(objects::CBioSource& src, objects::CSubSource::TSubtype subtype,
stringval)
83 if(src.IsSetSubtype()) {
84objects::CBioSource::TSubtype::iterator it = src.SetSubtype().begin();
85 while(it != src.SetSubtype().end()) {
86 if((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {
87it = src.SetSubtype().erase(it);
98src.SetSubtype().push_back(sub);
104 stringsNameOfSubtype =
106 if( sNameOfSubtype.empty() ) {
113BOOST_CHECK_EQUAL(eSubtype, eReverseSubtype);
123TSubtypeSet subtypesExpectedToFail;
125 #ifdef ESUBTYPE_SHOULD_FAIL 126 # error ESUBTYPE_SHOULD_FAIL already defined 129 #define ESUBTYPE_SHOULD_FAIL(name) \ 130 subtypesExpectedToFail.insert(CSeqFeatData::eSubtype_##name); 147 #undef ESUBTYPE_SHOULD_FAIL 156 if( subtypesExpectedToFail.find(eSubtype) ==
157subtypesExpectedToFail.end() )
183BOOST_CHECK_EQUAL(m->
GetSubname(),
"turkey");
189BOOST_CHECK_EQUAL(s->
GetName(),
"dioecious");
258 stringdegree =
"\xB0";
259 stringto_fix =
"9.93"+ degree +
"N and 78.12"+ degree +
"E";
261BOOST_CHECK_EQUAL(fixed,
"9.93 N 78.12 E");
263to_fix =
"Lattitude: 25.790544; longitude: -80.214930";
265BOOST_CHECK_EQUAL(fixed,
"25.790544 N 80.214930 W");
267to_fix =
"34.1030555556 , -118.357777778 34 degrees 6' 11'' North , 118 degrees 21' 28'' West";
269BOOST_CHECK_EQUAL(fixed,
"");
271to_fix =
"0031.02 N 00.01E";
273BOOST_CHECK_EQUAL(fixed,
"31.02 N 0.01 E");
275to_fix =
"000.00 N 0.12 E";
277BOOST_CHECK_EQUAL(fixed,
"0.00 N 0.12 E");
279to_fix =
"0.0023 N 0 E";
281BOOST_CHECK_EQUAL(fixed,
"0.0023 N 0 E");
283to_fix =
"78.32 -0092.25";
285BOOST_CHECK_EQUAL(fixed,
"78.32 N 92.25 W");
287to_fix =
"-0008.34 0.85";
289BOOST_CHECK_EQUAL(fixed,
"8.34 S 0.85 E");
291to_fix =
"0.067682S_76.39885W";
293BOOST_CHECK_EQUAL(fixed,
"0.067682 S 76.39885 W");
295to_fix =
"34degrees 20' 13'' N,47degrees 03' 24''E";
297BOOST_CHECK_EQUAL(fixed,
"34.3369 N 47.0567 E");
299to_fix =
"34degrees 20' 13' N,47deg 03' 24' E";
301BOOST_CHECK_EQUAL(fixed,
"34.3369 N 47.0567 E");
303to_fix =
"8 degrees 28 'N & 77 degrees 41 'E";
305BOOST_CHECK_EQUAL(fixed,
"8.47 N 77.68 E");
349BOOST_CHECK_EQUAL(
CSubSource::FixLatLonFormat(
"37.918 degrees N latitude, 119.258 degrees W longitude",
true),
"37.918 N 119.258 W");
367BOOST_CHECK_EQUAL(
CSubSource::FixLatLonFormat(
"N 16 degree 46 min 57 sec; E 99 degree 01 min 08 sec",
true),
"16.7825 N 99.0189 E");
368BOOST_CHECK_EQUAL(
CSubSource::FixLatLonFormat(
"N 16 degree 30 min 16 sec, E 99 degree 09 min 40 sec",
true),
"16.5044 N 99.1611 E");
377auth_list->
SetAffil().SetStd().SetAffil(
"Murdoch University");
378auth_list->
SetAffil().SetStd().SetDiv(
"School of Veterinary and Life Sciences");
379auth_list->
SetAffil().SetStd().SetCity(
"Murdoch");
380auth_list->
SetAffil().SetStd().SetSub(
"Western Australia");
381auth_list->
SetAffil().SetStd().SetCountry(
"Australia");
382auth_list->
SetAffil().SetStd().SetStreet(
"90 South Street");
383auth_list->
SetAffil().SetStd().SetPostal_code(
"6150");
385auth1->
SetName().SetName().SetLast(
"Yang");
386auth1->
SetName().SetName().SetFirst(
"Rongchang");
387auth1->
SetName().SetName().SetInitials(
"R.");
388auth_list->
SetNames().SetStd().push_back(auth1);
390auth2->
SetName().SetName().SetLast(
"Ryan");
391auth2->
SetName().SetName().SetFirst(
"Una");
392auth2->
SetName().SetName().SetInitials(
"U.");
393auth_list->
SetNames().SetStd().push_back(auth2);
400 if(auth_list.
SetNames().SetStd().size() == 0) {
402auth->
SetName().SetName().SetLast(
"Last");
403auth_list.
SetNames().SetStd().push_back(auth);
405auth_list.
SetNames().SetStd().back()->SetName().SetName().SetFirst(
"Uan");
411 if(auth_list.
SetNames().SetStd().size() == 0) {
413auth->
SetName().SetName().SetLast(
"Last");
414auth_list.
SetNames().SetStd().push_back(auth);
416auth_list.
SetNames().SetStd().back()->SetName().SetName().SetLast(
"Nyar");
423 switch(pub.
Which()) {
477imp->
SetDate().SetStr(
"?");
486 switch(pub.
Which()) {
522 t->SetName(
"a random title");
523title.
Set().push_back(
t);
529 if(title.
