/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/ |
H A D | seq_id_mapper.cpp | 100 if ( !idh ) { in x_GetTree() 103 else if ( idh.IsGi() ) { in x_GetTree() 107 return idh.m_Info->GetTree(); in x_GetTree() 130 return x_GetTree(idh).HaveMatch(idh); in HaveMatchingHandles() 137 x_GetTree(idh).FindMatch(idh, h_set); in GetMatchingHandles() 143 return x_GetTree(idh).HaveReverseMatch(idh); in HaveReverseMatch() 150 x_GetTree(idh).FindReverseMatch(idh, h_set); in GetReverseMatchingHandles() 157 if ( HaveMatchingHandles(idh) ) { in HaveMatchingHandles() 190 GetMatchingHandles(idh, h_set); in GetMatchingHandles() 209 tree->FindMatch(idh, h_set); in GetMatchingHandles() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seq/ |
H A D | seq_id_mapper.cpp | 100 if ( !idh ) { in x_GetTree() 103 else if ( idh.IsGi() ) { in x_GetTree() 107 return idh.m_Info->GetTree(); in x_GetTree() 130 return x_GetTree(idh).HaveMatch(idh); in HaveMatchingHandles() 137 x_GetTree(idh).FindMatch(idh, h_set); in GetMatchingHandles() 143 return x_GetTree(idh).HaveReverseMatch(idh); in HaveReverseMatch() 150 x_GetTree(idh).FindReverseMatch(idh, h_set); in GetReverseMatchingHandles() 157 if ( HaveMatchingHandles(idh) ) { in HaveMatchingHandles() 190 GetMatchingHandles(idh, h_set); in GetMatchingHandles() 209 tree->FindMatch(idh, h_set); in GetMatchingHandles() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/data_loaders/genbank/ |
H A D | psg_loader.cpp | 138 CPSGDataLoader::GetRecords(const CSeq_id_Handle& idh, in GetRecords() argument 205 m_Impl->GetIds(idh, ids); in GetIds() 210 CPSGDataLoader::GetGiFound(const CSeq_id_Handle& idh) in GetGiFound() argument 212 return m_Impl->GetGi(idh); in GetGiFound() 217 CPSGDataLoader::GetAccVerFound(const CSeq_id_Handle& idh) in GetAccVerFound() argument 219 return m_Impl->GetAccVer(idh); in GetAccVerFound() 225 auto taxid = m_Impl->GetTaxId(idh); in GetTaxId() 232 return m_Impl->GetSequenceLength(idh); in GetSequenceLength() 239 return m_Impl->GetSequenceHash(idh); in GetSequenceHashFound() 246 return m_Impl->GetSequenceType(idh); in GetSequenceTypeFound() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/data_loaders/genbank/impl/ |
H A D | psg_loader_impl.hpp | 115 void GetIds(const CSeq_id_Handle& idh, TIds& ids); 116 void GetIdsOnce(const CSeq_id_Handle& idh, TIds& ids); 117 CDataLoader::SGiFound GetGi(const CSeq_id_Handle& idh); 121 TTaxId GetTaxId(const CSeq_id_Handle& idh); 122 TTaxId GetTaxIdOnce(const CSeq_id_Handle& idh); 123 TSeqPos GetSequenceLength(const CSeq_id_Handle& idh); 124 TSeqPos GetSequenceLengthOnce(const CSeq_id_Handle& idh); 129 int GetSequenceState(const CSeq_id_Handle& idh); 130 int GetSequenceStateOnce(const CSeq_id_Handle& idh); 138 CRef<CPsgBlobId> GetBlobId(const CSeq_id_Handle& idh); [all …]
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/dports/devel/idutils/idutils-4.6/src/ |
H A D | fid.c | 43 struct idhead idh; variable 102 idh.idh_file_name = 0; in main() 128 idh.idh_file_name = optarg; in main() 159 idh.idh_file_name = locate_id_file_name (idh.idh_file_name); in main() 160 if (idh.idh_file_name == 0) in main() 163 init_idh_obstacks (&idh); in main() 164 init_idh_tables (&idh); in main() 170 members_0 = read_id_file (idh.idh_file_name, &idh); in main() 181 hits_buf = xmalloc (idh.idh_buf_size); in main() 182 fseek (idh.idh_FILE, idh.idh_tokens_offset, SEEK_SET); in main() [all …]
