| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/util/ |
| H A D | seq_loc_util.hpp | 377 CRef<CSeq_loc> Seq_loc_Merge(const CSeq_loc& loc,
392 return Seq_loc_Merge(temp, flags, scope); in Seq_locs_Merge()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/util/ |
| H A D | seq_loc_util.hpp | 377 CRef<CSeq_loc> Seq_loc_Merge(const CSeq_loc& loc,
392 return Seq_loc_Merge(temp, flags, scope); in Seq_locs_Merge()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
| H A D | compare_feats.cpp | 289 loc1 = sequence::Seq_loc_Merge(*m_loc1, CSeq_loc::fSort, m_scope_t); in x_Compare()
290 loc2 = sequence::Seq_loc_Merge(*m_loc2, CSeq_loc::fSort, m_scope_t); in x_Compare()
440 CRef<CSeq_loc> merged_loc1 = sequence::Seq_loc_Merge(*m_loc1, CSeq_loc::fMerge_All, m_scope_t); in x_ComputeOverlapValues()
441 CRef<CSeq_loc> merged_loc2 = sequence::Seq_loc_Merge(*m_loc2, CSeq_loc::fMerge_All, m_scope_t); in x_ComputeOverlapValues()
862 …CConstRef<CSeq_loc> feat1_mapped_range_loc = sequence::Seq_loc_Merge(*feat1_mapped_loc, CSeq_loc::… in x_GetPutativeMatches()
956 new_loc = sequence::Seq_loc_Merge( in x_GetSelfLoc()
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| H A D | project_exons.cpp | 1434 sequence::Seq_loc_Merge( in ProjectAndCollapseCDS()
1698 sequence::Seq_loc_Merge( in s_ProjectRNA()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/hgvs/ |
| H A D | variation_util.cpp | 293 …CRef<CSeq_loc> range_loc = sequence::Seq_loc_Merge(v.GetLocation(), CSeq_loc::fMerge_SingleRange, … in s_ResolveIntronicOffsets()
308 …CRef<CSeq_loc> range_loc = sequence::Seq_loc_Merge(v.GetLocation(), CSeq_loc::fMerge_SingleRange, … in s_ResolveIntronicOffsets()
370 CRef<CSeq_loc> loc = sequence::Seq_loc_Merge(vloc, CSeq_loc::fMerge_SingleRange, NULL); in s_AddIntronicOffsets()
444 …CRef<CSeq_loc> merged_mapped_loc = sequence::Seq_loc_Merge(*mapped_loc, CSeq_loc::fSortAndMerge_Al… in s_Remap()
452 …CRef<CSeq_loc> merged_mapped_loc = sequence::Seq_loc_Merge(*mapped_loc, CSeq_loc::fSortAndMerge_Al… in s_Remap()
762 v2->SetLocation(*sequence::Seq_loc_Merge(*nuc_loc, CSeq_loc::fSortAndMerge_All, NULL)); in x_ProtToPrecursor()
952 CRef<CSeq_loc> tmp_loc = sequence::Seq_loc_Merge(loc, CSeq_loc::fMerge_SingleRange, NULL); in AdjustDelinsToInterval()
956 tmp_loc = sequence::Seq_loc_Merge(loc, CSeq_loc::fMerge_SingleRange, NULL); in AdjustDelinsToInterval()
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| H A D | variation_util2.cpp | 346 sequence::Seq_loc_Merge( in s_ResolveIntronicOffsets()
387 loc = sequence::Seq_loc_Merge(*loc, CSeq_loc::fSortAndMerge_All, NULL); in s_ResolveIntronicOffsets()
458 … CRef<CSeq_loc> int_loc = sequence::Seq_loc_Merge(p.GetLoc(), CSeq_loc::fMerge_SingleRange, NULL); in s_AddIntronicOffsets()
951 mapped_loc = sequence::Seq_loc_Merge( in x_Remap()
1580 p2->SetLoc(*sequence::Seq_loc_Merge(*nuc_loc, CSeq_loc::fSortAndMerge_All, NULL)); in x_InferNAfromAA()
2204 CRef<CSeq_loc> range_loc = sequence::Seq_loc_Merge(loc, CSeq_loc::fMerge_SingleRange, NULL); in x_AdjustDelinsToInterval()
3187 cds_loc = sequence::Seq_loc_Merge(*cds_loc, CSeq_loc::fMerge_SingleRange, NULL); in FindLocationProperties()
3638 sequence::Seq_loc_Merge( in x_Index()
3897 p.first = sequence::Seq_loc_Merge(cds_loc, CSeq_loc::fMerge_SingleRange, NULL); in s_GetStartAndStopCodonsLocs()
3946 p.first = sequence::Seq_loc_Merge(gene_loc, CSeq_loc::fMerge_SingleRange, NULL); in s_GetNeighborhoodLocs()
[all …]
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| H A D | hgvs_writer2.cpp | 108 sequence::Seq_loc_Merge( p.GetLoc(), in x_AdjustPlacementForHgvs()
733 int_loc = sequence::Seq_loc_Merge(vp.GetLoc(), CSeq_loc::fMerge_SingleRange, m_scope); in x_PlacementCoordsToStr()
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| H A D | hgvs_parser2.cpp | 193 CRef<CSeq_loc> loc1 = sequence::Seq_loc_Merge(loc, CSeq_loc::fMerge_SingleRange, NULL); in FindSSRLoc()
223 …CRef<CSeq_loc> merged_repeats = sequence::Seq_loc_Merge(*container, CSeq_loc::fSortAndMerge_All, N… in FindSSRLoc()
