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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/editing_action_features.cpp Source File

changed_loc.

();

(

subloc(loc, objects::CSeq_loc_CI::eEmpty_Skip); subloc; ++subloc)

(

gene(bsh, subtype); gene; ++gene)

feature_handles.

(gene->GetSeq_feat_Handle());

(

gene : feature_handles)

& gene_loc = gene.GetLocation();

any_match =

;

(

bsh : seen_bsh)

(!subloc || !gene_subloc)

sub_exact =

;

exact = exact && sub_exact;

(sub_diff < INT_MAX)

best_non_exact = gene;

best_non_exact;

CRangeWithFuzz(

TParent& rg)

: TParent(it.GetRange()),

(m_Fuzz_from, rg.m_Fuzz_from, rg.m_Strand);

(

CRangeWithFuzz& rg)

(m_Fuzz_to, rg.m_Fuzz_to, rg.m_Strand);

(

CRangeWithFuzz& rg)

(

CRangeWithFuzz& rg)

(old_from == rg.GetFrom()) {

(old_to !=

()) {

(old_to == rg.GetTo()) {

(old_to !=

()) {

TFuzz copy_from_cref;

(copy_from == fuzz) copy_from_cref.

(copy_from);

new_fuzz->

(*copy_from);

fuzz.Reset(new_fuzz);

(fuzz, other.GetPointerOrNull());

(fuzz->Which() != other->Which()) {

( fz.

() ) {

other_rev =

(other_strand);

( fz.

() ) {

((!this_rev && other_lt) ||

(this_rev && other_gt)) {

((!this_rev && other_gt) ||

(this_rev && other_lt)) {

(other_lim == this_lim) {

new_fuzz->

().insert(

new_fuzz->

().end(),

(min1 > min2 || max1 < max2) {

(fz.

() < pct) {

CSeq_id_Handle_Wrapper

(

.IsLocal() &&

.GetLocal().IsStr()) {

(

CSeq_id_Handle_Wrapper& handle)

(

CSeq_id_Handle_Wrapper& handle)

(

CSeq_id_Handle_Wrapper& handle)

TSynonymMap::iterator id_syn = m_SynMap.find(idh);

(id_syn != m_SynMap.end()) {

id_syn->second;

(rank < best_rank) {

m_SynMap[syn_set->GetSeq_id_Handle(syn_it)] = best;

<<

<< gi);

CDefaultSynonymMapper syn_mapper(&scope);

CRangeWithFuzz total_rg(CRangeWithFuzz::GetEmpty());

CSeq_id_Handle_Wrapper prev_id;

CSeq_id_Handle_Wrapper next_id(syn_mapper.GetBestSynonym(it.GetSeq_id()), it.GetSeq_id());

(prev_id != next_id || prev_strand != next_strand)

->Assign(*prev_id.GetSeqId());

( total_rg.IsSetFuzzFrom() )

interval->

().Assign(total_rg.GetFuzzFrom());

( total_rg.IsSetFuzzTo() )

interval->

().Assign(total_rg.GetFuzzTo());

total_rg = CRangeWithFuzz(CRangeWithFuzz::GetEmpty());

total_rg += CRangeWithFuzz(it);

prev_strand = next_strand;

(!total_rg.Empty())

->Assign(*prev_id.GetSeqId());

( total_rg.IsSetFuzzFrom() )

interval->

().Assign(total_rg.GetFuzzFrom());

( total_rg.IsSetFuzzTo() )

interval->

().Assign(total_rg.GetFuzzTo());

gene_loc->

(*interval);

new_prot_loc->

(prot_loc);

((*annot_ci).IsFtable())

new_prot_loc->

(prot_loc);

((*it)->IsSetData() && (*it)->GetData().IsGene())

:

(seh, subtype, feat_type, ncRNA_class,

)

:

(seh, subtype, feat_type, ncRNA_class,

)

&qual,

&name)

found =

;

((*gbqual_it) && (*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

(!