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H A D | fnid.c | 41 struct idhead idh; variable 88 idh.idh_file_name = 0; in main() 113 idh.idh_file_name = optarg; in main() 153 idh.idh_file_name = locate_id_file_name (idh.idh_file_name); in main() 154 if (idh.idh_file_name == 0) in main() 157 init_idh_obstacks (&idh); in main() 158 init_idh_tables (&idh); in main() 162 struct file_link **members = read_id_file (idh.idh_file_name, &idh); in main() 163 struct file_link **members_N = &members[idh.idh_files]; in main() 164 struct file_link **flinkv_0 = xmalloc (sizeof(struct file_link *) * (idh.idh_files + 1)); in main()
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H A D | lid.c | 149 struct idhead idh; variable 292 idh.idh_file_name = 0; in main() 437 idh.idh_file_name = locate_id_file_name (idh.idh_file_name); in main() 441 init_idh_obstacks (&idh); in main() 442 init_idh_tables (&idh); in main() 448 members_0 = read_id_file (idh.idh_file_name, &idh); in main() 475 fclose (idh.idh_FILE); in main() 916 fseek (idh.idh_FILE, idh.idh_tokens_offset, SEEK_SET); in query_regexp() 981 fseek (idh.idh_FILE, idh.idh_tokens_offset, SEEK_SET); in query_number() 1032 fseek (idh.idh_FILE, idh.idh_tokens_offset, SEEK_SET); in query_ambiguous_prefix() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/wgs/test/ |
H A D | test_wgs_loader.cpp | 633 if ( idh == main_idh ) { in sx_CheckSeq() 1028 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1044 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1060 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1082 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1096 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1112 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1128 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1144 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() 1180 sx_ReportState(bsh, idh); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | data_loader.cpp | 134 return GetRecords(idh, choice); in GetRecordsNoBlobState() 170 return GetRecords(idh, eOrphanAnnot); in GetOrphanAnnotRecords() 178 return GetRecords(idh, eExtAnnot); in GetExternalAnnotRecords() 318 GetIds(idh, ids); in SequenceExists() 327 GetIds(idh, ids); in GetAccVer() 347 ret.acc_ver = GetAccVer(idh); in GetAccVerFound() 371 GetIds(idh, ids); in GetGi() 390 ret.gi = GetGi(idh); in GetGiFound() 414 GetIds(idh, ids); in GetLabel() 476 ret.type = GetSequenceType(idh); in GetSequenceTypeFound() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | data_loader.cpp | 134 return GetRecords(idh, choice); in GetRecordsNoBlobState() 170 return GetRecords(idh, eOrphanAnnot); in GetOrphanAnnotRecords() 178 return GetRecords(idh, eExtAnnot); in GetExternalAnnotRecords() 318 GetIds(idh, ids); in SequenceExists() 327 GetIds(idh, ids); in GetAccVer() 347 ret.acc_ver = GetAccVer(idh); in GetAccVerFound() 371 GetIds(idh, ids); in GetGi() 390 ret.gi = GetGi(idh); in GetGiFound() 414 GetIds(idh, ids); in GetLabel() 476 ret.type = GetSequenceType(idh); in GetSequenceTypeFound() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/data_loaders/genbank/ |