235 return sequence::Seq_loc_Merge(*result, CSeq_loc::fSortAndMerge_All, NULL); in FindSSRLoc()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/demo/ |
| H A D | xcompareannotsdemo.cpp | 218 CRef<CSeq_loc> mapped_interval_merged = sequence::Seq_loc_Merge( in Map()
420 CRef<CSeq_loc> tmp_loc = sequence::Seq_loc_Merge(loc, CSeq_loc::fMerge_SingleRange, &scope); in GetIdStartStopStrandStr()
895 …CRef<CSeq_loc> qry_rgn_loc = sequence::Seq_loc_Merge(*m_q_loc, CSeq_loc::fMerge_SingleRange, m_sco… in x_ProcessMappingRanges()
920 …CRef<CSeq_loc> rgn_loc = sequence::Seq_loc_Merge(*m_q_loc, CSeq_loc::fMerge_SingleRange, m_scope_… in x_ProcessMappingRanges()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/ngalign/ |
| H A D | sequence_set.cpp | 232 MaskLoc = sequence::Seq_loc_Merge(*MaskLoc, CSeq_loc::fSortAndMerge_All, in s_GetMaskLoc()
351 UngapLoc = sequence::Seq_loc_Merge(*UngapLoc, CSeq_loc::fSortAndMerge_All, in s_GetUngapLoc()
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| H A D | banded_aligner.cpp | 99 Merged = sequence::Seq_loc_Merge(*Accum, CSeq_loc::fSortAndMerge_All, &Scope); in s_CoverageSeqLoc()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/ |
| H A D | compare_feats.hpp | 439 … CRef<CSeq_loc> merged_loc = sequence::Seq_loc_Merge(loc, CSeq_loc::fMerge_SingleRange, NULL); in s_GetLocLabel()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/alnmgr/ |
| H A D | alntext.cpp | 432 genomic = sequence::Seq_loc_Merge(*genomic, CSeq_loc::fMerge_SingleRange, NULL); in GetGenomicBounds()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/alnmgr/ |
| H A D | alntext.cpp | 432 genomic = sequence::Seq_loc_Merge(*genomic, CSeq_loc::fMerge_SingleRange, NULL); in GetGenomicBounds()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | gap_trim.cpp | 76 …CRef<CSeq_loc> total_loc = sequence::Seq_loc_Merge(feat_loc, CSeq_loc::fMerge_SingleRange, &scope); in CollectGaps()
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| H A D | loc_edit.cpp | 640 …CRef<CSeq_loc> new_loc = sequence::Seq_loc_Merge(feat.GetLocation(), CSeq_loc::fMerge_SingleRange,… in ApplyPolicyToFeature()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | gap_trim.cpp | 76 …CRef<CSeq_loc> total_loc = sequence::Seq_loc_Merge(feat_loc, CSeq_loc::fMerge_SingleRange, &scope); in CollectGaps()
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| H A D | loc_edit.cpp | 640 …CRef<CSeq_loc> new_loc = sequence::Seq_loc_Merge(feat.GetLocation(), CSeq_loc::fMerge_SingleRange,… in ApplyPolicyToFeature()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
| H A D | gather_items.cpp | 3601 feat_loc = Seq_loc_Merge(*feat_loc, CSeq_loc::fMerge_Abutting, &scope); in x_GatherFeaturesOnRangeIdx()
4375 loc = Seq_loc_Merge(*loc, CSeq_loc::fMerge_Abutting, &scope); in x_GetFeatsOnCdsProductIdx()
4488 loc = Seq_loc_Merge(*loc, CSeq_loc::fMerge_Abutting, &scope); in x_GetFeatsOnCdsProduct()
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| H A D | reference_item.cpp | 237 m_Loc = Seq_loc_Merge(*m_Loc, merge_flags, &ctx.GetScope()); in CReferenceItem()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
| H A D | gather_items.cpp | 3601 feat_loc = Seq_loc_Merge(*feat_loc, CSeq_loc::fMerge_Abutting, &scope); in x_GatherFeaturesOnRangeIdx()
4373 loc = Seq_loc_Merge(*loc, CSeq_loc::fMerge_Abutting, &scope); in x_GetFeatsOnCdsProductIdx()
4486 loc = Seq_loc_Merge(*loc, CSeq_loc::fMerge_Abutting, &scope); in x_GetFeatsOnCdsProduct()
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| H A D | reference_item.cpp | 237 m_Loc = Seq_loc_Merge(*m_Loc, merge_flags, &ctx.GetScope()); in CReferenceItem()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
| H A D | seq_loc_util.cpp | 2098 CRef<CSeq_loc> Seq_loc_Merge(const CSeq_loc& loc, in Seq_loc_Merge() function
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| H A D | sequence.cpp | 3202 = sequence::Seq_loc_Merge(*location, merge_flags, &scope); in WriteSequence()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/ |
| H A D | seq_loc_util.cpp | 2098 CRef<CSeq_loc> Seq_loc_Merge(const CSeq_loc& loc, in Seq_loc_Merge() function
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