/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
H A D | biosource_tests.cpp | 124 …biosrc->GetOrg().IsSetOrgname() && biosrc->GetOrg().GetOrgname().IsSetMod() && biosrc->GetOrg().Is… 199 if (biosrc->GetOrg().IsSetOrgname() && biosrc->GetOrg().GetOrgname().IsSetMod()) { 241 …->GetOrg().IsSetTaxname() && NStr::StartsWith(biosrc->GetOrg().GetTaxname(), "Influenza A virus ")… 270 if (biosrc->GetOrg().IsSetOrgname() && biosrc->GetOrg().GetOrgname().IsSetMod()) { 450 if (!src.IsSetOrg() || !src.GetOrg().IsSetOrgMod() || !src.GetOrg().GetOrgname().IsSetMod()) { in SetCultureCollectionFromStrain() 878 if (src.IsSetOrg() && src.GetOrg().IsSetOrgname() && src.GetOrg().GetOrgname().IsSetMod()) { in HasAmplifiedWithSpeciesSpecificPrimerNote() 1374 GetOrgrefDifferences(first_biosrc.GetOrg(), second_biosrc.GetOrg(), diffs); in GetBiosourceDifferences() 1590 … if (biosrc->GetOrg().IsSetOrgname() && biosrc->GetOrg().GetOrgname().IsSetMod()) { 1821 …g() && biosrc->GetOrg().CanGetOrgname() && biosrc->GetOrg().GetOrgname().CanGetMod() && biosrc->Ge… 1879 if (bs.GetOrg().CanGetOrgname() && bs.GetOrg().GetOrgname().CanGetMod()) { in GetSrcQual() [all …]
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H A D | division_code_conflicts.cpp | 51 …g() && src->GetSource().GetOrg().IsSetOrgname() && src->GetSource().GetOrg().GetOrgname().IsSetDiv… 52 …m_Objs[kDivCodeConfl]["[n] bioseq[s] [has] division code " + src->GetSource().GetOrg().GetOrgname(…
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqfeat/ |
H A D | BioSource.cpp | 625 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetAttrib()) { in SetDisableStrainForwarding() 636 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetAttrib()) { in SetDisableStrainForwarding() 650 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetAttrib() in GetDisableStrainForwarding() 718 if (GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetName()) { in UpdateWithBioSample() 1318 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetLineage() in x_ShouldIgnoreNoteForBiosample() 1401 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetMod()) { in AutoFix() 1631 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetMod()) { in RemoveOrgMod() 1653 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetMod()) { in RemoveOrgMod() 1852 if (!IsSetOrg() || !GetOrg().IsSetOrgname() || !GetOrg().GetOrgname().IsSetLineage()) { in AllowSexQualifier() 1884 if (!IsSetOrg() || !GetOrg().IsSetOrgname() || !GetOrg().GetOrgname().IsSetLineage()) { in AllowMatingTypeQualifier() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqfeat/ |
H A D | BioSource.cpp | 625 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetAttrib()) { in SetDisableStrainForwarding() 636 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetAttrib()) { in SetDisableStrainForwarding() 650 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetAttrib() in GetDisableStrainForwarding() 718 if (GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetName()) { in UpdateWithBioSample() 1318 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetLineage() in x_ShouldIgnoreNoteForBiosample() 1401 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetMod()) { in AutoFix() 1631 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetMod()) { in RemoveOrgMod() 1653 if (IsSetOrg() && GetOrg().IsSetOrgname() && GetOrg().GetOrgname().IsSetMod()) { in RemoveOrgMod() 1852 if (!IsSetOrg() || !GetOrg().IsSetOrgname() || !GetOrg().GetOrgname().IsSetLineage()) { in AllowSexQualifier() 1884 if (!IsSetOrg() || !GetOrg().IsSetOrgname() || !GetOrg().GetOrgname().IsSetLineage()) { in AllowMatingTypeQualifier() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/unit_test/ |