Set().size() == 0) {
532title.
Set().front()->SetName() +=
" plus";
539 t->SetJta(
"a random title");
540title.
Set().push_back(
t);
546 if(title.
Set().size() == 0) {
549title.
Set().front()->SetJta() +=
" plus";
554 switch(pub.
Which()) {
607imp.
SetPub().SetStr(
"Publisher");
643auth_list2->
Assign(*auth_list1);
646BOOST_CHECK_EQUAL(auth_list1->
SameCitation(*auth_list2),
true);
650BOOST_CHECK_EQUAL(auth_list1->
SameCitation(*auth_list2),
true);
654BOOST_CHECK_EQUAL(auth_list1->
SameCitation(*auth_list2),
false);
663j_title->SetJta(
"Experimental Parasitology");
664jour->SetTitle().Set().push_back(j_title);
675title->SetName(
"Isospora streperae n. sp. (Apicomplexa: Eimeriidae) from a Grey Currawong (Strepera versicolour plumbea) (Passeriformes: Artamidae) in Western Australia");
687b_title->SetName(
"Book Title");
688book->
SetTitle().Set().push_back(b_title);
700title->SetName(
"Isospora streperae n. sp. (Apicomplexa: Eimeriidae) from a Grey Currawong (Strepera versicolour plumbea) (Passeriformes: Artamidae) in Western Australia");
934eq1->
Set().push_back(pub);
945eq2->
Set().push_back(pmid2);
955eq1->
Set().push_back(pmid1);
960 #define CHECK_COMMON_FIELD(o1,o2,c,Field,val1,val2) \ 961 o1->Set##Field(val1); \ 962 o2->Reset##Field(); \ 963 c = o1->MakeCommon(*o2); \ 964 BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \ 965 o2->Set##Field(val2); \ 966 c = o1->MakeCommon(*o2); \ 967 BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \ 968 o2->Set##Field(val1); \ 969 c = o1->MakeCommon(*o2); \ 970 BOOST_CHECK_EQUAL(c->IsSet##Field(), true); \ 971 BOOST_CHECK_EQUAL(c->Get##Field(), o1->Get##Field()); 980BOOST_ASSERT(
"common OrgName should not have been created");
983on1->
SetDiv(
"bacteria");
986BOOST_ASSERT(
"common OrgName should not have been created");
988on2->
SetDiv(
"archaea");
991BOOST_ASSERT(
"common OrgName should not have been created");
993on2->
SetDiv(
"bacteria");
995BOOST_CHECK_EQUAL(common->
GetDiv(),
"bacteria");
1001on1->
SetMod().push_back(m1);
1003BOOST_CHECK_EQUAL(common->
IsSetMod(),
false);
1008on2->
SetMod().push_back(m2);
1011BOOST_CHECK_EQUAL(common->
IsSetMod(),
false);
1015BOOST_CHECK_EQUAL(common->
IsSetMod(),
true);
1016BOOST_CHECK_EQUAL(common->
GetMod().size(), 1);
1017BOOST_CHECK_EQUAL(common->
GetMod().front()->Equals(*m2),
true);
1028 #define CHECK_COMMON_STRING_LIST(o1,o2,c,Field,val1,val2) \ 1029 o1->Set##Field().push_back(val1); \ 1030 c = o1->MakeCommon(*o2); \ 1031 BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \ 1032 o2->Set##Field().push_back(val2); \ 1033 c = o1->MakeCommon(*o2); \ 1034 BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \ 1035 o2->Set##Field().push_back(val1); \ 1036 c = o1->MakeCommon(*o2); \ 1037 BOOST_CHECK_EQUAL(c->IsSet##Field(), true); \ 1038 BOOST_CHECK_EQUAL(c->Get##Field().size(), 1); \ 1039 BOOST_CHECK_EQUAL(c->Get##Field().front(), val1); 1047BOOST_ASSERT(
"common OrgRef should not have been created");
1053BOOST_ASSERT(
"common OrgRef should not have been created");
1076BOOST_ASSERT(
"common BioSource should not have been created");
1101BOOST_CHECK_EQUAL(common->
GetSubtype().size(), 1);
1102BOOST_CHECK_EQUAL(common->
GetSubtype().front()->Equals(*s2),
true);
1150src1->
SetOrg().SetOrgname().SetLineage(
"Viruses; ssDNA viruses; Nanoviridae; Nanovirus");
1218ss->
SetName(
"a; [mixed bacterial source]; b");
1220BOOST_CHECK_EQUAL(ss->
GetName(),
"a; b");
1221ss->
SetName(
"[uncultured (using species-specific primers) bacterial source]");
1223BOOST_CHECK_EQUAL(ss->
GetName(),
"amplified with species-specific primers");
1224ss->
SetName(
"[BankIt_uncultured16S_wizard]; [universal primers]; [tgge]");
1226BOOST_CHECK_EQUAL(ss->
IsSetName(),
false);
1227ss->
SetName(
"[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]");
1229BOOST_CHECK_EQUAL(ss->
GetName(),
"amplified with species-specific primers");
1232ss->
SetName(
"a; [mixed bacterial source]; b");
1235BOOST_CHECK_EQUAL(ss->
GetName(),
"a; b");
1236ss->
SetName(
"[BankIt_uncultured16S_wizard]; [universal primers]; [tgge]");
1240ss->
SetName(
"[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]");
1242BOOST_CHECK_EQUAL(ss->
GetName(),
"[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]");
1244ss->
SetName(
"[BankIt_cultured16S_wizard]");
1273BOOST_CHECK_EQUAL(
msg,
"The International Cell Line Authentication Committee database indicates that 222 from Homo sapiens is known to be contaminated by PA1 from Human. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1276BOOST_CHECK_EQUAL(
msg,
"");
1279BOOST_CHECK_EQUAL(
msg,
"");
1282BOOST_CHECK_EQUAL(
msg,
"The International Cell Line Authentication Committee database indicates that ARO81-1 from Homo sapiens is known to be contaminated by HT-29 from Human. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1285BOOST_CHECK_EQUAL(
