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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/convert__feat_8cpp_source.html below:

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

66

: m_To(feat_to) , m_From(feat_from)

90 if

(subtype ==

m_To

) {

207 if

(!remove_transcript || (remove_transcript && remove_transcript->IsBool() && remove_transcript->GetBool()->GetVal())) {

213 if

(ncrna_class && ncrna_class->IsString() && !

NStr::IsBlank

(ncrna_class->GetString()->GetVal())) {

214

new_feat->

SetData

().SetRna().SetExt().SetGen().SetClass(ncrna_class->GetString()->GetVal());

219 if

(site_type && site_type->IsString() && !

NStr::IsBlank

(site_type->GetString()->GetVal())) {

220

new_feat->

SetData

().SetSite(

m_SiteList

.GetSiteType(site_type->GetString()->GetVal()));

225 if

(bond_type && bond_type->IsString() && !

NStr::IsBlank

(bond_type->GetString()->GetVal())) {

226

new_feat->

SetData

().SetBond(

m_BondList

.GetBondType(bond_type->GetString()->GetVal()));

231 if

(on_prot && on_prot->IsBool() && on_prot->GetBool()->GetVal()) {

253 if

(remove_gene && remove_gene->IsBool() && remove_gene->GetBool()->GetVal() && !(

orig

.IsSetData() &&

orig

.GetData().IsGene())) {

277

vector<string> products)

279 bool

make_pseudo =

false

;

281 if

(is_pseudo && is_pseudo->IsBool() && is_pseudo->GetBool()->GetVal()) {

287 ITERATE

(vector<string>, it, products) {

298 ITERATE

(vector<string>, it, products) {

299 prot

->SetData().SetProt().SetName().push_back(*it);

317 string

product =

""

;

318 if

(

orig

.IsSetProduct()) {

322 if

(

->IsSetData() &&

->GetData().IsProt()

323

->GetData().GetProt().IsSetName()

324

->GetData().GetProt().GetName().size() > 0) {

325

product =

->GetData().GetProt().GetName().front();

328

}

else if

(

orig

.IsSetXref()) {

330 if

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

331

&& (*it)->GetData().GetProt().IsSetName()

332

&& (*it)->GetData().GetProt().GetName().size() > 0) {

333

product = (*it)->GetData().GetProt().GetName().front();

361 if

(

orig

.GetData().IsCdregion() && keep_orig) {

362 if

orig

.IsSetProduct()) {

398

CSeq_feat::TQual::iterator it = new_feat->

SetQual

().begin();

399 while

(it != new_feat->

SetQual

().end()) {

401 if

((*it)->IsSetVal() && !

NStr::IsBlank

((*it)->GetVal())) {

402

vals.push_back((*it)->GetVal());

404

it = new_feat->

SetQual

().erase(it);

409 if

(new_feat->

GetQual

().size() == 0) {

466

remove_mrna->SetBool();

469

remove_gene->SetBool();

472

remove_transcript->SetBool();

480

is_pseudo->SetBool();

491 ITERATE

(vector<string>, it, class_vals) {

492 val

->AddSuggestedValue(*it);

494 val

->SetOnlySuggested(

false

);

507 val

->AddSuggestedValue(it->first);

510 val

->SetDefaultVal(

"active"

);

511 val

->SetOnlySuggested(

true

);

522 val

->AddSuggestedValue(it->first);

525 val

->SetDefaultVal(

"disulfide"

);

526 val

->SetOnlySuggested(

true

);

631 while

(it !=

m_SiteList

.end() && site_type != it->second) {

646

new_feat->

SetData

().SetGene();

647 if

(

orig

.IsSetComment()) {

648

new_feat->

SetData

().SetGene().SetLocus(

orig

.GetComment());

650 if

(pos == string::npos) {

681 string

remainder =

""

;

682

new_feat->

SetData

().SetRna().SetRnaProductName(product, remainder);

699

}

else if

(

NStr::Find

(product, field) == string::npos &&

NStr::Find

(comment, field) == string::npos) {

700

comment = comment +

"; "

+ field;

707 string

product =

""

;

708 string

comment =

""

;

