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  C++/include/objects/seq/seq_macros.hpp


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#ifndef OBJECTS_SEQ___SEQ_MACROS__HPP #define OBJECTS_SEQ___SEQ_MACROS__HPP /* $Id: seq_macros.hpp 59539 2013-09-03 19:16:46Z kornbluh $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Authors: Jonathan Kans, Michael Kornbluh, Colleen Bollin * */ /// @file seq_macros.hpp /// Utility macros and typedefs for exploring NCBI objects from seq.asn. #include <objects/misc/sequence_util_macros.hpp> #include <objects/seq/seq__.hpp> /// @NAME Convenience macros for NCBI objects /// @{ BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) ///////////////////////////////////////////////////////////////////////////// /// Macros and typedefs for object subtypes ///////////////////////////////////////////////////////////////////////////// /// CSeq_inst definitions #define NCBI_SEQREPR(Type) CSeq_inst::eRepr_##Type typedef CSeq_inst::TRepr TSEQ_REPR; // virtual raw seg const ref // consen map delta other #define NCBI_SEQMOL(Type) CSeq_inst::eMol_##Type typedef CSeq_inst::TMol TSEQ_MOL; // dna rna aa na other #define NCBI_SEQTOPOLOGY(Type) CSeq_inst::eTopology_##Type typedef CSeq_inst::TTopology TSEQ_TOPOLOGY; // linear circular tandem other #define NCBI_SEQSTRAND(Type) CSeq_inst::eStrand_##Type typedef CSeq_inst::TStrand TSEQ_STRAND; // ss ds mixed other /// CSeq_annot definitions #define NCBI_SEQANNOT(Type) CSeq_annot::TData::e_##Type typedef CSeq_annot::TData::E_Choice TSEQANNOT_CHOICE; // Ftable Align Graph Ids Locs Seq_table /// CAnnotdesc definitions #define NCBI_ANNOTDESC(Type) CAnnotdesc::e_##Type typedef CAnnotdesc::E_Choice TANNOTDESC_CHOICE; // Name Title Comment Pub // User Create_date Update_date // Src Align Region /// CSeqdesc definitions #define NCBI_SEQDESC(Type) CSeqdesc::e_##Type typedef CSeqdesc::E_Choice TSEQDESC_CHOICE; // Mol_type Modif Method Name // Title Org Comment Num // Maploc Pir Genbank Pub // Region User Sp Dbxref // Embl Create_date Update_date Prf // Pdb Het Source Molinfo /// CMolInfo definitions #define NCBI_BIOMOL(Type) CMolInfo::eBiomol_##Type typedef CMolInfo::TBiomol TMOLINFO_BIOMOL; // genomic pre_RNA mRNA rRNA // tRNA snRNA scRNA peptide // other_genetic genomic_mRNA cRNA snoRNA // transcribed_RNA ncRNA tmRNA other #define NCBI_TECH(Type) CMolInfo::eTech_##Type typedef CMolInfo::TTech TMOLINFO_TECH; // standard est sts // survey genemap physmap // derived concept_trans seq_pept // both seq_pept_overlap seq_pept_homol // concept_trans_a htgs_1 htgs_2 // htgs_3 fli_cdna htgs_0 // htc wgs barcode // composite_wgs_htgs tsa other #define NCBI_COMPLETENESS(Type) CMolInfo::eCompleteness_##Type typedef CMolInfo::TCompleteness TMOLINFO_COMPLETENESS; // complete partial no_left no_right // no_ends has_left has_right other ///////////////////////////////////////////////////////////////////////////// /// Macros for obtaining closest specific CSeqdesc applying to a CBioseq ///////////////////////////////////////////////////////////////////////////// /// IF_EXISTS_CLOSEST base macro calls GetClosestDescriptor with generated components // If Lvl is not NULL, it must be a pointer to an int #define IF_EXISTS_CLOSEST(Cref, Var, Lvl, Chs) \ if (CConstRef<CSeqdesc> Cref = (Var).GetClosestDescriptor (Chs, Lvl)) /// IF_EXISTS_CLOSEST_MOLINFO // CBioseq& as input, dereference with const CMolInfo& molinf = (*cref).GetMolinfo(); #define IF_EXISTS_CLOSEST_MOLINFO(Cref, Var, Lvl) \ IF_EXISTS_CLOSEST (Cref, Var, Lvl, NCBI_SEQDESC(Molinfo)) /// IF_EXISTS_CLOSEST_BIOSOURCE // CBioseq& as input, dereference with const CBioSource& source = (*cref).GetSource(); #define IF_EXISTS_CLOSEST_BIOSOURCE(Cref, Var, Lvl) \ IF_EXISTS_CLOSEST (Cref, Var, Lvl, NCBI_SEQDESC(Source)) /// IF_EXISTS_CLOSEST_TITLE // CBioseq& as input, dereference with const string& title = (*cref).GetTitle(); #define IF_EXISTS_CLOSEST_TITLE(Cref, Var, Lvl) \ IF_EXISTS_CLOSEST (Cref, Var, Lvl, NCBI_SEQDESC(Title)) /// IF_EXISTS_CLOSEST_GENBANKBLOCK // CBioseq& as input, dereference with const CGB_block& gbk = (*cref).GetGenbank(); #define IF_EXISTS_CLOSEST_GENBANKBLOCK(Cref, Var, Lvl) \ IF_EXISTS_CLOSEST (Cref, Var, Lvl, NCBI_SEQDESC(Genbank)) /// IF_EXISTS_CLOSEST_EMBLBLOCK // CBioseq& as input, dereference with const CEMBL_block& ebk = (*cref).GetEmbl(); #define IF_EXISTS_CLOSEST_EMBLBLOCK(Cref, Var, Lvl) \ IF_EXISTS_CLOSEST (Cref, Var, Lvl, NCBI_SEQDESC(Embl)) /// IF_EXISTS_CLOSEST_PDBBLOCK // CBioseq& as input, dereference with const CPDB_block& pbk = (*cref).GetPdb(); #define IF_EXISTS_CLOSEST_PDBBLOCK(Cref, Var, Lvl) \ IF_EXISTS_CLOSEST (Cref, Var, Lvl, NCBI_SEQDESC(Pdb)) // "FOR_EACH_XXX_ON_YYY" does a linear const traversal of STL containers // "EDIT_EACH_XXX_ON_YYY" does a linear non-const traversal of STL containers // "SWITCH_ON_XXX_CHOICE" switches on the item subtype // "ADD_XXX_TO_YYY" adds an element to a specified object // "ERASE_XXX_ON_YYY" deletes a specified object within an iterator // Miscellaneous macros for testing objects include // "XXX_IS_YYY" or "XXX_HAS_YYY" // "XXX_CHOICE_IS" /// /// CBioseq macros /// SEQDESC_ON_BIOSEQ macros #define SEQDESC_ON_BIOSEQ_Type