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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/test/
H A Dtest_fix_feature_ids.cpp71 auto orig_feat = fh_feat.first; in sx_RunTest_Unique_Feature_Ids() local
73 CSeq_feat_EditHandle feh(orig_feat); in sx_RunTest_Unique_Feature_Ids()
117 auto orig_feat = fh_feat.first; in sx_RunTest_Reassign_Feature_Ids() local
119 CSeq_feat_EditHandle feh(orig_feat); in sx_RunTest_Reassign_Feature_Ids()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/
H A Dseq_loc_cvt.hpp121 const CSeq_feat& orig_feat,
124 const CSeq_feat& orig_feat,
127 const CSeq_feat& orig_feat,
378 const CSeq_feat& orig_feat,
381 const CSeq_feat& orig_feat,
384 const CSeq_feat& orig_feat,
H A Dannot_collector.hpp160 const CSeq_feat* orig_feat) const;
289 const CSeq_feat& orig_feat);
293 const CSeq_feat& orig_feat);
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/
H A Dseq_loc_cvt.hpp121 const CSeq_feat& orig_feat,
124 const CSeq_feat& orig_feat,
127 const CSeq_feat& orig_feat,
378 const CSeq_feat& orig_feat,
381 const CSeq_feat& orig_feat,
384 const CSeq_feat& orig_feat,
H A Dannot_collector.hpp160 const CSeq_feat* orig_feat) const;
289 const CSeq_feat& orig_feat);
293 const CSeq_feat& orig_feat);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dseq_loc_cvt.cpp1160 switch ( orig_feat.GetData().Which() ) { in ConvertFeature()
1162 ConvertCdregion(ref, orig_feat, mapped_feat); in ConvertFeature()
1165 ConvertRna(ref, orig_feat, mapped_feat); in ConvertFeature()
1182 CConstRef<CSeq_feat> orig_feat; in Convert() local
1184 orig_feat = obj.GetFeatFast(); in Convert()
1195 orig_feat = created_feat; in Convert()
1280 CConstRef<CSeq_feat> orig_feat; in Convert() local
1282 orig_feat = obj.GetFeatFast(); in Convert()
1293 orig_feat = created_feat; in Convert()
1683 switch ( orig_feat.GetData().Which() ) { in ConvertFeature()
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H A Dannot_collector.cpp252 orig_feat->GetProduct(): orig_feat->GetLocation(); in UpdateMappedSeq_loc()
1532 CRef<CSeq_feat> orig_feat; in GetOriginalFeature() local
1536 snp_info.UpdateSeq_feat(orig_feat, in GetOriginalFeature()
1540 ret = orig_feat; in GetOriginalFeature()
1549 CRef<CSeq_feat> orig_feat; in GetOriginalFeature() local
1554 orig_feat, in GetOriginalFeature()
1557 ret = orig_feat; in GetOriginalFeature()
1602 &orig_feat); in GetMappedLocation()
1644 const CSeq_feat& orig_feat) in GetMappedFeature() argument
1651 ret = &orig_feat; in GetMappedFeature()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dseq_loc_cvt.cpp1160 switch ( orig_feat.GetData().Which() ) { in ConvertFeature()
1162 ConvertCdregion(ref, orig_feat, mapped_feat); in ConvertFeature()
1165 ConvertRna(ref, orig_feat, mapped_feat); in ConvertFeature()
1182 CConstRef<CSeq_feat> orig_feat; in Convert() local
1184 orig_feat = obj.GetFeatFast(); in Convert()
1195 orig_feat = created_feat; in Convert()
1280 CConstRef<CSeq_feat> orig_feat; in Convert() local
1282 orig_feat = obj.GetFeatFast(); in Convert()
1293 orig_feat = created_feat; in Convert()
1683 switch ( orig_feat.GetData().Which() ) { in ConvertFeature()
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H A Dannot_collector.cpp252 orig_feat->GetProduct(): orig_feat->GetLocation(); in UpdateMappedSeq_loc()