.empty())

&qual1,

&qual2)

:

(seh, subtype, feat_type, ncRNA_class, qual1,

), m_qual2(qual2)

found =

;

((*gbqual_it) && (*gbqual_it)->IsSetQual() && ((*gbqual_it)->GetQual() ==

|| (*gbqual_it)->GetQual() ==

))

element_type, element_name;

!element_type.empty();

element_type, element_name;

element_type =

;

(!element_name.empty())

element_type +=

+ element_name;

element_type, element_name;

element_type;

element_type, element_name;

(!element_name.empty())

element_type, element_name;

!element_name.empty();

element_type, element_name;

element_name =

;

(!element_type.empty())

element_name = element_type +

+ element_name;

element_type, element_name;

element_name;

element_type, element_name;

(!element_type.empty())

found =

;

(!db.empty() && !

.empty())

dbtag->

().SetId(

);

db +

+

;

:

(seh, subtype, feat_type, ncRNA_class,

)

:

(seh, subtype, feat_type, ncRNA_class,

)

:

(seh, subtype, feat_type, ncRNA_class,

,

)

is_trna || is_qual;

(ch ==

|| ch ==

|| ch ==

|| ch ==

|| ch ==

) {

,

,

,

,

,

,

,

,

,

,

};

(pos != string::npos) {

vector<string> replacements;

(codon.length() == 3 &&

(codon.c_str()[0])) {

this_codon = codon.substr(0, 1);

replacements.push_back(this_codon);

(

= 1;

< 3;

++) {

num_now = replacements.size();

(

j = 1; j < ch.length(); j++) {

(

k = 0; k < num_now; k++) {

cpy = replacements[k];

replacements.push_back(cpy);

(

k = 0; k < num_now; k++) {

(

j = 0; j < ch.length(); j++) {

replacements[j * num_now + k].append(ch.substr(j, 1));

replacements.push_back(codon);

replacements;

(

j = 0; j <

.size(); j++)

:

(seh, subtype, feat_type, ncRNA_class,

,

)

found =

;

loc_label = v[0];

cb_loc->

().SetPoint(start);

cb_loc->

().SetId().Assign(*loc.

());

vector<char> seqData;

(!loc_label.empty())

is_trna || is_qual;

rval = (

)

+ (partial3 ?

:

)

+

+ (partial5 ?

:

)

rval = (partial5 ?

:

)

+

+ (partial3 ?

:

)

(loc.

())

( (*it)->IsInt())

=

;

:

(seh, subtype, feat_type, ncRNA_class,

), m_qual(qual), m_erase(

)

found =

;

((*rnaqual_it)->IsSetQual() && (*rnaqual_it)->GetQual() ==

)

((*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

= (*it)->GetName();

= (*it)->GetId();

= (*it)->GetName();

= (*it)->GetId();

:

(seh, subtype, feat_type, ncRNA_class,

)

(!before && after)

(!before && after)

:

(seh, subtype, feat_type, ncRNA_class,

), m_erase(

), m_syn(

), m_qual(

)

found =

;

(!before && after)

((*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

(!before && after)

:

(seh, subtype, feat_type, ncRNA_class,

), m_erase(

), m_activity(

), m_qual(

)

found =

;

((*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

:

(seh, subtype, feat_type, ncRNA_class,

)

:

(seh, subtype, feat_type, ncRNA_class,

,

)

:

(seh, subtype, feat_type, ncRNA_class,

), m_erase(

), m_ec(

), m_qual(

)

found =

;

((*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

& ncRNA_class)

:

(seh, subtype, feat_type, ncRNA_class,

), m_erase(

), m_name(

), m_qual(

)

found =

;

((*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

(

==

||

==

)

(

==

||

==

)

is_gene || is_xref || is_qual;

(!before && after)

((*annot_ci).IsFtable())

vector<CRef<CSeq_loc>> already_created;

(!

(action))

= find_if(already_created.begin(), already_created.end(),[gene_loc](

loc) {return loc->Equals(*gene_loc);});

(

== already_created.end())

already_created.push_back(gene_loc);

vector<CSeq_feat_Handle> feat_handles;

feat_handles.push_back(fh);

feat_handles.push_back(fh);

vector<CRef<CSeq_loc>> already_created;

(

= 0;

< feat_handles.size();

++)

= find_if(already_created.begin(), already_created.end(),[gene_loc](

loc) {return loc->Equals(*gene_loc);});

(

== already_created.end())

already_created.push_back(gene_loc);

=

;

=

;

=

;

=

;

=

;

:

(seh, subtype, feat_type, ncRNA_class,

), m_erase(

), m_function(

), m_qual(

)

found =

;

((*gbqual_it)->IsSetQual() && (*gbqual_it)->GetQual() ==

)