CBioseq::TDescr::Tdata #define SEQDESC_ON_BIOSEQ_Test(Var) (Var).IsSetDescr() #define SEQDESC_ON_BIOSEQ_Get(Var) (Var).GetDescr().Get() #define SEQDESC_ON_BIOSEQ_Set(Var) (Var).SetDescr().Set() /// BIOSEQ_HAS_SEQDESC #define BIOSEQ_HAS_SEQDESC(Var) \ ITEM_HAS (SEQDESC_ON_BIOSEQ, Var) /// FOR_EACH_SEQDESC_ON_BIOSEQ /// EDIT_EACH_SEQDESC_ON_BIOSEQ // CBioseq& as input, dereference with [const] CSeqdesc& desc = **itr #define FOR_EACH_SEQDESC_ON_BIOSEQ(Itr, Var) \ FOR_EACH (SEQDESC_ON_BIOSEQ, Itr, Var) #define EDIT_EACH_SEQDESC_ON_BIOSEQ(Itr, Var) \ EDIT_EACH (SEQDESC_ON_BIOSEQ, Itr, Var) /// ADD_SEQDESC_TO_BIOSEQ #define ADD_SEQDESC_TO_BIOSEQ(Var, Ref) \ ADD_ITEM (SEQDESC_ON_BIOSEQ, Var, Ref) /// ERASE_SEQDESC_ON_BIOSEQ #define ERASE_SEQDESC_ON_BIOSEQ(Itr, Var) \ LIST_ERASE_ITEM (SEQDESC_ON_BIOSEQ, Itr, Var) /// BIOSEQ_HAS_DESCRIPTOR /// FOR_EACH_DESCRIPTOR_ON_BIOSEQ /// EDIT_EACH_DESCRIPTOR_ON_BIOSEQ /// ADD_DESCRIPTOR_TO_BIOSEQ /// ERASE_DESCRIPTOR_ON_BIOSEQ #define BIOSEQ_HAS_DESCRIPTOR BIOSEQ_HAS_SEQDESC #define FOR_EACH_DESCRIPTOR_ON_BIOSEQ FOR_EACH_SEQDESC_ON_BIOSEQ #define EDIT_EACH_DESCRIPTOR_ON_BIOSEQ EDIT_EACH_SEQDESC_ON_BIOSEQ #define ADD_DESCRIPTOR_TO_BIOSEQ ADD_SEQDESC_TO_BIOSEQ #define ERASE_DESCRIPTOR_ON_BIOSEQ ERASE_SEQDESC_ON_BIOSEQ /// SEQANNOT_ON_BIOSEQ macros #define SEQANNOT_ON_BIOSEQ_Type CBioseq::TAnnot #define SEQANNOT_ON_BIOSEQ_Test(Var) (Var).IsSetAnnot() #define SEQANNOT_ON_BIOSEQ_Get(Var) (Var).GetAnnot() #define SEQANNOT_ON_BIOSEQ_Set(Var) (Var).SetAnnot() /// BIOSEQ_HAS_SEQANNOT #define BIOSEQ_HAS_SEQANNOT(Var) \ ITEM_HAS (SEQANNOT_ON_BIOSEQ, Var) /// FOR_EACH_SEQANNOT_ON_BIOSEQ /// EDIT_EACH_SEQANNOT_ON_BIOSEQ // CBioseq& as input, dereference with [const] CSeq_annot& annot = **itr; #define FOR_EACH_SEQANNOT_ON_BIOSEQ(Itr, Var) \ FOR_EACH (SEQANNOT_ON_BIOSEQ, Itr, Var) #define EDIT_EACH_SEQANNOT_ON_BIOSEQ(Itr, Var) \ EDIT_EACH (SEQANNOT_ON_BIOSEQ, Itr, Var) /// ADD_SEQANNOT_TO_BIOSEQ #define ADD_SEQANNOT_TO_BIOSEQ(Var, Ref) \ ADD_ITEM (SEQANNOT_ON_BIOSEQ, Var, Ref) /// ERASE_SEQANNOT_ON_BIOSEQ #define ERASE_SEQANNOT_ON_BIOSEQ(Itr, Var) \ LIST_ERASE_ITEM (SEQANNOT_ON_BIOSEQ, Itr, Var) /// BIOSEQ_HAS_ANNOT /// FOR_EACH_ANNOT_ON_BIOSEQ /// EDIT_EACH_ANNOT_ON_BIOSEQ /// ADD_ANNOT_TO_BIOSEQ /// ERASE_ANNOT_ON_BIOSEQ #define BIOSEQ_HAS_ANNOT BIOSEQ_HAS_SEQANNOT #define FOR_EACH_ANNOT_ON_BIOSEQ FOR_EACH_SEQANNOT_ON_BIOSEQ #define EDIT_EACH_ANNOT_ON_BIOSEQ EDIT_EACH_SEQANNOT_ON_BIOSEQ #define ADD_ANNOT_TO_BIOSEQ ADD_SEQANNOT_TO_BIOSEQ #define ERASE_ANNOT_ON_BIOSEQ ERASE_SEQANNOT_ON_BIOSEQ /// SEQID_ON_BIOSEQ macros #define