msg,
"The International Cell Line Authentication Committee database indicates that aRO81-1 from Homo sapiens is known to be contaminated by HT-29 from Human. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1288BOOST_CHECK_EQUAL(
msg,
"The International Cell Line Authentication Committee database indicates that IPRI-OL-7 from Orgyia leucostigma is known to be contaminated by IPRI-CF-124 from Choristoneura fumiferana. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1321BOOST_CHECK_EQUAL(
msg,
"The International Cell Line Authentication Committee database indicates that Yamada from Canis lupus familiaris is known to be contaminated by Unknown from Mouse. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1342 "Spain: Mediterranean, Malvarrosa Beach (Valencia)");
1350 "China: Guangdong Province, Guangzhou City, Tianlu Lake Forest Park");
1360 bool ambig=
false;
1362BOOST_CHECK_EQUAL(
ambig,
true);
1378 bool ambig=
false;
1380BOOST_CHECK_EQUAL(
ambig,
false);
1427{
"1952",
"1952"},
1428{
"1952-10-21T11:43Z",
"1952-10-21T11:43Z"},
1429{
"1952-10-21T11Z",
"1952-10-21T11Z"},
1430{
"1952-10-21",
"1952-10-21"},
1431{
"1952-10",
"1952-10"},
1432{
"1952/1953",
"1952/1953"},
1433{
"1952-10-21/1953-02-15",
"1952-10-21/1953-02-15"},
1434{
"1952-10/1953-02",
"1952-10/1953-02"},
1435{
"1952-10-21T11:43Z/1952-10-21T17:43Z",
1436 "1952-10-21T11:43Z/1952-10-21T17:43Z"},
1440{
"21-Oct-1952",
"21-Oct-1952"},
1441{
"Oct-1952",
"Oct-1952"},
1442{
"21-Oct-1952/15-Feb-1953",
"21-Oct-1952/15-Feb-1953"},
1443{
"Oct-1952/Feb-1953",
"Oct-1952/Feb-1953"},
1446{
"1-1-1952",
"01-Jan-1952"},
1447{
"1-1-1952/2-2-1952",
"01-Jan-1952/02-Feb-1952"}
1451 const stringfixed_date =
1453 const stringexpected_date(
1454kGoodCollectionDates[idx].expected_result);
1455BOOST_CHECK_EQUAL(fixed_date, expected_date);
1458 boolbad_format =
false;
1459 boolin_future =
false;
1461fixed_date, bad_format, in_future);
1462BOOST_CHECK_MESSAGE( ! bad_format, fixed_date );
1463BOOST_CHECK_MESSAGE( ! in_future, fixed_date );
1467BOOST_CHECK_MESSAGE(
1472vector<string> date_pieces_strs;
1475 ITERATE( vector<string>, date_piece_ci, date_pieces_strs ) {
1476 const string& date_piece_str = *date_piece_ci;
1480BOOST_CHECK_MESSAGE(
1483BOOST_CHECK_MESSAGE(
1494BOOST_CHECK_EQUAL(
rna->GetRnaProductName(),
kEmptyStr);
1496 stringproduct(
"mRNA product");
1497 rna->SetExt().SetName(product);
1498BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1502 rna->SetExt().SetGen(*rna_gen);
1503BOOST_CHECK_EQUAL(
rna->GetRnaProductName(),
kEmptyStr);
1505product.assign(
"miscRNA product");
1506rna_gen->SetProduct(product);
1507BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1511BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1514product.assign(
"tRNA-Ser");
1515 rna->SetExt().SetTRNA().SetAa().SetNcbieaa(83);
1516BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1519BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1521product.assign(
"tRNA-Met");
1523 rna->SetExt().SetTRNA().SetAa().SetIupacaa(77);
1524BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1526product.assign(
"tRNA-OTHER");
1527 rna->SetExt().SetTRNA().SetAa().SetIupacaa(88);
1528BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1530 rna->SetExt().SetTRNA().SetAa().SetNcbieaa(88);
1531BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1533product.assign(
"tRNA-TERM");
1534 rna->SetExt().SetTRNA().SetAa().SetNcbieaa(42);
1535BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1537 rna->SetExt().SetTRNA().SetAa().SetIupacaa(42);
1538BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1541 rna->SetExt().SetTRNA().SetAa().SetIupacaa(43);
1542BOOST_CHECK_EQUAL(
rna->GetRnaProductName(), product);
1550 stringproduct(
"mRNA product");
1552 rna->SetRnaProductName(product, remainder);
1553BOOST_CHECK_EQUAL(
rna->IsSetExt(),
true);
1554BOOST_CHECK_EQUAL(
rna->GetExt().GetName(), product);
1555BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1558 rna->SetRnaProductName(product, remainder);
1559BOOST_CHECK_EQUAL(
rna->IsSetExt(),
false);
1560BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1562product.assign(
"rRNA product");
1564 rna->SetRnaProductName(product, remainder);
1565BOOST_CHECK_EQUAL(
rna->IsSetExt(),
true);
1566BOOST_CHECK_EQUAL(
rna->GetExt().GetName(), product);
1567BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1570 rna->SetRnaProductName(product, remainder);
1571BOOST_CHECK_EQUAL(
rna->IsSetExt(),
false);
1572BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1574product.assign(
"miscRNA product");
1576 rna->SetRnaProductName(product, remainder);
1577BOOST_CHECK_EQUAL(
rna->IsSetExt(),
true);
1578BOOST_CHECK_EQUAL(