& ncRNA_class)

(field ==

|| field ==

)

(field ==

)

(field ==

|| field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

|| field ==

)

(field ==

|| field ==

)

(field ==

)

(field ==

|| field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

|| field ==

|| field ==

)

(field ==

|| field ==

)

(field ==

|| field ==

)

(field ==

)

(field ==

)

(field ==

|| field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

|| field ==

|| field ==

)

(field ==

)

(field ==

)

(field ==

)

(field ==

|| field ==

|| field ==

|| field ==

|| field ==

)

(field ==

)

(field ==

)

(field ==

|| field ==

)

(field ==

|| field ==

|| field ==

)

(field ==

|| field ==

)

(field ==

|| field ==

)

(field ==

)

static CRef< CScope > m_Scope

bool IsReverse(ENa_strand s)

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

virtual ~CDefaultSynonymMapper(void)

CDefaultSynonymMapper(CScope *scope)

map< CSeq_id_Handle, CSeq_id_Handle > TSynonymMap

CRef< CSeq_id_Mapper > m_IdMapper

virtual CSeq_id_Handle GetBestSynonym(const CSeq_id &id)

virtual bool Match(const string &value)

CEditingActionFeatActivity(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void SetValue(const string &value)

virtual bool IsSetValue(void)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual void Modify(EActionType action)

CRef< CGb_qual > m_GBqual

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

CEditingActionFeatAllele(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void SetValue(const string &value)

CEditingActionFeatAnticodon(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual string GetValue(void)

string GetIntervalString(const CSeq_interval &seq_int)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

CEditingActionFeatCodonStart(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual string GetValue(void)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

CEditingActionFeatCodonsRecognized(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void Modify(EActionType action)

virtual bool IsSetValue(void)

virtual string GetValue(void)

virtual void ResetValue(void)

CEditingActionFeatDbxref(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void SetValue(const string &value)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

virtual void ResetValue(void)

virtual string GetValue(void)

CEditingActionFeatDesc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual bool IsSetValue(void)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

CEditingActionFeatDualVal1(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual)

virtual void ResetValue(void)

CEditingActionFeatDualVal2(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual void Modify(EActionType action)

virtual void FindRelated(EActionType action)

virtual bool IsSetValue(void)

virtual void Find(EActionType action)

CEditingActionFeatEcNumber(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void ResetValue(void)

virtual string GetValue(void)

CRef< CGb_qual > m_GBqual

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual void SetValue(const string &value)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

CEditingActionFeatEvidence(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

CEditingActionFeatException(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

virtual bool IsSetValue(void)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

virtual void ResetValue(void)

CEditingActionFeatFunction(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual string GetValue(void)

CRef< CGb_qual > m_GBqual

virtual void Modify(EActionType action)

virtual void Modify(EActionType action)

CEditingActionFeatGbQualTwoNames(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual1, const string &qual2)

virtual void SetValue(const string &value)

virtual void ResetValue(void)

CRef< CGb_qual > m_GBqual

virtual void Modify(EActionType action)

virtual bool IsSetValue(void)

CEditingActionFeatGbQual(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual, const string &name="CEditingActionFeatGbQual")

virtual string GetValue(void)

virtual void SetFeat(CSeq_feat_Handle fh)

virtual void Find(EActionType action)

virtual void Find(EActionType action)

virtual void Find(EActionType action)

virtual bool SameObject()

virtual void SetFeat(CSeq_feat_Handle fh)

CEditingActionFeatGeneLocus(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &name)

virtual void FindRelated(EActionType action)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual bool IsSetValue(void)

CEditingActionFeatLocus_tag(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

CEditingActionFeatMaploc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual bool IsSetValue(void)

CEditingActionFeatNcRnaClass(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual string GetValue(void)

virtual void SetValue(const string &value)

CEditingActionFeatPartial(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

virtual void Modify(EActionType action)

virtual void SetValue(const string &value)

CRef< CGb_qual > m_GBqual

virtual void Find(EActionType action)

virtual string GetValue(void)

virtual void FindRelated(EActionType action)

CEditingActionFeatProduct(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void ResetValue(void)

CEditingActionFeatPseudo(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual string GetValue(void)

virtual bool IsSetValue(void)

virtual void ResetValue(void)

