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Searched refs:taxid_list (Results 1 – 13 of 13) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/seqdb_reader/
H A Dseqdb_lmdb_unit_test.cpp308 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
309 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
328 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
329 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
346 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
366 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
367 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
382 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
441 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
442 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/seqdb_reader/
H A Dseqdb_lmdb_unit_test.cpp308 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
309 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
328 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
329 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
346 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
366 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
367 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
382 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
441 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in BOOST_AUTO_TEST_CASE() local
442 taxid_list->AddTaxIds(tax_ids); in BOOST_AUTO_TEST_CASE()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastdb/unit_test/
H A Ddefline_unit_test.cpp285 list<int> taxid_list; // initially empty in BOOST_AUTO_TEST_CASE() local
288 taxid_list.push_back(200003); in BOOST_AUTO_TEST_CASE()
289 taxid_list.push_back(200002); in BOOST_AUTO_TEST_CASE()
290 taxid_list.push_back(200001); in BOOST_AUTO_TEST_CASE()
292 def_line.SetLinks() = taxid_list; in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/
H A Dseqdb_lmdb.cpp656 inline void GetTaxIdListForOid(blastdb::TOid oid, vector<TTaxId> & taxid_list);
663 void CLookupTaxIds::GetTaxIdListForOid(blastdb::TOid oid, vector<TTaxId> & taxid_list) in GetTaxIdListForOid() argument
665 taxid_list.clear(); in GetTaxIdListForOid()
671 taxid_list.push_back(TAX_ID_FROM(Int4, *begin)); in GetTaxIdListForOid()
711 vector<TTaxId> taxid_list; in GetTaxIdsForOids() local
712 lookup.GetTaxIdListForOid(oids[i], taxid_list); in GetTaxIdsForOids()
713 tax_ids.insert(taxid_list.begin(), taxid_list.end()); in GetTaxIdsForOids()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/
H A Dseqdb_lmdb.cpp656 inline void GetTaxIdListForOid(blastdb::TOid oid, vector<TTaxId> & taxid_list);
663 void CLookupTaxIds::GetTaxIdListForOid(blastdb::TOid oid, vector<TTaxId> & taxid_list) in GetTaxIdListForOid() argument
665 taxid_list.clear(); in GetTaxIdListForOid()
671 taxid_list.push_back(TAX_ID_FROM(Int4, *begin)); in GetTaxIdListForOid()
711 vector<TTaxId> taxid_list; in GetTaxIdsForOids() local
712 lookup.GetTaxIdListForOid(oids[i], taxid_list); in GetTaxIdsForOids()
713 tax_ids.insert(taxid_list.begin(), taxid_list.end()); in GetTaxIdsForOids()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_options_builder.cpp401 list<TTaxId> taxid_list; in x_ProcessOneOption() local
403 taxid_list.push_back(TAX_ID_FROM(int, *it)); in x_ProcessOneOption()
405 m_NegativeTaxidList = taxid_list; in x_ProcessOneOption()
481 list<TTaxId> taxid_list; in x_ProcessOneOption() local
483 taxid_list.push_back(TAX_ID_FROM(int, *it)); in x_ProcessOneOption()
485 m_TaxidList = taxid_list; in x_ProcessOneOption()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_options_builder.cpp405 list<TTaxId> taxid_list; in x_ProcessOneOption() local
407 taxid_list.push_back(TAX_ID_FROM(int, *it)); in x_ProcessOneOption()
409 m_NegativeTaxidList = taxid_list; in x_ProcessOneOption()
485 list<TTaxId> taxid_list; in x_ProcessOneOption() local
487 taxid_list.push_back(TAX_ID_FROM(int, *it)); in x_ProcessOneOption()
489 m_TaxidList = taxid_list; in x_ProcessOneOption()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blastdb/
H A Dblastdb_aliastool.cpp469 string taxid_list = args[kArgTaxIdListFile].AsString(); in CreateAliasFile() local
470 if ( !taxid_list.empty() ) { in CreateAliasFile()
471 if ( !CFile(taxid_list).Exists() ) { in CreateAliasFile()
472 NCBI_THROW(CSeqDBException, eFileErr, taxid_list + " not found"); in CreateAliasFile()
477 seq_type, taxid_list, in CreateAliasFile()
H A Dblastdbcmd.cpp342 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in x_InitBlastDB_TaxIdList() local
343 taxid_list->AddTaxIds(m_TaxIdList); in x_InitBlastDB_TaxIdList()
344 m_BlastDb.Reset(new CSeqDBExpert(args[kArgDb].AsString(), seqtype, taxid_list.GetPointer())); in x_InitBlastDB_TaxIdList()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blastdb/
H A Dblastdb_aliastool.cpp469 string taxid_list = args[kArgTaxIdListFile].AsString(); in CreateAliasFile() local
470 if ( !taxid_list.empty() ) { in CreateAliasFile()
471 if ( !CFile(taxid_list).Exists() ) { in CreateAliasFile()
472 NCBI_THROW(CSeqDBException, eFileErr, taxid_list + " not found"); in CreateAliasFile()
477 seq_type, taxid_list, in CreateAliasFile()
H A Dblastdbcmd.cpp342 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in x_InitBlastDB_TaxIdList() local
343 taxid_list->AddTaxIds(m_TaxIdList); in x_InitBlastDB_TaxIdList()
344 m_BlastDb.Reset(new CSeqDBExpert(args[kArgDb].AsString(), seqtype, taxid_list.GetPointer())); in x_InitBlastDB_TaxIdList()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/
H A Dblast_args.cpp2343 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in s_GetTaxIDList() local
2344 taxid_list->AddTaxIds(tax_ids); in s_GetTaxIDList()
2346 sdb->SetNegativeGiList(taxid_list.GetPointer()); in s_GetTaxIDList()
2349 sdb->SetGiList(taxid_list.GetPointer()); in s_GetTaxIDList()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/
H A Dblast_args.cpp2343 CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList()); in s_GetTaxIDList() local
2344 taxid_list->AddTaxIds(tax_ids); in s_GetTaxIDList()
2346 sdb->SetNegativeGiList(taxid_list.GetPointer()); in s_GetTaxIDList()
2349 sdb->SetGiList(taxid_list.GetPointer()); in s_GetTaxIDList()