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NCBI C++ ToolKit: src/objtools/edit/promote.cpp Source File

);

);

rna_map[

] = *it;

CSeq_feat::TXref::iterator it = feat.

().begin();

( it != feat.

().end() ) {

it = feat.

().erase(it);

(

[

.length() - 1] ==

) {

descr->

().push_back(desc);

.SetDescr(*descr);

( feat.

().empty() ) {

( (rna_map == 0) || (rna_map->

(mrna) == rna_map->

()) ) {

annot->

().SetFtable().push_back(mcds);

descr->

().push_back(desc);

&

,

&

,

kRNA =

;

kCDS =

;

* ftype = feat.

().

() ? &kRNA : &kCDS;

CSeq_feat::TQual::iterator it = feat.

().begin();

( it != feat.

().end() ) {

( !

.

() ) {

<< qual.

() <<

<<

);

it = feat.

().erase(it);

( feat.

().empty() ) {

( !

.

() ) {

( it != sc_BiomolMap.end() ) {

feat.

().SetWhole().Assign(*prod_id);

partial_left,

partial_right)

->SetData().SetProt(prp);

->SetLocation(*loc);

include_stop,

remove_trailingX)

( include_stop ) {

( remove_trailingX ) {

changed =

;

( partial5 && partial3 ) {

}

( partial5 ) {

}

( partial3 ) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

@Gb_qual.hpp User-defined methods of the data storage class.

ESubtype GetSubtype(void) const

@Seq_descr.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

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

TBase::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const struct type types[]

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define LOG_POST_X(err_subcode, message)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

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

Set object to copy of another one.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

static void TranslateCdregion(string &prot, const CBioseq_Handle &bsh, const CSeq_loc &loc, const CCdregion &cdr, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0, ETranslationLengthProblemOptions options=eThrowException)

translation coding region into ncbieaa protein sequence

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

@ eLocationToProduct

Map from the feature's location to product.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

void SetDescr(TDescr &v) const

CBioseq_EditHandle MoveTo(const CSeq_entry_EditHandle &entry, int index=-1) const

Move current bioseq into seq-entry.

void Remove(void) const

Remove current annot.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

void SetInst_Mol(TInst_Mol v) const

void SetInst_Seq_data(TInst_Seq_data &v) const

void SetInst_Length(TInst_Length v) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

void SetInst_Repr(TInst_Repr v) const

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetExactComplexityLevel(CBioseq_set::EClass cls) const

Return level with exact complexity, or empty handle if not found.

CSeqFeatData::E_Choice GetFeatType(void) const

SAnnotSelector & SetResolveNone(void)

SetResolveNone() is equivalent to SetResolveMethod(eResolve_None).

TCoding GetCoding(void) const

Target sequence coding.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * ReleaseOrNull(void)

Release a reference to the object and return a pointer to the object.

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

#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.

const TVal & GetVal(void) const

Get the Val member data.

TXref & SetXref(void)

Assign a value to Xref data member.

void SetData(TData &value)

Assign a value to Data data member.

const TData & GetData(void) const

Get the Data member data.

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TLocation & GetLocation(void) const

Get the Location member data.

list< CRef< CCode_break > > TCode_break

const TData & GetData(void) const

Get the Data member data.

bool CanGetData(void) const

Check if it is safe to call GetData method.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsPub(void) const

Check if variant Pub is selected.

void SetData(TData &value)

Assign a value to Data data member.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetQual(void) const

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

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TXref & GetXref(void) const

Get the Xref member data.

bool CanGetProduct(void) const

Check if it is safe to call GetProduct method.

const TQual & GetQual(void) const

Get the Qual member data.

void ResetXref(void)

Reset Xref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetVal(void) const

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

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsRna(void) const

Check if variant Rna is selected.

void ResetQual(void)

Reset Qual data member.

@ e_Pub

publication applies to this seq

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetCompleteness(void) const

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

TId & SetId(void)

Assign a value to Id data member.

E_Choice

Choice variants.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

EMol

molecule class in living organism

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

Tdata & Set(void)

Assign a value to data member.

void SetTech(TTech value)

Assign a value to Tech data member.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eRepr_raw

continuous sequence

@ eCompleteness_complete

complete biological entity

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ eTech_concept_trans

conceptual translation

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

constexpr bool empty(list< Ts... >) noexcept

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

bool AddSeqEntryToSeqEntry(const objects::CSeq_entry *entry, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool &has_nuc, bool &has_prot, bool create_general_only)

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