CEditingActionFeatRegion(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void SetValue(const string &value)

virtual bool IsSetValue(void)

CEditingActionFeatRnaQual(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual)

virtual void ResetValue(void)

virtual void Modify(EActionType action)

virtual string GetValue(void)

CRef< CGb_qual > m_GBqual

virtual void SetValue(const string &value)

CRef< CRNA_qual > m_RnaQual

virtual void SetFeat(CSeq_feat_Handle fh)

virtual void Find(EActionType action)

virtual bool SameObject()

virtual void FindRelated(EActionType action)

CEditingActionFeatRnaToGeneDesc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

virtual void FindRelated(EActionType action)

virtual void Find(EActionType action)

virtual void SetFeat(CSeq_feat_Handle fh)

virtual bool SameObject()

CEditingActionFeatRnaToGeneLocus_tag(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

virtual void SetFeat(CSeq_feat_Handle fh)

virtual void Find(EActionType action)

virtual void FindRelated(EActionType action)

virtual bool SameObject()

CEditingActionFeatRnaToGeneMaploc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

CEditingActionFeatRnaToGeneSynonym(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

virtual void SetFeat(CSeq_feat_Handle fh)

virtual bool SameObject()

virtual void FindRelated(EActionType action)

virtual void Find(EActionType action)

virtual bool IsSetValue(void)

virtual string GetValue(void)

CEditingActionFeatSynonym(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void ResetValue(void)

virtual void Modify(EActionType action)

virtual void SetValue(const string &value)

CRef< CGb_qual > m_GBqual

virtual bool IsSetValue(void)

virtual void ResetValue(void)

CEditingActionFeatTranscriptId(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual void SetValue(const string &value)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

virtual void Modify(EActionType action)

virtual string GetValue(void)

CEditingActionFeatTranslExcept(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual bool IsSetValue(void)

CRef< CCode_break > m_CodeBreak

const CGenetic_code_table & m_code_table

virtual string GetValue(void)

CEditingActionFeatTranslTable(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

virtual bool IsSetValue(void)

virtual void SetValue(const string &value)

virtual void ResetValue(void)

virtual bool IsSetValue(void)

virtual string GetValue(void)

virtual void ResetValue(void)

virtual void SetValue(const string &value)

CEditingActionFeatTranslation(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

static string IndexToCodon(int index)

static int CodonToIndex(char base1, char base2, char base3)

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

string GetRnaProductName(void) const

void AddFuzzFrom(const CRangeWithFuzz &rg)

bool IsSetFuzzFrom(void) const

CRef< CInt_fuzz > x_SetFuzz(TFuzz &fuzz, const CInt_fuzz *copy_from)

const CInt_fuzz & GetFuzzTo(void) const

void x_AddFuzz(TFuzz &fuzz, const TFuzz &other, ENa_strand other_strand)

const CInt_fuzz & GetFuzzFrom(void) const

bool IsSetFuzzTo(void) const

CRangeWithFuzz(const TParent &rg)

void AddFuzzTo(const CRangeWithFuzz &rg)

void CopyTo(const CRangeWithFuzz &rg)

void CopyFrom(const CRangeWithFuzz &rg)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

static E_Choice GetTypeFromSubtype(ESubtype subtype)

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

void AddOrReplaceQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature, or replace the value for the first one if it already exists.

void AddQualifier(const string &qual_name, const string &qual_val)

Add a qualifier to this feature.

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name; do nothing if no such qualifier exists.

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

void SetGeneXref(CGene_ref &value)

void SetProtXref(CProt_ref &value)

const CSeq_id_Handle & GetHandle(void) const

CConstRef< CSeq_id > m_Id

CSeq_id_Handle_Wrapper(void)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStart(ESeqLocExtremes ext) const

bool IsPartialStart(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

CRef< CSeq_loc > x_GetSublocOnBioseq(CBioseq_Handle bsh, const CSeq_loc &loc)

void SetFeatForAnotherFeat(CSeq_feat_Handle fh, const CSeqFeatData::ESubtype subtype)

CSeq_feat_Handle x_FindGeneForFeature(const CSeq_loc &loc, CScope &scope, CSeqFeatData::ESubtype subtype)

virtual void SwapContext(IEditingAction *source)