H A D | unit_test_source_edit.cpp | 122 FOR_EACH_DBXREF_ON_ORGREF ( db, src.GetOrg() ) { in BOOST_AUTO_TEST_CASE() 152 FOR_EACH_DBXREF_ON_ORGREF ( db, src.GetOrg() ) { in BOOST_AUTO_TEST_CASE() 162 BOOST_CHECK_EQUAL(src.GetOrg().IsSetSyn(), false); in BOOST_AUTO_TEST_CASE() 207 BOOST_CHECK_EQUAL(common->GetOrg().GetTaxname(), "Pneumocystis carinii"); in BOOST_AUTO_TEST_CASE() 208 BOOST_CHECK_EQUAL(common->GetOrg().GetTaxId(), TAX_ID_CONST(4754)); in BOOST_AUTO_TEST_CASE() 228 BOOST_CHECK_EQUAL(common->GetOrg().GetTaxname(), "Eremothecium gossypii ATCC 10895"); in BOOST_AUTO_TEST_CASE() 229 BOOST_CHECK_EQUAL(common->GetOrg().GetTaxId(), TAX_ID_CONST(284811)); in BOOST_AUTO_TEST_CASE() 245 BOOST_CHECK_EQUAL(common->GetOrg().GetTaxId(), TAX_ID_CONST(99287)); in BOOST_AUTO_TEST_CASE() 247 BOOST_CHECK_EQUAL(s_HasOrgMod(common->GetOrg(), COrgMod::eSubtype_strain, "LT2"), true); in BOOST_AUTO_TEST_CASE() 257 BOOST_CHECK_EQUAL(common->GetOrg().GetTaxId(), TAX_ID_CONST(90371)); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
H A D | source_edit.cpp | 56 if (src.IsSetOrg() && src.GetOrg().IsSetCommon()) { in BEGIN_SCOPE() 60 if (src.IsSetOrg() && src.GetOrg().IsSetSyn()) { in BEGIN_SCOPE() 75 if (src.IsSetOrg() && src.GetOrg().IsSetOrgname() in RemoveMod() 76 && src.GetOrg().GetOrgname().IsSetMod()) { in RemoveMod() 86 if (src.GetOrg().GetOrgname().GetMod().empty()) { in RemoveMod() 96 if (src.IsSetOrg() && src.GetOrg().IsSetDb()) { in RemoveTaxId() 106 if (src.GetOrg().GetDb().empty()) { in RemoveTaxId() 117 org->Assign(reply.GetData().GetOrg()); in s_ProcessReply() 176 o1->Assign(src1.GetOrg()); in MakeCommonBioSource() 179 o2->Assign(src2.GetOrg()); in MakeCommonBioSource() [all …]
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H A D | mail_report.cpp | 71 if (di && di->GetSource().IsSetOrg() && di->GetSource().GetOrg().IsSetTaxname()) { in BEGIN_SCOPE() 72 taxname = di->GetSource().GetOrg().GetTaxname(); in BEGIN_SCOPE() 106 if (di->GetSource().GetOrg().IsSetTaxname()) { in MakeMailReportPostReport() 107 taxname = di->GetSource().GetOrg().GetTaxname(); in MakeMailReportPostReport() 109 org->Assign(di->GetSource().GetOrg()); in MakeMailReportPostReport() 138 … if ((*reply_it)->GetData().IsSetOrg() && (*reply_it)->GetData().GetOrg().IsSetDb()) { in MakeMailReportPostReport() 139 ITERATE(COrg_ref::TDb, db_it, (*reply_it)->GetData().GetOrg().GetDb()) { in MakeMailReportPostReport()
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H A D | autodef_with_tax.cpp | 119 TTaxId taxid = desc_ci->GetSource().GetOrg().GetTaxId(); in GetDocsumOrgDescription() 136 && (*reply_it)->GetData().GetOrg().IsSetTaxname()) { in GetDocsumOrgDescription() 137 joined_org = (*reply_it)->GetData().GetOrg().GetTaxname(); in GetDocsumOrgDescription()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
