/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/ |
H A D | blast_asn1_input.cpp | 70 CASN1InputSourceOMF::GetNextSequence(CBioseq_set& bioseq_set) in GetNextSequence() argument 75 x_ReadFromTwoFiles(bioseq_set); in GetNextSequence() 78 x_ReadFromSingleFile(bioseq_set); in GetNextSequence() 148 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromSingleFile() 155 bioseq_set.SetSeq_set().push_back(second); in x_ReadFromSingleFile() 161 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromSingleFile() 170 CASN1InputSourceOMF::x_ReadFromTwoFiles(CBioseq_set& bioseq_set) in x_ReadFromTwoFiles() argument 189 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromTwoFiles() 190 bioseq_set.SetSeq_set().push_back(second); in x_ReadFromTwoFiles() 195 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromTwoFiles() [all …]
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H A D | blast_fasta_input.cpp | 562 x_ReadFromTwoFiles(bioseq_set, m_Format); in GetNextSequence() 565 x_ReadFastaOrFastq(bioseq_set); in GetNextSequence() 571 x_ReadFromTwoFiles(bioseq_set, m_Format); in GetNextSequence() 574 x_ReadFastaOrFastq(bioseq_set); in GetNextSequence() 579 x_ReadFastc(bioseq_set); in GetNextSequence() 641 bioseq_set.SetSeq_set().push_back(first); in x_ReadFastaOrFastq() 648 bioseq_set.SetSeq_set().push_back(second); in x_ReadFastaOrFastq() 654 bioseq_set.SetSeq_set().push_back(first); in x_ReadFastaOrFastq() 758 bioseq_set.SetSeq_set().push_back(seq_entry); in x_ReadFastc() 997 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromTwoFiles() [all …]
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H A D | blast_input.cpp | 306 CBlastInputOMF::GetNextSeqBatch(CBioseq_set& bioseq_set) in GetNextSeqBatch() argument 318 bioseq_set.SetSeq_set().push_back(it); in GetNextSeqBatch() 328 CRef<CBioseq_set> bioseq_set(new CBioseq_set); in GetNextSeqBatch() local 329 GetNextSeqBatch(*bioseq_set); in GetNextSeqBatch() 330 return bioseq_set; in GetNextSeqBatch()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/ |
H A D | blast_asn1_input.cpp | 70 CASN1InputSourceOMF::GetNextSequence(CBioseq_set& bioseq_set) in GetNextSequence() argument 75 x_ReadFromTwoFiles(bioseq_set); in GetNextSequence() 78 x_ReadFromSingleFile(bioseq_set); in GetNextSequence() 148 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromSingleFile() 155 bioseq_set.SetSeq_set().push_back(second); in x_ReadFromSingleFile() 161 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromSingleFile() 170 CASN1InputSourceOMF::x_ReadFromTwoFiles(CBioseq_set& bioseq_set) in x_ReadFromTwoFiles() argument 189 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromTwoFiles() 190 bioseq_set.SetSeq_set().push_back(second); in x_ReadFromTwoFiles() 195 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromTwoFiles() [all …]
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H A D | blast_fasta_input.cpp | 562 x_ReadFromTwoFiles(bioseq_set, m_Format); in GetNextSequence() 565 x_ReadFastaOrFastq(bioseq_set); in GetNextSequence() 571 x_ReadFromTwoFiles(bioseq_set, m_Format); in GetNextSequence() 574 x_ReadFastaOrFastq(bioseq_set); in GetNextSequence() 579 x_ReadFastc(bioseq_set); in GetNextSequence() 641 bioseq_set.SetSeq_set().push_back(first); in x_ReadFastaOrFastq() 648 bioseq_set.SetSeq_set().push_back(second); in x_ReadFastaOrFastq() 654 bioseq_set.SetSeq_set().push_back(first); in x_ReadFastaOrFastq() 758 bioseq_set.SetSeq_set().push_back(seq_entry); in x_ReadFastc() 997 bioseq_set.SetSeq_set().push_back(first); in x_ReadFromTwoFiles() [all …]
