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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/rna__names_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/discrepancy/rna_names.cpp Source File

44 "4.5S ribosomal RNA"

46 "5.8S ribosomal RNA"

56 "large subunit ribosomal RNA"

57 "small subunit ribosomal RNA" 63

{

"16S rRNA. Bacterial SSU"

"16S ribosomal RNA"

64

{

"23S rRNA. Bacterial LSU"

"23S ribosomal RNA"

65

{

"5S rRNA. Bacterial TSU"

"5S ribosomal RNA"

66

{

"Large Subunit Ribosomal RNA; lsuRNA; 23S ribosomal RNA"

"23S ribosomal RNA"

67

{

"Small Subunit Ribosomal RNA; ssuRNA; 16S ribosomal RNA"

"16S ribosomal RNA"

68

{

"Small Subunit Ribosomal RNA; ssuRNA; SSU ribosomal RNA"

"small subunit ribosomal RNA"

69

{

"Large Subunit Ribosomal RNA; lsuRNA; LSU ribosomal RNA"

"large subunit ribosomal RNA"

}

77 for

(

auto

& feat :

context

.GetFeat()) {

78 if

(feat.IsSetData() && feat.GetData().IsRna() && feat.GetData().GetRna().CanGetExt() && feat.GetData().GetRna().GetType() ==

CRNA_ref::eType_rRNA

) {

79 const string

& name = feat.GetData().GetRna().GetExt().GetName();

81 bool

autofix =

false

;

102

m_Objs[

"[n] rRNA product name[s] [is] not standard. Correct the names to the standard format, eg \"16S ribosomal RNA\""

].Add(*

context

.SeqFeatObjRef(feat, autofix ? &feat :

nullptr

)).Fatal();

118 context

.ReplaceSeq_feat(*obj, *sf, *new_feat);

128 context

.ReplaceSeq_feat(*obj, *sf, *new_feat);

namespace ncbi::objects::

#define DISCREPANCY_AUTOFIX(name)

#define DISCREPANCY_CASE(name, type, group, descr)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

constexpr size_t ArraySize(const Element(&)[Size])

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TRna & GetRna(void) const

Get the variant data.

static const size_t rrna_standard_name_len

static const size_t rrna_name_replace_len

static const char * rrna_standard_name[]

static const pair< const char *, const char * > rrna_name_replace[]

static CS_CONTEXT * context

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