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NCBI C++ ToolKit: src/gui/objutils/cmd_add_cds.cpp Source File

CSeq_descr::Tdata::iterator desc_it = seq_descr.begin();

(desc_it != seq_descr.end()) {

((*desc_it)->IsSource() || (*desc_it)->IsPub()) {

desc_it = seq_descr.erase(desc_it);

(; annot_ci; ++annot_ci) {

((*annot_ci).IsFtable()) {

((*annot_ci).IsFtable())

(

->IsSetProduct())

(

->IsSetProduct() && !prot_h) {

prot_id->

(*(

->GetProduct().GetId()));

->SetProduct().SetWhole().Assign(*prot_id);

protein->

().push_back(prot_id);

->SetPartial(

);

->SetPartial(

);

->SetLocation().SetInt().SetId(*prot_id);

->SetLocation().SetInt().SetFrom(0);

;

(!

.empty()) {

CSeq_descr::Tdata::iterator desc_it = seq_descr.begin();

(desc_it != seq_descr.end()) {

((*desc_it)->IsSource() || (*desc_it)->IsPub()) {

desc_it = seq_descr.erase(desc_it);

(; annot_ci; ++annot_ci) {

((*annot_ci).IsFtable()) {

(!

.empty()) {

protein->

().ResetExt();

protein->

().SetSeq_data().SetIupacaa().Set(

);

protein->

().SetSeq_data().SetNcbieaa().Set(

);

protein->

().push_back(new_prot_id);

->SetPartial(

);

->SetPartial(

);

->SetLocation().SetInt().SetFrom(0);

->SetLocation().SetInt().SetTo(seq_length - 1);

;

@ eExtreme_Biological

5' and 3'

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

TSeqPos GetLength(void) const

objects::CSeq_feat_EditHandle m_feh_CDS

CRef< objects::CSeq_feat > m_CDS

objects::CSeq_annot_EditHandle m_FTableCreated

virtual string GetLabel()

objects::CSeq_entry_Handle m_seh

virtual void Unexecute()

Undo (opposite to Execute())

bool m_create_general_only

objects::CBioseq_EditHandle m_ProtHandle

CRef< objects::CSeq_feat > m_Prot

virtual void Execute()

Do the editing action.

objects::CSeq_annot_EditHandle m_FTableCreated

objects::CBioseq_EditHandle m_ProtHandle

virtual string GetLabel()

vector< CRef< objects::CSeq_feat > > m_other_prot_feats

virtual void Unexecute()

Undo (opposite to Execute())

objects::CSeq_feat_EditHandle m_feh_CDS

CRef< objects::CSeq_feat > m_CDS

vector< CRef< objects::CSeq_id > > m_prot_id

void x_AddMolinfoDescriptorToProtein()

objects::CSeq_entry_Handle m_seh

CRef< objects::CSeq_feat > m_Prot

virtual void Execute()

Do the editing action.

void x_AddProteinFeatures(const TSeqPos &seq_length)

static string s_GetProductSequence(const objects::CSeq_feat &cds, objects::CScope &scope)

SeqVector related exceptions.

namespace ncbi::objects::

unsigned int TSeqPos

Type for sequence locations and lengths.

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

Set object to copy of another one.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static CRef< CBioseq > TranslateToProtein(const CSeq_feat &cds, CScope &scope)

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.

TSeq ConvertSetToSeq(void) const

Do the same as CollapseSet() when sub-entry is of type bioseq.

void SetDescr(TDescr &v) const

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

TSet ConvertSeqToSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the entry from Bioseq to Bioseq-set.

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from the TSE of this Seq-entry.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CBioseq_EditHandle AttachBioseq(CBioseq &seq, int index=-1) const

Attach an existing bioseq.

bool AddSeqdesc(CSeqdesc &v) const

#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 SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

@ eClass_nuc_prot

nuc acid and coded proteins

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

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

@ eMol_na

just a nucleic acid

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