H A D | psg_loader.hpp | 70 virtual TBlobId GetBlobId(const CSeq_id_Handle& idh) override; 78 virtual TTSE_LockSet GetOrphanAnnotRecordsNA(const CSeq_id_Handle& idh, 81 virtual TTSE_LockSet GetExternalAnnotRecordsNA(const CSeq_id_Handle& idh, 93 virtual void GetIds(const CSeq_id_Handle& idh, TIds& ids) override; 94 virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle& idh) override; 95 virtual SGiFound GetGiFound(const CSeq_id_Handle& idh) override; 96 virtual TTaxId GetTaxId(const CSeq_id_Handle& idh) override; 97 virtual TSeqPos GetSequenceLength(const CSeq_id_Handle& idh) override; 98 virtual SHashFound GetSequenceHashFound(const CSeq_id_Handle& idh) override; 100 virtual int GetSequenceState(const CSeq_id_Handle& idh) override; [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/genbank/ |
H A D | psg_loader.cpp | 214 CPSGDataLoader::GetRecords(const CSeq_id_Handle& idh, in GetRecords() argument 333 m_Impl->GetIds(idh, ids); in GetIds() 338 CPSGDataLoader::GetGiFound(const CSeq_id_Handle& idh) in GetGiFound() argument 340 return m_Impl->GetGi(idh); in GetGiFound() 345 CPSGDataLoader::GetAccVerFound(const CSeq_id_Handle& idh) in GetAccVerFound() argument 347 return m_Impl->GetAccVer(idh); in GetAccVerFound() 353 auto taxid = m_Impl->GetTaxId(idh); in GetTaxId() 360 return m_Impl->GetSequenceLength(idh); in GetSequenceLength() 367 return m_Impl->GetSequenceHash(idh); in GetSequenceHashFound() 374 return m_Impl->GetSequenceType(idh); in GetSequenceTypeFound() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/ |
H A D | data_loader.hpp | 245 virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh, 288 virtual void GetIds(const CSeq_id_Handle& idh, TIds& ids); 291 bool SequenceExists(const CSeq_id_Handle& idh); 297 virtual CSeq_id_Handle GetAccVer(const CSeq_id_Handle& idh); 312 virtual TGi GetGi(const CSeq_id_Handle& idh); 321 virtual SGiFound GetGiFound(const CSeq_id_Handle& idh); 326 virtual string GetLabel(const CSeq_id_Handle& idh); 331 virtual TTaxId GetTaxId(const CSeq_id_Handle& idh); 356 virtual int GetSequenceState(const CSeq_id_Handle& idh); 361 virtual int GetSequenceHash(const CSeq_id_Handle& idh); [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/ |
H A D | data_loader.hpp | 245 virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh, 288 virtual void GetIds(const CSeq_id_Handle& idh, TIds& ids); 291 bool SequenceExists(const CSeq_id_Handle& idh); 297 virtual CSeq_id_Handle GetAccVer(const CSeq_id_Handle& idh); 312 virtual TGi GetGi(const CSeq_id_Handle& idh); 321 virtual SGiFound GetGiFound(const CSeq_id_Handle& idh); 326 virtual string GetLabel(const CSeq_id_Handle& idh); 331 virtual TTaxId GetTaxId(const CSeq_id_Handle& idh); 356 virtual int GetSequenceState(const CSeq_id_Handle& idh); 361 virtual int GetSequenceHash(const CSeq_id_Handle& idh); [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/wgs/ |
H A D | wgsloader.cpp | 195 CWGSDataLoader::GetRecords(const CSeq_id_Handle& idh, in GetRecords() argument 263 m_Impl->GetIds(idh, ids); in GetIds() 268 CWGSDataLoader::GetAccVerFound(const CSeq_id_Handle& idh) in GetAccVerFound() argument 270 return m_Impl->GetAccVer(idh); in GetAccVerFound() 275 CWGSDataLoader::GetGiFound(const CSeq_id_Handle& idh) in GetGiFound() argument 277 return m_Impl->GetGi(idh); in GetGiFound() 281 TTaxId CWGSDataLoader::GetTaxId(const CSeq_id_Handle& idh) in GetTaxId() argument 283 return m_Impl->GetTaxId(idh); in GetTaxId() 289 return m_Impl->GetSequenceLength(idh); in GetSequenceLength() 296 return m_Impl->GetSequenceHash(idh); in GetSequenceHashFound() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/data_loaders/genbank/ |
