetLiteral().IsSetSeq_data()

1667

|| (*seg_it)->GetLiteral().GetSeq_data().IsGap())) {

1669  len

-= (*seg_it)->GetLiteral().GetLength();

1670

seg_it = entry->

SetSeq

().

SetInst

().SetExt().SetDelta().Set().erase(seg_it);

1682  size_t

add_len = seq.length();

1685

gap_seg->SetLiteral().SetSeq_data().SetGap();

1686

gap_seg->SetLiteral().SetLength(10);

1687

entry->

SetSeq

().

SetInst

().SetExt().SetDelta().Set().push_back(gap_seg);

1689

entry->

SetSeq

().

SetInst

().SetLength(orig_len + 10 + add_len);

1698

part->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set(

"AATTGGCCAAAATTGGCCAAAATTGGCCAAAATTGGCCAAAATTGGCCAAAATTGGCCAA"

);

1717

loc1->

SetWhole

().SetLocal().SetStr(

"part1"

);

1719

loc2->

SetWhole

().SetLocal().SetStr(

"part2"

);

1721

loc3->

SetWhole

().SetLocal().SetStr(

"part3"

);

1723

seg_seq->

SetSeq

().

SetInst

().SetExt().SetSeg().Set().push_back(loc1);

1724

seg_seq->

SetSeq

().

SetInst

().SetExt().SetSeg().Set().push_back(loc2);

1725

seg_seq->

SetSeq

().

SetInst

().SetExt().SetSeg().Set().push_back(loc3);

1729  id

->SetLocal().SetStr (

"master"

);

1753

odesc->

SetSource

().

SetOrg

().SetOrgname().SetLineage(

"some lineage"

);

1755

taxon_id->

SetDb

(

"taxon"

);

1756

taxon_id->

SetTag

().SetId(592768);

1762

segset->

SetDescr

().Set().push_back(odesc);

1783

desc->

SetTitle

(

"popset title"

);

1800  id

->Assign(*(s->GetSeq().GetId().front()));

1801

align->

SetSegs

().SetDenseg().SetIds().push_back(

id

);

1803  const string

&

orig

= s->SetSeq().SetInst().SetSeq_data().SetIupacna().Set();

1804  size_t

orig_len = s->GetSeq().GetInst().GetLength();

1806  for

(

auto i

= (

size_t

)0;

i

<

offset

;

i

++) {

1809

s->SetSeq().SetInst().SetSeq_data().SetIupacna().Set(add +

orig

);

1810

s->SetSeq().SetInst().SetLength(orig_len +

offset

);

1812

align->

SetSegs

().SetDenseg().SetStarts().push_back(

offset

);

1815

align->

SetSegs

().SetDenseg().SetNumseg(1);

1816

align->

SetSegs

().SetDenseg().SetLens().push_back(entry->

GetSet

().

GetSeq_set

().front()->GetSeq().GetInst().GetLength());

1817

align->

SetSegs

().SetDenseg().SetDim(3);

1820

annot->

SetData

().SetAlign().push_back(align);

1832  for

(

auto i

= 0;

i

< num_pieces;

i

++) {

1835

}

else if

(denseg.

GetStrands

().size() < num_pieces) {

1836  for

(

auto i

= denseg.

GetStrands

().size();

i

< num_pieces;

i

++) {

1866

align->

SetSegs

().SetDenseg().SetIds().push_back(id1);

1867

align->

SetSegs

().SetDenseg().SetIds().push_back(id2);

1868

align->

SetSegs

().SetDenseg().SetDim(2);

1869

align->

SetSegs

().SetDenseg().SetStarts().push_back(0);

1870

align->

SetSegs

().SetDenseg().SetStarts().push_back(0);

1871

align->

SetSegs

().SetDenseg().SetNumseg(1);

1872

align->

SetSegs

().SetDenseg().SetLens().push_back(812);

1881

graph->

SetLoc

().SetInt().SetFrom(0);

1882

graph->

SetLoc

().SetInt().SetTo(10);

1883

graph->

SetLoc

().SetInt().SetId().SetLocal().SetStr(

id

);

1886

annot->

SetData

().SetGraph().push_back(graph);

1895  if

((*dit)->Which() == desc_choice) {

1905

feat->

SetLocation

().SetInt().SetId().Assign(*

id

);

1910

feat->

SetData

().SetRna().SetExt().SetTRNA().SetAa().SetIupacaa(

'N'

);

1911

feat->

SetData

().SetRna().SetExt().SetTRNA().SetAnticodon().SetInt().SetId().Assign(*

id

);

