/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objects/seq/ |
H A D | seq_id_handle.hpp | 324 void Swap(CSeq_id_Handle& idh) in Swap() argument 326 m_Info.Swap(idh.m_Info); in Swap() 327 swap(m_Packed, idh.m_Packed); in Swap() 328 swap(m_Variant, idh.m_Variant); in Swap() 350 CConstRef<CSeq_id> Get_ConstRef_Seq_id(const CSeq_id_Handle& idh) in Get_ConstRef_Seq_id() argument 352 return idh.GetSeqId(); in Get_ConstRef_Seq_id() 379 CNcbiOstream& operator<<(CNcbiOstream& out, const CSeq_id_Handle& idh);
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H A D | seq_loc_mapper_base.hpp | 599 ESeqType GetSeqType(const CSeq_id_Handle& idh) const; 765 void x_AdjustSeqTypesToProt(const CSeq_id_Handle& idh); 850 void x_PushSourceRange(const CSeq_id_Handle& idh, 858 CRef<CSeq_loc> x_RangeToSeq_loc(const CSeq_id_Handle& idh, 980 ESeqType GetSeqTypeById(const CSeq_id_Handle& idh) const; 993 int GetWidthById(const CSeq_id_Handle& idh) const; 1026 virtual TSeqType GetSequenceType(const CSeq_id_Handle& idh) = 0; 1029 virtual TSeqPos GetSequenceLength(const CSeq_id_Handle& idh) = 0; 1295 CSeq_loc_Mapper_Base::GetSeqTypeById(const CSeq_id_Handle& idh) const in GetSeqTypeById() 1297 CSeq_id_Handle primary_id = CollectSynonyms(idh); in GetSeqTypeById() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objects/seq/ |
H A D | seq_id_handle.hpp | 324 void Swap(CSeq_id_Handle& idh) in Swap() argument 326 m_Info.Swap(idh.m_Info); in Swap() 327 swap(m_Packed, idh.m_Packed); in Swap() 328 swap(m_Variant, idh.m_Variant); in Swap() 350 CConstRef<CSeq_id> Get_ConstRef_Seq_id(const CSeq_id_Handle& idh) in Get_ConstRef_Seq_id() argument 352 return idh.GetSeqId(); in Get_ConstRef_Seq_id() 379 CNcbiOstream& operator<<(CNcbiOstream& out, const CSeq_id_Handle& idh);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | align_group.cpp | 178 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(*id_iter); in GroupBySeqIds() local 181 sequence::GetId(idh, scope, sequence::eGetId_ForceGi); in GroupBySeqIds() 183 idh = gi_idh; in GroupBySeqIds() 186 ids.insert(idh); in GroupBySeqIds() 315 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(*id_iter); in GroupBySequenceType() local 316 idh = sequence::GetId(idh, scope, sequence::eGetId_Best); in GroupBySequenceType() 319 idh.GetSeqId()->GetLabel(&id_str); in GroupBySequenceType() 320 CSeq_id::EAccessionInfo info = idh.GetSeqId()->IdentifyAccession(); in GroupBySequenceType() 467 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(*id_iter); in x_SeparateByTaxId() local 468 TTaxId tax_id = x_GetTaxId(idh, scope); in x_SeparateByTaxId()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/lds2/ |
H A D | lds2_db.hpp | 305 Int8 GetBioseqId(const CSeq_id_Handle& idh) const; 315 void GetSynonyms(const CSeq_id_Handle& idh, TLdsIdSet& ids); 319 void GetSynonyms(const CSeq_id_Handle& idh, TSeqIds& ids); 323 SLDS2_Blob GetBlobInfo(const CSeq_id_Handle& idh); 335 void GetBioseqBlobs(const CSeq_id_Handle& idh, TBlobSet& blobs); 347 void GetAnnotBlobs(const CSeq_id_Handle& idh, 405 CSQLITE_Statement& x_InitGetBioseqsSql(const CSeq_id_Handle& idh) const;
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/dports/games/megaglest-data/megaglest-data-3.13.0/scenarios/lobby_access/ |
