| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/demo/ |
| H A D | alnmrg.cpp | 75 CScope& GetScope (void) const;
300 CScope& CAlnMrgApp::GetScope(void) const in GetScope() function in CAlnMrgApp
379 GetScope(); // first call creates the scope in SetOptions()
411 GetScope().AddTopLevelSeqEntry(*se); in LoadSeqEntry()
423 GetScope().AddTopLevelSeqEntry(*fasta_reader.ReadSet()); in LoadFasta()
433 GetScope(); /* make sure m_ObjMgr and m_Scope are created */ in LoadBlastDb()
443 GetScope().AddDataLoader(blast_loader->GetName()); in LoadBlastDb()
471 CAlnVec aln_vec(m_Mix->GetDenseg(), GetScope()); in ViewMergedAln()
520 CAlnAsnReader reader(&GetScope()); in LoadInputAlns()
534 m_Mix = m_Scope ? new CAlnMix(GetScope()) : new CAlnMix(); in Run()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/ |
| H A D | heap_scope.hpp | 94 NCBI_XOBJMGR_EXPORT CScope& GetScope(void) const;
98 return GetScope(); in operator CScope&()
102 return &GetScope(); in operator CScope*()
106 return GetScope(); in operator *()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/ |
| H A D | heap_scope.hpp | 94 NCBI_XOBJMGR_EXPORT CScope& GetScope(void) const;
98 return GetScope(); in operator CScope&()
102 return &GetScope(); in operator CScope*()
106 return GetScope(); in operator *()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/seqqa/ |
| H A D | prot_prod_tests.cpp | 63 CBioseq_Handle handle = ctx->GetScope().GetBioseqHandle(*id); in CanTest()
92 int len = ctx->GetScope() in RunTest()
115 CBioseq_Handle hand = ctx->GetScope().GetBioseqHandle(*id); in RunTest()
169 CBioseq_Handle hand = ctx->GetScope().GetBioseqHandle(*id); in CanTest()
195 CBioseq_Handle hand = ctx->GetScope().GetBioseqHandle(*id); in RunTest()
245 ctx->GetScope().GetBioseqHandle(neigh_id).GetBioseqLength(); in RunTest()
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| H A D | xcript_tests.cpp | 72 CBioseq_Handle handle = ctx->GetScope().GetBioseqHandle(*id); in CanTest()
99 CFeat_CI feat_iter(ctx->GetScope(), loc, sel); in RunTest()
161 CScope& scope = ctx->GetScope(); in s_GetCdregionPlusUpstream()
379 int len = ctx->GetScope() in RunTest()
468 CSeqVector vec(feat_iter->GetLocation(), ctx->GetScope()); in s_CdsStopCodon()
538 CSeqVector vec(feat_iter->GetLocation(), ctx->GetScope()); in s_PrematureStopCodon()
630 CSeqVector prod_vec(prod_loc, ctx->GetScope()); in s_CompareProtProdToTrans()
658 = ctx->GetScope().GetBioseqHandle(*updated_id); in s_CompareProtProdToTrans()
894 ctx->GetScope()); in s_Code_break()
999 CSeqVector vec(feat_iter->GetLocation(), ctx->GetScope()); in s_CdsCountAmbiguities()
[all …]
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| /dports/www/chromium-legacy/chromium-88.0.4324.182/chrome/browser/chromeos/cert_provisioning/ |
| H A D | cert_provisioning_invalidator_unittest.cc | 28 GetScope(), in CertProvisioningInvalidationHandlerTest()
44 CertScope GetScope() const { return GetParam(); } in GetScope() function in chromeos::cert_provisioning::internal::CertProvisioningInvalidationHandlerTest
47 switch (GetScope()) { in GetExpectedOwnerName()
115 GetScope(), &invalidation_service_, kInvalidatorTopic, in TEST_P()
126 GetScope(), &invalidation_service_, kSomeOtherTopic, base::DoNothing()); in TEST_P()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/ |
| H A D | seq_feat_handle.hpp | 90 CScope& GetScope(void) const;
285 CScope& CSeq_feat_Handle::GetScope(void) const in GetScope() function in CSeq_feat_Handle
287 return GetAnnot().GetScope(); in GetScope()
727 CScope& GetScope(void) const;
763 CScope& CSeq_annot_ftable_CI::GetScope(void) const in GetScope() function in CSeq_annot_ftable_CI
765 return GetAnnot().GetScope(); in GetScope()
806 CScope& GetScope(void) const;
844 CScope& CSeq_annot_ftable_I::GetScope(void) const in GetScope() function in CSeq_annot_ftable_I
846 return GetAnnot().GetScope(); in GetScope()
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| H A D | seq_annot_ci.hpp | 114 CScope& GetScope(void) const;