rna->GetExt().GetGen().GetProduct(), product);
1579BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1582 rna->SetRnaProductName(product, remainder);
1583BOOST_CHECK_EQUAL(
rna->IsSetExt(),
false);
1584BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1587product.assign(
"tRNA_Ala");
1589 rna->SetRnaProductName(product, remainder);
1590BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1591BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().IsSetAa(),
false);
1592BOOST_CHECK_EQUAL(remainder, product);
1595product.assign(
"TRNA-Ala");
1596 rna->SetRnaProductName(product, remainder);
1597BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1598BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().IsSetAa(),
false);
1599BOOST_CHECK_EQUAL(remainder, product);
1601product.assign(
"tRNA-Ala");
1602 rna->SetRnaProductName(product, remainder);
1603BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().IsSetAa(),
true);
1604BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 65);
1605BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1608 rna->SetRnaProductName(product, remainder);
1609BOOST_CHECK_EQUAL(
rna->IsSetExt(),
true);
1610BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().IsSetAa(),
false);
1611BOOST_CHECK_EQUAL(
rna->GetRnaProductName(),
kEmptyStr);
1612BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1614product.assign(
"Ser");
1615 rna->SetRnaProductName(product, remainder);
1616BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1617BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 83);
1618BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1620product.assign(
"TERM");
1621 rna->SetRnaProductName(product, remainder);
1622BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1623BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 42);
1624BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1626product.assign(
"tRNA-other");
1627 rna->SetRnaProductName(product, remainder);
1628BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1629BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 88);
1630BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1633product.assign(
"tRNA-A(gct)");
1634 rna->SetRnaProductName(product, remainder);
1635BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1636BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 65);
1637BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1639product.assign(
"tRNA-*(gct)");
1640 rna->SetRnaProductName(product, remainder);
1641BOOST_CHECK_EQUAL(
rna->GetExt().IsTRNA(),
true);
1642BOOST_CHECK_EQUAL(
rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 42);
1643BOOST_CHECK_EQUAL(remainder,
kEmptyStr);
1669BOOST_CHECK_EQUAL(obj->
GetData().front()->GetLabel().GetStr(),
"BaseModification-FileTrackURL");
1670BOOST_CHECK_EQUAL(obj->
GetData().front()->GetData().GetStr(),
"https://submit.ncbi.nlm.nih.gov/ft/byid/7azalbch/brev2_motif_summary.csv");
1679src->
SetOrg().SetTaxname(
"uncultured x");
1685src->
SetOrg().SetTaxname(
"Homo sapiens");
1693src->
SetOrg().SetOrgname().SetDiv(
"ENV");
1699src->
SetOrg().SetOrgname().ResetDiv();
1700src->
SetOrg().SetOrgname().SetLineage(
"metagenomes");
1707src->
SetOrg().SetOrgname().ResetLineage();
1735BOOST_CHECK_EQUAL(
om->RemoveAbbreviation(),
true);
1736BOOST_CHECK_EQUAL(
om->GetSubname(),
"x");
1740BOOST_CHECK_EQUAL(om2->
GetSubname(),
"y");
1749src->
SetOrg().SetOrgname().SetLineage(
"Viruses; foo");
1752src->
SetOrg().SetOrgname().SetLineage(
"Bacteria; foo");
1755src->
SetOrg().SetOrgname().SetLineage(
"Archaea; foo");
1758src->
SetOrg().SetOrgname().SetLineage(
"Eukaryota; Fungi; foo");
1761src->
SetOrg().SetOrgname().SetLineage(
"Eukaryota; Metazoa; foo");
1764src->
SetOrg().SetOrgname().SetLineage(
"Eukaryota; Viridiplantae; Streptophyta; Embryophyta; foo");
1767src->
SetOrg().SetOrgname().SetLineage(
"Eukaryota; Rhodophyta; foo");
1770src->
SetOrg().SetOrgname().SetLineage(
"Eukaryota; stramenopiles; Phaeophyceae; foo");
1777BOOST_CHECK_EQUAL(src->
GetSubtype().size(), 1);
1781BOOST_CHECK_EQUAL(src->
GetSubtype().size(), 1);
1789src->
SetOrg().SetOrgname().SetLineage(
"Viruses; foo");
1813src->
SetOrg().SetOrgname().SetLineage(
"Viruses; foo");
1853BOOST_ASSERT(recomb_values.
find(
"chromosome_breakpoint") != recomb_values.
end());
1856 stringold_recomb_value(
"meiotic_recombination");
1858BOOST_CHECK_EQUAL(old_recomb_value,
"meiotic");
1860old_recomb_value = (
"other:non_allelic_homologous_recombination");
1862BOOST_CHECK_EQUAL(old_recomb_value,
"non_allelic_homologous");
1864 stringvalid_recomb_value(
"mitotic");
1866BOOST_CHECK_EQUAL(valid_recomb_value,
"mitotic");
1879src.
SetOrg().SetOrgname().SetLineage(
"viruses");
1882src.
SetOrg().SetOrgname().SetLineage(
"viroids");
1885src.