713 if

(

orig

.IsSetLocus()) {

716 if

(

orig

.IsSetAllele()) {

719 if

(

orig

.IsSetDesc()) {

722 if

(

orig

.IsSetMaploc()) {

725 if

(

orig

.IsSetLocus_tag()) {

729 string

remainder =

""

;

730

new_feat->

SetData

().SetRna().SetRnaProductName(product, remainder);

732

comment = comment +

"; "

+ remainder;

735

comment = comment.substr(1);

760

new_feat->

SetData

().SetImp().SetKey(

"repeat_region"

);

762 bool

is_transposon =

false

;

763 bool

is_insertion =

false

;

764 string

transposon_name =

""

;

765 string

insertion_name =

""

;

766 string

comment =

""

;

767 if

(

orig

.IsSetComment()) {

768

comment =

orig

.GetComment();

771 if

(

orig

.IsSetData() &&

orig

.GetData().IsBiosrc()) {

772 if

(

orig

.GetData().GetBiosrc().IsSetSubtype()) {

774 if

((*it)->IsSetSubtype()) {

776

is_transposon =

true

;

777 if

((*it)->IsSetName() && !

NStr::IsBlank

((*it)->GetName())) {

779

transposon_name = (*it)->GetName();

781

transposon_name = transposon_name +

";"

+ (*it)->GetName();

785

is_insertion =

true

;

786 if

((*it)->IsSetName() && !

NStr::IsBlank

((*it)->GetName())) {

788

insertion_name = (*it)->GetName();

790

insertion_name = insertion_name +

";"

+ (*it)->GetName();

794

&& (*it)->IsSetName()

797

comment = (*it)->GetName();

799

comment = comment +

";"

+ (*it)->GetName();

805 if

(

orig

.GetData().GetBiosrc().IsSetOrg()

806

orig

.GetData().GetBiosrc().GetOrg().IsSetOrgname()

807

orig

.GetData().GetBiosrc().GetOrg().GetOrgname().IsSetMod()) {

810

&& (*it)->IsSetSubname() && !

NStr::IsBlank

((*it)->GetSubname())) {

812

comment = (*it)->GetSubname();

814

comment = comment +

";"

+ (*it)->GetSubname();

822

new_feat->

SetQual

().push_back(q);

827

new_feat->

SetQual

().push_back(q);

845

new_feat->

SetData

().SetImp().SetKey(

"misc_feature"

);

850 const string

& qual_str = (*qual)->GetQual();

862 bool

cross_origin =

false

;

886 id

->Assign(*

orig

.GetLocation().GetId());

891

new_loc->

SetInt

(*new_int);

896 if

(!product.empty())

898 string

comment = product;

901

comment =

"similar to "

+product;

905

comment =

"nonfunctional "

+product+

" due to mutation"

;

928 if

(

->IsSetData() &&

->GetData().IsProt()

929

->GetData().GetProt().IsSetDesc()) {

930

desc =

->GetData().GetProt().GetDesc();

949

new_feat->

SetData

().SetProt().SetName().push_back(product);

952

CSeq_feat::TQual::iterator it = new_feat->

SetQual

().begin();

953 while

(it != new_feat->

SetQual

().end()) {

955 if

((*it)->IsSetVal()) {

956 val

= (*it)->GetVal();

958 if

(!(*it)->IsSetQual()) {

963

new_feat->

SetData

().SetProt().SetName().push_back((*it)->GetVal());

965

it = new_feat->

SetQual

().erase(it);

969

new_feat->

SetData

().SetProt().SetEc().push_back((*it)->GetVal());

971

it = new_feat->

SetQual

().erase(it);

975

new_feat->

SetData

().SetProt().SetActivity().push_back((*it)->GetVal());

977

it = new_feat->

SetQual

().erase(it);

983 if

(pos == string::npos) {

987

db->

SetTag

().SetStr(

val

.substr(pos));

989

new_feat->

SetData

().SetProt().SetDb().push_back(db);

991

it = new_feat->

SetQual

().erase(it);

1012 if

(!overlapping_cds) {

1032 if

(

prot

.IsSetName()

