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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cmd__add__seqentry_8cpp_source.html below:

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

: m_SEH(seh), m_Add(seqentry)

(nuc_parent && nuc_parent.

() && nuc_parent.

() == objects::CBioseq_set::eClass_nuc_prot) {

(

&&

->IsSetSeq_set()) {

CBioseq_set::TDescr::Tdata::const_iterator it =

->GetDescr().Get().begin();

(it !=

->GetDescr().Get().end()) {

(!(*it)->IsMolinfo()

(

->IsSetDescr()) {

it =

->GetDescr().Get().begin();

(entry->

()) {

CBioseq_set::TSeq_set::const_iterator it =

.GetSeq_set().

();

(it !=

.GetSeq_set().

()) {

(

.GetSeq_set().

() == 1) {

;

changed =

;

( partial5 && partial3 ) {

}

( partial5 ) {

}

( partial3 ) {

((*it)->IsMolinfo()) {

pdesc =

objects::CSeqdesc();

protein->SetDescr().Set().push_back(pdesc);

pdesc->SetMolinfo().SetBiomol(objects::CMolInfo::eBiomol_peptide);

(objects::CSeq_entry::TAnnot, annot_it, protein->SetSeq().SetAnnot()) {

((*annot_it)->IsFtable()) {

=

objects::CSeq_annot();

protein->SetSeq().SetAnnot().push_back(

);

((*feat_it)->IsSetData() && (*feat_it)->GetData().IsProt() && !(*feat_it)->GetData().GetProt().IsSetProcessed()) {

prot_feat = *feat_it;

prot_feat =

objects::CSeq_feat();

prot_feat->SetData().SetProt();

->SetData().SetFtable().push_back(prot_feat);

prot_id->Assign(*(protein->GetSeq().GetId().front()));

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

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

prot_feat->SetLocation().SetInt().SetTo(protein->GetSeq().GetLength() - 1);

(partial5 || partial3) {

prot_feat->SetPartial(

);

prot_feat->ResetPartial();

objects::CSourceModParser

(

objects::CSourceModParser::eHandleBadMod_Ignore );

= protein->GetSeq().GetClosestDescriptor(objects::CSeqdesc::e_Title);

& title(

&

(title_desc->GetTitle()));

.ApplyAllMods(protein->SetSeq());

objects::CSeqTranslator::ChangeDeltaProteinToRawProtein(protein);

(cds->IsSetProduct()) {

prot_id->Assign(*(cds->GetProduct().GetId()));

local_offset = 1;

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

protein->SetId().push_back(prot_id);

entry->SetSeq().Assign(*protein);

@ eExtreme_Biological

5' and 3'

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

virtual string GetLabel()

virtual void Unexecute()

Undo (opposite to Execute())

CCmdAddSeqEntry(CSeq_entry *seqentry, CSeq_entry_Handle seh)

virtual void Execute()

Do the editing action.

@ eObjectType_AutodefOptions

const_iterator begin() const

const_iterator end() const

bool SetMolinfoCompleteness(CMolInfo &mi, bool partial5, bool partial3)

void SetMolinfoForProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

CRef< objects::CSeq_feat > AddEmptyProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

CRef< objects::CSeq_entry > CreateTranslatedProteinSequence(CRef< objects::CSeq_feat > cds, objects::CBioseq_Handle nuc_h, bool create_general_only, int *offset)

CRef< objects::CSeq_feat > AddProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CSeq_entry_EditHandle GetSeq_entryEditHandle(const CSeq_entry &entry)

TSeq ConvertSetToSeq(void) const

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

TClass GetClass(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &v) const

CBioseq_set_EditHandle GetParentBioseq_set(void) const

Get parent bioseq-set edit handle.

void Remove(void) const

Remove this Seq-entry from parent, or scope if it's top level Seq-entry.

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

Convert the entry from Bioseq to Bioseq-set.

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

bool IsSetClass(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

bool AddSeqdesc(CSeqdesc &v) const

int GetSeq_entry_Index(const CSeq_entry_Handle &handle) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

@ eClass_nuc_prot

nuc acid and coded proteins

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

bool IsSetCompleteness(void) const

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

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

@ 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

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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