NCBI C++ ToolKit
Typedefs | Functions | Variables
Gb_qual.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <serial/enumvalues.hpp>
#include <serial/serialimpl.hpp>
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Typedefs

typedef CStaticArraySet< const char *, PNocase_CStrTLegalMobileElementStrings
 
typedef SStaticPair< const char *, const char * > TInferenceTypeSynonymPairElem
 
typedef CStaticArrayMap< const char *, const char *, PNocase_CStrTInferenceTypeSynonymPairMap
 

Functions

static string GetRptTypeValue (const string &val, bool &open_bracket, bool &close_bracket)
 
 DEFINE_STATIC_ARRAY_MAP (TLegalMobileElementStrings, sc_LegalMobileElementStrings, s_LegalMobileElementStrings)
 
static string s_FindInArray (const string &val, const char **arr)
 
 DEFINE_STATIC_ARRAY_MAP (TInferenceTypeSynonymPairMap, sc_InferenceTypeSynonymPairMap, k_inference_type_synonym_pair_map)
 
static void ReplaceIfNotFound (string &inference, const string &find, const string &replace)
 

Variables

static const char * valid_inf_categories []
 
static const char * valid_inf_prefixes []
 
static const char * s_LegalMobileElementStrings []
 
static const char * s_IllegalQualNameStrings []
 
static const char * kInferenceDBChoices []
 
size_t kNumInferenceDBChoices = sizeof(kInferenceDBChoices) / sizeof(char *)
 
static const TInferenceTypeSynonymPairElem k_inference_type_synonym_pair_map []
 

Typedef Documentation

◆ TInferenceTypeSynonymPairElem

Definition at line 547 of file Gb_qual.cpp.

◆ TInferenceTypeSynonymPairMap

Definition at line 569 of file Gb_qual.cpp.

◆ TLegalMobileElementStrings

Definition at line 428 of file Gb_qual.cpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP() [1/2]

DEFINE_STATIC_ARRAY_MAP ( TInferenceTypeSynonymPairMap  ,
sc_InferenceTypeSynonymPairMap  ,
k_inference_type_synonym_pair_map   
)

◆ DEFINE_STATIC_ARRAY_MAP() [2/2]

DEFINE_STATIC_ARRAY_MAP ( TLegalMobileElementStrings  ,
sc_LegalMobileElementStrings  ,
s_LegalMobileElementStrings   
)

◆ GetRptTypeValue()

static string GetRptTypeValue ( const string val,
bool open_bracket,
bool close_bracket 
)
static

◆ ReplaceIfNotFound()

static void ReplaceIfNotFound ( string inference,
const string find,
const string replace 
)
static

Definition at line 720 of file Gb_qual.cpp.

References NStr::Find(), NPOS, and NStr::ReplaceInPlace().

Referenced by CGb_qual::CleanupAndRepairInference().

◆ s_FindInArray()

static string s_FindInArray ( const string val,
const char **  arr 
)
static

Definition at line 518 of file Gb_qual.cpp.

References arr, i, result, and val.

Referenced by CGb_qual::ParseInferenceString().

Variable Documentation

◆ k_inference_type_synonym_pair_map

const TInferenceTypeSynonymPairElem k_inference_type_synonym_pair_map[]
static
Initial value:
= {
{ "ab initio prediction", "ab initio prediction" },
{ "alignment", "alignment" },
{ "nucleotide motif", "nucleotide motif" },
{ "profile", "profile" },
{ "protein motif", "protein motif" },
{ "similar to AA", "similar to AA sequence" },
{ "similar to AA sequence", "similar to AA sequence" },
{ "similar to DNA", "similar to DNA sequence" },
{ "similar to DNA sequence", "similar to DNA sequence" },
{ "similar to EST", "similar to RNA sequence, EST" },
{ "similar to mRNA", "similar to RNA sequence, mRNA" },
{ "similar to RNA", "similar to RNA sequence" },
{ "similar to RNA sequence", "similar to RNA sequence" },
{ "similar to RNA sequence, EST", "similar to RNA sequence, EST" },
{ "similar to RNA sequence, mRNA", "similar to RNA sequence, mRNA" },
{ "similar to RNA sequence, other", "similar to RNA sequence, other" },
{ "similar to sequence", "similar to sequence" }
}

Definition at line 548 of file Gb_qual.cpp.

◆ kInferenceDBChoices

const char* kInferenceDBChoices[]
static
Initial value:
= {
"GenBank",
"EMBL",
"DDBJ",
"INSD",
"RefSeq",
"UniProt",
"PDB",
"UniProtKB",
"SwissProt",
"KEGG",
"GeneDB",
"Other",
"\0" }

Definition at line 530 of file Gb_qual.cpp.

Referenced by CGb_qual::CleanupAndRepairInference(), CGb_qual::IsLegalInferenceDatabase(), and CGb_qual::ParseInferenceString().

◆ kNumInferenceDBChoices

size_t kNumInferenceDBChoices = sizeof(kInferenceDBChoices) / sizeof(char *)

◆ s_IllegalQualNameStrings

const char* s_IllegalQualNameStrings[]
static
Initial value:
= {
"anticodon",
"citation",
"codon_start",
"db_xref",
"evidence",
"exception",
"gene",
"note",
"protein_id",
"pseudo",
"transcript_id",
"translation",
"transl_except",
"transl_table"
}

Definition at line 491 of file Gb_qual.cpp.

Referenced by CGb_qual::IsIllegalQualName().

◆ s_LegalMobileElementStrings

const char* s_LegalMobileElementStrings[]
static
Initial value:
= {
"insertion sequence",
"integron",
"LINE",
"MITE",
"non-LTR retrotransposon",
"other",
"P-element",
"retrotransposon",
"SINE",
"superintegron",
"transposable element",
"transposon"
}

Definition at line 413 of file Gb_qual.cpp.

◆ valid_inf_categories

const char* valid_inf_categories[]
static
Initial value:
= {
"EXISTENCE",
"COORDINATES",
"DESCRIPTION"
}

Definition at line 61 of file Gb_qual.cpp.

Referenced by CInferencePrefixList::GetPrefixAndRemainder(), and CGb_qual::ParseExperiment().

◆ valid_inf_prefixes

const char* valid_inf_prefixes[]
static
Initial value:
= {
"ab initio prediction",
"nucleotide motif",
"profile",
"protein motif",
"similar to AA sequence",
"similar to DNA sequence",
"similar to RNA sequence",
"similar to RNA sequence, EST",
"similar to RNA sequence, mRNA",
"similar to RNA sequence, other RNA",
"similar to sequence",
"alignment"
}

Definition at line 67 of file Gb_qual.cpp.

Referenced by CGb_qual::CleanupAndRepairInference(), and CInferencePrefixList::GetPrefixAndRemainder().

Modified on Thu Feb 29 12:20:34 2024 by modify_doxy.py rev. 669887