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NCBI C++ ToolKit: src/objtools/flatfile/genref.cpp File Reference

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  USING_SCOPE (objects)   static void  GetLocationStr (const CSeq_loc &loc, string &str)   static bool  fta_seqid_same (const CSeq_id &sid, const Char *acnum, const CSeq_id *id)   static void  fta_seqloc_del_far (CSeq_loc &locs, const Char *acnum, const CSeq_id *id)   static CRef< CSeq_loc >  fta_seqloc_local (const CSeq_loc &orig, const Char *acnum)   static Int4  fta_cmp_gene_syns (const TSynSet &syn1, const TSynSet &syn2)   static Int4  fta_cmp_gene_refs (const CGene_ref &grp1, const CGene_ref &grp2)   static Int4  fta_cmp_locusyn (const Gene &g1, const Gene &g2)   static bool  CompareGeneListName (const Gene &g1, const Gene &g2)   static SeqlocInfoblkPtr  GetLowHighFromSeqLoc (const CSeq_loc *origslp, Int4 length, const CSeq_id &orig_id)   static bool  DoWeHaveGeneInBetween (Gene &g, SeqlocInfoblkPtr second, const GeneNode *gnp)   static bool  DoWeHaveCdssInBetween (const Gene &g, Int4 to, const TCdsList &cdsl)   static void  AddGeneFeat (Gene &g, const string &maploc, TSeqFeatList &feats)   static bool  s_IdsMatch (const CRef< CSeq_id > &pId1, const CRef< CSeq_id > &pId2)   static TMixLocList  EasySeqLocMerge (const TMixLocList &first, const TMixLocList &second, bool join)   static TMixLocList  CircularSeqLocCollect (const TMixLocList &first, const TMixLocList &second)   static void  fta_add_wormbase (Gene &fromg, Gene &tog)   static void  fta_add_olt (Gene &fromg, Gene &tog)   static void  fta_check_pseudogene (Gene &tg, Gene &g)   static bool  fta_check_feat_overlap (const TGeneLocList &gelocs, Gene &g, const MixLoc &ml, Int4 from, Int4 to)   static bool  ConfirmCircular (TMixLocList &mll)   static void  FixMixLoc (Gene &g, const TGeneLocList &gelocs)   static void  fta_make_seq_int (MixLoc &ml, bool noleft, bool noright, CSeq_interval &interval)   static void  fta_make_seq_pnt (MixLoc &ml, bool noleft, bool noright, CSeq_point &point)   static CRef< CSeq_loc >  MakeCLoc (TMixLocList &mll, bool noleft, bool noright)   static Int2  GetMergeOrder (const TMixLocList &first, const TMixLocList &second)   static void  CircularSeqLocFormat (Gene &g)   static void  SortMixLoc (TMixLocList &mll)   static void  ScannGeneName (GeneNodePtr gnp, Int4 seqlen)   static CRef< CSeq_id >  CpSeqIdAcOnly (const CSeq_id &id, bool accver)   static bool  WeDontNeedToJoinThis (const CSeqFeatData &data)   static void  GetGeneSyns (const TQualVector &quals, const string &name, TSynSet &syns)   static bool  fta_rnas_cds_feat (const CSeq_feat &feat)   static bool  IfCDSGeneFeat (const CSeq_feat &feat, Uint1 choice, const char *key)   static bool  GetFeatNameAndLoc (Gene *glp, const CSeq_feat &feat, GeneNodePtr gnp)   static list< AccMinMax >  fta_get_acc_minmax_strand (const CSeq_loc *location, GeneLoc *gelop)   static void  fta_append_feat_list (GeneNodePtr gnp, const CSeq_loc *location, const string &gene, const string &locus_tag)   static bool  CompareGeneLocsMinMax (const GeneLoc &sp1, const GeneLoc &sp2)   static void  fta_collect_wormbases (Gene &g, CSeq_feat &feat)   static void  fta_collect_olts (Gene &g, CSeq_feat &feat)   static void  SrchGene (CSeq_annot::C_Data::TFtable &feats, GeneNodePtr gnp, Int4 length, const CSeq_id &id)   static void  SrchCDSs (CSeq_annot::C_Data::TFtable &feats, TCdsList &cdsl, const CSeq_id &id)   static void  FindGene (CBioseq &bioseq, GeneNodePtr gene_node)   static void  GeneCheckForStrands (const TGeneList &gl)   static bool  LocusTagCheck (TGeneList &gl, bool &resort)   static void  MiscFeatsWithoutGene (GeneNodePtr gnp)   static void  RemoveUnneededMiscFeats (GeneNodePtr gnp)   static bool  GeneLocusCheck (const TSeqFeatList &feats, bool diff_lt)   static void  CheckGene (CRef< CSeq_entry > entry, ParserPtr pp, GeneRefFeats &gene_refs)   bool  GenelocContained (const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)   static CRef< CSeqFeatXref >  GetXrpForOverlap (const char *acnum, GeneRefFeats &gene_refs, const TSeqLocInfoList &llocs, const CSeq_feat &feat, CGene_ref &gerep)   static void  FixAnnot (CBioseq::TAnnot &annots, const char *acnum, GeneRefFeats &gene_refs, TSeqLocInfoList &llocs)   static void  GeneQuals (CSeq_entry &entry, const char *acnum, GeneRefFeats &gene_refs)   static void  fta_collect_genes (const CBioseq &bioseq, std::set< string > &genes)   static void  fta_fix_labels (CBioseq &bioseq, const std::set< string > &genes)   void  DealWithGenes (CRef< CSeq_entry > &pEntry, ParserPtr pp)   ◆ THIS_FILE #define THIS_FILE   "genref.cpp"