H A D | source_edit.cpp | 56 if (src.IsSetOrg() && src.GetOrg().IsSetCommon()) { in BEGIN_SCOPE() 60 if (src.IsSetOrg() && src.GetOrg().IsSetSyn()) { in BEGIN_SCOPE() 75 if (src.IsSetOrg() && src.GetOrg().IsSetOrgname() in RemoveMod() 76 && src.GetOrg().GetOrgname().IsSetMod()) { in RemoveMod() 86 if (src.GetOrg().GetOrgname().GetMod().empty()) { in RemoveMod() 96 if (src.IsSetOrg() && src.GetOrg().IsSetDb()) { in RemoveTaxId() 106 if (src.GetOrg().GetDb().empty()) { in RemoveTaxId() 117 org->Assign(reply.GetData().GetOrg()); in s_ProcessReply() 176 o1->Assign(src1.GetOrg()); in MakeCommonBioSource() 179 o2->Assign(src2.GetOrg()); in MakeCommonBioSource() [all …]
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H A D | mail_report.cpp | 71 if (di && di->GetSource().IsSetOrg() && di->GetSource().GetOrg().IsSetTaxname()) { in BEGIN_SCOPE() 72 taxname = di->GetSource().GetOrg().GetTaxname(); in BEGIN_SCOPE() 106 if (di->GetSource().GetOrg().IsSetTaxname()) { in MakeMailReportPostReport() 107 taxname = di->GetSource().GetOrg().GetTaxname(); in MakeMailReportPostReport() 109 org->Assign(di->GetSource().GetOrg()); in MakeMailReportPostReport() 138 … if ((*reply_it)->GetData().IsSetOrg() && (*reply_it)->GetData().GetOrg().IsSetDb()) { in MakeMailReportPostReport() 139 ITERATE(COrg_ref::TDb, db_it, (*reply_it)->GetData().GetOrg().GetDb()) { in MakeMailReportPostReport()
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H A D | autodef_with_tax.cpp | 119 TTaxId taxid = desc_ci->GetSource().GetOrg().GetTaxId(); in GetDocsumOrgDescription() 136 && (*reply_it)->GetData().GetOrg().IsSetTaxname()) { in GetDocsumOrgDescription() 137 joined_org = (*reply_it)->GetData().GetOrg().GetTaxname(); in GetDocsumOrgDescription()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
H A D | autodef_source_desc.cpp | 55 if (bs.CanGetOrg() && bs.GetOrg().CanGetTaxname()) { in BEGIN_SCOPE() 56 m_DescStrings.push_back (bs.GetOrg().GetTaxname()); in BEGIN_SCOPE() 58 if (bs.CanGetOrg() && bs.GetOrg().CanGetOrgname() && bs.GetOrg().GetOrgname().CanGetMod()) { in BEGIN_SCOPE() 59 ITERATE (COrgName::TMod, modI, bs.GetOrg().GetOrgname().GetMod()) { in BEGIN_SCOPE() 201 return m_BS.GetOrg().GetTaxname(); in GetComboDescription() 213 … if (m_BS.CanGetOrg() && m_BS.GetOrg().CanGetOrgname() && m_BS.GetOrg().GetOrgname().IsSetMod()) { in GetAvailableModifiers() 214 ITERATE (COrgName::TMod, modI, m_BS.GetOrg().GetOrgname().GetMod()) { in GetAvailableModifiers() 241 string tax_name = m_BS.GetOrg().GetTaxname(); in IsTrickyHIV() 260 … if (m_BS.CanGetOrg() && m_BS.GetOrg().CanGetOrgname() && m_BS.GetOrg().GetOrgname().IsSetMod()) { in IsTrickyHIV() 261 ITERATE (COrgName::TMod, modI, m_BS.GetOrg().GetOrgname().GetMod()) { in IsTrickyHIV()
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H A D | autodef_mod_combo.cpp | 328 if (!src.IsSetOrg() || !src.GetOrg().IsSetOrgname() || !src.GetOrg().GetOrgname().IsSetMod()) { in x_BioSourceHasOrgMod() 331 ITERATE(COrgName::TMod, it, src.GetOrg().GetOrgname().GetMod()) { in x_BioSourceHasOrgMod() 419 … if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetOrgname() || !bsrc.GetOrg().GetOrgname().IsSetMod()) { in x_AddOrgModString() 481 if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetTaxname()) { in x_AddHIVModifiers() 484 string source_description = bsrc.GetOrg().GetTaxname(); in x_AddHIVModifiers() 638 …bsrc.IsSetOrg() && bsrc.GetOrg().IsSetTaxname() && NStr::StartsWith(bsrc.GetOrg().GetTaxname(), "I… in x_AddRequiredSubSourceModifiers() 646 … if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetOrgname() || !bsrc.GetOrg().GetOrgname().IsSetMod()) { in x_HasTypeStrainComment() 650 ITERATE(COrgName::TMod, it, bsrc.GetOrg().GetOrgname().GetMod()) { in x_HasTypeStrainComment() 791 source_description += bsrc.GetOrg().GetTaxname(); in GetSourceDescriptionString() 858 for (auto& it : bsrc.GetOrg().GetOrgname().GetMod()) { in GetSourceDescriptionString() [all …]