SEQID_ON_BIOSEQ_Type CBioseq::TId #define SEQID_ON_BIOSEQ_Test(Var) (Var).IsSetId() #define SEQID_ON_BIOSEQ_Get(Var) (Var).GetId() #define SEQID_ON_BIOSEQ_Set(Var) (Var).SetId() /// BIOSEQ_HAS_SEQID #define BIOSEQ_HAS_SEQID(Var) \ ITEM_HAS (SEQID_ON_BIOSEQ, Var) /// FOR_EACH_SEQID_ON_BIOSEQ /// EDIT_EACH_SEQID_ON_BIOSEQ // CBioseq& as input, dereference with [const] CSeq_id& sid = **itr; #define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var) \ FOR_EACH (SEQID_ON_BIOSEQ, Itr, Var) #define EDIT_EACH_SEQID_ON_BIOSEQ(Itr, Var) \ EDIT_EACH (SEQID_ON_BIOSEQ, Itr, Var) /// ADD_SEQID_TO_BIOSEQ #define ADD_SEQID_TO_BIOSEQ(Var, Ref) \ ADD_ITEM (SEQID_ON_BIOSEQ, Var, Ref) /// ERASE_SEQID_ON_BIOSEQ #define ERASE_SEQID_ON_BIOSEQ(Itr, Var) \ LIST_ERASE_ITEM (SEQID_ON_BIOSEQ, Itr, Var) /// SEQID_ON_BIOSEQ_IS_SORTED #define SEQID_ON_BIOSEQ_IS_SORTED(Var, Func) \ IS_SORTED (SEQID_ON_BIOSEQ, Var, Func) /// SORT_SEQID_ON_BIOSEQ #define SORT_SEQID_ON_BIOSEQ(Var, Func) \ DO_LIST_SORT (SEQID_ON_BIOSEQ, Var, Func) /// SEQID_ON_BIOSEQ_IS_UNIQUE #define SEQID_ON_BIOSEQ_IS_UNIQUE(Var, Func) \ IS_UNIQUE (SEQID_ON_BIOSEQ, Var, Func) /// UNIQUE_SEQID_ON_BIOSEQ #define UNIQUE_SEQID_ON_BIOSEQ(Var, Func) \ DO_UNIQUE (SEQID_ON_BIOSEQ, Var, Func) /// /// CSeq_annot macros /// SEQANNOT_CHOICE macros #define SEQANNOT_CHOICE_Test(Var) (Var).IsSetData() #define SEQANNOT_CHOICE_Chs(Var) (Var).GetData().Which() /// SEQANNOT_CHOICE_IS #define SEQANNOT_CHOICE_IS(Var, Chs) \ CHOICE_IS (SEQANNOT_CHOICE, Var, Chs) /// SEQANNOT_IS_FTABLE #define SEQANNOT_IS_FTABLE(Var) \ SEQANNOT_CHOICE_IS (Var, NCBI_SEQANNOT(Ftable)) /// SEQANNOT_IS_ALIGN #define SEQANNOT_IS_ALIGN(Var) \ SEQANNOT_CHOICE_IS (Var, NCBI_SEQANNOT(Align)) /// SEQANNOT_IS_GRAPH #define SEQANNOT_IS_GRAPH(Var) \ SEQANNOT_CHOICE_IS (Var, NCBI_SEQANNOT(Graph)) /// SEQANNOT_IS_IDS #define SEQANNOT_IS_IDS(Var) \ SEQANNOT_CHOICE_IS (Var, NCBI_SEQANNOT(Ids)) /// SEQANNOT_IS_LOCS #define SEQANNOT_IS_LOCS(Var) \ SEQANNOT_CHOICE_IS (Var, NCBI_SEQANNOT(Locs)) /// SEQANNOT_IS_SEQ_TABLE #define SEQANNOT_IS_SEQ_TABLE(Var) \ SEQANNOT_CHOICE_IS (Var, NCBI_SEQANNOT(Seq_table)) /// SWITCH_ON_SEQANNOT_CHOICE #define SWITCH_ON_SEQANNOT_CHOICE(Var) \ SWITCH_ON (SEQANNOT_CHOICE, Var) /// SEQFEAT_ON_SEQANNOT macros #define SEQFEAT_ON_SEQANNOT_Type CSeq_annot::TData::TFtable #define SEQFEAT_ON_SEQANNOT_Test(Var) (Var).IsFtable() #define SEQFEAT_ON_SEQANNOT_Get(Var) (Var).GetData().GetFtable() #define SEQFEAT_ON_SEQANNOT_Set(Var) (Var).SetData().SetFtable() /// SEQANNOT_IS_SEQFEAT #define SEQANNOT_IS_SEQFEAT(Var) \ ITEM_HAS (SEQFEAT_ON_SEQANNOT, Var) /// FOR_EACH_SEQFEAT_ON_SEQANNOT /// EDIT_EACH_SEQFEAT_ON_SEQANNOT // CSeq_annot& as input, dereference with [const] CSeq_feat& feat = **itr; #define FOR_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var) \ FOR_EACH (SEQFEAT_ON_SEQANNOT, Itr, Var) #define EDIT_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var) \ EDIT_EACH (SEQFEAT_ON_SEQANNOT, Itr, Var) /// ADD_SEQFEAT_TO_SEQANNOT #define ADD_SEQFEAT_TO_SEQANNOT(Var, Ref) \ ADD_ITEM (SEQFEAT_ON_SEQANNOT, Var, Ref) /// ERASE_SEQFEAT_ON_SEQANNOT #define ERASE_SEQFEAT_ON_SEQANNOT(Itr, Var) \ LIST_ERASE_ITEM (SEQFEAT_ON_SEQANNOT, Itr, Var) /// ANNOT_IS_FEATURE /// FOR_EACH_FEATURE_ON_ANNOT /// EDIT_EACH_FEATURE_ON_ANNOT /// ADD_FEATURE_TO_ANNOT /// ERASE_FEATURE_ON_ANNOT #define ANNOT_IS_FEATURE SEQANNOT_IS_SEQFEAT #define FOR_EACH_FEATURE_ON_ANNOT FOR_EACH_SEQFEAT_ON_SEQANNOT #define EDIT_EACH_FEATURE_ON_ANNOT EDIT_EACH_SEQFEAT_ON_SEQANNOT #define ADD_FEATURE_TO_ANNOT ADD_SEQFEAT_TO_SEQANNOT #define ERASE_FEATURE_ON_ANNOT ERASE_SEQFEAT_ON_SEQANNOT /// SEQALIGN_ON_SEQANNOT macros #define SEQALIGN_ON_SEQANNOT_Type CSeq_annot::TData::TAlign #define SEQALIGN_ON_SEQANNOT_Test(Var) (Var).IsAlign() #define SEQALIGN_ON_SEQANNOT_Get(Var) (Var).GetData().GetAlign() #define SEQALIGN_ON_SEQANNOT_Set(Var) (Var).SetData().SetAlign() /// SEQANNOT_IS_SEQALIGN #define SEQANNOT_IS_SEQALIGN(Var) \ ITEM_HAS (SEQALIGN_ON_SEQANNOT, Var) /// FOR_EACH_SEQALIGN_ON_SEQANNOT /// EDIT_EACH_SEQALIGN_ON_SEQANNOT // CSeq_annot& as input, dereference with [const] CSeq_align& align = **itr; #define FOR_EACH_SEQALIGN_ON_SEQANNOT(Itr, Var) \ FOR_EACH (SEQALIGN_ON_SEQANNOT, Itr, Var) #define EDIT_EACH_SEQALIGN_ON_SEQANNOT(Itr, Var) \ EDIT_EACH (SEQALIGN_ON_SEQANNOT, Itr, Var) /// ADD_SEQALIGN_TO_SEQANNOT #define ADD_SEQALIGN_TO_SEQANNOT(Var, Ref) \ ADD_ITEM (SEQALIGN_ON_SEQANNOT, Var, Ref) /// ERASE_SEQALIGN_ON_SEQANNOT #define ERASE_SEQALIGN_ON_SEQANNOT(Itr, Var) \ LIST_ERASE_ITEM (SEQALIGN_ON_SEQANNOT, Itr, Var) /// ANNOT_IS_ALIGN /// FOR_EACH_ALIGN_ON_ANNOT /// EDIT_EACH_ALIGN_ON_ANNOT /// ADD_ALIGN_TO_ANNOT /// ERASE_ALIGN_ON_ANNOT #define ANNOT_IS_ALIGN SEQANNOT_IS_SEQALIGN #define FOR_EACH_ALIGN_ON_ANNOT FOR_EACH_SEQALIGN_ON_SEQANNOT #define EDIT_EACH_ALIGN_ON_ANNOT EDIT_EACH_SEQALIGN_ON_SEQANNOT #define ADD_ALIGN_TO_ANNOT ADD_SEQALIGN_TO_SEQANNOT #define ERASE_ALIGN_ON_ANNOT ERASE_SEQALIGN_ON_SEQANNOT /// SEQGRAPH_ON_SEQANNOT macros #define SEQGRAPH_ON_SEQANNOT_Type CSeq_annot::TData::TGraph #define SEQGRAPH_ON_SEQANNOT_Test(Var) (Var).IsGraph() #define SEQGRAPH_ON_SEQANNOT_Get(Var) (Var).GetData().GetGraph() #define