#include <ncbi_pch.hpp>#include <corelib/ncbiapp.hpp>#include <corelib/ncbienv.hpp>#include <corelib/ncbiargs.hpp>#include <corelib/request_ctx.hpp>#include <corelib/ncbi_signal.hpp>#include <util/static_map.hpp>#include <util/stream_source.hpp>#include <util/compress/stream.hpp>#include <util/compress/zlib.hpp>#include <serial/serial.hpp>#include <serial/objistr.hpp>#include <serial/objostr.hpp>#include <objects/seqset/Seq_entry.hpp>#include <objects/seq/Bioseq.hpp>#include <objects/seq/Seq_descr.hpp>#include <objects/seq/Seq_inst.hpp>#include <objects/seq/Seq_ext.hpp>#include <objects/seq/Delta_ext.hpp>#include <objects/seq/Delta_seq.hpp>#include <objects/seq/Seqdesc.hpp>#include <objects/seq/MolInfo.hpp>#include <objects/seqfeat/BioSource.hpp>#include <objects/taxon1/taxon1.hpp>#include <objects/taxon1/local_taxon.hpp>#include <objects/submit/Submit_block.hpp>#include <objects/general/Object_id.hpp>#include <objtools/readers/fasta.hpp>#include <objtools/readers/message_listener.hpp>#include <objmgr/object_manager.hpp>#include <objmgr/bioseq_handle.hpp>#include <objmgr/bioseq_ci.hpp>#include <objmgr/scope.hpp>#include <objmgr/util/sequence.hpp>#include <objtools/data_loaders/asn_cache/Cache_blob.hpp>#include <objtools/data_loaders/asn_cache/asn_index.hpp>#include <objtools/data_loaders/asn_cache/chunk_file.hpp>#include <objtools/data_loaders/asn_cache/seq_id_chunk_file.hpp>#include <objtools/data_loaders/asn_cache/asn_cache_util.hpp>#include <objtools/data_loaders/genbank/gbloader.hpp>
Include dependency graph for prime_cache.cpp:
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Classes | |
| class | CPrimeCacheApplication |
| class | CPrimeCacheApplication::CCacheBioseq |
| struct | CPrimeCacheApplication::SOrgData |
| class | CObjectEnum< T, Consumer > |
Typedefs | |
| typedef SStaticPair< const char *, const CMolInfo::EBiomol > | TBiomolTypeKey |
| typedef CStaticPairArrayMap< const char *, const CMolInfo::EBiomol, PCase > | TBiomolTypeMap |
| typedef SStaticPair< const char *, const CBioSource::EGenome > | TGenomeTypeKey |
| typedef CStaticPairArrayMap< const char *, const CBioSource::EGenome, PCase > | TGenomeTypeMap |
| typedef SStaticPair< const char *, const CSeq_inst::EMol > | TInstMolTypeKey |
| typedef CStaticPairArrayMap< const char *, const CSeq_inst::EMol, PCase > | TInstMolTypeMap |
Functions | |
| USING_SCOPE (objects) | |
| DEFINE_STATIC_ARRAY_MAP (TBiomolTypeMap, sm_BiomolTypes, db_biomol_type_name_to_enum) | |
| DEFINE_STATIC_ARRAY_MAP (TGenomeTypeMap, sm_GenomeTypes, db_genome_type_name_to_enum) | |
| DEFINE_STATIC_ARRAY_MAP (TInstMolTypeMap, sm_InstMolTypes, db_inst_mol_type_name_to_enum) | |
| int | main (int argc, const char *argv[]) |
Typedef Documentation
◆ TBiomolTypeKey
| typedef SStaticPair<const char*, const CMolInfo::EBiomol> TBiomolTypeKey |
Definition at line 87 of file prime_cache.cpp.
◆ TBiomolTypeMap
| typedef CStaticPairArrayMap<const char*, const CMolInfo::EBiomol, PCase> TBiomolTypeMap |
Definition at line 108 of file prime_cache.cpp.