1912

feat->

SetData

().SetRna().SetExt().SetTRNA().SetAnticodon().SetInt().SetFrom(11);

1913

feat->

SetData

().SetRna().SetExt().SetTRNA().SetAnticodon().SetInt().SetTo(13);

1922

trna->

SetData

().SetRna().SetExt().SetTRNA().SetAnticodon().SetInt().SetFrom(8);

1923

trna->

SetData

().SetRna().SetExt().SetTRNA().SetAnticodon().SetInt().SetTo(10);

1924

trna->

SetData

().SetRna().SetExt().SetTRNA().SetAa().SetIupacaa(

'F'

);

1932

loc1->

SetInt

().SetFrom(0);

1933

loc1->

SetInt

().SetTo(15);

1934

loc1->

SetInt

().SetId().Assign(*

id

);

1936

loc2->

SetInt

().SetFrom(46);

1937

loc2->

SetInt

().SetTo(56);

1938

loc2->

SetInt

().SetId().Assign(*

id

);

1940

mixloc->

SetMix

().Set().push_back(loc1);

1941

mixloc->

SetMix

().Set().push_back(loc2);

1949

intron->

SetData

().SetImp().SetKey(

"intron"

);

1952

intron->

SetLocation

().SetInt().SetId().Assign(*

id

);

1959

seq.

SetInst

().SetSeq_data().SetIupacna().Set()[16] =

'G'

;

1960

seq.

SetInst

().SetSeq_data().SetIupacna().Set()[17] =

'T'

;

1961

seq.

SetInst

().SetSeq_data().SetIupacna().Set()[44] =

'A'

;

1962

seq.

SetInst

().SetSeq_data().SetIupacna().Set()[45] =

'G'

;

1969

gene->

SetData

().SetGene().SetLocus(

"gene locus"

);

1986

imp_feat->

SetData

().SetImp().SetKey(

key

);

1990

entry->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set()[0] =

'G'

;

1991

entry->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set()[1] =

'T'

;

1992

entry->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set()[9] =

'A'

;

1993

entry->

SetSeq

().

SetInst

().SetSeq_data().SetIupacna().Set()[10] =

'G'

;

2003

imp_feat->

SetLocation

().SetPnt().SetId().SetLocal().SetStr(

"good"

);

2015  struct

SFileRememberer

2017  void

operator()(

const CDirEntry

& dir_entry ) {

2018

m_filesFound.push_back(

CFile

(dir_entry));

2021

vector<CFile> m_filesFound;

2027  template

<

typename

Pair>

2030  typename

Pair::first_type operator()(

const

Pair & a_pair )

const 2032  return

a_pair.first;

2039  CDir

dirWithTestCases,

2045  if

( ! pTestRunner ) {

2048  if

( ! dirWithTestCases.

Exists

() ) {

2049

pTestRunner->

OnError

(

"Top-level test-cases dir not found: "

+ dirWithTestCases.

GetPath

() );

2052  if

( ! dirWithTestCases.

IsDir

() ) {

2053

pTestRunner->

OnError

(

"Top-level test-cases dir is actually not a dir: "

+ dirWithTestCases.

GetPath

() );

2057  const

vector<string> kEmptyVectorOfStrings;

2059

SFileRememberer fileRememberer;

2062

kEmptyVectorOfStrings,

2063

kEmptyVectorOfStrings,

2072

TMapTestNameToItsFiles mapTestNameToItsFiles;

2074  ITERATE

( vector<CFile>, file_it, fileRememberer.m_filesFound ) {

2075  const string

sFileName = file_it->GetName();

2094  if

( sTestName.empty() || sSuffix.empty() ) {

2095

pTestRunner->

OnError

(

"Bad file name: "

+ file_it->GetPath());

2099  if

( setOfIgnoredSuffixes.

find

(sSuffix) != setOfIgnoredSuffixes.

end

() ) {

2105  const bool

bWasInserted =

2106

mapTestNameToItsFiles[sTestName].insert(make_pair(sSuffix, *file_it)).second;

2107  if

( ! bWasInserted ) {

2109  "File with same name appears multiple times in different dirs: "

+

2110

file_it->GetPath() );

2116  ERASE_ITERATE

(TMapTestNameToItsFiles, test_it, mapTestNameToItsFiles) {

2117  const string

& sTestName = test_it->first;

2124

inserter(setOfAllSuffixes, setOfAllSuffixes.

begin

()),

2125

SFirstOfPair<ITestRunner::TMapSuffixToFile::value_type>() );

2129

set_difference( setOfAllSuffixes.

begin

(), setOfAllSuffixes.

end

(),

2130

setOfRequiredSuffixes.