CSeq_feat_Handle GetFeatHandle(void)

void FindFeatForAnotherFeat(EActionType action, SAnnotSelector other_selector)

virtual void SetFeat(CSeq_feat_Handle fh)

void RemoveGeneXref(void)

CRef< CSeq_feat > m_EditedFeat

IEditingActionFeat(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &name)

CSeq_entry_Handle GetCurrentSeqEntryHandleFromFeatHandle(CSeq_feat_Handle fh)

virtual void Find(EActionType action)

bool MatchBioseqConstraintForFeatHandle(CSeq_feat_Handle fh)

CRef< CSeq_feat > m_SavedEditedFeat

bool m_saved_feat_enabled

virtual void FindRelated(EActionType action)

void GoToOrigFeature(void)

static const string & s_GetncRNAClass(const objects::CRNA_ref &rna_ref)

bool OtherFeatIs(const CSeqFeatData::ESubtype subtype)

virtual void ResetScope()

CRef< CSeq_loc > x_MergeFeatureLocation(const CSeq_loc &loc, CScope &scope)

static bool s_IsSetncRNAClass(const objects::CRNA_ref &rna_ref)

virtual void Modify(EActionType action)

void GoToProtFeature(void)

SAnnotSelector m_selector

CSeq_feat_Handle m_SavedFeat

bool x_TestGeneForFeature(const CSeq_loc &gene_loc, const CSeq_loc &feat_loc, CScope &scope, bool &exact, TSeqPos &diff)

void FindRelatedFeatForAnotherFeat(EActionType action, SAnnotSelector other_selector)

void FindRelatedOrCreateProtFeat(EActionType action)

void FindOrCreateProtFeat(EActionType action)

virtual bool SameObject()

edit::EExistingText m_existing_text

CSeq_entry_Handle m_TopSeqEntry

map< CSeq_feat_Handle, CRef< CSeq_feat > > m_ChangedFeatures

CSeq_entry_Handle m_CurrentSeqEntry

void Action(EActionType action)

map< CSeq_feat_Handle, CSeq_entry_Handle > m_CreatedFeatures

virtual void SwapContext(IEditingAction *source)

bool IsFrom(EActionType action)

CRef< CEditingActionConstraint > m_constraint

bool IsCreateNew(EActionType action)

bool IsNOOP(EActionType action)

Interface for mapping IDs to the best synonym.

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static bool s_IsATGC(char ch)

static vector< string > ParseDegenerateCodons(string codon)

IEditingActionFeat * CreateActionCdsGeneProt(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

static const string s_GetExpansion(const string &ch)

static const string kAmbiguities

IEditingActionFeat * CreateActionFeat(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

static const string kReplacements[]

IEditingActionFeat * CreateActionRna(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const char * str(char *buf, int n)

const TResidue codons[4][4]

#define DECLARE_OPERATOR_BOOL(Expr)

Declaration of safe bool operator from boolean expression.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

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

Set object to copy of another one.

#define ENUM_METHOD_NAME(EnumName)

CConstRef< CSeq_id > GetSeqId(void) const

int BestRankScore(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

@ eContent

Untagged human-readable accession or the like.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void SetPacked_int(TPacked_int &v)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

void Delete(void)

Delete current element, and make iterator to point to the next element.

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

size_t GetSize(void) const

Get number of ranges.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eEmpty_Allow

ignore empty locations

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

TSeqPos GetCoverage(const CSeq_loc &loc, CScope *scope)

Get number of unique bases in the location.

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

@ eContains

First CSeq_loc contains second.

@ eOverlap

CSeq_locs overlap.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

void ResetHistory(EActionIfLocked action=eKeepIfLocked)

Clean all unused TSEs from the scope's cache and release the memory.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id &id)

Get bioseq synonyms, resolving to the bioseq in this scope.

@ kPriority_Default

Use default priority for added data.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeqFeatData & GetData(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

CConstRef< CSeq_id > GetSeqId(void) const

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

virtual const CSeq_loc & GetLocation(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

bool HasParentEntry(void) const

Check if current seq-entry has a parent.

CSeqFeatData::E_Choice GetFeatType(void) const

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_entry > GetSeq_entryCore(void) const

Get const reference to the seq-entry.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

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

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

void SetCoding(TCoding coding)

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TThisType & operator+=(const TThisType &r)

TParent::position_type position_type

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fAllowTrailingSpaces

Ignore trailing whitespace characters.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSpaces

Ignore leading whitespace characters in converted string.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

bool IsSetAllele(void) const

Official allele designation Check if a value has been assigned to Allele data member.

bool IsSetMaploc(void) const

descriptive map location Check if a value has been assigned to Maploc data member.

