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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objects/seq/
H A Dseq_id_handle.hpp324 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);
H A Dseq_loc_mapper_base.hpp599 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objects/seq/
H A Dseq_id_handle.hpp324 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);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dalign_group.cpp178 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/lds2/
H A Dlds2_db.hpp305 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;
/dports/games/megaglest-data/megaglest-data-3.13.0/scenarios/lobby_access/
H A Dlobby_access_irish.lng3 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…
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/
H A Dhuge_asn_loader.cpp78 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/asn_cache/
H A Dasn_cache_store.cpp103 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
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/agp_validate/
H A DAgpFastaComparator.cpp437 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/sra/
H A Dsraloader.hpp105 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);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/
H A Dbuf_data_loader.h61 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()
/dports/devel/idutils/idutils-4.6/src/
H A Dxtokid.c49 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()
H A Dmkid.c122 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/
H A Dsra_test.cpp171 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()
/dports/security/snort/snort-2.9.18/src/side-channel/
H A Drbmq.c150 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/bam/test/
H A Dtest_bam_loader.cpp135 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/
H A Dscope_impl.hpp337 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,
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/
H A Dscope_impl.hpp337 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,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/cdd/cdd_access/
H A Dcdd_client.cpp190 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/blastdb/
H A Dlocal_blastdb_adapter.cpp52 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/data_loaders/blastdb/
H A Dlocal_blastdb_adapter.cpp52 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/asn_cache/
H A Dprime_cache.cpp494 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/data_loaders/vdbgraph/impl/
H A Dvdbgraphloader_impl.hpp65 TBlobId GetBlobId(const CSeq_id_Handle& idh);
69 const CSeq_id_Handle& idh,
72 const CSeq_id_Handle& idh,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/
H A Dtest_sra.cpp123 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/data_loaders/lds2/
H A Dlds2_dataloader.hpp109 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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