H A D | lobby_access_irish.lng | 3 m1=An bhfuil tú réidh? 4 why=Faigh bua sa gcnámhscéal seo mar dheimhniú go bhfuil tú réidh do chluichí ilimreoirí ar líne. 6 DESCRIPTION=Faigh bua sa gcnámhscéal seo mar dheimhniú go bhfuil tú\nréidh do chluichí ilimreoirí a…
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/ |
H A D | huge_asn_loader.cpp | 78 CDataLoader::TBlobId CHugeAsnDataLoader::GetBlobId(const CSeq_id_Handle& idh) in GetBlobId() argument 88 size_t info = m_reader->FindTopObject(idh.GetSeqId()); in GetBlobId() 115 CHugeAsnDataLoader::GetRecords(const CSeq_id_Handle& idh, EChoice choice) in GetRecords() argument 118 TBlobId blob_id = GetBlobId(idh); in GetRecords()
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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_store.cpp | 103 bool CAsnCacheStore::s_GetChunkAndOffset(const CSeq_id_Handle& idh, in s_GetChunkAndOffset() argument 115 GetNormalizedSeqId(idh, seq_id, version); in s_GetChunkAndOffset() 157 bool CAsnCacheStore::s_GetChunkAndOffset(const CSeq_id_Handle& idh, in s_GetChunkAndOffset() argument 162 if (!s_GetChunkAndOffset(idh, index, info_vector, false)) { in s_GetChunkAndOffset() 169 bool CAsnCacheStore::GetIdInfo(const CSeq_id_Handle& idh, in GetIdInfo() argument 259 bool CAsnCacheStore::GetBlob(const CSeq_id_Handle& idh, in GetBlob() argument 266 was_blob_found = s_GetChunkAndOffset(idh, *m_Index, info); in GetBlob() 329 bool CAsnCacheStore::GetRaw(const CSeq_id_Handle& idh, in GetRaw() argument 333 if ( !GetBlob(idh, blob) ) { in GetRaw() 360 CRef<CSeq_entry> CAsnCacheStore::GetEntry(const CSeq_id_Handle& idh) in GetEntry() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/agp_validate/ |
H A D | AgpFastaComparator.cpp | 437 CSeq_id_Handle idh = sequence::GetId(*bioseq_it, in WriteData() local 482 const string initial_seq_id = idh.AsString(); in GetFileName() 524 CSeq_id_Handle idh = sequence::GetId(*bioseq_it, in x_Process() local 532 "doesn't exist) for " << idh in x_Process() 548 << idh << Endl() << Endl() in x_Process() 555 x_WriteDataAsFasta( *pDataOutFile, idh, data ); in x_Process() 566 seqs[key].insert(idh); in x_Process() 578 COMP_LOG(" " << idh << ": " in x_Process() 591 const CSeq_id_Handle & idh, in x_WriteDataAsFasta() argument 596 dataOutFile << '>' << idh << endl; in x_WriteDataAsFasta() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/sra/ |
H A D | sraloader.hpp | 105 virtual TBlobId GetBlobId(const CSeq_id_Handle& idh); 111 virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh, EChoice choice); 112 virtual TSeqPos GetSequenceLength(const CSeq_id_Handle& idh); 113 virtual STypeFound GetSequenceTypeFound(const CSeq_id_Handle& idh);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
H A D | buf_data_loader.h | 61 virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh, EChoice choice); in BEGIN_SCOPE() 63 virtual TBlobId GetBlobId(const CSeq_id_Handle& idh); in BEGIN_SCOPE() 72 void x_LoadData(const CSeq_id_Handle& idh, CTSE_LoadLock& lock); in BEGIN_SCOPE()
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/dports/devel/idutils/idutils-4.6/src/ |
H A D | xtokid.c | 49 struct idhead idh; variable 163 cw_dlink = init_walker (&idh); in main() 217 cw_dlink = init_walker (&idh); in main() 288 mark_member_file_links (&idh); in main() 290 scan_files (&idh); in main()