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H A D | blast_input.cpp | 306 CBlastInputOMF::GetNextSeqBatch(CBioseq_set& bioseq_set) in GetNextSeqBatch() argument 318 bioseq_set.SetSeq_set().push_back(it); in GetNextSeqBatch() 328 CRef<CBioseq_set> bioseq_set(new CBioseq_set); in GetNextSeqBatch() local 329 GetNextSeqBatch(*bioseq_set); in GetNextSeqBatch() 330 return bioseq_set; in GetNextSeqBatch()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | objmgrfree_query_data.cpp | 70 CObjMgrFree_LocalQueryData(CConstRef<CBioseq_set> bioseq_set, 93 (CConstRef<CBioseq_set> bioseq_set, const CBlastOptions* options) in CObjMgrFree_LocalQueryData() argument 94 : m_Options(options), m_BioseqSet(bioseq_set) in CObjMgrFree_LocalQueryData() 98 m_QuerySource.Reset(new CBlastQuerySourceBioseqSet(*bioseq_set, is_prot)); in CObjMgrFree_LocalQueryData() 161 s_ConstBioseqSetToSeqLocs(CConstRef<CBioseq_set> bioseq_set) in s_ConstBioseqSetToSeqLocs() argument 163 CTypeConstIterator<CBioseq> itr(ConstBegin(*bioseq_set, eDetectLoops)); in s_ConstBioseqSetToSeqLocs() 164 CBlastQuerySourceBioseqSet query_source(*bioseq_set, itr->IsAa()); in s_ConstBioseqSetToSeqLocs() 184 CObjMgrFree_RemoteQueryData(CConstRef<CBioseq_set> bioseq_set); 198 (CConstRef<CBioseq_set> bioseq_set) in CObjMgrFree_RemoteQueryData() argument 199 : m_ClientBioseqSet(bioseq_set) in CObjMgrFree_RemoteQueryData()
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H A D | search_strategy.cpp | 572 CRef<CBioseq_set> bioseq_set = remote_query->GetBioseqSet(); in x_Process_Query() local 575 if (bioseq_set.Empty() && seqloc_list.empty()) in x_Process_Query() 595 _ASSERT(bioseq_set->CanGetSeq_set()); in x_Process_Query() 596 _ASSERT(!bioseq_set->GetSeq_set().empty()); in x_Process_Query() 597 _ASSERT(bioseq_set->GetSeq_set().front()->IsSeq()); in x_Process_Query() 598 _ASSERT(bioseq_set->GetSeq_set().front()->GetSeq().CanGetInst()); in x_Process_Query() 600 bioseq_set->GetSeq_set().front()->GetSeq().GetInst().GetLength(); in x_Process_Query() 651 Q->SetBioseq_set(*bioseq_set); in x_Process_Query() 664 CRef<CBioseq_set> bioseq_set = remote_query->GetBioseqSet(); in x_Process_Subject() local 666 if (bioseq_set.Empty()) in x_Process_Subject() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | objmgrfree_query_data.cpp | 70 CObjMgrFree_LocalQueryData(CConstRef<CBioseq_set> bioseq_set, 93 (CConstRef<CBioseq_set> bioseq_set, const CBlastOptions* options) in CObjMgrFree_LocalQueryData() argument 94 : m_Options(options), m_BioseqSet(bioseq_set) in CObjMgrFree_LocalQueryData() 98 m_QuerySource.Reset(new CBlastQuerySourceBioseqSet(*bioseq_set, is_prot)); in CObjMgrFree_LocalQueryData() 161 s_ConstBioseqSetToSeqLocs(CConstRef<CBioseq_set> bioseq_set) in s_ConstBioseqSetToSeqLocs() argument 163 CTypeConstIterator<CBioseq> itr(ConstBegin(*bioseq_set, eDetectLoops)); in s_ConstBioseqSetToSeqLocs() 164 CBlastQuerySourceBioseqSet query_source(*bioseq_set, itr->IsAa()); in s_ConstBioseqSetToSeqLocs() 184 CObjMgrFree_RemoteQueryData(CConstRef<CBioseq_set> bioseq_set); 198 (CConstRef<CBioseq_set> bioseq_set) in CObjMgrFree_RemoteQueryData() argument 199 : m_ClientBioseqSet(bioseq_set) in CObjMgrFree_RemoteQueryData()