Definition at line 66 of file genref.cpp.

◆ GeneNodePtr ◆ SeqlocInfoblkPtr ◆ TCdsList ◆ TGeneList ◆ TGeneLocList ◆ TLocusTagSet ◆ TMixLocList ◆ TSeqLocInfoList ◆ TSynSet ◆ TWormbaseSet ◆ AddGeneFeat()

Definition at line 571 of file genref.cpp.

References ERR_FEATURE_MultipleOldLocusTags, ERR_FEATURE_MultipleWBGeneXrefs, FtaErrPost, g(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetDbxref(), CSeq_feat_Base::SetLocation(), CGene_ref_Base::SetLocus(), CGene_ref_Base::SetLocus_tag(), CGene_ref_Base::SetMaploc(), CSeq_feat_Base::SetPseudo(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CGene_ref_Base::SetSyn(), CGb_qual_Base::SetVal(), SEV_WARNING, and tag.

Referenced by ScannGeneName().

◆ CheckGene()

Definition at line 2192 of file genref.cpp.

References Parser::accver, GeneNode::accver, Begin(), GeneNode::bioseq, GeneNode::circular, CompareGeneListName(), Parser::curindx, Parser::diff_lt, Indexblk::division, Indexblk::drop, Parser::entrylist, GeneNode::feats, FindGene(), GeneRefFeats::first, GeneCheckForStrands(), GeneLocusCheck(), CBioseq::GetLength(), GeneNode::gl, GeneNode::got_misc, Indexblk::got_plastid, GeneRefFeats::last, LocusTagCheck(), MiscFeatsWithoutGene(), RemoveUnneededMiscFeats(), ScannGeneName(), CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), Parser::simple_genes, GeneNode::simple_genes, GeneNode::skipdiv, StringEqu(), and GeneRefFeats::valid.

Referenced by DealWithGenes().

◆ CircularSeqLocCollect() ◆ CircularSeqLocFormat() ◆ CompareGeneListName() ◆ CompareGeneLocsMinMax() ◆ ConfirmCircular() ◆ CpSeqIdAcOnly() ◆ DealWithGenes()

Definition at line 2520 of file genref.cpp.

References Begin(), CheckGene(), Parser::curindx, Parser::entrylist, eSeqlocPartial_Start, eSeqlocPartial_Stop, GeneRefFeats::first, Parser::Flybase, fta_collect_genes(), fta_fix_labels(), Parser::genenull, GeneQuals(), GetScope(), GeneRefFeats::last, ProcNucProt(), SeqLocPartialCheck(), CSeq_loc_mix_Base::Set(), CSeq_loc::SetNull(), Parser::source, and GeneRefFeats::valid.

Referenced by OutputEmblAsn(), CGenbank2Asn::xGetEntry(), and CXml2Asn::xGetEntry().

◆ DoWeHaveCdssInBetween() ◆ DoWeHaveGeneInBetween() ◆ EasySeqLocMerge() ◆ FindGene()

Definition at line 1933 of file genref.cpp.

References GeneNode::accver, GeneNode::bioseq, GeneNode::cdsl, GeneNode::circular, CpSeqIdAcOnly(), CSeq_inst_Base::eTopology_circular, GeneNode::flag, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CBioseq::GetLength(), CSeq_inst_Base::GetTopology(), GeneNode::gl, CBioseq_Base::IsSetAnnot(), CBioseq_Base::SetAnnot(), GeneNode::skipdiv, SrchCDSs(), and SrchGene().