SetOrg().SetOrgname().ResetLineage();
1956 stringtaxname =
"Zea mays";
1960BOOST_CHECK_EQUAL(
"", taxname);
1963BOOST_CHECK_EQUAL(
lookup->GetTaxname(), taxname);
1964BOOST_CHECK_EQUAL(
lookup->GetOrgname().GetDiv(),
"PLN");
1985 stringvoucher_type;
1986 boolis_miscapitalized;
1989 boolerroneous_country;
1990 stringinst_code =
"ARBH";
1991BOOST_CHECK_EQUAL(
COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country),
true);
1992BOOST_CHECK_EQUAL(voucher_type,
"s");
1993BOOST_CHECK_EQUAL(is_miscapitalized,
false);
1994BOOST_CHECK_EQUAL(correct_cap,
"ARBH");
1995BOOST_CHECK_EQUAL(needs_country,
false);
1996BOOST_CHECK_EQUAL(erroneous_country,
false);
1998inst_code =
"NMNH";
1999BOOST_CHECK_EQUAL(
COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country),
true);
2000BOOST_CHECK_EQUAL(voucher_type,
"sb");
2001BOOST_CHECK_EQUAL(is_miscapitalized,
false);
2002BOOST_CHECK_EQUAL(correct_cap,
"NMNH");
2003BOOST_CHECK_EQUAL(needs_country,
false);
2004BOOST_CHECK_EQUAL(erroneous_country,
false);
2007BOOST_CHECK_EQUAL(
COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country),
true);
2008BOOST_CHECK_EQUAL(voucher_type,
"s");
2009BOOST_CHECK_EQUAL(is_miscapitalized,
false);
2010BOOST_CHECK_EQUAL(correct_cap,
"ZMM");
2011BOOST_CHECK_EQUAL(needs_country,
false);
2012BOOST_CHECK_EQUAL(erroneous_country,
false);
2014inst_code =
"ZMUM";
2015BOOST_CHECK_EQUAL(
COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country),
true);
2016BOOST_CHECK_EQUAL(voucher_type,
"s");
2017BOOST_CHECK_EQUAL(is_miscapitalized,
false);
2018BOOST_CHECK_EQUAL(correct_cap,
"ZMUM");
2019BOOST_CHECK_EQUAL(needs_country,
false);
2020BOOST_CHECK_EQUAL(erroneous_country,
false);
2056 string val=
"p-element";
2058BOOST_CHECK_EQUAL(
val,
"P-element");
2064 string val=
"Exon";
2066BOOST_CHECK_EQUAL(
val,
"exon");
2086 inthour,
min, sec;
2089BOOST_CHECK_EQUAL(hour, 11);
2090BOOST_CHECK_EQUAL(
min, 13);
2091BOOST_CHECK_EQUAL(sec, 0);
2096BOOST_CHECK_EQUAL(hour, 11);
2097BOOST_CHECK_EQUAL(
min, 13);
2098BOOST_CHECK_EQUAL(sec, 0);
2108BOOST_CHECK_EQUAL(user->
GetType().
GetStr(),
"RefGeneTracking");
2117BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"Status");
2118BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"PIPELINE");
2121BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"Status");
2122BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"INFERRED");
2123BOOST_CHECK_EQUAL(user->
GetData().size(), 1);
2130BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"GenomicSource");
2131BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"XXX");
2135BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"GenomicSource");
2136BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"XXX2");
2138BOOST_CHECK_EQUAL(user->
GetData().size(), 2);
2145BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"Collaborator");
2146BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"YYY");
2149BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"Collaborator");
2150BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"YYY2");
2153BOOST_CHECK_EQUAL(user->
GetData().size(), 3);
2160BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"CollaboratorURL");
2161BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetStr(),
"ZZZ");
2165BOOST_CHECK_EQUAL(user->
GetData().size(), 4);
2170BOOST_CHECK_EQUAL(user->
GetData().back()->GetLabel().GetStr(),
"Generated");
2171BOOST_CHECK_EQUAL(user->
GetData().back()->GetData().GetBool(),
true);
2177BOOST_CHECK_EQUAL(user->
GetData().size(), 5);
2185BOOST_CHECK_EQUAL(r_ident->GetAccession(),
"AY12345");
2186BOOST_CHECK_EQUAL(user->
GetData().size(), 6);
2189vector<CConstRef<CUser_object::CRefGeneTrackingAccession> > assembly;
2192(
"XXX",
GI_CONST(123), 0, 100,
"comment1",
"name1")));
2195(
"YYY",
GI_CONST(124), 10, 1100,
"comment2",
"name2")));
2197BOOST_CHECK_EQUAL(user->
GetData().size(), 7);
2200BOOST_CHECK_EQUAL(r_assembly.size(), 2);
2201BOOST_CHECK_EQUAL(r_assembly.front()->GetAccession(),
"XXX");
2202BOOST_CHECK_EQUAL(r_assembly.front()->GetGI(),
GI_CONST(123));
2203BOOST_CHECK_EQUAL(r_assembly.front()->GetFrom(), 0);
2204BOOST_CHECK_EQUAL(r_assembly.front()->GetTo(), 100);
2205BOOST_CHECK_EQUAL(r_assembly.front()->GetName(),
"name1");
2206BOOST_CHECK_EQUAL(r_assembly.front()->GetComment(),
"comment1");
2207BOOST_CHECK_EQUAL(r_assembly.back()->GetAccession(),
"YYY");
2208BOOST_CHECK_EQUAL(r_assembly.back()->GetGI(),
GI_CONST(124));
2209BOOST_CHECK_EQUAL(r_assembly.back()->GetFrom(), 10);
2210BOOST_CHECK_EQUAL(r_assembly.back()->GetTo(), 1100);
2211BOOST_CHECK_EQUAL(r_assembly.back()->GetName(),
"name2");
2212BOOST_CHECK_EQUAL(r_assembly.back()->GetComment(),
"comment2");
2216BOOST_CHECK_EQUAL(user->
GetData().size(), 6);
2219BOOST_CHECK_EQUAL(user->
GetData().size(), 5);
2222BOOST_CHECK_EQUAL(user->
GetData().size(), 4);
2225BOOST_CHECK_EQUAL(user->