begin

(), setOfRequiredSuffixes.

end

(),

2131

inserter(setOfNonRequiredSuffixes, setOfNonRequiredSuffixes.

begin

() ) );

2136  const size_t

szNumOfSuffixes = setOfAllSuffixes.

size

();

2137  const size_t

szNumOfNonRequiredSuffixes = setOfNonRequiredSuffixes.

size

();

2138  if

( (szNumOfSuffixes - szNumOfNonRequiredSuffixes) != setOfRequiredSuffixes.

size

() )

2140

pTestRunner->

OnError

(

"Skipping this test because it's missing some files: "

+ sTestName);

2141

mapTestNameToItsFiles.erase(test_it);

2146  if

( ! includes( setOfOptionalSuffixes.

begin

(), setOfOptionalSuffixes.

end

(),

2147

setOfNonRequiredSuffixes.

begin

(), setOfNonRequiredSuffixes.

end

() ) )

2149

pTestRunner->

OnError

(

"Skipping this test because it has unexpected suffix(es): "

+ sTestName);

2150

mapTestNameToItsFiles.erase(test_it);

2156  if

( mapTestNameToItsFiles.empty() ) {

2157

pTestRunner->

OnError

(

"There are no tests to run"

);

2162  ITERATE

(TMapTestNameToItsFiles, test_it, mapTestNameToItsFiles) {

2163  const string

& sTestName = test_it->first;

2167

cerr <<

"Running test: "

<< sTestName << endl;

2168

pTestRunner->

RunTest

(sTestName, mapSuffixToFile);

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.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

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.

void transform(Container &c, UnaryFunction *op)

TSeqPos GetLength(void) const

@OrgMod.hpp User-defined methods of the data storage class.

bool IsFtable(void) const

void SetDescr(CSeq_descr &value)

list< CRef< CSeq_annot > > TAnnot

namespace ncbi::objects::

void AddQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature.

virtual void RunTest(const string &sTestNAme, const TMapSuffixToFile &mapSuffixToFile)=0

This function is called for each test.

virtual void OnError(const string &sErrorText)=0

This is called when an error occurs, and if ITestRunner is using boost it should indicate that using,...

const_iterator begin() const

const_iterator end() const

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define ENTREZ_ID_CONST(id)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

void FindFilesInDir(const CDir &dir, const vector< string > &masks, const vector< string > &masks_subdir, TFindFunc &find_func, TFindFiles flags=fFF_Default)

Find files in the specified directory.

virtual bool Exists(void) const

Check if directory "dirname" exists.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

const string & GetPath(void) const

Get entry path.

@ fFF_Recursive

descend into sub-dirs

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

Set object to copy of another one.

const TPrim & Get(void) const

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

#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.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

void SetTitle(TTitle &value)

Assign a value to Title data member.

void SetDate(TDate &value)

Assign a value to Date data member.

void SetName(TName &value)

Assign a value to Name data member.

void SetFrom(TFrom &value)

Assign a value to From data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetSerial_number(TSerial_number value)

Assign a value to Serial_number data member.

void SetDate(TDate &value)

Assign a value to Date data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

void SetAuthors(TAuthors &value)

Assign a value to Authors data member.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

bool IsSetOrg(void) const

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

bool IsSetSubtype(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

void SetName(const TName &value)

Assign a value to Name data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

void SetTag(TTag &value)

Assign a value to Tag data member.

TStr & SetStr(void)

Select the variant.

void SetDb(const TDb &value)

Assign a value to Db data member.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

bool IsSetMod(void) const

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

bool IsSetOrgname(void) const

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

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

TPmid & SetPmid(void)

Select the variant.

TSub & SetSub(void)

Select the variant.

TGen & SetGen(void)

Select the variant.

TArticle & SetArticle(void)

Select the variant.

bool IsSetStrands(void) const

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

const TStarts & GetStarts(void) const

Get the Starts member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TLens & GetLens(void) const

Get the Lens member data.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

TDim GetDim(void) const

Get the Dim member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

TNumseg GetNumseg(void) const

Get the Numseg member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void SetData(TData &value)

Assign a value to Data data member.

TPartial GetPartial(void) const

Get the Partial member data.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

bool IsMix(void) const

Check if variant Mix is selected.

void SetAccession(const TAccession &value)

Assign a value to Accession data member.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

TLocal & SetLocal(void)

Select the variant.

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

TGenbank & SetGenbank(void)

Select the variant.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

void SetVersion(TVersion value)

Assign a value to Version data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetClass(void) const

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

TSet & SetSet(void)

Select the variant.