Referenced by CheckGene().

◆ FixAnnot() ◆ FixMixLoc()

Definition at line 890 of file genref.cpp.

References CSeq_id::Assign(), CSeq_loc::begin(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, CSeq_loc::end(), fta_check_feat_overlap(), g(), CSeq_interval_Base::GetFrom(), CSeq_point_Base::GetFuzz(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc_Base::GetInt(), CInt_fuzz_Base::GetLim(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc::GetStrand(), CSeq_interval_Base::GetTo(), i, CSeq_loc_Base::IsInt(), CInt_fuzz_Base::IsLim(), CSeq_loc_Base::IsPnt(), CSeq_interval_Base::IsSetFrom(), CSeq_point_Base::IsSetFuzz(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetId(), CSeq_point_Base::IsSetId(), CSeq_point_Base::IsSetPoint(), CSeq_loc::IsSetStrand(), CSeq_interval_Base::IsSetTo(), next(), Ref(), and s_IdsMatch().

Referenced by ScannGeneName().

◆ fta_add_olt() ◆ fta_add_wormbase() ◆ fta_append_feat_list() ◆ fta_check_feat_overlap() ◆ fta_check_pseudogene() ◆ fta_cmp_gene_refs() ◆ fta_cmp_gene_syns() ◆ fta_cmp_locusyn() ◆ fta_collect_genes() ◆ fta_collect_olts() ◆ fta_collect_wormbases() ◆ fta_fix_labels() ◆ fta_get_acc_minmax_strand()

Definition at line 1667 of file genref.cpp.

References _ASSERT, CSeq_id::Assign(), eNa_strand_unknown, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_interval_Base::GetStrand(), CSeq_point_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPnt(), CSeq_interval_Base::IsSetId(), CSeq_point_Base::IsSetId(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), location, AccMinMax::max, AccMinMax::min, AccMinMax::pId, Ref(), s_IdsMatch(), GeneLoc::strand, GeneLoc::verymax, and GeneLoc::verymin.

Referenced by fta_append_feat_list().

◆ fta_make_seq_int()

Definition at line 1027 of file genref.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, MixLoc::max, MixLoc::min, MixLoc::noleft, MixLoc::noright, MixLoc::pId, CSeq_interval_Base::SetFrom(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_interval_Base::SetId(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), and MixLoc::strand.

Referenced by MakeCLoc().

◆ fta_make_seq_pnt()

Definition at line 1047 of file genref.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, MixLoc::min, MixLoc::noleft, MixLoc::noright, MixLoc::pId, CSeq_point_Base::SetFuzz(), CSeq_point_Base::SetId(), CSeq_point_Base::SetPoint(), CSeq_point_Base::SetStrand(), and MixLoc::strand.

Referenced by MakeCLoc().

◆ fta_rnas_cds_feat()

Definition at line 1537 of file genref.cpp.

References CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::GetType(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsImp(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), CImp_feat_Base::IsSetKey(), CRNA_ref_Base::IsSetType(), and ncbi::grid::netcache::search::fields::key.

Referenced by SrchGene().

◆ fta_seqid_same() ◆ fta_seqloc_del_far()

Definition at line 256 of file genref.cpp.

References CSeq_loc::Assign(), CSeq_loc_CI::eEmpty_Allow, CSeq_loc::end(), fta_seqid_same(), CSeq_bond_Base::GetA(), CSeq_loc_Base::GetBond(), CPacked_seqpnt_Base::GetId(), CSeq_interval_Base::GetId(), CSeq_loc::GetId(), CSeq_point_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::IsBond(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPacked_pnt(), CSeq_loc_Base::IsPnt(), CSeq_bond_Base::IsSetA(), CSeq_loc_Base::IsWhole(), and CSeq_loc::Subtract().

Referenced by fta_seqloc_local().

◆ fta_seqloc_local() ◆ GeneCheckForStrands() ◆ GenelocContained() ◆ GeneLocusCheck() ◆ GeneQuals() ◆ GetFeatNameAndLoc()

Definition at line 1580 of file genref.cpp.

References feat_no_gene, Gene::fname, CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CSeq_feat_Base::GetLocation(), GetLocationStr(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::GetType(), GeneNode::got_misc, if(), CSeqFeatData_Base::IsBiosrc(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CSeqFeatData_Base::IsImp(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), CImp_feat_Base::IsSetKey(), CSeq_feat_Base::IsSetLocation(), CRNA_ref_Base::IsSetType(), Gene::location, MatchArrayString(), and StringEqu().

