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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/
H A Dseq_id_mapper.cpp100 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seq/
H A Dseq_id_mapper.cpp100 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/data_loaders/genbank/
H A Dpsg_loader.cpp138 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/data_loaders/genbank/impl/
H A Dpsg_loader_impl.hpp115 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);
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/dports/devel/idutils/idutils-4.6/src/
H A Dfid.c43 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()
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H A Dfnid.c41 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()
H A Dlid.c149 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/wgs/test/
H A Dtest_wgs_loader.cpp633 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Ddata_loader.cpp134 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Ddata_loader.cpp134 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/data_loaders/genbank/
H A Dpsg_loader.hpp70 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;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/genbank/
H A Dpsg_loader.cpp214 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/
H A Ddata_loader.hpp245 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);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/
H A Ddata_loader.hpp245 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);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/wgs/
H A Dwgsloader.cpp195 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/data_loaders/genbank/
H A Dpsg_loader.hpp105 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;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/hgvs/
H A Did_resolver.cpp29 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/wgs/
H A Dwgsloader.hpp84 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);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/
H A Dgenbank_id_resolve.cpp65 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/asn_cache/
H A Dasn_cache_loader.cpp133 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
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/data_loaders/genbank/impl/
H A Dpsg_loader_impl.hpp147 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);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Didmapper.cpp124 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Didmapper.cpp124 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/
H A Ddbsource_item.cpp91 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/
H A Ddbsource_item.cpp91 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()
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