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H A D | mkid.c | 122 struct idhead idh; variable 218 idh.idh_file_name = DEFAULT_ID_FILE_NAME; in main() 244 idh.idh_file_name = optarg; in main() 269 cw_dlink = init_walker (&idh); in main() 330 assert_writeable (idh.idh_file_name); in main() 332 cw_dlink = init_walker (&idh); in main() 405 mark_member_file_links (&idh); in main() 425 if (idh.idh_member_file_table.ht_fill) in main() 427 scan_files (&idh); in main() 433 write_id_file (&idh); in main() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/ |
H A D | sra_test.cpp | 171 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle("gnl|SRA|"+sra); in Run() local 172 NcbiCout << "Loading data for " << idh << NcbiEndl; in Run() 177 CBioseq_Handle bh = scope.GetBioseqHandle(idh); in Run() 181 "GetBioseqHandle("<<idh<<") unexpectedly succeeded"); in Run() 209 bh = seh.GetTSE_Handle().GetBioseqHandle(idh); in Run()
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/dports/security/snort/snort-2.9.18/src/side-channel/ |
H A D | rbmq.c | 150 RBMQ_InternalDataHdr *idh; in RBMQ_ReserveMsg() local 179 idh = (RBMQ_InternalDataHdr *) (mq->data_ring.data + start_offset); in RBMQ_ReserveMsg() 180 idh->msg_index = msg_index; in RBMQ_ReserveMsg() 181 idh->prev_offset = mq->data_ring.write_offset; in RBMQ_ReserveMsg() 192 msg_info->data = (uint8_t *) idh + sizeof(RBMQ_InternalDataHdr); in RBMQ_ReserveMsg() 249 RBMQ_InternalDataHdr *idh; in RBMQ_DiscardReservedMsg() local 275 idh = (RBMQ_InternalDataHdr *) (msg_info->data - sizeof(RBMQ_InternalDataHdr)); in RBMQ_DiscardReservedMsg() 276 mq->data_ring.write_offset = idh->prev_offset; in RBMQ_DiscardReservedMsg()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/bam/test/ |
H A D | test_bam_loader.cpp | 135 if ( idh == main_idh ) { in sx_CheckSeq() 141 BOOST_CHECK_EQUAL(ids[0], idh); in sx_CheckSeq() 199 sx_CheckSeq(scope, idh, **j); in BOOST_AUTO_TEST_CASE() 259 sx_CheckSeq(scope, idh, **j); in BOOST_AUTO_TEST_CASE() 318 sx_CheckSeq(scope, idh, **j); in BOOST_AUTO_TEST_CASE() 414 main_idh = idh; in BOOST_AUTO_TEST_CASE() 623 main_idh = idh; in BOOST_AUTO_TEST_CASE() 713 main_idh = idh; in BOOST_AUTO_TEST_CASE() 1257 main_idh = idh; in BOOST_AUTO_TEST_CASE() 1363 main_idh = idh; in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/ |
H A D | scope_impl.hpp | 337 TIds GetIds(const CSeq_id_Handle& idh, TGetFlags flags = 0); 338 CSeq_id_Handle GetAccVer(const CSeq_id_Handle& idh, TGetFlags flags); 339 TGi GetGi(const CSeq_id_Handle& idh, TGetFlags flags); 340 string GetLabel(const CSeq_id_Handle& idh, TGetFlags flags); 341 TTaxId GetTaxId(const CSeq_id_Handle& idh, TGetFlags flags); 412 void GetTSESetWithAnnots(const CSeq_id_Handle& idh, 416 void GetTSESetWithAnnots(const CSeq_id_Handle& idh, 477 const CSeq_id_Handle& idh, 480 const CSeq_id_Handle& idh, 483 const CSeq_id_Handle& idh, [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/ |
H A D | scope_impl.hpp | 337 TIds GetIds(const CSeq_id_Handle& idh, TGetFlags flags = 0); 338 CSeq_id_Handle GetAccVer(const CSeq_id_Handle& idh, TGetFlags flags); 339 TGi GetGi(const CSeq_id_Handle& idh, TGetFlags flags); 340 string GetLabel(const CSeq_id_Handle& idh, TGetFlags flags); 341 TTaxId GetTaxId(const CSeq_id_Handle& idh, TGetFlags flags); 412 void GetTSESetWithAnnots(const CSeq_id_Handle& idh, 416 void GetTSESetWithAnnots(const CSeq_id_Handle& idh, 477 const CSeq_id_Handle& idh, 480 const CSeq_id_Handle& idh, 483 const CSeq_id_Handle& idh, [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/cdd/cdd_access/ |