SEQGRAPH_ON_SEQANNOT_Set(Var) SetData().SetGraph() /// SEQANNOT_IS_SEQGRAPH #define SEQANNOT_IS_SEQGRAPH(Var) \ ITEM_HAS (SEQGRAPH_ON_SEQANNOT, Var) /// FOR_EACH_SEQGRAPH_ON_SEQANNOT /// EDIT_EACH_SEQGRAPH_ON_SEQANNOT // CSeq_annot& as input, dereference with [const] CSeq_graph& graph = **itr; #define FOR_EACH_SEQGRAPH_ON_SEQANNOT(Itr, Var) \ FOR_EACH (SEQGRAPH_ON_SEQANNOT, Itr, Var) #define EDIT_EACH_SEQGRAPH_ON_SEQANNOT(Itr, Var) \ EDIT_EACH (SEQGRAPH_ON_SEQANNOT, Itr, Var) /// ADD_SEQGRAPH_TO_SEQANNOT #define ADD_SEQGRAPH_TO_SEQANNOT(Var, Ref) \ ADD_ITEM (SEQGRAPH_ON_SEQANNOT, Var, Ref) /// ERASE_SEQGRAPH_ON_SEQANNOT #define ERASE_SEQGRAPH_ON_SEQANNOT(Itr, Var) \ LIST_ERASE_ITEM (SEQGRAPH_ON_SEQANNOT, Itr, Var) /// ANNOT_IS_GRAPH /// FOR_EACH_GRAPH_ON_ANNOT /// EDIT_EACH_GRAPH_ON_ANNOT /// ADD_GRAPH_TO_ANNOT /// ERASE_GRAPH_ON_ANNOT #define ANNOT_IS_GRAPH SEQANNOT_IS_SEQGRAPH #define FOR_EACH_GRAPH_ON_ANNOT FOR_EACH_SEQGRAPH_ON_SEQANNOT #define EDIT_EACH_GRAPH_ON_ANNOT EDIT_EACH_SEQGRAPH_ON_SEQANNOT #define ADD_GRAPH_TO_ANNOT ADD_SEQGRAPH_TO_SEQANNOT #define ERASE_GRAPH_ON_ANNOT ERASE_SEQGRAPH_ON_SEQANNOT /// SEQTABLE_ON_SEQANNOT macros #define SEQTABLE_ON_SEQANNOT_Type CSeq_annot::TData::TSeq_table #define SEQTABLE_ON_SEQANNOT_Test(Var) (Var).IsSeq_table() #define SEQTABLE_ON_SEQANNOT_Get(Var) (Var).GetData().GetSeq_table() #define SEQTABLE_ON_SEQANNOT_Set(Var) SetData().SetSeq_table() /// SEQANNOT_IS_SEQTABLE #define SEQANNOT_IS_SEQTABLE(Var) \ ITEM_HAS (SEQTABLE_ON_SEQANNOT, Var) /// ANNOT_IS_TABLE #define ANNOT_IS_TABLE SEQANNOT_IS_SEQTABLE /// ANNOTDESC_ON_SEQANNOT macros #define ANNOTDESC_ON_SEQANNOT_Type CSeq_annot::TDesc::Tdata #define ANNOTDESC_ON_SEQANNOT_Test(Var) (Var).IsSetDesc() && (Var).GetDesc().IsSet() #define ANNOTDESC_ON_SEQANNOT_Get(Var) (Var).GetDesc().Get() #define ANNOTDESC_ON_SEQANNOT_Set(Var) (Var).SetDesc().Set() /// SEQANNOT_HAS_ANNOTDESC #define SEQANNOT_HAS_ANNOTDESC(Var) \ ITEM_HAS (ANNOTDESC_ON_SEQANNOT, Var) /// FOR_EACH_ANNOTDESC_ON_SEQANNOT /// EDIT_EACH_ANNOTDESC_ON_SEQANNOT // CSeq_annot& as input, dereference with [const] CAnnotdesc& desc = **itr; #define FOR_EACH_ANNOTDESC_ON_SEQANNOT(Itr, Var) \ FOR_EACH (ANNOTDESC_ON_SEQANNOT, Itr, Var) #define EDIT_EACH_ANNOTDESC_ON_SEQANNOT(Itr, Var) \ EDIT_EACH (ANNOTDESC_ON_SEQANNOT, Itr, Var) /// ADD_ANNOTDESC_TO_SEQANNOT #define ADD_ANNOTDESC_TO_SEQANNOT(Var, Ref) \ ADD_ITEM (ANNOTDESC_ON_SEQANNOT, Var, Ref) /// ERASE_ANNOTDESC_ON_SEQANNOT #define ERASE_ANNOTDESC_ON_SEQANNOT(Itr, Var) \ LIST_ERASE_ITEM (ANNOTDESC_ON_SEQANNOT, Itr, Var) /// ANNOT_HAS_ANNOTDESC /// FOR_EACH_ANNOTDESC_ON_ANNOT /// EDIT_EACH_ANNOTDESC_ON_ANNOT /// ADD_ANNOTDESC_TO_ANNOT /// ERASE_ANNOTDESC_ON_ANNOT #define ANNOT_HAS_ANNOTDESC SEQANNOT_HAS_ANNOTDESC #define FOR_EACH_ANNOTDESC_ON_ANNOT FOR_EACH_ANNOTDESC_ON_SEQANNOT #define EDIT_EACH_ANNOTDESC_ON_ANNOT EDIT_EACH_ANNOTDESC_ON_SEQANNOT #define ADD_ANNOTDESC_TO_ANNOT ADD_ANNOTDESC_TO_SEQANNOT #define ERASE_ANNOTDESC_ON_ANNOT ERASE_ANNOTDESC_ON_SEQANNOT /// /// SEQFEAT_ON_MAPEXT macros #define SEQFEAT_ON_MAPEXT_Type CMap_ext::Tdata #define SEQFEAT_ON_MAPEXT_Test(Var) (Var).IsSet() #define SEQFEAT_ON_MAPEXT_Get(Var) (Var).Get() #define SEQFEAT_ON_MAPEXT_Set(Var) (Var).Set() /// SEQANNOT_IS_SEQFEAT /// FOR_EACH_SEQFEAT_ON_MAPEXT /// EDIT_EACH_SEQFEAT_ON_MAPEXT #define FOR_EACH_SEQFEAT_ON_MAPEXT(Itr, Var) \ FOR_EACH (SEQFEAT_ON_MAPEXT, Itr, Var) #define EDIT_EACH_SEQFEAT_ON_MAPEXT(Itr, Var) \ EDIT_EACH (SEQFEAT_ON_MAPEXT, Itr, Var) /// ADD_SEQFEAT_ON_MAPEXT #define ADD_SEQFEAT_TO_MAPEXT(Var, Ref) \ ADD_ITEM (SEQFEAT_ON_MAPEXT, Var, Ref) /// ERASE_SEQFEAT_ON_MAPEXT #define ERASE_SEQFEAT_ON_MAPEXT(Itr, Var) \ LIST_ERASE_ITEM (SEQFEAT_ON_MAPEXT, Itr, Var) /// /// CAnnotdesc macros /// ANNOTDESC_CHOICE macros #define ANNOTDESC_CHOICE_Test(Var) (Var).Which() != CAnnotdesc::e_not_set #define ANNOTDESC_CHOICE_Chs(Var) (Var).Which() /// ANNOTDESC_CHOICE_IS #define ANNOTDESC_CHOICE_IS(Var, Chs) \ CHOICE_IS (ANNOTDESC_CHOICE, Var, Chs) /// SWITCH_ON_ANNOTDESC_CHOICE #define SWITCH_ON_ANNOTDESC_CHOICE(Var) \ SWITCH_ON (ANNOTDESC_CHOICE, Var) /// /// CSeq_descr macros /// SEQDESC_ON_SEQDESCR macros #define SEQDESC_ON_SEQDESCR_Type CSeq_descr::Tdata #define SEQDESC_ON_SEQDESCR_Test(Var) (Var).IsSet() #define SEQDESC_ON_SEQDESCR_Get(Var) (Var).Get() #define SEQDESC_ON_SEQDESCR_Set(Var) (Var).Set() /// SEQDESCR_HAS_SEQDESC #define SEQDESCR_HAS_SEQDESC(Var) \ ITEM_HAS (SEQDESC_ON_SEQDESCR, Var) /// FOR_EACH_SEQDESC_ON_SEQDESCR /// EDIT_EACH_SEQDESC_ON_SEQDESCR // CSeq_descr& as input, dereference with [const] CSeqdesc& desc = **itr; #define FOR_EACH_SEQDESC_ON_SEQDESCR(Itr, Var) \ FOR_EACH (SEQDESC_ON_SEQDESCR, Itr, Var) #define EDIT_EACH_SEQDESC_ON_SEQDESCR(Itr, Var) \ EDIT_EACH (SEQDESC_ON_SEQDESCR, Itr, Var) /// ADD_SEQDESC_TO_SEQDESCR #define ADD_SEQDESC_TO_SEQDESCR(Var, Ref) \ ADD_ITEM (SEQDESC_ON_SEQDESCR, Var, Ref) /// ERASE_SEQDESC_ON_SEQDESCR #define ERASE_SEQDESC_ON_SEQDESCR(Itr, Var) \ LIST_ERASE_ITEM (SEQDESC_ON_SEQDESCR, Itr, Var) /// DESCR_HAS_DESCRIPTOR /// FOR_EACH_DESCRIPTOR_ON_DESCR /// EDIT_EACH_DESCRIPTOR_ON_DESCR /// ADD_DESCRIPTOR_TO_DESCR /// ERASE_DESCRIPTOR_ON_DESCR #define DESCR_HAS_DESCRIPTOR