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H A D | search_strategy.cpp | 572 CRef<CBioseq_set> bioseq_set = remote_query->GetBioseqSet(); in x_Process_Query() local 575 if (bioseq_set.Empty() && seqloc_list.empty()) in x_Process_Query() 595 _ASSERT(bioseq_set->CanGetSeq_set()); in x_Process_Query() 596 _ASSERT(!bioseq_set->GetSeq_set().empty()); in x_Process_Query() 597 _ASSERT(bioseq_set->GetSeq_set().front()->IsSeq()); in x_Process_Query() 598 _ASSERT(bioseq_set->GetSeq_set().front()->GetSeq().CanGetInst()); in x_Process_Query() 600 bioseq_set->GetSeq_set().front()->GetSeq().GetInst().GetLength(); in x_Process_Query() 651 Q->SetBioseq_set(*bioseq_set); in x_Process_Query() 664 CRef<CBioseq_set> bioseq_set = remote_query->GetBioseqSet(); in x_Process_Subject() local 666 if (bioseq_set.Empty()) in x_Process_Subject() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blast_sra_input/ |
H A D | blast_sra_input.cpp | 87 CSraInputSource::GetNextSequence(CBioseq_set& bioseq_set) in GetNextSequence() argument 93 x_ReadPairs(bioseq_set); in GetNextSequence() 100 x_ReadOneSeq(bioseq_set); in GetNextSequence() 132 CSraInputSource::x_ReadOneSeq(CBioseq_set& bioseq_set) in x_ReadOneSeq() argument 135 bioseq_set.SetSeq_set().push_back(seq_entry); in x_ReadOneSeq() 136 return bioseq_set.SetSeq_set().back().GetNonNullPointer(); in x_ReadOneSeq() 141 CSraInputSource::x_ReadPairs(CBioseq_set& bioseq_set) in x_ReadPairs() argument 162 CSeq_entry* first = x_ReadOneSeq(bioseq_set); in x_ReadPairs() 173 CSeq_entry* second = x_ReadOneSeq(bioseq_set); in x_ReadPairs()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/ |
H A D | newcleanupp.hpp | 491 void x_ClearEmptyDescr( CBioseq_set& bioseq_set ); 512 void x_RemoveDupBioSource( CBioseq_set & bioseq_set ); 557 void x_BioseqSetEC( CBioseq_set & bioseq_set ); 558 void x_ChangePopToPhy(CBioseq_set& bioseq_set); 566 void x_BioseqSetNucProtEC( CBioseq_set & bioseq_set ); 567 void x_BioseqSetGenBankEC(CBioseq_set & bioseq_set); 568 void x_RemoveNestedGenBankSet(CBioseq_set & bioseq_set); 570 void x_MoveNpDBlinks(CBioseq_set& bioseq_set); 571 void x_MoveNpSrc(CBioseq_set& bioseq_set); 575 void x_MoveNpPub(CBioseq_set& bioseq_set); [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/ |
H A D | newcleanupp.hpp | 492 void x_ClearEmptyDescr( CBioseq_set& bioseq_set ); 513 void x_RemoveDupBioSource( CBioseq_set & bioseq_set ); 559 void x_BioseqSetEC( CBioseq_set & bioseq_set ); 560 void x_ChangePopToPhy(CBioseq_set& bioseq_set); 568 void x_BioseqSetNucProtEC( CBioseq_set & bioseq_set ); 569 void x_BioseqSetGenBankEC(CBioseq_set & bioseq_set); 570 void x_RemoveNestedGenBankSet(CBioseq_set & bioseq_set); 572 void x_MoveNpDBlinks(CBioseq_set& bioseq_set); 573 void x_MoveNpSrc(CBioseq_set& bioseq_set); 577 void x_MoveNpPub(CBioseq_set& bioseq_set); [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/blastinput/ |
H A D | blast_fasta_input.hpp | 135 virtual int GetNextSequence(CBioseq_set& bioseq_set); 148 void x_ReadFastaOrFastq(CBioseq_set& bioseq_set); 157 bool x_ReadFromTwoFiles(CBioseq_set& bioseq_set, EInputFormat format); 161 void x_ReadFastc(CBioseq_set& bioseq_set);
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H A D | blast_asn1_input.hpp | 68 virtual int GetNextSequence(CBioseq_set& bioseq_set); 81 bool x_ReadFromSingleFile(CBioseq_set& bioseq_set); 84 bool x_ReadFromTwoFiles(CBioseq_set& bioseq_set);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blastinput/ |