1532 CRef<CSeq_feat> orig_feat; in GetOriginalFeature() local
1536 snp_info.UpdateSeq_feat(orig_feat, in GetOriginalFeature()
1540 ret = orig_feat; in GetOriginalFeature()
1549 CRef<CSeq_feat> orig_feat; in GetOriginalFeature() local
1554 orig_feat, in GetOriginalFeature()
1557 ret = orig_feat; in GetOriginalFeature()
1602 &orig_feat); in GetMappedLocation()
1644 const CSeq_feat& orig_feat) in GetMappedFeature() argument
1651 ret = &orig_feat; in GetMappedFeature()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/
H A Dloc_edit.cpp301 (const CSeq_feat& orig_feat, in Interpret5Policy() argument
308 const CSeq_loc& loc = orig_feat.GetLocation(); in Interpret5Policy()
335 && orig_feat.GetData().IsCdregion()) { in Interpret5Policy()
353 && orig_feat.GetData().IsCdregion() in Interpret5Policy()
354 && orig_feat.GetData().GetCdregion().IsSetFrame() in Interpret5Policy()
375 && orig_feat.GetData().IsCdregion() in Interpret5Policy()
400 (const CSeq_feat& orig_feat, in Interpret3Policy() argument
407 const CSeq_loc& loc = orig_feat.GetLocation(); in Interpret3Policy()
435 && orig_feat.GetData().IsCdregion()) { in Interpret3Policy()
470 && orig_feat.GetData().IsCdregion()) { in Interpret3Policy()
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H A Dapply_object.cpp124 const CSeq_feat* orig_feat = dynamic_cast<const CSeq_feat * >(m_Original.GetPointer()); in ApplyChange() local
133 } else if (orig_feat) { in ApplyChange()
134 CSeq_feat_Handle oh = m_SEH.GetScope().GetSeq_featHandle(*orig_feat); in ApplyChange()
H A Dfeature_propagate.cpp129 CRef<CSeq_feat> CFeaturePropagator::Propagate(const CSeq_feat& orig_feat) in Propagate() argument
132 rval->Assign(orig_feat); in Propagate()
136 m_FeatIdMap.emplace(orig_feat.GetId().GetLocal().GetId(), rval->GetId().GetLocal().GetId()); in Propagate()
142 CRef<CSeq_loc> new_loc = x_MapLocation(orig_feat.GetLocation(), *pTargetId); in Propagate()
146 orig_feat.GetLocation().GetLabel(&loc_label); in Propagate()
165 const CSeq_loc& location = orig_feat.GetLocation(); in Propagate()
169 switch(orig_feat.GetData().GetSubtype()) { in Propagate()
H A Dcds_fix.cpp977 bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat) in DemoteCDSToNucSeq() argument
979 CSeq_feat_EditHandle feh(orig_feat); in DemoteCDSToNucSeq()
996 const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot(); in DemoteCDSToNucSeq()
1018 orig_feat = new_annot.TakeFeat(feh); in DemoteCDSToNucSeq()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/
H A Dloc_edit.cpp301 (const CSeq_feat& orig_feat, in Interpret5Policy() argument
308 const CSeq_loc& loc = orig_feat.GetLocation(); in Interpret5Policy()
335 && orig_feat.GetData().IsCdregion()) { in Interpret5Policy()
353 && orig_feat.GetData().IsCdregion() in Interpret5Policy()
354 && orig_feat.GetData().GetCdregion().IsSetFrame() in Interpret5Policy()
375 && orig_feat.GetData().IsCdregion() in Interpret5Policy()
400 (const CSeq_feat& orig_feat, in Interpret3Policy() argument
407 const CSeq_loc& loc = orig_feat.GetLocation(); in Interpret3Policy()
435 && orig_feat.GetData().IsCdregion()) { in Interpret3Policy()
470 && orig_feat.GetData().IsCdregion()) { in Interpret3Policy()