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H A D | seqtitle.cpp | 329 && source->GetOrg().IsSetTaxname()) { in GetTitle() 530 org = &source->GetOrg(); in GetTitle() 534 org = &it->GetOrg(); in GetTitle() 713 && source->GetOrg().IsSetTaxname()) { in GetTitle() 853 org = &source->GetOrg(); in GetTitle() 857 org = &desc->GetOrg(); in GetTitle() 925 const COrg_ref& org = source.GetOrg(); in s_TitleFromBioSource() 1082 if (source.GetOrg().IsSetTaxname()) { in x_TitleFromChromosome() 1083 name = source.GetOrg().GetTaxname(); in x_TitleFromChromosome() 1280 org = &it->GetSource().GetOrg(); in s_TitleFromProtein() [all …]
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H A D | autodef_source_group.cpp | 343 if (bsrc.CanGetOrg() && bsrc.GetOrg().CanGetTaxname()) { in GetDefaultExcludeSp() 344 string taxname1 = bsrc.GetOrg().GetTaxname(); in GetDefaultExcludeSp() 348 if (bsrc2.CanGetOrg() && bsrc2.GetOrg().CanGetTaxname()) { in GetDefaultExcludeSp() 349 string taxname2 = bsrc.GetOrg().GetTaxname(); in GetDefaultExcludeSp()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/ |
H A D | autodef_source_desc.cpp | 55 if (bs.CanGetOrg() && bs.GetOrg().CanGetTaxname()) { in BEGIN_SCOPE() 56 m_DescStrings.push_back (bs.GetOrg().GetTaxname()); in BEGIN_SCOPE() 58 if (bs.CanGetOrg() && bs.GetOrg().CanGetOrgname() && bs.GetOrg().GetOrgname().CanGetMod()) { in BEGIN_SCOPE() 59 ITERATE (COrgName::TMod, modI, bs.GetOrg().GetOrgname().GetMod()) { in BEGIN_SCOPE() 201 return m_BS.GetOrg().GetTaxname(); in GetComboDescription() 213 … if (m_BS.CanGetOrg() && m_BS.GetOrg().CanGetOrgname() && m_BS.GetOrg().GetOrgname().IsSetMod()) { in GetAvailableModifiers() 214 ITERATE (COrgName::TMod, modI, m_BS.GetOrg().GetOrgname().GetMod()) { in GetAvailableModifiers() 241 string tax_name = m_BS.GetOrg().GetTaxname(); in IsTrickyHIV() 260 … if (m_BS.CanGetOrg() && m_BS.GetOrg().CanGetOrgname() && m_BS.GetOrg().GetOrgname().IsSetMod()) { in IsTrickyHIV() 261 ITERATE (COrgName::TMod, modI, m_BS.GetOrg().GetOrgname().GetMod()) { in IsTrickyHIV()
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H A D | autodef_mod_combo.cpp | 328 if (!src.IsSetOrg() || !src.GetOrg().IsSetOrgname() || !src.GetOrg().GetOrgname().IsSetMod()) { in x_BioSourceHasOrgMod() 331 ITERATE(COrgName::TMod, it, src.GetOrg().GetOrgname().GetMod()) { in x_BioSourceHasOrgMod() 419 … if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetOrgname() || !bsrc.GetOrg().GetOrgname().IsSetMod()) { in x_AddOrgModString() 481 if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetTaxname()) { in x_AddHIVModifiers() 484 string source_description = bsrc.GetOrg().GetTaxname(); in x_AddHIVModifiers() 638 …bsrc.IsSetOrg() && bsrc.GetOrg().IsSetTaxname() && NStr::StartsWith(bsrc.GetOrg().GetTaxname(), "I… in x_AddRequiredSubSourceModifiers() 646 … if (!bsrc.IsSetOrg() || !bsrc.GetOrg().IsSetOrgname() || !bsrc.GetOrg().GetOrgname().IsSetMod()) { in x_HasTypeStrainComment() 650 ITERATE(COrgName::TMod, it, bsrc.GetOrg().GetOrgname().GetMod()) { in x_HasTypeStrainComment() 791 source_description += bsrc.GetOrg().GetTaxname(); in GetSourceDescriptionString() 858 for (auto& it : bsrc.GetOrg().GetOrgname().GetMod()) { in GetSourceDescriptionString() [all …]