H A D | psg_loader.hpp | 105 virtual TBlobId GetBlobId(const CSeq_id_Handle& idh) override; 113 virtual TTSE_LockSet GetOrphanAnnotRecordsNA(const CSeq_id_Handle& idh, 116 virtual TTSE_LockSet GetExternalAnnotRecordsNA(const CSeq_id_Handle& idh, 128 virtual void GetIds(const CSeq_id_Handle& idh, TIds& ids) override; 129 virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle& idh) override; 130 virtual SGiFound GetGiFound(const CSeq_id_Handle& idh) override; 131 virtual TTaxId GetTaxId(const CSeq_id_Handle& idh) override; 132 virtual TSeqPos GetSequenceLength(const CSeq_id_Handle& idh) override; 133 virtual SHashFound GetSequenceHashFound(const CSeq_id_Handle& idh) override; 135 virtual int GetSequenceState(const CSeq_id_Handle& idh) override; [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/hgvs/ |
H A D | id_resolver.cpp | 29 CSeq_id_Handle idh; in GetAccessionVersion() local 31 if (x_TryProcessLRG(identifier, idh)) { in GetAccessionVersion() 32 return idh; in GetAccessionVersion() 41 idh = sequence::GetId(temp_idh, in GetAccessionVersion() 47 if (!idh) { // Failed to resolve id in GetAccessionVersion() 53 return idh; in GetAccessionVersion() 57 bool CIdResolver::x_TryProcessGenomicLRG(const string& identifier, CSeq_id_Handle& idh) const in x_TryProcessGenomicLRG() 78 idh = sequence::GetId(*lrg_seqid, in x_TryProcessGenomicLRG() 87 bool CIdResolver::x_TryProcessLRG(const string& identifier, CSeq_id_Handle& idh) const in x_TryProcessLRG() 104 idh = genome_idh; // No need to search for products. in x_TryProcessLRG() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/wgs/ |
H A D | wgsloader.hpp | 84 virtual TBlobId GetBlobId(const CSeq_id_Handle& idh); 90 virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh, EChoice choice); 92 virtual TTSE_LockSet GetExternalAnnotRecords(const CSeq_id_Handle& idh, 96 virtual TTSE_LockSet GetOrphanAnnotRecords(const CSeq_id_Handle& idh, 102 virtual void GetIds(const CSeq_id_Handle& idh, TIds& ids); 103 virtual SAccVerFound GetAccVerFound(const CSeq_id_Handle& idh); 104 virtual SGiFound GetGiFound(const CSeq_id_Handle& idh); 105 virtual TTaxId GetTaxId(const CSeq_id_Handle& idh); 106 virtual TSeqPos GetSequenceLength(const CSeq_id_Handle& idh); 107 virtual SHashFound GetSequenceHashFound(const CSeq_id_Handle& idh); [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
H A D | genbank_id_resolve.cpp | 65 CSeq_id_Handle idh, in GetBestId() argument 70 if (!idh) { in GetBestId() 73 CSeq_id_Handle best_idh = sequence::GetId(idh, scope, sequence::eGetId_Best); in GetBestId() 75 best_idh = idh; in GetBestId() 100 CSeq_id_Handle idh = mf.GetLocationId(); in GetBestId() local 101 if (idh) { in GetBestId() 102 return GetBestId(idh, mf.GetScope(), best_id); in GetBestId() 105 idh = sequence::GetIdHandle(loc, &mf.GetScope()); in GetBestId() 106 return GetBestId(idh, mf.GetScope(), best_id); in GetBestId()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/asn_cache/ |
H A D | asn_cache_loader.cpp | 133 CAsnCache_DataLoader::GetBlobId(const CSeq_id_Handle& idh) in GetBlobId() argument 140 if (index.cache->GetIndexEntry(idh, info)) { in GetBlobId() 141 blob_id = new CBlobIdSeq_id(idh); in GetBlobId() 154 TGi CAsnCache_DataLoader::GetGi(const CSeq_id_Handle& idh) in GetGi() argument 161 if (index.cache->GetIdInfo(idh, gi, timestamp)) { in GetGi() 179 if (index.cache->GetIdInfo(idh, acc, gi, in GetSequenceLength() 221 if (index.cache->GetIdInfo(idh, acc, gi, in GetTaxId() 255 CSeq_id_Handle idh = in GetBlobById() local 273 idh.AsString() + " not found"); in GetBlobById() 281 CAsnCache_DataLoader::GetRecords(const CSeq_id_Handle& idh, in GetRecords() argument [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/data_loaders/genbank/impl/ |