◆ TGenomeTypeKey
| typedef SStaticPair<const char*, const CBioSource::EGenome> TGenomeTypeKey |
Definition at line 112 of file prime_cache.cpp.
◆ TGenomeTypeMap
| typedef CStaticPairArrayMap<const char*, const CBioSource::EGenome, PCase> TGenomeTypeMap |
Definition at line 122 of file prime_cache.cpp.
◆ TInstMolTypeKey
| typedef SStaticPair<const char*, const CSeq_inst::EMol> TInstMolTypeKey |
Definition at line 126 of file prime_cache.cpp.
◆ TInstMolTypeMap
| typedef CStaticPairArrayMap<const char*, const CSeq_inst::EMol, PCase> TInstMolTypeMap |
Definition at line 136 of file prime_cache.cpp.
Function Documentation
◆ DEFINE_STATIC_ARRAY_MAP() [1/3]
| DEFINE_STATIC_ARRAY_MAP | ( | TBiomolTypeMap | , |
| sm_BiomolTypes | , | ||
| db_biomol_type_name_to_enum | |||
| ) |
◆ DEFINE_STATIC_ARRAY_MAP() [2/3]
| DEFINE_STATIC_ARRAY_MAP | ( | TGenomeTypeMap | , |
| sm_GenomeTypes | , | ||
| db_genome_type_name_to_enum | |||
| ) |
◆ DEFINE_STATIC_ARRAY_MAP() [3/3]
| DEFINE_STATIC_ARRAY_MAP | ( | TInstMolTypeMap | , |
| sm_InstMolTypes | , | ||
| db_inst_mol_type_name_to_enum | |||
| ) |
◆ main()
Definition at line 1408 of file prime_cache.cpp.
References CPrimeCacheApplication::CPrimeCacheApplication().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ db_biomol_type_name_to_enum
|
static |
Initial value:
= {
{ "crna", CMolInfo::eBiomol_cRNA },
{ "genomic", CMolInfo::eBiomol_genomic },
{ "genomic-mrna", CMolInfo::eBiomol_genomic_mRNA },
{ "mrna", CMolInfo::eBiomol_mRNA },
{ "ncrna", CMolInfo::eBiomol_ncRNA },
{ "other", CMolInfo::eBiomol_other },
{ "other-genetic", CMolInfo::eBiomol_other_genetic },
{ "peptide", CMolInfo::eBiomol_peptide },
{ "pre-rna", CMolInfo::eBiomol_pre_RNA },
{ "rrna", CMolInfo::eBiomol_rRNA },
{ "scrna", CMolInfo::eBiomol_scRNA },
{ "snorna", CMolInfo::eBiomol_snoRNA },
{ "snrna", CMolInfo::eBiomol_snRNA },
{ "tmrna", CMolInfo::eBiomol_tmRNA },
{ "transcribed-rna", CMolInfo::eBiomol_transcribed_RNA },
{ "trna", CMolInfo::eBiomol_tRNA }
}
Definition at line 89 of file prime_cache.cpp.
◆ db_genome_type_name_to_enum
|
static |
Initial value:
= {
{ "chromosome", CBioSource::eGenome_chromosome },
{ "genomic", CBioSource::eGenome_genomic },
{ "mitochondrion", CBioSource::eGenome_mitochondrion },
{ "plasmid", CBioSource::eGenome_plasmid },
{ "plastid", CBioSource::eGenome_plastid }
}
Definition at line 114 of file prime_cache.cpp.
◆ db_inst_mol_type_name_to_enum
|
static |
Initial value:
= {
{ "aa", CSeq_inst::eMol_aa },
{ "dna", CSeq_inst::eMol_dna },
{ "na", CSeq_inst::eMol_na },
{ "other", CSeq_inst::eMol_other },
{ "rna", CSeq_inst::eMol_rna }
}
Definition at line 128 of file prime_cache.cpp.
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 84 of file prime_cache.cpp.