TClass GetClass(void) const

Get the Class member data.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetAnnot(void) const

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

bool IsSetSeq_set(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void SetClass(TClass value)

Assign a value to Class data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

@ eClass_parts

parts for 2 or 3

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_segset

segmented sequence + parts

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

const TInst & GetInst(void) const

Get the Inst member data.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TIupacna & GetIupacna(void) const

Get the variant data.

bool IsSetAnnot(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

TSource & SetSource(void)

Select the variant.

E_Choice

Choice variants.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

void SetTech(TTech value)

Assign a value to Tech data member.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eRepr_seg

segmented sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eCompleteness_complete

complete biological entity

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

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

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::KEY key

static const GLdouble origin[]

#define EDIT_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var)

#define EDIT_EACH_SEQANNOT_ON_BIOSEQ(Itr, Var)

#define ERASE_DESCRIPTOR_ON_SEQENTRY

#define EDIT_EACH_DESCRIPTOR_ON_SEQENTRY

#define EDIT_EACH_SEQANNOT_ON_SEQSET(Itr, Var)

CRef< CSeq_feat > GetCDSFromGenProdSet(CRef< CSeq_entry > entry)

CRef< CSeq_annot > BuildGoodGraphAnnot(string id)

CRef< CSeq_entry > BuildGoodEcoSet()

CRef< CSeq_feat > AddMiscFeature(CRef< CSeq_entry > entry, size_t right_end)

CRef< CSeq_loc > MakeMixLoc(CRef< CSeq_id > id)

void MakeSeqLong(CBioseq &seq)

CRef< CSeq_feat > GetProtFeatFromGoodNucProtSet(CRef< CSeq_entry > entry)

void RemoveDescriptorType(CRef< CSeq_entry > entry, CSeqdesc::E_Choice desc_choice)

CRef< CSeq_entry > GetGenomicFromGenProdSet(CRef< CSeq_entry > entry)

CRef< CSeq_entry > BuildSegSetPart(string id_str)

CRef< CSeq_entry > BuildGoodDeltaSeq()

void RemoveDeltaSeqGaps(CRef< CSeq_entry > entry)

void SetCompleteness(CRef< CSeq_entry > entry, CMolInfo::TCompleteness completeness)

void SetSpliceForMixLoc(CBioseq &seq)

CRef< CPub > BuildGoodCitSubPub()

CRef< CSeq_feat > AddGoodImpFeat(CRef< CSeq_entry > entry, string key)

void ChangeProtId(CRef< CSeq_entry > np_set, CRef< CSeq_id > id)

void SetLineage(CRef< CSeq_entry > entry, string lineage)

void SetNucProtSetPartials(CRef< CSeq_entry > entry, bool partial5, bool partial3)

void SetSynthetic_construct(CRef< CSeq_entry > entry)

void ResetOrgname(CRef< CSeq_entry > entry)

void AdjustProtFeatForNucProtSet(CRef< CSeq_entry > entry)

void SetDiv(CRef< CSeq_entry > entry, string div)

CRef< CSeq_feat > GetmRNAFromGenProdSet(CRef< CSeq_entry > entry)

CRef< CSeq_feat > BuildGoodFeat()

void ReverseAlignmentStrand(CDense_seg &denseg, size_t pos, size_t seq_len)

CRef< CSeq_entry > BuildGoodSeq()

CRef< CSeq_feat > MakemRNAForCDS(CRef< CSeq_feat > feat)

CRef< CSeq_annot > AddFeat(CRef< CSeq_feat > feat, CRef< CSeq_entry > entry)

void SetBiomol(CRef< CSeq_entry > entry, CMolInfo::TBiomol biomol)

void SetDrosophila_melanogaster(CRef< CSeq_entry > entry)

CRef< CSeq_entry > BuildGoodProtSeq()

CRef< CSeq_feat > MakeCDSForGoodNucProtSet(const string &nuc_id, const string &prot_id)

void ChangeProductId(CRef< CSeq_annot > annot, CRef< CSeq_id > id)

void AddToDeltaSeq(CRef< CSeq_entry > entry, string seq)

CRef< CSeq_id > BuildRefSeqId()

void SetGenome(CRef< CSeq_entry > entry, CBioSource::TGenome genome)

void SetChromosome(CBioSource &src, string chromosome)

void SetOrgMod(CBioSource &src, COrgMod::TSubtype subtype, string val)

CRef< CSeq_feat > MakeMiscFeature(CRef< CSeq_id > id, size_t right_end, size_t left_end)

