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Searched refs:bioseq_set (Results 1 – 25 of 63) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/
H A Dblast_asn1_input.cpp70 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()
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H A Dblast_fasta_input.cpp562 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()
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H A Dblast_input.cpp306 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/
H A Dblast_asn1_input.cpp70 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()
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H A Dblast_fasta_input.cpp562 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()
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H A Dblast_input.cpp306 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dobjmgrfree_query_data.cpp70 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()
H A Dsearch_strategy.cpp572 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dobjmgrfree_query_data.cpp70 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()
H A Dsearch_strategy.cpp572 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blast_sra_input/
H A Dblast_sra_input.cpp87 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/
H A Dnewcleanupp.hpp491 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);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/
H A Dnewcleanupp.hpp492 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);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/blastinput/
H A Dblast_fasta_input.hpp135 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);
H A Dblast_asn1_input.hpp68 virtual int GetNextSequence(CBioseq_set& bioseq_set);
81 bool x_ReadFromSingleFile(CBioseq_set& bioseq_set);
84 bool x_ReadFromTwoFiles(CBioseq_set& bioseq_set);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blastinput/
H A Dblast_fasta_input.hpp135 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);
H A Dblast_asn1_input.hpp68 virtual int GetNextSequence(CBioseq_set& bioseq_set);
81 bool x_ReadFromSingleFile(CBioseq_set& bioseq_set);
84 bool x_ReadFromTwoFiles(CBioseq_set& bioseq_set);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dmake_cdr_prods.cpp61 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/blast_sra_input/
H A Dblast_sra_input.hpp62 virtual int GetNextSequence(CBioseq_set& bioseq_set);
80 CSeq_entry* x_ReadOneSeq(CBioseq_set& bioseq_set);
83 void x_ReadPairs(CBioseq_set& bioseq_set);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dbioseq_ci.cpp246 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()
H A Dseq_annot_ci.cpp98 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dbioseq_ci.cpp246 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()
H A Dseq_annot_ci.cpp98 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Dphrap.cpp1246 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Dphrap.cpp1246 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()
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