NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
prime_cache.cpp File Reference
#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::EBiomolTBiomolTypeKey
 
typedef CStaticPairArrayMap< const char *, const CMolInfo::EBiomol, PCaseTBiomolTypeMap
 
typedef SStaticPair< const char *, const CBioSource::EGenomeTGenomeTypeKey
 
typedef CStaticPairArrayMap< const char *, const CBioSource::EGenome, PCaseTGenomeTypeMap
 
typedef SStaticPair< const char *, const CSeq_inst::EMolTInstMolTypeKey
 
typedef CStaticPairArrayMap< const char *, const CSeq_inst::EMol, PCaseTInstMolTypeMap
 

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[])
 

Variables

 USING_NCBI_SCOPE
 
static const TBiomolTypeKey db_biomol_type_name_to_enum []
 
static const TGenomeTypeKey db_genome_type_name_to_enum []
 
static const TInstMolTypeKey db_inst_mol_type_name_to_enum []
 

Typedef Documentation

◆ TBiomolTypeKey

Definition at line 87 of file prime_cache.cpp.

◆ TBiomolTypeMap

Definition at line 108 of file prime_cache.cpp.

◆ TGenomeTypeKey

Definition at line 112 of file prime_cache.cpp.

◆ TGenomeTypeMap

Definition at line 122 of file prime_cache.cpp.

◆ TInstMolTypeKey

Definition at line 126 of file prime_cache.cpp.

◆ 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()

int main ( int  argc,
const char *  argv[] 
)

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ db_biomol_type_name_to_enum

const TBiomolTypeKey db_biomol_type_name_to_enum[]
static
Initial value:
= {
{ "genomic", CMolInfo::eBiomol_genomic },
{ "genomic-mrna", CMolInfo::eBiomol_genomic_mRNA },
{ "other-genetic", CMolInfo::eBiomol_other_genetic },
{ "peptide", CMolInfo::eBiomol_peptide },
{ "pre-rna", CMolInfo::eBiomol_pre_RNA },
{ "snorna", CMolInfo::eBiomol_snoRNA },
{ "transcribed-rna", CMolInfo::eBiomol_transcribed_RNA },
}
@ eBiomol_pre_RNA
precursor RNA of any sort really
Definition: MolInfo_.hpp:102
@ eBiomol_cRNA
viral RNA genome copy intermediate
Definition: MolInfo_.hpp:111
@ eBiomol_snoRNA
small nucleolar RNA
Definition: MolInfo_.hpp:112
@ eBiomol_genomic_mRNA
reported a mix of genomic and cdna sequence
Definition: MolInfo_.hpp:110
@ eBiomol_transcribed_RNA
transcribed RNA other than existing classes
Definition: MolInfo_.hpp:113
@ eBiomol_other_genetic
other genetic material
Definition: MolInfo_.hpp:109

Definition at line 89 of file prime_cache.cpp.

◆ db_genome_type_name_to_enum

const TGenomeTypeKey db_genome_type_name_to_enum[]
static
Initial value:

Definition at line 114 of file prime_cache.cpp.

◆ db_inst_mol_type_name_to_enum

const TInstMolTypeKey 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 },
}
@ eMol_na
just a nucleic acid
Definition: Seq_inst_.hpp:113

Definition at line 128 of file prime_cache.cpp.

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 84 of file prime_cache.cpp.

Modified on Thu Dec 07 10:07:13 2023 by modify_doxy.py rev. 669887