1033

prot

.GetName().size() > 0

1036

new_feat->

SetQual

().push_back(q);

1037

}

else if

(

prot

.IsSetDesc()

1040

new_feat->

SetQual

().push_back(q);

1044 if

(

prot

.IsSetEc()) {

1047

new_feat->

SetQual

().push_back(q);

1052 if

(

prot

.IsSetActivity()) {

1055

new_feat->

SetQual

().push_back(q);

1060 if

(

prot

.IsSetDb()) {

1063

(*it)->GetLabel(&

val

);

1065

new_feat->

SetQual

().push_back(q);

1093 if

(products.size() > 0) {

1094 string

product = products[0];

1095 for

(

size_t i

= 1;

< products.size();

++) {

1096

product +=

"; "

+ products[

];

1098 string

remainder =

""

;

1099

new_feat->

SetData

().SetRna().SetRnaProductName(product, remainder);

1113

new_feat->

SetData

().SetCdregion();

1116

products.push_back(new_feat->

GetComment

());

1128

new_feat->

SetData

().SetGene();

1132

gene_vals.push_back(new_feat->

GetComment

());

1136 if

(gene_vals.size() > 0) {

1137 string

gene = gene_vals[0];

1138 for

(

size_t i

= 1;

< gene_vals.size();

++) {

1139

gene +=

"; "

+ gene_vals[

];

1141

new_feat->

SetData

().SetGene().SetLocus(gene);

1169 string

product =

orig

.GetData().GetRegion();

1170 string

remainder =

""

;

1171

new_feat->

SetData

().SetRna().SetRnaProductName(product, remainder);

1197 string

orig_comment =

""

;

1224 string

product =

orig

.GetData().GetRna().GetRnaProductName();

1237

new_feat->

SetData

().SetCdregion();

1239

vector<string> products;

1240

products.push_back(

orig

.GetData().GetRna().GetRnaProductName());

1251 string

product =

orig

.GetData().GetRna().GetRnaProductName();

1252

new_feat->

SetData

().SetGene().SetDesc(product);

1281

new_feat->

SetData

().SetProt().SetName().push_back(

orig

.GetData().GetRegion());

1294 string

product =

orig

.GetData().GetRna().GetRnaProductName();

1295 string

remainder =

""

;

1296

new_feat->

SetData

().SetRna().SetRnaProductName(product, remainder);

1348 return "Create region feature with the protein name as the region name"

;

1350 return "Create Region feature on nucleotide sequence or protein product sequence of overlapping coding region as specified. Use comment on feature for region name.\n\ 1351 All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded."

;

1360

new_feat->

SetData

().SetRegion();

1362 if

(

orig

.GetData().IsProt()) {

1363 if

(

orig

.GetData().GetProt().IsSetName() &&

orig

.GetData().GetProt().GetName().size() > 0) {

1364

new_feat->

SetData

().SetRegion(

orig

.GetData().GetProt().GetName().front());

1366

}

else if

(

orig

.IsSetComment()) {

1367

new_feat->

SetData

().SetRegion(

orig

.GetComment());

1378 string

desc =

"If coding region is overlapped by another coding region, convert the coding region to a " 1380

" on the overlapping coding region's protein sequence, otherwise if you have checked \"Leave Original Feature\" it will create a " 1381

+ subtype_name +

" with the same protein names and description on the protein sequence for the coding region."

;

1394

new_feat->

SetData

().SetProt().SetName().push_back(product);

1398 if

(

orig

.IsSetProduct())

1422

new_feat->

SetData

().SetGene();

1424 if

(

orig

.IsSetProduct()) {

1428 if

(

->IsSetData() &&

->GetData().IsProt()) {

1430 if

(

prot

.IsSetName()) {

1435 if

(

prot

.IsSetDesc()) {

1438 if

(

prot

.IsSetActivity()) {

1443 if

(

prot

.IsSetDb()) {

1446

(*it)->GetLabel(&

val

);

1450 if

(

prot

.IsSetEc()) {

1472 if

(subtype_from != subtype_to) {

1652

new_feat->

SetData

().SetGene();

1656

copy_gene->

Assign

(*gene);