H A D | cdd_client.cpp | 190 SCDDCacheInfo(const CSeq_id_Handle idh, const TBlob& b) in SCDDCacheInfo() 191 : id(idh), blob(b), deadline(kMaxCacheLifespanSeconds) {} in SCDDCacheInfo() 254 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(blob.info->GetSeq_id()); in Add() local 256 auto found = m_SeqIdMap.find(idh); in Add() 259 shared_ptr<SCDDCacheInfo> info = make_shared<SCDDCacheInfo>(idh, blob); in Add() 267 m_SeqIdMap[idh] = info; in Add() 343 CCDDClientPool::SCDDBlob CCDDClientPool::GetBlobBySeq_id(CSeq_id_Handle idh) in GetBlobBySeq_id() argument 345 SCDDBlob ret = m_Cache->Get(idh); in GetBlobBySeq_id() 364 CConstRef<CSeq_id> id(idh.GetSeqId()); in GetBlobBySeq_id() 455 SCDDBlob blob = m_Cache->Get(idh); in GetBlobIdBySeq_id() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/blastdb/ |
H A D | local_blastdb_adapter.cpp | 52 CLocalBlastDbAdapter::GetTaxId(const CSeq_id_Handle& idh) in GetTaxId() argument 55 CConstRef<CSeq_id> id = idh.GetSeqId(); in GetTaxId() 61 if (idh.IsGi()) { in GetTaxId() 62 retval = gi_to_taxid[idh.GetGi()]; in GetTaxId()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/data_loaders/blastdb/ |
H A D | local_blastdb_adapter.cpp | 52 CLocalBlastDbAdapter::GetTaxId(const CSeq_id_Handle& idh) in GetTaxId() argument 55 CConstRef<CSeq_id> id = idh.GetSeqId(); in GetTaxId() 61 if (idh.IsGi()) { in GetTaxId() 62 retval = gi_to_taxid[idh.GetGi()]; in GetTaxId()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/asn_cache/ |
H A D | prime_cache.cpp | 494 if (m_PreviousExecutionIds.count(idh)) { in x_Process_Fasta() 595 ostr_seqids << idh << endl; in x_Process_Fasta() 631 if (m_PreviousExecutionIds.count(idh)) { in x_Process_SRA() 668 ostr_seqids << idh << endl; in x_Process_SRA() 772 CSeq_id_Handle idh = sequence::GetId(*bioseq_it, m_id_type); in x_CacheSeqEntry() local 774 ostr_seqids << idh << '\n'; in x_CacheSeqEntry() 818 CSeq_id_Handle idh = *id_it; in x_Process_Ids() local 819 if (m_CachedIds.count(idh)) { in x_Process_Ids() 823 CBioseq_Handle bsh = scope.GetBioseqHandle(idh); in x_Process_Ids() 856 ostr_seqids << idh << '\n'; in x_Process_Ids() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/vdbgraph/impl/ |
H A D | vdbgraphloader_impl.hpp | 65 TBlobId GetBlobId(const CSeq_id_Handle& idh); 69 const CSeq_id_Handle& idh, 72 const CSeq_id_Handle& idh,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/ |
H A D | test_sra.cpp | 123 CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(line); in Run() local 124 CBioseq_Handle bsh = scope->GetBioseqHandle(idh); in Run() 129 ostr << idh << '\t' << data << '\n'; in Run()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/data_loaders/lds2/ |
H A D | lds2_dataloader.hpp | 109 virtual TTSE_LockSet GetRecords(const CSeq_id_Handle& idh, 114 virtual TTSE_LockSet GetExternalAnnotRecords(const CSeq_id_Handle& idh, 122 virtual TBlobId GetBlobId(const CSeq_id_Handle& idh); 128 virtual void GetIds(const CSeq_id_Handle& idh, TIds& ids);
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