149 CScope& CSeq_annot_CI::GetScope(void) const in GetScope() function in CSeq_annot_CI
151 return m_CurrentEntry.GetScope(); in GetScope()
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| H A D | bioseq_ci.hpp | 111 CScope& GetScope(void) const;
163 CScope& CBioseq_CI::GetScope(void) const in GetScope() function in CBioseq_CI
165 return m_Scope.GetScope(); in GetScope()
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| H A D | seq_align_handle.hpp | 81 CScope& GetScope(void) const;
155 CScope& CSeq_align_Handle::GetScope(void) const in GetScope() function in CSeq_align_Handle
157 return GetAnnot().GetScope(); in GetScope()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/ |
| H A D | seq_feat_handle.hpp | 90 CScope& GetScope(void) const;
285 CScope& CSeq_feat_Handle::GetScope(void) const in GetScope() function in CSeq_feat_Handle
287 return GetAnnot().GetScope(); in GetScope()
727 CScope& GetScope(void) const;
763 CScope& CSeq_annot_ftable_CI::GetScope(void) const in GetScope() function in CSeq_annot_ftable_CI
765 return GetAnnot().GetScope(); in GetScope()
806 CScope& GetScope(void) const;
844 CScope& CSeq_annot_ftable_I::GetScope(void) const in GetScope() function in CSeq_annot_ftable_I
846 return GetAnnot().GetScope(); in GetScope()
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| H A D | seq_annot_ci.hpp | 114 CScope& GetScope(void) const;
149 CScope& CSeq_annot_CI::GetScope(void) const in GetScope() function in CSeq_annot_CI
151 return m_CurrentEntry.GetScope(); in GetScope()
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| H A D | bioseq_ci.hpp | 111 CScope& GetScope(void) const;
163 CScope& CBioseq_CI::GetScope(void) const in GetScope() function in CBioseq_CI
165 return m_Scope.GetScope(); in GetScope()
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| H A D | seq_align_handle.hpp | 81 CScope& GetScope(void) const;
155 CScope& CSeq_align_Handle::GetScope(void) const in GetScope() function in CSeq_align_Handle
157 return GetAnnot().GetScope(); in GetScope()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
| H A D | annot_types_ci.cpp | 102 : m_DataCollector(new CAnnot_Collector(bioseq.GetScope())) in CAnnotTypes_CI()
179 : m_DataCollector(new CAnnot_Collector(annot.GetScope())) in CAnnotTypes_CI()
194 : m_DataCollector(new CAnnot_Collector(annot.GetScope())) in CAnnotTypes_CI()
199 x_Init(annot.GetScope(), loc, sel); in CAnnotTypes_CI()
206 : m_DataCollector(new CAnnot_Collector(entry.GetScope())) in CAnnotTypes_CI()
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| H A D | seq_loc_mapper.cpp | 100 m_Scope.GetScope().GetSynonyms(id); in CollectSynonyms()
114 switch ( m_Scope.GetScope().GetSequenceType(idh) ) { in GetSequenceType()
133 h = m_Scope.GetScope().GetBioseqHandle(idh); in GetSequenceLength()
254 m_Scope(&target_seq.GetScope()) in CSeq_loc_Mapper()
297 m_Scope(&target_seq.GetScope()) in CSeq_loc_Mapper()
343 m_Scope(&top_level_seq.GetScope()) in CSeq_loc_Mapper()
399 m_Scope.GetScope().AddScope(*scope); in CSeq_loc_Mapper()
422 m_Scope.GetScope().AddScope(*scope); in CSeq_loc_Mapper()
428 m_Scope.GetScope().AddTopLevelSeqEntry(*entry); in CSeq_loc_Mapper()
431 CBioseq_Handle h = m_Scope.GetScope().GetBioseqHandle(*id); in CSeq_loc_Mapper()
[all …]
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| H A D | seq_map_ci.cpp | 178 : m_Scope(&bioseq.GetScope()), in CSeqMap_CI()
192 : m_Scope(&bioseq.GetScope()), in CSeqMap_CI()
243 TSeqPos len = seqMap->GetLength(GetScope()); in x_Select()
376 return m_Selector.x_GetLimitTSE(GetScope()).GetBioseqHandle(id); in x_RefTSEMatch()
396 if ( !GetScope() ) { in x_GetBioseq()
401 bh = GetScope()->GetBioseqHandle(seq_id); in x_GetBioseq()
533 seqMap->x_GetSegmentLength(push.m_Index, GetScope()); in x_Push()
562 if ( !top.x_Move(top.m_MinusStrand, GetScope()) ) { in x_TopNext()
576 if ( !top.x_Move(!top.m_MinusStrand, GetScope()) ) { in x_TopPrev()
758 &bioseq.GetScope(), in CSeqMap_I()
[all …]