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H A D | seqtitle.cpp | 329 && source->GetOrg().IsSetTaxname()) { in GetTitle() 530 org = &source->GetOrg(); in GetTitle() 534 org = &it->GetOrg(); in GetTitle() 713 && source->GetOrg().IsSetTaxname()) { in GetTitle() 853 org = &source->GetOrg(); in GetTitle() 857 org = &desc->GetOrg(); in GetTitle() 925 const COrg_ref& org = source.GetOrg(); in s_TitleFromBioSource() 1082 if (source.GetOrg().IsSetTaxname()) { in x_TitleFromChromosome() 1083 name = source.GetOrg().GetTaxname(); in x_TitleFromChromosome() 1280 org = &it->GetSource().GetOrg(); in s_TitleFromProtein() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | tax_validation_and_cleanup.cpp | 166 …m_HostLineage = reply.GetData().GetOrg().IsSetLineage() ? reply.GetData().GetOrg().GetLineage() : … in AddReply() 174 …m_HostLineage = reply.GetData().GetOrg().IsSetLineage() ? reply.GetData().GetOrg().GetLineage() : … in AddReply() 183 …m_HostLineage = reply.GetData().GetOrg().IsSetLineage() ? reply.GetData().GetOrg().GetLineage() : … in AddReply() 189 …m_HostLineage = reply.GetData().GetOrg().IsSetLineage() ? reply.GetData().GetOrg().GetLineage() : … in AddReply() 193 …m_HostLineage = reply.GetData().GetOrg().IsSetLineage() ? reply.GetData().GetOrg().GetLineage() : … in AddReply() 386 const COrg_ref& org = desc->GetSource().GetOrg(); in AddDesc() 418 const COrg_ref& org = feat->GetData().GetBiosrc().GetOrg(); in AddFeat() 719 const COrg_ref& org = (*desc_it)->GetSource().GetOrg(); in GetTaxonomyLookupRequest() 952 cpy->Assign((*reply_it)->GetData().GetOrg()); in AdjustOrgRefsWithTaxLookupReply() 956 (*reply_it)->GetError().GetOrg().IsSetTaxname() && in AdjustOrgRefsWithTaxLookupReply() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/biosample_chk/ |
H A D | src_table_column.cpp | 80 if (in_out_bioSource.IsSetOrg() && in_out_bioSource.GetOrg().IsSetTaxname()) { in GetFromBioSource() 81 val = in_out_bioSource.GetOrg().GetTaxname(); in GetFromBioSource() 101 if (in_out_bioSource.IsSetOrg() && in_out_bioSource.GetOrg().IsSetDb()) { in ClearInBioSource() 120 int taxid = in_out_bioSource.GetOrg().GetTaxId(); in GetFromBioSource() 227 …f (in_out_bioSource.IsSetOrg() && in_out_bioSource.GetOrg().IsSetOrgname() && in_out_bioSource.Get… in ClearInBioSource() 244 …f (in_out_bioSource.IsSetOrg() && in_out_bioSource.GetOrg().IsSetOrgname() && in_out_bioSource.Get… in GetFromBioSource() 246 while (it != in_out_bioSource.GetOrg().GetOrgname().GetMod().end()) { in GetFromBioSource() 594 if (src.GetOrg().IsSetTaxname()) { in GetSourceFields() 597 src.GetOrg().GetTaxId(); in GetSourceFields() 602 if (src.GetOrg().IsSetOrgname() && src.GetOrg().GetOrgname().IsSetMod()) { in GetSourceFields() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/taxon1/unit_test/ |