GetData().size(), 3);
2228BOOST_CHECK_EQUAL(user->
GetData().size(), 2);
2231BOOST_CHECK_EQUAL(user->
GetData().size(), 1);
2234BOOST_CHECK_EQUAL(user->
GetData().size(), 0);
2258BOOST_CHECK_EQUAL(
CSeq_id::IsValidLocalID(
"ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXY"),
false);
2351 const size_tnumExpectedQuals = 138;
2354BOOST_CHECK_EQUAL(all_quals.size(), numExpectedQuals);
2357BOOST_CHECK_EQUAL(
count, numExpectedQuals);
2360BOOST_CHECK_EQUAL(empty_quals.size(), 0);
2364BOOST_CHECK_EQUAL(
count, 0);
2368 for(
autorec: mandatory)
2370std::cout << rec << std::endl;
2378BOOST_CHECK_EQUAL(test1.second,
"host");
2381BOOST_CHECK_EQUAL(
test2.second,
"host");
2384BOOST_CHECK_EQUAL(test3.second,
"specific_host");
2387BOOST_CHECK_EQUAL(test4.second,
"specific_host");
2390BOOST_CHECK_EQUAL(test5,
"host");
2395 size_torig_size =
orig.size();
2396BOOST_CHECK(orig_size == 2);
2397std::vector<CSeqFeatData::EQualifier> mandatory =
orig;
2400 ERASE_ITERATE(std::vector<CSeqFeatData::EQualifier>, it, mandatory) {
2401 if(*it == not_mandatory) {
2407BOOST_CHECK(mandatory.size() == 1);
2409 automandatory_copy =
orig;
2410 boolres2 = mandatory_copy.reset(not_mandatory);
2411BOOST_CHECK(res == res2);
2412BOOST_CHECK(mandatory_copy.size() == 1);
2414 boolres3 = mandatory_copy.set(not_mandatory);
2415BOOST_CHECK(res != res3);
2416BOOST_CHECK(mandatory_copy.size() == 2);
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
@Auth_list.hpp User-defined methods of the data storage class.
bool SameCitation(const CAuth_list &other) const
bool FixEnvironmentalSample()
string GetRepliconName(void) const
static bool ShouldIgnoreConflict(const string &label, string src_val, string sample_val, bool is_local_copy=false)
static bool AllowSexQualifier(const string &lineage)
void RemoveCultureNotes(bool is_species_level=true)
string GetBioprojectLocation(void) const
bool FixSexMatingTypeInconsistencies()
CRef< CBioSource > MakeCommon(const CBioSource &other) const
static bool AllowMatingTypeQualifier(const string &lineage)
bool FixGenomeForQualifiers()
string GetBioprojectType(void) const
bool RemoveUnexpectedViralQualifiers()
static string CountryFixupItem(const string &input, bool capitalize_after_colon)
static bool IsLegalMobileElementValue(const string &val)
static bool IsIllegalQualName(const string &val)
static bool FixRecombinationClassValue(string &val)
static string CleanupAndRepairInference(const string &orig_inference)
static bool FixMobileElementValue(string &val)
static const TLegalRecombinationClassSet & GetSetOfLegalRecombinationClassValues(void)
@OrgMod.hpp User-defined methods of the data storage class.
static string FixCapitalization(TSubtype subtype, const string &value)
static bool IsINSDCValidTypeMaterial(const string &type_material)
static bool IsInstitutionCodeValid(const string &inst_coll, string &voucher_type, bool &is_miscapitalized, string &correct_cap, bool &needs_country, bool &erroneous_country)
static bool IsDiscouraged(const TSubtype stype, bool indexer=false)
static string FixHost(const string &value)
bool RemoveAbbreviation()
static bool IsValidTypeMaterial(const string &type_material)
static string FixHostCapitalization(const string &value)
static string FixStrain(const string &strain)
CRef< COrgName > MakeCommon(const COrgName &other) const
static CConstRef< COrg_ref > TableLookup(const string &taxname)
TTaxId SetTaxId(TTaxId tax_id)
CRef< COrg_ref > MakeCommon(const COrg_ref &other) const
static bool IsECNumberSplit(const string &old_ecno)
static bool IsValidECNumberFormat(const string &ecno)
Verify correct form of EC number.
bool SameCitation(const CPub_equiv &other) const
bool SameCitation(const CPub &other) const
static vector< string > GetncRNAClassList()
bool IsLegalClass() const
@RNA_ref.hpp User-defined methods of the data storage class.
static const string & GetRegulatoryClass(ESubtype subtype)
bool IsLegalQualifier(EQualifier qual) const
Test wheather a certain qualifier is legal for the feature.
static bool IsDiscouragedQual(EQualifier qual)
static EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype)
EQualifier
List of available qualifiers for feature keys.
@ eQual_recombination_class
@ eFeatureLocationAllowed_NucOnly
@ eFeatureLocationAllowed_Error
@ eFeatureLocationAllowed_ProtOnly
@ eFeatureLocationAllowed_Any
static bool ProhibitXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)
const TLegalQualifiers & GetLegalQualifiers(void) const
Get a list of all the legal qualifiers for the feature.
const TQualifiers & GetMandatoryQualifiers(void) const
Get the list of all mandatory qualifiers for the feature.
static bool IsDiscouragedSubtype(ESubtype subtype)
static std::pair< EQualifier, CTempString > GetQualifierTypeAndValue(CTempString qual)
static bool FixImportKey(string &key)
@ eSubtype_bad
These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.