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| H A D | heap_scope.cpp | 68 CScope& CHeapScope::GetScope(void) const in GetScope() function in CHeapScope
82 return GetScope().m_Impl.GetPointer(); in GetImpl()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
| H A D | annot_types_ci.cpp | 102 : m_DataCollector(new CAnnot_Collector(bioseq.GetScope())) in CAnnotTypes_CI()
179 : m_DataCollector(new CAnnot_Collector(annot.GetScope())) in CAnnotTypes_CI()
194 : m_DataCollector(new CAnnot_Collector(annot.GetScope())) in CAnnotTypes_CI()
199 x_Init(annot.GetScope(), loc, sel); in CAnnotTypes_CI()
206 : m_DataCollector(new CAnnot_Collector(entry.GetScope())) in CAnnotTypes_CI()
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| H A D | seq_loc_mapper.cpp | 100 m_Scope.GetScope().GetSynonyms(id); in CollectSynonyms()
114 switch ( m_Scope.GetScope().GetSequenceType(idh) ) { in GetSequenceType()
133 h = m_Scope.GetScope().GetBioseqHandle(idh); in GetSequenceLength()
254 m_Scope(&target_seq.GetScope()) in CSeq_loc_Mapper()
297 m_Scope(&target_seq.GetScope()) in CSeq_loc_Mapper()
343 m_Scope(&top_level_seq.GetScope()) in CSeq_loc_Mapper()
399 m_Scope.GetScope().AddScope(*scope); in CSeq_loc_Mapper()
422 m_Scope.GetScope().AddScope(*scope); in CSeq_loc_Mapper()
428 m_Scope.GetScope().AddTopLevelSeqEntry(*entry); in CSeq_loc_Mapper()
431 CBioseq_Handle h = m_Scope.GetScope().GetBioseqHandle(*id); in CSeq_loc_Mapper()
[all …]
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| H A D | seq_map_ci.cpp | 178 : m_Scope(&bioseq.GetScope()), in CSeqMap_CI()
192 : m_Scope(&bioseq.GetScope()), in CSeqMap_CI()
243 TSeqPos len = seqMap->GetLength(GetScope()); in x_Select()
376 return m_Selector.x_GetLimitTSE(GetScope()).GetBioseqHandle(id); in x_RefTSEMatch()
396 if ( !GetScope() ) { in x_GetBioseq()
401 bh = GetScope()->GetBioseqHandle(seq_id); in x_GetBioseq()
533 seqMap->x_GetSegmentLength(push.m_Index, GetScope()); in x_Push()
562 if ( !top.x_Move(top.m_MinusStrand, GetScope()) ) { in x_TopNext()
576 if ( !top.x_Move(!top.m_MinusStrand, GetScope()) ) { in x_TopPrev()
758 &bioseq.GetScope(), in CSeqMap_I()
[all …]
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| H A D | heap_scope.cpp | 68 CScope& CHeapScope::GetScope(void) const in GetScope() function in CHeapScope
82 return GetScope().m_Impl.GetPointer(); in GetImpl()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
| H A D | genbank_id_resolve.cpp | 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()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/unit_test/ |
| H A D | unit_test_get_label.cpp | 91 feature::GetLabel(*(f->GetSeq_feat()), &label, feature::fFGL_Content, &(bsh.GetScope())); in CheckOneFeatureType()
95 feature::GetLabel(*(f->GetSeq_feat()), &label, feature::fFGL_Type, &(bsh.GetScope())); in CheckOneFeatureType()
99 feature::GetLabel(*(f->GetSeq_feat()), &label, feature::fFGL_Both, &(bsh.GetScope())); in CheckOneFeatureType()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | splice_problems.cpp | 357 bsh.GetScope()); in ValidateSpliceExon()
372 bsh.GetScope()); in ValidateSpliceExon()
388 CBioseq_Handle bsh_si = bsh.GetScope().GetBioseqHandle(*cur_int); in ValidateSpliceExon()
458 bsh.GetScope()); in ValidateSpliceMrna()
481 CBioseq_Handle bsh_head = bsh.GetScope().GetBioseqHandle(*head.GetRangeAsSeq_loc()); in ValidateSpliceMrna()
505 CBioseq_Handle bsh_head = bsh.GetScope().GetBioseqHandle(*head.GetRangeAsSeq_loc()); in ValidateSpliceMrna()
506 CBioseq_Handle bsh_tail = bsh.GetScope().GetBioseqHandle(*tail.GetRangeAsSeq_loc()); in ValidateSpliceMrna()
532 CBioseq_Handle bsh_head = bsh.GetScope().GetBioseqHandle(*head.GetRangeAsSeq_loc()); in ValidateSpliceMrna()
561 CBioseq_Handle bsh_head = bsh.GetScope().GetBioseqHandle(*head.GetRangeAsSeq_loc()); in ValidateSpliceCdregion()
587 CBioseq_Handle bsh_head = bsh.GetScope().GetBioseqHandle(*head.GetRangeAsSeq_loc()); in ValidateSpliceCdregion()
[all …]
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