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H A Dapply_object.cpp124 const CSeq_feat* orig_feat = dynamic_cast<const CSeq_feat * >(m_Original.GetPointer()); in ApplyChange() local
133 } else if (orig_feat) { in ApplyChange()
134 CSeq_feat_Handle oh = m_SEH.GetScope().GetSeq_featHandle(*orig_feat); in ApplyChange()
H A Dfeature_propagate.cpp129 CRef<CSeq_feat> CFeaturePropagator::Propagate(const CSeq_feat& orig_feat) in Propagate() argument
132 rval->Assign(orig_feat); in Propagate()
136 m_FeatIdMap.emplace(orig_feat.GetId().GetLocal().GetId(), rval->GetId().GetLocal().GetId()); in Propagate()
142 CRef<CSeq_loc> new_loc = x_MapLocation(orig_feat.GetLocation(), *pTargetId); in Propagate()
146 orig_feat.GetLocation().GetLabel(&loc_label); in Propagate()
165 const CSeq_loc& location = orig_feat.GetLocation(); in Propagate()
169 switch(orig_feat.GetData().GetSubtype()) { in Propagate()
H A Dcds_fix.cpp977 bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat) in DemoteCDSToNucSeq() argument
979 CSeq_feat_EditHandle feh(orig_feat); in DemoteCDSToNucSeq()
996 const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot(); in DemoteCDSToNucSeq()
1018 orig_feat = new_annot.TakeFeat(feh); in DemoteCDSToNucSeq()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/edit/
H A Dloc_edit.hpp97 …bool Interpret5Policy(const CSeq_feat& orig_feat, CScope& scope, bool& do_set_5_partial, bool& do_…
98 …bool Interpret3Policy(const CSeq_feat& orig_feat, CScope& scope, bool& do_set_3_partial, bool& do_…
127 const CSeq_feat& orig_feat,
H A Dcds_fix.hpp58 NCBI_XOBJEDIT_EXPORT bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat);
H A Dfeature_propagate.hpp64 CRef<CSeq_feat> Propagate(const objects::CSeq_feat& orig_feat);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/edit/
H A Dloc_edit.hpp97 …bool Interpret5Policy(const CSeq_feat& orig_feat, CScope& scope, bool& do_set_5_partial, bool& do_…
98 …bool Interpret3Policy(const CSeq_feat& orig_feat, CScope& scope, bool& do_set_3_partial, bool& do_…
127 const CSeq_feat& orig_feat,
H A Dcds_fix.hpp58 NCBI_XOBJEDIT_EXPORT bool DemoteCDSToNucSeq(objects::CSeq_feat_Handle& orig_feat);
H A Dfeature_propagate.hpp64 CRef<CSeq_feat> Propagate(const objects::CSeq_feat& orig_feat);
/dports/games/stonesoup/crawl-0.27.1/crawl-ref/source/
H A Dterrain.cc1324 const dungeon_feature_type orig_feat = env.grid(dest_pos); in _announce_swap_real() local
1330 string prep = feat_preposition(orig_feat, false); in _announce_swap_real()
1610 const dungeon_feature_type orig_feat, in _ok_dest_cell() argument
1615 if (orig_feat == dest_feat) in _ok_dest_cell()
1628 if (dest_actor && !dest_actor->is_habitable_feat(orig_feat)) in _ok_dest_cell()
1639 const dungeon_feature_type orig_feat = env.grid(src); in slide_feature_over() local
1643 && _ok_dest_cell(orig_actor, orig_feat, preferred_dest)) in slide_feature_over()
1652 if (_ok_dest_cell(orig_actor, orig_feat, *ai) in slide_feature_over()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/
H A Dfix_feature_id.cpp327 auto orig_feat = entry.first; in s_ApplyToSeqInSet() local
329 CSeq_feat_EditHandle feh(orig_feat); in s_ApplyToSeqInSet()

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