H A D | taxon1_unit_test.cpp | 137 BOOST_REQUIRE( p->GetOrg().IsSetTaxname() != false ); in BOOST_AUTO_TEST_CASE() 349 BOOST_CHECK( t1p->GetOrg().IsSetOrgname() != false ); in BOOST_AUTO_TEST_CASE() 350 string s = s_OrgRef2String( t1p->GetOrg() ); in BOOST_AUTO_TEST_CASE() 368 BOOST_CHECK( t1p->GetOrg().IsSetOrgname() != false ); in BOOST_AUTO_TEST_CASE() 402 BOOST_CHECK( t2p->GetOrg().IsSetOrgname() != false ); in BOOST_AUTO_TEST_CASE() 406 string s = s_OrgRef2String( t2p->GetOrg() ); in BOOST_AUTO_TEST_CASE() 416 BOOST_CHECK( t2p->GetOrg().IsSetOrgname() != false ); in BOOST_AUTO_TEST_CASE() 420 s = s_OrgRef2String( t2p->GetOrg() ); in BOOST_AUTO_TEST_CASE() 435 BOOST_CHECK( ct2p->GetOrg().IsSetOrgname() != false ); in BOOST_AUTO_TEST_CASE() 439 string s = s_OrgRef2String( ct2p->GetOrg() ); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/biosample_chk/unit_test/ |
H A D | unit_test_biosample_chk.cpp | 142 BOOST_CHECK_EQUAL(test_src->GetOrg().GetTaxname(), "B"); in BOOST_AUTO_TEST_CASE() 156 BOOST_CHECK_EQUAL(test_src->GetOrg().IsSetOrgMod(), false); in BOOST_AUTO_TEST_CASE() 337 BOOST_CHECK_EQUAL(src.GetOrg().GetDb().front()->GetTag().GetId(), 123); in BOOST_AUTO_TEST_CASE() 379 BOOST_CHECK_EQUAL(src->GetOrg().GetDb().size(), 2); in BOOST_AUTO_TEST_CASE() 402 BOOST_CHECK_EQUAL(src->GetOrg().IsSetOrgMod(), false); in BOOST_AUTO_TEST_CASE() 415 BOOST_CHECK_EQUAL(src->GetOrg().IsSetOrgMod(), false); in BOOST_AUTO_TEST_CASE() 434 smpl->SetOrg().SetTaxname(src->GetOrg().GetTaxname()); in BOOST_AUTO_TEST_CASE() 469 BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().size(), 2); in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
H A D | cuTaxClient.cpp | 156 org = &((*j)->GetOrg()); in GetTaxIDFromBioseq() 158 org = &((*j)->GetSource().GetOrg()); in GetTaxIDFromBioseq() 218 if (data->IsSetOrg() && data->GetOrg().IsSetTaxname()) { in GetTaxNameForTaxID() 219 taxName = data->GetOrg().GetTaxname(); in GetTaxNameForTaxID()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/biosample_util/unit_test/ |
H A D | unit_test_biosample_util.cpp | 164 BOOST_CHECK_EQUAL(test_src->GetOrg().GetTaxname(), "B"); in BOOST_AUTO_TEST_CASE() 178 BOOST_CHECK_EQUAL(test_src->GetOrg().IsSetOrgMod(), false); in BOOST_AUTO_TEST_CASE() 364 BOOST_CHECK_EQUAL(src.GetOrg().GetDb().front()->GetTag().GetId(), 123); in BOOST_AUTO_TEST_CASE() 406 BOOST_CHECK_EQUAL(src->GetOrg().GetDb().size(), 2); in BOOST_AUTO_TEST_CASE() 429 BOOST_CHECK_EQUAL(src->GetOrg().IsSetOrgMod(), false); in BOOST_AUTO_TEST_CASE() 442 BOOST_CHECK_EQUAL(src->GetOrg().IsSetOrgMod(), false); in BOOST_AUTO_TEST_CASE() 461 smpl->SetOrg().SetTaxname(src->GetOrg().GetTaxname()); in BOOST_AUTO_TEST_CASE() 496 BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().size(), 2); in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
H A D | fta_src.cpp | 1939 if (bio.GetOrg().CanGetOrgname() && bio.GetOrg().GetOrgname().CanGetMod()) in CheckQualsInSourceFeat() 2184 bio.GetOrg().GetOrgname().CanGetDiv() && in UpdateRawBioSource() 2191 if (bio.GetOrg().CanGetTaxname() && in UpdateRawBioSource() 2192 !bio.GetOrg().GetTaxname().empty()) in UpdateRawBioSource() 2365 bio_src.GetOrg().GetTaxname().empty()) in CompareDescrFeatSources() 2373 if (bio_src.GetOrg().IsSetCommon()) in CompareDescrFeatSources() 2426 if (sfbp->bio_src->GetOrg().IsSetOrgname() && in CheckSourceLineage() 2464 sfbp->bio_src->GetOrg().GetTaxname().empty()) in PropogateSuppliedLineage() 2489 !bio_src.GetOrg().IsSetTaxname() || bio_src.GetOrg().GetTaxname().empty() || in PropogateSuppliedLineage() 3449 if (bio.GetOrg().IsSetTaxname() && in CheckMetagenome() [all …]
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