1662 if

(

orig

.IsSetProduct()) {

1666 if

(

->IsSetData() &&

->GetData().IsProt()) {

1669 if

(

->IsSetComment()) {

1672 if

(

prot

.IsSetDesc()) {

1676 if

(

prot

.IsSetName()) {

1684 string

protein_names;

1702

}

else if

(

orig

.IsSetData() &&

orig

.GetData().IsCdregion()) {

1725 string

orig_val = gene->

GetLocus

();

1741 string

orig_val = gene->

GetDesc

();

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

TBondMap::const_iterator const_iterator

CConstRef< CConversionOptionString > GetString() const

CRef< CConversionOptionBool > SetBool()

CRef< CConversionOptionString > SetString()

CConstRef< CConversionOptionBool > GetBool() const

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

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

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

virtual string GetDescription()

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

CConvertCDSToPseudoGene()

void x_AddToGeneDescr(string text, CRef< objects::CGene_ref > gene, objects::edit::EExistingText existing_text)

void x_AddToGeneLocus(string text, CRef< objects::CGene_ref > gene, objects::edit::EExistingText existing_text)

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

static CRef< CConvertFeatureBase > Create(objects::CSeqFeatData::ESubtype subtype_from, objects::CSeqFeatData::ESubtype subtype_to)

CRef< CConversionOption > x_FindPseudo()

void x_AddToComment(string comment, CRef< objects::CSeq_feat > new_feat, objects::edit::EExistingText existing_text=objects::edit::eExistingText_prefix_semi)

bool x_IsRnaSubtype(objects::CSeqFeatData::ESubtype subtype)

static const string s_PlaceOnProt

void x_AddRnaDestinationConversionOptions()

bool x_IsImportSubtype(objects::CSeqFeatData::ESubtype subtype)

static const string s_RemoveTranscriptID

vector< string > x_ExtractProductQuals(CRef< objects::CSeq_feat > new_feat)

void x_AddCDSSourceConversionOptions()

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype subtype)

CRef< CConversionOption > x_FindRemovemRNA()

CConvertFeatureBase(objects::CSeqFeatData::ESubtype feat_to=objects::CSeqFeatData::eSubtype_bad, objects::CSeqFeatData::ESubtype feat_from=objects::CSeqFeatData::eSubtype_bad)

void x_AddCDSDestinationConversionOptions()

bool x_MoveFeatureToProtein(const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope)

static const string s_SiteType

void x_AddRegionDestionationConversionOptions()

CRef< CConversionOption > x_FindRemoveGene()

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

CRef< CCmdComposite > x_ConvertToCDS(const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope, vector< string > product)

static const string s_BondType

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

void x_AddSiteDestinationConversionOptions()

CRef< CCmdComposite > x_SimpleConversion(const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope)

CRef< CConversionOption > x_FindSiteType()

static const string s_NcrnaClass

CRef< CConversionOption > x_FindNcrnaClass()

string x_GetCDSProduct(const objects::CSeq_feat &orig, objects::CScope &scope)

static const string s_IsPseudo

CRef< CConversionOption > FindRemoveTranscriptId()

bool m_create_general_only

static const string s_RemovemRNA

void x_ClearGenericFields(CRef< objects::CSeq_feat > new_feat)

vector< string > x_ExtractQuals(CRef< objects::CSeq_feat > new_feat, string qual_name)

objects::CBondList m_BondList

string GetSiteName(objects::CSeqFeatData::TSite site_type)

vector< CRef< CConversionOption > > TOptions

CRef< CConversionOption > x_FindPlaceOnProt()

objects::CSeqFeatData::ESubtype m_To

CRef< CConversionOption > x_FindBondType()

objects::CSeqFeatData::ESubtype m_From

static const string s_RemoveGene

CRef< CConversionOption > x_FindOption(const string &label)

void x_AddBondDestinationConversionOptions()

objects::CSiteList m_SiteList

bool x_IsProtSubtype(objects::CSeqFeatData::ESubtype subtype)

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

void x_AddGeneFieldsToComment(const objects::CGene_ref &orig, CRef< objects::CSeq_feat > new_feat)

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

void x_AddOneGeneField(string &product, string &comment, const string &field)

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

virtual string GetDescription()

virtual CRef< CCmdComposite > Convert(const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope)

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

static vector< string > GetncRNAClassList()

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

EQualifier

List of available qualifiers for feature keys.