H A D | blast_fasta_input.hpp | 135 virtual int GetNextSequence(CBioseq_set& bioseq_set); 148 void x_ReadFastaOrFastq(CBioseq_set& bioseq_set); 157 bool x_ReadFromTwoFiles(CBioseq_set& bioseq_set, EInputFormat format); 161 void x_ReadFastc(CBioseq_set& bioseq_set);
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H A D | blast_asn1_input.hpp | 68 virtual int GetNextSequence(CBioseq_set& bioseq_set); 81 bool x_ReadFromSingleFile(CBioseq_set& bioseq_set); 84 bool x_ReadFromTwoFiles(CBioseq_set& bioseq_set);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | make_cdr_prods.cpp | 61 CRef<CBioseq_set> bioseq_set(new CBioseq_set); in MakeCdrProds() local 65 return bioseq_set; in MakeCdrProds() 117 bioseq_set->SetSeq_set().push_back(seq_entry); in MakeCdrProds() 125 return bioseq_set; in MakeCdrProds()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blast_sra_input/ |
H A D | blast_sra_input.hpp | 62 virtual int GetNextSequence(CBioseq_set& bioseq_set); 80 CSeq_entry* x_ReadOneSeq(CBioseq_set& bioseq_set); 83 void x_ReadPairs(CBioseq_set& bioseq_set);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | bioseq_ci.cpp | 246 CBioseq_CI::CBioseq_CI(const CBioseq_set_Handle& bioseq_set, in CBioseq_CI() argument 249 : m_Scope(&bioseq_set.GetScope()), in CBioseq_CI() 254 x_Initialize(bioseq_set.GetParentEntry()); in CBioseq_CI()
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H A D | seq_annot_ci.cpp | 98 CSeq_annot_CI::CSeq_annot_CI(const CBioseq_set_Handle& bioseq_set, in CSeq_annot_CI() argument 102 x_Initialize(bioseq_set.GetParentEntry(), flags); in CSeq_annot_CI()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | bioseq_ci.cpp | 246 CBioseq_CI::CBioseq_CI(const CBioseq_set_Handle& bioseq_set, in CBioseq_CI() argument 249 : m_Scope(&bioseq_set.GetScope()), in CBioseq_CI() 254 x_Initialize(bioseq_set.GetParentEntry()); in CBioseq_CI()
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H A D | seq_annot_ci.cpp | 98 CSeq_annot_CI::CSeq_annot_CI(const CBioseq_set_Handle& bioseq_set, in CSeq_annot_CI() argument 102 x_Initialize(bioseq_set.GetParentEntry(), flags); in CSeq_annot_CI()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
H A D | phrap.cpp | 1246 x_CreateAlignAll(bioseq_set); in x_CreateAlign() 1249 x_CreateAlignPairs(bioseq_set); in x_CreateAlign() 1252 x_CreateAlignOptimized(bioseq_set); in x_CreateAlign() 1291 bioseq_set.SetAnnot().push_back(annot); in x_CreateAlignAll() 1328 bioseq_set.SetAnnot().push_back(annot); in x_CreateAlignPairs() 1369 bioseq_set.SetAnnot().push_back(annot); in x_CreateAlignOptimized() 1594 CBioseq_set& bioseq_set = set_entry->SetSet(); in CreateContig() local 1595 bioseq_set.SetLevel(level); in CreateContig() 1597 bioseq_set.SetSeq_set().push_back(cont_entry); in CreateContig() 1598 x_CreateAlign(bioseq_set); in CreateContig() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
H A D | phrap.cpp | 1246 x_CreateAlignAll(bioseq_set); in x_CreateAlign() 1249 x_CreateAlignPairs(bioseq_set); in x_CreateAlign() 1252 x_CreateAlignOptimized(bioseq_set); in x_CreateAlign() 1291 bioseq_set.SetAnnot().push_back(annot); in x_CreateAlignAll() 1328 bioseq_set.SetAnnot().push_back(annot); in x_CreateAlignPairs() 1369 bioseq_set.SetAnnot().push_back(annot); in x_CreateAlignOptimized() 1594 CBioseq_set& bioseq_set = set_entry->SetSet(); in CreateContig() local 1595 bioseq_set.SetLevel(level); in CreateContig() 1597 bioseq_set.SetSeq_set().push_back(cont_entry); in CreateContig() 1598 x_CreateAlign(bioseq_set); in CreateContig() [all …]
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