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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/RNA__ref_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqfeat/RNA_ref.cpp Source File

* rna_type_name =

;

( rna_type_it != sc_RnaTypeMap.end() ) {

rna_type_name = rna_type_it->second;

(

().IsName()) {

}

(

().IsGen() &&

().GetGen().IsSetProduct()) {

}

(

().IsTRNA()) {

= product;

trna.

().SetNcbieaa(42);

(

.length() > 9) {

remainder =

.substr(9);

found_three_letter_code =

;

trna.

().SetNcbieaa(

+ 64);

found_three_letter_code =

;

(!found_three_letter_code &&

.length() > 5) {

ch =

.c_str()[5];

after =

.c_str()[6];

aa = 65 + ch -

;

trna.

().SetNcbieaa(aa);

remainder =

.substr(6);

}

(ch ==

) {

trna.

().SetNcbieaa(42);

remainder =

.substr(6);

codon = remainder.substr(1, 3);

(!

().GetGen().IsSetClass() && !

().GetGen().IsSetQuals()) {

DEFINE_STATIC_ARRAY_MAP(TRnaTypeMap, sc_RnaTypeMap, sc_rna_type_map)

static const SStaticPair< CRNA_ref::EType, const char * > sc_rna_type_map[]

static const char * sc_TrnaList[]

static CTempString s_GetTrnaProduct(const CTrna_ext &trna)

static void s_SetTrnaProduct(CTrna_ext &trna, const string &product, string &remainder)

static CTempString s_AaName(int aa)

CStaticPairArrayMap< CRNA_ref::EType, const char * > TRnaTypeMap

User-defined methods of the data storage class.

string GetRnaProductName(void) const

static string GetRnaTypeName(const CRNA_ref::EType rna_type)

void SetRnaProductName(const string &product, string &remainder)

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

static bool ParseDegenerateCodon(CTrna_ext &tRNA, const string &codon)

#define test(a, b, c, d, e)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

size_type length(void) const

Return the length of the represented array.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ eNocase

Case insensitive compare.

TName & SetName(void)

Select the variant.

TType GetType(void) const

Get the Type member data.

const TAa & GetAa(void) const

Get the Aa member data.

void ResetAa(void)

Reset Aa data member.

bool IsSetAa(void) const

Check if a value has been assigned to Aa data member.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

EType

type of RNA feature

bool IsSetExt(void) const

generic fields for ncRNA, tmRNA, miscRNA Check if a value has been assigned to Ext data member.

TCodon & SetCodon(void)

Assign a value to Codon data member.

TNcbieaa GetNcbieaa(void) const

Get the variant data.

TIupacaa GetIupacaa(void) const

Get the variant data.

void SetAa(TAa &value)

Assign a value to Aa data member.

void ResetCodon(void)

Reset Codon data member.

const TGen & GetGen(void) const

Get the variant data.

void ResetExt(void)

Reset Ext data member.

const TName & GetName(void) const

Get the variant data.

TGen & SetGen(void)

Select the variant.

const TProduct & GetProduct(void) const

Get the Product member data.

const TExt & GetExt(void) const

Get the Ext member data.

void SetProduct(const TProduct &value)

Assign a value to Product data member.

TExt & SetExt(void)

Assign a value to Ext data member.

void ResetProduct(void)

Reset Product data member.

@ eType_scRNA

will become ncRNA, with RNA-gen.class = scRNA

@ eType_snoRNA

will become ncRNA, with RNA-gen.class = snoRNA

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

@ eType_snRNA

will become ncRNA, with RNA-gen.class = snRNA

unsigned int

A callback function used to compare two keys in a database.

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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