@ eSubtype_mat_peptide_aa
static CTempString GetQualifierAsString(EQualifier qual)
Convert a qualifier from an enumerated value to a string representation or empty if not found.
static ESubtype SubtypeNameToValue(CTempString sName)
Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.
static CTempString SubtypeValueToName(ESubtype eSubtype)
Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...
static bool IsRegulatory(ESubtype subtype)
static bool AllowXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)
const_iterator find(const key_type &key) const
Return a const_iterator pointing to the specified element, or to the end if the element is not found.
const_iterator end() const
Return the end of the controlled sequence.
static string FixCapitalization(TSubtype subtype, const string &value)
static string FixTissueTypeCapitalization(const string &value)
static bool IsISOFormatTime(const string &orig_time, int &hour, int &min, int &sec, bool require_time_zone=true)
static string GetCollectionDateProblem(const string &date_string)
static string FixLatLonFormat(string orig_lat_lon, bool guess=false)
static string FixIsolationSourceCapitalization(const string &value)
static string FixCellTypeCapitalization(const string &value)
static string FixDateFormat(const string &orig_date)
Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.
static string CheckCellLine(const string &cell_line, const string &organism)
static CRef< CDate > DateFromCollectionDate(const string &str) THROWS((CException))
static string FixDevStageCapitalization(const string &value)
static string FixAltitude(const string &value)
static void RemoveCultureNotes(string &value, bool is_species_level=true)
static void IsCorrectDateFormat(const string &date_string, bool &bad_format, bool &in_future)
const string & GetRefGeneTrackingCollaborator() const
void SetObjectType(EObjectType obj_type)
void ResetRefGeneTrackingAssembly()
void ResetRefGeneTrackingStatus()
void RemoveUnverifiedFeature()
void AddUnverifiedOrganism()
void SetRefGeneTrackingCollaboratorURL(const string &collaborator_url)
const string & GetRefGeneTrackingCollaboratorURL() const
void AddUnverifiedContaminant()
@ eRefGeneTrackingStatus_INFERRED
@ eRefGeneTrackingStatus_NotSet
@ eRefGeneTrackingStatus_PIPELINE
void ResetRefGeneTrackingCollaboratorURL()
bool IsRefGeneTracking() const
void SetRefGeneTrackingAssembly(const TRefGeneTrackingAccessions &acc_list)
void ResetRefGeneTrackingGenerated()
void RemoveUnverifiedMisassembled()
void ResetRefGeneTrackingGenomicSource()
bool IsSetRefGeneTrackingIdenticalTo() const
bool IsSetRefGeneTrackingGenomicSource() const
void SetRefGeneTrackingStatus(ERefGeneTrackingStatus status)
void RemoveUnverifiedContaminant()
void SetRefGeneTrackingCollaborator(const string &collaborator)
void SetRefGeneTrackingIdenticalTo(const CRefGeneTrackingAccession &accession)
void SetRefGeneTrackingGenomicSource(const string &genomic_source)
@ eObjectType_RefGeneTracking
bool IsUnverifiedMisassembled() const
bool IsSetRefGeneTrackingCollaboratorURL() const
void SetRefGeneTrackingGenerated(bool val=true)
void SetFileTrackUploadId(const string &upload_id)
vector< CConstRef< CRefGeneTrackingAccession > > TRefGeneTrackingAccessions
const string & GetRefGeneTrackingGenomicSource() const
bool IsSetRefGeneTrackingStatus() const
bool IsUnverifiedOrganism() const
bool GetRefGeneTrackingGenerated() const
void ResetRefGeneTrackingCollaborator()
ERefGeneTrackingStatus GetRefGeneTrackingStatus() const
bool IsUnverifiedContaminant() const
TRefGeneTrackingAccessions GetRefGeneTrackingAssembly() const
bool IsUnverifiedFeature() const
bool IsUnverified() const
void RemoveUnverifiedOrganism()
void AddUnverifiedMisassembled()
CConstRef< CRefGeneTrackingAccession > GetRefGeneTrackingIdenticalTo() const
bool IsSetRefGeneTrackingCollaborator() const
void ResetRefGeneTrackingIdenticalTo()
EObjectType GetObjectType() const
void AddUnverifiedFeature()
static int lookup(const char *name, const struct lookup_int *table)
#define test2(s, m, d, r)
#define ITERATE_0_IDX(idx, up_to)
idx loops from 0 (inclusive) to up_to (exclusive)
constexpr size_t ArraySize(const Element(&)[Size])
#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 VECTOR_ERASE(Var, Cont)
Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.
#define ENTREZ_ID_FROM(T, value)
virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)
Set object to copy of another one.
static bool IsValidLocalID(const CTempString &s)
Perform rudimentary validation on potential local IDs, whose contents should be pure ASCII and limite...
void Reset(void)
Reset reference object.
static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)
Split a string using specified delimiters.
static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)
Check if a string is blank (has no text).
static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)
Case-insensitive equality of a substring with another string.
void SetBook(TBook &value)
Assign a value to Book data member.
void SetIssue(const TIssue &value)
Assign a value to Issue data member.
void SetTitle(TTitle &value)
Assign a value to Title data member.
const TFrom & GetFrom(void) const
Get the From member data.
void SetJournal(TJournal &value)
Assign a value to Journal data member.
void SetImp(TImp &value)
Assign a value to Imp data member.
void SetTitle(TTitle &value)
Assign a value to Title 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 SetAffil(TAffil &value)
Assign a value to Affil data member.
bool IsSetFrom(void) const
Check if a value has been assigned 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 SetPages(const TPages &value)
Assign a value to Pages 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 SetPub(TPub &value)
Assign a value to Pub data member.
void SetTitle(TTitle &value)
Assign a value to Title data member.
void SetImp(TImp &value)
Assign a value to Imp data member.
void SetCit(TCit &value)
Assign a value to Cit data member.
void SetCit(const TCit &value)
Assign a value to Cit data member.
void SetVolume(const TVolume &value)
Assign a value to Volume data member.
void SetNames(TNames &value)
Assign a value to Names data member.
void SetAuthors(TAuthors &value)
Assign a value to Authors data member.
void SetDate(TDate &value)
Assign a value to Date data member.
void SetVolume(const TVolume &value)
Assign a value to Volume data member.
void SetTitle(const TTitle &value)
Assign a value to Title data member.
void SetMuid(TMuid value)
Assign a value to Muid data member.
bool IsBook(void) const
Check if variant Book is selected.
bool IsJournal(void) const
Check if variant Journal is selected.
void SetPrepub(TPrepub value)
Assign a value to Prepub data member.
void SetImp(TImp &value)
Assign a value to Imp data member.
void SetAuthors(TAuthors &value)
Assign a value to Authors data member.