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

const TLocus & GetLocus(void) const

Get the Locus member data.

const TAllele & GetAllele(void) const

Get the Allele member data.

const TMaploc & GetMaploc(void) const

Get the Maploc member data.

void SetMin(TMin value)

Assign a value to Min data member.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

const TTag & GetTag(void) const

Get the Tag member data.

void SetTag(TTag &value)

Assign a value to Tag data member.

bool IsId(void) const

Check if variant Id is selected.

TRange & SetRange(void)

Select the variant.

bool IsSetTag(void) const

appropriate tag Check if a value has been assigned to Tag data member.

TAlt & SetAlt(void)

Select the variant.

TPct GetPct(void) const

Get the variant data.

const TDb & GetDb(void) const

Get the Db member data.

void ResetTag(void)

Reset Tag data member.

TLim GetLim(void) const

Get the variant data.

TP_m & SetP_m(void)

Select the variant.

TMin GetMin(void) const

Get the Min member data.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

void SetMax(TMax value)

Assign a value to Max data member.

E_Choice Which(void) const

Which variant is currently selected.

TLim & SetLim(void)

Select the variant.

const TAlt & GetAlt(void) const

Get the variant data.

TPct & SetPct(void)

Select the variant.

TMax GetMax(void) const

Get the Max member data.

TP_m GetP_m(void) const

Get the variant data.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId GetId(void) const

Get the variant data.

const TRange & GetRange(void) const

Get the variant data.

@ eLim_tl

space to left of position

@ eLim_tr

space to right of position

@ e_Pct

% plus or minus (x10) 0-1000

@ e_Alt

set of alternatives for the integer

@ e_P_m

plus or minus fixed amount

bool IsSetDesc(void) const

description (instead of name) Check if a value has been assigned to Desc data member.

const TDesc & GetDesc(void) const

Get the Desc member data.

void SetQual(const TQual &value)

Assign a value to Qual data member.

void SetVal(const TVal &value)

Assign a value to Val data member.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

TType GetType(void) const

Get the Type member data.

const TCodon & GetCodon(void) const

Get the Codon member data.

bool IsTRNA(void) const

Check if variant TRNA is selected.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

bool IsSetExt(void) const

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

bool IsSetCodon(void) const

codon(s) as in Genetic-code Check if a value has been assigned to Codon data member.

bool IsGen(void) const

Check if variant Gen is selected.

bool IsSetVal(void) const

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

bool IsSetQuals(void) const

e.g., tag_peptide qualifier for tmRNAs Check if a value has been assigned to Quals data member.

const TGen & GetGen(void) const

Get the variant data.

bool IsSetType(void) const

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

bool IsSetClass(void) const

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value h...

const TVal & GetVal(void) const

Get the Val member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TTRNA & GetTRNA(void) const

Get the variant data.

const TClass & GetClass(void) const

Get the Class member data.

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

void SetAa(TAa &value)

Assign a value to Aa data member.

const TVal & GetVal(void) const

Get the Val member data.

bool IsSetComment(void) const

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

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void ResetPartial(void)

Reset Partial data member.

bool IsSetData(void) const

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

bool IsSetQual(void) const

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

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

bool IsProt(void) const

Check if variant Prot is selected.

TNcbi8aa GetNcbi8aa(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TRegion & GetRegion(void) const

Get the variant data.

const TLoc & GetLoc(void) const

Get the Loc member data.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void ResetExcept(void)

Reset Except data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

void ResetExp_ev(void)

Reset Exp_ev data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

void ResetExcept_text(void)

Reset Except_text data member.

list< CRef< CGenetic_code > > Tdata

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

void SetExcept(TExcept value)

Assign a value to Except data member.

bool IsGene(void) const

Check if variant Gene is selected.

EExp_ev

evidence for existence of feature

void ResetPseudo(void)

Reset Pseudo data member.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetExcept(void) const

something funny about this? Check if a value has been assigned to Except data member.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

void ResetData(void)

Reset Data data member.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TCode & GetCode(void) const

Get the Code member data.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetExp_ev(void) const

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

void ResetComment(void)

Reset Comment data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetAa(void) const

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

void SetExp_ev(TExp_ev value)

Assign a value to Exp_ev data member.

const TAa & GetAa(void) const

Get the Aa member data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TProduct & GetProduct(void) const

Get the Product member data.