H A D | psg_loader_impl.hpp | 147 void GetIds(const CSeq_id_Handle& idh, TIds& ids); 148 CDataLoader::SGiFound GetGi(const CSeq_id_Handle& idh); 149 CDataLoader::SAccVerFound GetAccVer(const CSeq_id_Handle& idh); 150 TTaxId GetTaxId(const CSeq_id_Handle& idh); 151 TSeqPos GetSequenceLength(const CSeq_id_Handle& idh); 152 CDataLoader::SHashFound GetSequenceHash(const CSeq_id_Handle& idh); 153 CDataLoader::STypeFound GetSequenceType(const CSeq_id_Handle& idh); 154 int GetSequenceState(const CSeq_id_Handle& idh); 157 const CSeq_id_Handle& idh, 159 CRef<CPsgBlobId> GetBlobId(const CSeq_id_Handle& idh); [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
H A D | idmapper.cpp | 124 return idh; in Map() 147 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(*id); in Map() local 148 TMapperCache::iterator it = m_Cache.find(idh); in Map() 189 string CIdMapper::MapErrorString(const CSeq_id_Handle& idh ) in MapErrorString() argument 191 string strId = idh.AsString(); in MapErrorString() 218 if ( !idh ) { in MapObject() 221 id.Assign(*idh.GetSeqId()); in MapObject() 238 CSeq_id_Handle CIdMapperComposite::Map(const CSeq_id_Handle& idh) in Map() argument 242 ret = it->m_Mapper->Map(idh); in Map() 243 if (ret && ret != idh) break; in Map() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
H A D | idmapper.cpp | 124 return idh; in Map() 147 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(*id); in Map() local 148 TMapperCache::iterator it = m_Cache.find(idh); in Map() 189 string CIdMapper::MapErrorString(const CSeq_id_Handle& idh ) in MapErrorString() argument 191 string strId = idh.AsString(); in MapErrorString() 218 if ( !idh ) { in MapObject() 221 id.Assign(*idh.GetSeqId()); in MapObject() 238 CSeq_id_Handle CIdMapperComposite::Map(const CSeq_id_Handle& idh) in Map() argument 242 ret = it->m_Mapper->Map(idh); in Map() 243 if (ret && ret != idh) break; in Map() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
H A D | dbsource_item.cpp | 91 CConstRef<CSeq_id> id = idh.GetSeqId(); in s_ScoreForDBSource() 115 if (idh == *it) { in s_AddToUniqueIdList() 119 unique_ids.push_back(idh); in s_AddToUniqueIdList() 145 if (!idh) { in x_GatherInfo() 150 switch (idh.Which()) { in x_GatherInfo() 152 m_DBSource.push_back(x_FormatDBSourceID(idh)); in x_GatherInfo() 157 m_DBSource.push_back(x_FormatDBSourceID(idh)); in x_GatherInfo() 162 m_DBSource.push_back(x_FormatDBSourceID(idh)); in x_GatherInfo() 410 best = idh; in x_AddSPBlock() 553 if (idh) { in x_FormatDBSourceID() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
H A D | dbsource_item.cpp | 91 CConstRef<CSeq_id> id = idh.GetSeqId(); in s_ScoreForDBSource() 115 if (idh == *it) { in s_AddToUniqueIdList() 119 unique_ids.push_back(idh); in s_AddToUniqueIdList() 145 if (!idh) { in x_GatherInfo() 150 switch (idh.Which()) { in x_GatherInfo() 152 m_DBSource.push_back(x_FormatDBSourceID(idh)); in x_GatherInfo() 157 m_DBSource.push_back(x_FormatDBSourceID(idh)); in x_GatherInfo() 162 m_DBSource.push_back(x_FormatDBSourceID(idh)); in x_GatherInfo() 410 best = idh; in x_AddSPBlock() 553 if (idh) { in x_FormatDBSourceID() [all …]
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