SEQDESCR_HAS_SEQDESC #define FOR_EACH_DESCRIPTOR_ON_DESCR FOR_EACH_SEQDESC_ON_SEQDESCR #define EDIT_EACH_DESCRIPTOR_ON_DESCR EDIT_EACH_SEQDESC_ON_SEQDESCR #define ERASE_DESCRIPTOR_ON_DESCR ERASE_SEQDESC_ON_SEQDESCR #define ADD_DESCRIPTOR_TO_DESCR ADD_SEQDESC_TO_SEQDESCR /// /// CSeqdesc macros /// SEQDESC_CHOICE macros #define SEQDESC_CHOICE_Test(Var) (Var).Which() != CSeqdesc::e_not_set #define SEQDESC_CHOICE_Chs(Var) (Var).Which() /// SEQDESC_CHOICE_IS #define SEQDESC_CHOICE_IS(Var, Chs) \ CHOICE_IS (SEQDESC_CHOICE, Var, Chs) /// SWITCH_ON_SEQDESC_CHOICE #define SWITCH_ON_SEQDESC_CHOICE(Var) \ SWITCH_ON (SEQDESC_CHOICE, Var) /// DESCRIPTOR_CHOICE_IS /// SWITCH_ON_DESCRIPTOR_CHOICE #define DESCRIPTOR_CHOICE_IS SEQDESC_CHOICE_IS #define SWITCH_ON_DESCRIPTOR_CHOICE SWITCH_ON_SEQDESC_CHOICE /// /// CMolInfo macros /// MOLINFO_BIOMOL macros #define MOLINFO_BIOMOL_Test(Var) (Var).IsSetBiomol() #define MOLINFO_BIOMOL_Chs(Var) (Var).GetBiomol() /// MOLINFO_BIOMOL_IS #define MOLINFO_BIOMOL_IS(Var, Chs) \ CHOICE_IS (MOLINFO_BIOMOL, Var, Chs) /// SWITCH_ON_MOLINFO_BIOMOL #define SWITCH_ON_MOLINFO_BIOMOL(Var) \ SWITCH_ON (MOLINFO_BIOMOL, Var) /// MOLINFO_TECH macros #define MOLINFO_TECH_Test(Var) (Var).IsSetTech() #define MOLINFO_TECH_Chs(Var) (Var).GetTech() /// MOLINFO_TECH_IS #define MOLINFO_TECH_IS(Var, Chs) \ CHOICE_IS (MOLINFO_TECH, Var, Chs) /// SWITCH_ON_MOLINFO_TECH #define SWITCH_ON_MOLINFO_TECH(Var) \ SWITCH_ON (MOLINFO_TECH, Var) /// MOLINFO_COMPLETENESS macros #define MOLINFO_COMPLETENESS_Test(Var) (Var).IsSetCompleteness() #define MOLINFO_COMPLETENESS_Chs(Var) (Var).GetCompleteness() /// MOLINFO_COMPLETENESS_IS #define MOLINFO_COMPLETENESS_IS(Var, Chs) \ CHOICE_IS (MOLINFO_COMPLETENESS, Var, Chs) /// SWITCH_ON_MOLINFO_COMPLETENESS #define SWITCH_ON_MOLINFO_COMPLETENESS(Var) \ SWITCH_ON (MOLINFO_COMPLETENESS, Var) /// /// CDelta_ext macros #define DELTASEQ_IN_DELTAEXT_Type list< CRef< CDelta_seq > > #define DELTASEQ_IN_DELTAEXT_Test(Var) ( (Var).IsSet() && ! (Var).Get().empty() ) #define DELTASEQ_IN_DELTAEXT_Get(Var) (Var).Get() #define DELTASEQ_IN_DELTAEXT_Set(Var) (Var).Set() #define DELTASEQ_IN_DELTAEXT_Reset(Var) (Var).Reset() #define FOR_EACH_DELTASEQ_IN_DELTAEXT(Itr, Var) \ FOR_EACH( DELTASEQ_IN_DELTAEXT, Itr, Var ) #define EDIT_EACH_DELTASEQ_IN_DELTAEXT(Itr, Var) \ EDIT_EACH( DELTASEQ_IN_DELTAEXT, Itr, Var ) #define ERASE_DELTASEQ_IN_DELTAEXT(Itr, Var) \ LIST_ERASE_ITEM (DELTASEQ_IN_DELTAEXT, Itr, Var) END_SCOPE(objects) END_NCBI_SCOPE /* @} */ #endif /* OBJECTS_SEQ___SEQ_MACROS__HPP */

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