CRef< CSeq_feat > GetCDSFromGoodNucProtSet(CRef< CSeq_entry > entry)

void ChangeNucProtSetNucId(CRef< CSeq_entry > entry, CRef< CSeq_id > id)

void ChangeId(CRef< CSeq_annot > annot, CRef< CSeq_id > id)

void SetTaxname(CRef< CSeq_entry > entry, string taxname)

CRef< CSeq_feat > BuildGoodtRNA(CRef< CSeq_id > id)

void SetFocus(CRef< CSeq_entry > entry)

CRef< CSeq_feat > MakeGeneForFeature(CRef< CSeq_feat > feat)

void MakeNucProtSet3Partial(CRef< CSeq_entry > entry)

CRef< CSeq_entry > BuildGoodNucProtSet()

void TraverseAndRunTestCases(ITestRunner *pTestRunner, CDir dirWithTestCases, const set< string > &setOfRequiredSuffixes, const set< string > &setOfOptionalSuffixes, const set< string > &setOfIgnoredSuffixes, TTraverseAndRunTestCasesFlags fFlags)

This is for running data-driven test cases below the given top-level test directory.

void SetMGcode(CRef< CSeq_entry > entry, COrgName::TGcode mgcode)

CRef< CSeq_feat > BuildtRNA(CRef< CSeq_id > id)

void SetNucProtSetProductName(CRef< CSeq_entry > entry, string new_name)

void RevComp(CBioseq &bioseq)

CRef< CSeq_entry > BuildGenProdSetNucProtSet(CRef< CSeq_id > nuc_id, CRef< CSeq_id > prot_id)

void SetDbxref(CBioSource &src, string db, CObject_id::TId id)

void ChangeNucId(CRef< CSeq_entry > np_set, CRef< CSeq_id > id)

void SetSebaea_microphylla(CRef< CSeq_entry > entry)

void RemoveDbxref(CBioSource &src, string db, CObject_id::TId id)

void SetTaxon(CBioSource &src, size_t taxon)

void RetranslateCdsForNucProtSet(CRef< CSeq_entry > entry, CScope &scope)

CRef< CSeq_entry > MakeProteinForGoodNucProtSet(string id)

CRef< CSeq_id > IdFromEntry(CRef< CSeq_entry > entry)

void AddFeatAnnotToSeqEntry(CRef< CSeq_annot > annot, CRef< CSeq_entry > entry)

CRef< CSeq_feat > AddProtFeat(CRef< CSeq_entry > entry)

void SetGcode(CRef< CSeq_entry > entry, COrgName::TGcode gcode)

CRef< CAuthor > BuildGoodAuthor()

void ChangeNucProtSetProteinId(CRef< CSeq_entry > entry, CRef< CSeq_id > id)

CRef< CSeq_entry > GetNucleotideSequenceFromGoodNucProtSet(CRef< CSeq_entry > entry)

CRef< CSeq_feat > AddGoodSourceFeature(CRef< CSeq_entry > entry)

void SetProteinPartial(CRef< CSeq_entry > pentry, bool partial5, bool partial3)

CRef< CSeq_align > BuildGoodAlign()

CRef< CSeqdesc > BuildGoodPubSeqdesc()

CRef< CSeq_entry > GetNucProtSetFromGenProdSet(CRef< CSeq_entry > entry)

void SetTech(CRef< CSeq_entry > entry, CMolInfo::TTech tech)

void AddGoodSource(CRef< CSeq_entry > entry)

CRef< CSeq_entry > BuildGoodGenProdSet()

void SetOrigin(CRef< CSeq_entry > entry, CBioSource::TOrigin origin)

CRef< CSeq_entry > GetProteinSequenceFromGoodNucProtSet(CRef< CSeq_entry > entry)

void SetSubSource(CBioSource &src, CSubSource::TSubtype subtype, string val)

void SetCommon(CRef< CSeq_entry > entry, string common)

CRef< CSeq_feat > MakeIntronForMixLoc(CRef< CSeq_id > id)

CRef< CSeq_entry > BuildGoodSegSet()

void SetTransgenic(CBioSource &src, bool do_set)

void AddGoodPub(CRef< CSeq_entry > entry)

void ClearFocus(CRef< CSeq_entry > entry)

void SetPGcode(CRef< CSeq_entry > entry, COrgName::TGcode pgcode)

CRef< CSeq_entry > BuildGoodEcoSetWithAlign(size_t front_insert)

CRef< CPub > BuildGoodCitGenPub(CRef< CAuthor > author, int serial_number)

CRef< CPub > BuildGoodArticlePub()

@ fTraverseAndRunTestCasesFlags_DoNOTIgnoreREADMEFiles

Overrides default behavior (which is to disregard files whose prefix is "README")

int TTraverseAndRunTestCasesFlags


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