Referenced by SrchGene().

◆ GetGeneSyns() ◆ GetLocationStr() ◆ GetLowHighFromSeqLoc()

Definition at line 440 of file genref.cpp.

References CSeq_id::Assign(), CSeq_id::Compare(), CSeq_id::e_NO, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, SeqlocInfoblk::from, CSeq_interval_Base::GetFrom(), CSeq_point_Base::GetFuzz(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc_Base::GetInt(), CInt_fuzz_Base::GetLim(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_interval_Base::GetStrand(), CSeq_point_Base::GetStrand(), CSeq_interval_Base::GetTo(), SeqlocInfoblk::ids, CSeq_loc_Base::IsInt(), CInt_fuzz_Base::IsLim(), CSeq_loc_Base::IsPnt(), CSeq_point_Base::IsSetFuzz(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), SeqlocInfoblk::length, SeqlocInfoblk::noleft, SeqlocInfoblk::noright, SeqlocInfoblk::strand, and SeqlocInfoblk::to.

Referenced by SrchCDSs(), and SrchGene().

◆ GetMergeOrder() ◆ GetXrpForOverlap()

Definition at line 2320 of file genref.cpp.

References count, CConstRef< C, Locker >::Empty(), GeneRefFeats::first, fta_cmp_gene_refs(), fta_seqloc_local(), GenelocContained(), CSeq_feat_Base::GetLocation(), GeneRefFeats::last, CConstRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), and GeneRefFeats::valid.

Referenced by FixAnnot().

◆ IfCDSGeneFeat() ◆ LocusTagCheck() ◆ MakeCLoc() ◆ MiscFeatsWithoutGene() ◆ RemoveUnneededMiscFeats() ◆ s_IdsMatch() ◆ ScannGeneName()

Definition at line 1286 of file genref.cpp.

References AddGeneFeat(), GeneNode::cdsl, GeneNode::circular, CircularSeqLocCollect(), CircularSeqLocFormat(), Compare(), ConfirmCircular(), DoWeHaveCdssInBetween(), DoWeHaveGeneInBetween(), EasySeqLocMerge(), eContains, NStr::EqualNocase(), ERR_GENEREF_NoUniqMaploc, eSame, fCompareOverlapping, GeneNode::feats, FixMixLoc(), fta_add_olt(), fta_add_wormbase(), fta_check_pseudogene(), fta_cmp_locusyn(), FtaErrPost, GeneNode::gelocs, GetMergeOrder(), GeneNode::gl, join(), MakeCLoc(), next(), SEV_WARNING, GeneNode::simple_genes, GeneNode::skipdiv, and SortMixLoc().

Referenced by CheckGene().

◆ SortMixLoc() ◆ SrchCDSs() ◆ SrchGene()

Definition at line 1824 of file genref.cpp.

References Gene::allpseudo, CSeq_loc::Assign(), CSerialObject::Assign(), CompareGeneLocsMinMax(), CpTheQualValue(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, Gene::feat, fta_append_feat_list(), fta_collect_olts(), fta_collect_wormbases(), fta_rnas_cds_feat(), GeneNode::gelocs, Gene::genefeat, GetFeatNameAndLoc(), GetGeneSyns(), GetLowHighFromSeqLoc(), GetTheQualValue(), GeneNode::gl, IfCDSGeneFeat(), CSeq_loc_Base::IsMix(), Gene::leave, Gene::loc, Gene::locus, Gene::locus_tag, Gene::maploc, SeqlocInfoblk::noleft, Gene::noleft, SeqlocInfoblk::noright, Gene::noright, Gene::pseudo, Gene::pseudogene, CRef< C, Locker >::Reset(), GeneNode::simple_genes, Gene::slibp, Gene::syn, Gene::todel, and WeDontNeedToJoinThis().

Referenced by FindGene().

◆ USING_SCOPE() ◆ WeDontNeedToJoinThis()

Definition at line 1475 of file genref.cpp.

References b, data, CRNA_ref_Base::eType_other, CRNA_ref_Base::GetExt(), CRNA_ref_Base::C_Ext::GetName(), CRNA_ref_Base::GetType(), i, CRNA_ref_Base::C_Ext::IsName(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::IsSetType(), leave_imp_feat, and leave_rna_feat.

Referenced by SrchGene().

◆ feat_no_gene const char* feat_no_gene[] = { "gap", "operon", "source", nullptr } ◆ leave_imp_feat const char* leave_imp_feat[] ◆ leave_rna_feat

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