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NCBI C++ ToolKit: src/algo/sequence/make_cdr_prods.cpp Source File

list<CRef<CSeq_feat> >&

= annot->

().SetFtable();

(!(*feat)->GetData().IsCdregion()) {

((*feat)->IsSetProduct()) {

num.insert(

(0), 5 - num.size(),

);

acc =

+ num;

full_acc =

+ acc;

bio_seq->

().push_back(

);

title->

(

(

) + acc);

bio_seq->

().Set().push_back(title);

bio_seq->

().Set().push_back(mol_type);

seq_entry->

(*bio_seq);

bioseq_set->

().push_back(seq_entry);

(*feat)->SetProduct(*prod_loc);

User-defined methods of the data storage class.

static CAtomicCounter sm_Counter

static CRef< objects::CBioseq_set > MakeCdrProds(CRef< objects::CSeq_annot > annot, objects::CBioseq_Handle handle)

Given an annot containing a feature table with Cdregions, translate those without products.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

TValue Add(int delta) THROWS_NONE

Atomically add value (=delta), and return new counter value.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

CScope & GetScope(void) const

Get scope this handle belongs to.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

TTitle & SetTitle(void)

Select the variant.

TMol_type & SetMol_type(void)

Select the variant.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void SetMol(TMol value)

Assign a value to Mol data member.

@ eRepr_raw

continuous sequence

@ e_Iupacaa

IUPAC 1 letter amino acid code.

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