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ eSubtype_transit_peptide

@ eSubtype_transit_peptide_aa

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

static EQualifier GetQualifierType(CTempString qual)

convert qual string to enumerated value

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

namespace ncbi::objects::

void SetPartialStart(bool val, ESeqLocExtremes ext)

void SetPartialStop(bool val, ESeqLocExtremes ext)

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

TSiteMap::const_iterator const_iterator

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

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

CProt_ref::EProcessed GetProtProcessedFromFeatureSubtype(CSeqFeatData::ESubtype subtype)

CRNA_ref::EType GetRnaTypeFromFeatureSubtype(CSeqFeatData::ESubtype subtype)

static void AdjustMappedStop(CRef< CSeq_loc > loc, const CSeq_loc &product, CScope &scope)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

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.

const CSeq_id * GetId(void) const

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

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestOverlappingFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype need_subtype, sequence::EOverlapType overlap_type, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

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.

@ eOverlap_Contained

2nd contained within 1st extremes

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

Get the encoding CDS feature of a given protein sequence.

CConstRef< CSeq_feat > GetOverlappingmRNA(const CSeq_loc &loc, CScope &scope)

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

@ fBestFeat_FavorLonger

favor longer features over shorter features

@ fBestFeat_Defaults

default options: do everything

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

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.

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

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

bool IsProtein(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 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 bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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 bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static const char label[]

list< CRef< CSubSource > > TSubtype

@ eSubtype_insertion_seq_name

@ eSubtype_transposon_name

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

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.

void SetLocus(const TLocus &value)

Assign a value to Locus data member.

const TLocus & GetLocus(void) const

Get the Locus member data.

void SetDesc(const TDesc &value)

Assign a value to Desc data member.

void SetTag(TTag &value)

Assign a value to Tag data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

list< CRef< COrgMod > > TMod

@ eSubtype_other

ASN5: old-name (254) will be added to next spec.

bool IsSetDesc(void) const

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

EProcessed

processing status

vector< CRef< CDbtag > > TDb

const TDesc & GetDesc(void) const

Get the Desc member data.

@ eProcessed_signal_peptide

@ eProcessed_transit_peptide

EType

type of RNA feature

@ eType_scRNA

will become ncRNA, with RNA-gen.class = scRNA

@ eType_snoRNA

will become ncRNA, with RNA-gen.class = snoRNA

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

@ eType_snRNA

will become ncRNA, with RNA-gen.class = snRNA

bool IsSetComment(void) const

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

void ResetTitle(void)

Reset Title 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 IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void ResetExcept(void)

Reset Except data member.

const TQual & GetQual(void) const

Get the Qual member data.

void ResetExcept_text(void)

Reset Except_text data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void ResetPseudo(void)

Reset Pseudo data member.

void ResetId(void)

Reset Id data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

void ResetComment(void)

Reset Comment data member.

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

void SetPseudo(TPseudo value)

Assign a value to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

vector< CRef< CSeqFeatXref > > TXref

void ResetProduct(void)

Reset Product data member.

void ResetDbxref(void)

Reset Dbxref data member.

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetProduct(void) const

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

void ResetQual(void)

Reset Qual data member.

void ResetCit(void)

Reset Cit data member.

ENa_strand

strand of nucleic acid

E_Choice Which(void) const

Which variant is currently selected.

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

static void text(MDB_val *v)

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

#define EDIT_EACH_GBQUAL_ON_SEQFEAT(Itr, Var)

#define ERASE_GBQUAL_ON_SEQFEAT(Itr, Var)

ERASE_GBQUAL_ON_SEQFEAT.

bool QualifierNamesAreEquivalent(string name1, string name2)

@ eExistingText_append_semi

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

CRef< CCmdComposite > GetDeleteFeatureCommand(const objects::CSeq_feat_Handle &fh, bool remove_proteins=true)

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