Tdata & Set(void)
Assign a value to data member.
@ ePrepub_in_press
accepted, not published
@ ePrepub_submitted
submitted, not accepted
const TSubtype & GetSubtype(void) const
Get the Subtype member data.
TGenome GetGenome(void) const
Get the Genome member data.
void ResetGenome(void)
Reset Genome data member.
void SetSubtype(TSubtype value)
Assign a value to Subtype 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 SetGenome(TGenome value)
Assign a value to Genome data member.
void SetOrg(TOrg &value)
Assign a value to Org data member.
void SetName(const TName &value)
Assign a value to Name data member.
const TName & GetName(void) const
Get the Name member data.
EGenome
biological context
bool IsSetName(void) const
Check if a value has been assigned to Name data member.
TSubtype & SetSubtype(void)
Assign a value to Subtype data member.
void ResetSubtype(void)
Reset Subtype data member.
@ eSubtype_insertion_seq_name
@ eSubtype_environmental_sample
@ eSubtype_endogenous_virus_name
@ eOrigin_mut
artificially mutagenized
@ eOrigin_artificial
artificially engineered
@ eGenome_endogenous_virus
@ eGenome_plasmid_in_mitochondrion
@ eGenome_plasmid_in_plastid
void SetYear(TYear value)
Assign a value to Year data member.
TStd & SetStd(void)
Select the variant.
const TStr & GetStr(void) const
Get the variant data.
const TData & GetData(void) const
Get the Data member data.
const TType & GetType(void) const
Get the Type member data.
const TMod & GetMod(void) const
Get the Mod member data.
const TDiv & GetDiv(void) const
Get the Div member data.
const TSubname & GetSubname(void) const
Get the Subname member data.
void SetDiv(const TDiv &value)
Assign a value to Div data member.
void SetSubtype(TSubtype value)
Assign a value to Subtype data member.
bool IsSetMod(void) const
Check if a value has been assigned to Mod data member.
bool IsSetTaxname(void) const
preferred formal name Check if a value has been assigned to Taxname data member.
TMod & SetMod(void)
Assign a value to Mod data member.
void SetSubname(const TSubname &value)
Assign a value to Subname data member.
const TOrgname & GetOrgname(void) const
Get the Orgname member data.
@ eSubtype_nat_host
natural host of this specimen
@ eSubtype_metagenome_source
@ eSubtype_specimen_voucher
TProc & SetProc(void)
Select the variant.
TPmid & SetPmid(void)
Select the variant.
TBook & SetBook(void)
Select the variant.
Tdata & Set(void)
Assign a value to data member.
const TArticle & GetArticle(void) const
Get the variant data.
E_Choice Which(void) const
Which variant is currently selected.
TMan & SetMan(void)
Select the variant.
TSub & SetSub(void)
Select the variant.
TGen & SetGen(void)
Select the variant.
TJournal & SetJournal(void)
Select the variant.
TArticle & SetArticle(void)
Select the variant.
bool IsGen(void) const
Check if variant Gen is selected.
@ e_Gen
general or generic unparsed
@ e_Proc
proceedings of a meeting
@ e_Man
manuscript, thesis, or letter
@ eType_ncRNA
non-coding RNA; subsumes snRNA, scRNA, snoRNA
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
const struct ncbi::grid::netcache::search::fields::SIZE size
const CharType(& source)[N]
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
Miscellaneous common-use basic types and functionality.
void s_ChangeAuthorLastName(CAuth_list &auth_list)
void s_TestAuthorChanges(CPub &pub)
void s_ChangeNameTitle(CTitle &title)
#define ESUBTYPE_SHOULD_FAIL(name)
#define CHECK_COMMON_FIELD(o1, o2, c, Field, val1, val2)
CRef< CImprint > s_SetImprint(CPub &pub)
CRef< CPub > s_MakeJournalArticlePub()
void s_ChangeImprintNoMatch(CImprint &imp, int change_no)
CRef< CCit_book > s_MakeBook()
static void SetSubSource(objects::CBioSource &src, objects::CSubSource::TSubtype subtype, string val)
BOOST_AUTO_TEST_CASE(s_TestSubtypeMaps)
CRef< CPub > s_MakeBookChapterPub()
CRef< CAuth_list > s_SetAuthList(CPub &pub)
void s_ChangeImprintMatch(CImprint &imp, int change_no)
CRef< CCit_jour > s_MakeJournal()
void s_TestImprintChanges(CPub &pub)
void CheckBioProjectLocationVals(CBioSource::EGenome genome, const string &bioprojectlocation)
void s_ChangeJTATitle(CTitle &title)
void s_AddJTATitle(CTitle &title)
void s_AddNameTitle(CTitle &title)
CRef< CImprint > s_MakeImprint()
void s_ChangeTitle(CPub &pub)
void s_ChangeDate(CDate &date)
void CheckPlasmid(CBioSource &src)
void s_TestTitleChange(CPub &pub)
CRef< CAuth_list > s_MakeAuthList()
void CheckViruses(CBioSource &src)
void s_ChangeAuthorFirstName(CAuth_list &auth_list)
#define CHECK_COMMON_STRING_LIST(o1, o2, c, Field, val1, val2)
static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)
CRef< objects::CObjectManager > om
const char * expected_result
Utility stuff for more convenient using of Boost.Test library.
#define NCBITEST_CHECK(P)
static bool ambig(char c)
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