TNcbieaa GetNcbieaa(void) const

Get the variant data.

bool IsSetPseudo(void) const

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

const TComment & GetComment(void) const

Get the Comment member data.

void SetVal(const TVal &value)

Assign a value to Val data member.

void SetPseudo(TPseudo value)

Assign a value to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

TPartial GetPartial(void) const

Get the Partial member data.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

const TProt & GetProt(void) const

Get the variant data.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

void ResetProduct(void)

Reset Product data member.

void ResetXref(void)

Reset Xref data member.

const TRna & GetRna(void) const

Get the variant data.

void ResetDbxref(void)

Reset Dbxref data member.

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

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 IsSetLoc(void) const

location of exception Check if a value has been assigned to Loc data member.

bool IsRna(void) const

Check if variant Rna is selected.

TExp_ev GetExp_ev(void) const

Get the Exp_ev member data.

bool IsRegion(void) const

Check if variant Region is selected.

void ResetQual(void)

Reset Qual data member.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

bool IsSetFrame(void) const

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

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

@ e_Ncbi8aa

NCBI8aa code.

@ e_Ncbieaa

ASCII value of NCBIeaa code.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

E_Choice Which(void) const

Which variant is currently selected.

const Tdata & Get(void) const

Get the member data.

void SetFuzz_to(TFuzz_to &value)

Assign a value to Fuzz_to data member.

void SetFuzz_from(TFuzz_from &value)

Assign a value to Fuzz_from data member.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

TLocal & SetLocal(void)

Select the variant.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

bool IsSetVersion(void) const

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

const TMix & GetMix(void) const

Get the variant data.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_not_set

No variant selected.

@ e_not_set

No variant selected.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ eMol_na

just a nucleic acid

CNcbiMatrix< T > & operator+=(CNcbiMatrix< T > &, const CNcbiMatrix< U > &)

global addition: matrix += matrix

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

const struct ncbi::grid::netcache::search::fields::CREATED created

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define EDIT_EACH_QUAL_ON_RNAGEN(Itr, Var)

#define EDIT_EACH_ECNUMBER_ON_PROTREF(Itr, Var)

#define ERASE_ECNUMBER_ON_PROTREF(Itr, Var)

ERASE_ECNUMBER_ON_PROTREF.

#define EDIT_EACH_ACTIVITY_ON_PROTREF(Itr, Var)

#define ERASE_ACTIVITY_ON_PROTREF(Itr, Var)

ERASE_ACTIVITY_ON_PROTREF.

#define EDIT_EACH_DBXREF_ON_SEQFEAT(Itr, Var)

#define EDIT_EACH_NAME_ON_PROTREF(Itr, Var)

#define ERASE_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

ERASE_SEQFEATXREF_ON_SEQFEAT.

#define EDIT_EACH_CODEBREAK_ON_CDREGION(Itr, Var)

#define ERASE_SYNONYM_ON_GENEREF(Itr, Var)

ERASE_SYNONYM_ON_GENEREF.

#define EDIT_EACH_SEQFEATXREF_ON_SEQFEAT(Itr, Var)

#define EDIT_EACH_SYNONYM_ON_GENEREF(Itr, Var)

#define EDIT_EACH_GBQUAL_ON_SEQFEAT(Itr, Var)

#define ERASE_NAME_ON_PROTREF(Itr, Var)

ERASE_NAME_ON_PROTREF.

#define ERASE_QUAL_ON_RNAGEN(Itr, Var)

ERASE_QUAL_ON_RNAGEN.

#define ERASE_DBXREF_ON_SEQFEAT(Itr, Var)

ERASE_DBXREF_ON_SEQFEAT.

#define ERASE_CODEBREAK_ON_CDREGION(Itr, Var)

ERASE_CODEBREAK_ON_CDREGION.

#define ERASE_GBQUAL_ON_SEQFEAT(Itr, Var)

ERASE_GBQUAL_ON_SEQFEAT.

TFeatSubtype GetFeatSubtype(void) const

TAnnotType GetAnnotType(void) const

TFeatType GetFeatType(void) const

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