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NCBI C++ ToolKit: src/objmgr/util/autodef_feature_clause.cpp Source File

sequence;

m_pMainFeat(&main_feat),

(

(comment,

) != string::npos

||

(comment,

) != string::npos) {

( ; desc_iter; ++desc_iter) {

is_pseudo =

;

(

.CanGetPseudo() &&

.IsSetPseudo()) {

}

(

.IsSetQual()) {

(

& it :

.GetQual()) {

qual, comment;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

((*q)->IsSetQual() &&

((*q)->GetQual(),

) &&

typeword = (*q)->GetVal();

typeword =

;

typeword =

;

typeword =

;

typeword =

;

typeword =

;

string::size_type start_pos = 0;

(start_pos != NCBI_NS_STD::string::npos) {

start_pos =

(comment, keyword, start_pos);

(start_pos != NCBI_NS_STD::string::npos) {

= comment.substr(start_pos + keyword.length());

string::size_type end =

(product_name,

);

(end != NCBI_NS_STD::string::npos) {

product_name = product_name.substr(0, end);

product_name = product_name.substr(0, product_name.length() - 9);

product_name +=

;

start_pos += keyword.length();

string::size_type start_pos =

(comment,

);

(start_pos != NCBI_NS_STD::string::npos) {

string::size_type sep_pos =

(comment,

, start_pos);

(sep_pos != NCBI_NS_STD::string::npos) {

product_name = comment.substr(start_pos, sep_pos - start_pos);

comment = comment.substr (0, comment.length() - 5);

comment = comment.substr (0, comment.length() - 6);

string::size_type pos =

(comment,

);

(pos == NCBI_NS_STD::string::npos) {

product_name = comment;

product_name = comment.substr(0, pos);

comment = comment.substr (pos + 1);

(pos == NCBI_NS_STD::string::npos) {

gene_name = comment.substr (0, pos);

(product_name.length() < 8

|| !

(product_name.c_str()[5]) || !

(product_name.c_str()[5])

|| !

(product_name.c_str()[6]) || !

(product_name.c_str()[6])

|| !

(product_name.c_str()[7]) || !

(product_name.c_str()[7])) {

&& (gene_name.length() < 4

|| !

(gene_name.c_str()[3])

|| !

(gene_name.c_str()[3]))) {

(pos != NCBI_NS_STD::string::npos) {

string::size_type pos =

(comment,

);

(pos != NCBI_NS_STD::string::npos) {

comment = comment.substr(0, pos);

product_name = comment;

product_name =

;

((*q)->IsSetQual() &&

((*q)->GetQual(),

) &&

product_name = (*q)->GetVal();

(!mat_pi && !m_name.empty()) {

(

.empty()) {

+=

+ m_name +

;

product_name =

;

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

description = (*it)->GetVal();

description = description.substr(0, description.length() - 4);

description = (*subSrcI)->GetName();

comment = comment.substr(4);

comment = comment.substr(0, comment.length() - 4);

description = comment;

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

((*it)->GetVal(),

) != string::npos) {

has_promoter =

;

(it->IsPromoter()) {

has_promoter =

;

interval +=

;

interval =

;

(*it)->Label(suppress_allele);

suppress_final_and =

;

suppress_final_and =

;

interval +=

(

, suppress_final_and, suppress_allele);

(utr3 !=

) {

interval +=

;

interval +=

;

interval +=

;

interval +=

;

interval +=

;

interval +=

;

product_name;

interval +=

;

(utr3 !=

) {

interval +=

;

interval +=

;

(also_set_partials) {

(also_set_partials) {

used_mRNA =

;

clause_product, mRNA_product;

adjust_partials =

;

adjust_partials =

;

used_gene =

;

noncoding_product_name;

(suppress_allele);

(suppress_allele);

ok_to_group =

;

(parent_clause ==

) {

ok_to_group =

;

ok_to_group =

;

ok_to_group =

;

ok_to_group =

;

ok_to_group =

;

(parent_clause ==

) {

|| (parent_clause->

() && gene_cluster_opp_strand)) {

(promoter_stop == parent_start + 1) {

}

(promoter_stop + 1 == parent_start) {

CSeq_loc_CI seq_loc_it(*(parent_clause->

()));

prev_start = seq_loc_it.GetRange().GetFrom();

prev_stop = seq_loc_it.GetRange().GetTo();

(seq_loc_it) {

cds_start = seq_loc_it.GetRange().GetFrom();

cds_stop = seq_loc_it.GetRange().GetTo();

((intron_start == prev_stop + 1 && intron_stop == cds_start - 1)

|| (intron_start == cds_stop + 1 && intron_stop == prev_start - 1)) {

prev_start = cds_start;

prev_stop = cds_stop;

(intron_start > prev_stop && intron_start - 1 == prev_stop) {

}

(prev_start > intron_stop && prev_start - 1 == intron_stop) {

(subclause ==

|| subclause ==

) {

best_parent =

;

(

k = 0; k <

.size(); k++) {

((*it)->IsSetQual() &&

(*it)->IsSetVal() &&

m_UseComment (m_Opts.GetUseNcRNAComment())

ncrna_product;

ncrna_product = ext.

();

ncrna_product =

;

}

(ext.

()) {

ncrna_comment;

string::size_type pos =

(ncrna_comment,

);

(pos != NCBI_NS_STD::string::npos) {

ncrna_comment = ncrna_comment.substr(0, pos);

product_name = ncrna_product;

product_name +=

+ ncrna_class;

product_name = ncrna_class;

product_name = ncrna_comment;

product_name =

;

,

,

,

mobile_element_name = mobile_element_name.substr(6);

found_keyword =

;

(

k = 0; k <

(

) /

(

) && !found_keyword; k++) {

found_keyword =

;

found_keyword =

;

&&

(mobile_element_name.c_str()[pos])) {

(!found_keyword) {

string::size_type pos =

(comment,

);

(pos != NCBI_NS_STD::string::npos) {

comment = comment.substr(0, pos);

comment = prefix +

+ comment;

comment = comment.substr (0,

) +

+ comment.substr (

+ 1);

comment = comment.substr(9);

comment = comment.substr(17);

string::size_type pos =

(comment,

);

(pos != NCBI_NS_STD::string::npos) {

string::size_type pos =

(comment,

);

(pos != NCBI_NS_STD::string::npos) {

comment = comment.substr(0, pos);

& description,

is_first,

is_last,

& opts)

(pos != string::npos) {

product_name;

gene_name,

product_name,

string::size_type pos =

(comment,

);

(pos == NCBI_NS_STD::string::npos) {

(pos != NCBI_NS_STD::string::npos) {

comment = comment.substr(0, pos);

(pos != NCBI_NS_STD::string::npos) {

(elements.empty()) {

(vector<string>, it, elements) {

(*it == elements.back()) {

(parent_clause ==

) {

ok_to_group =

;

(parent_clause ==

) {

ok_to_group =

;

vector<CRef<CAutoDefFeatureClause > > rval;

string::size_type pos;

is_region =

;

(pos != string::npos) {

comment = comment.substr(0, pos);

(!elements.empty()) {

(

s : elements) {

(s == elements.front()), (s == elements.back()), opts));

new_clause->SetMiscRNAWord(s);

rval.push_back(new_clause);

(!elements.empty()) {

(

s : elements) {

pos =

(s,

);

(pos != string::npos) {

(s == elements.front()),

(s == elements.back()), opts)));

vector<CRef<CAutoDefFeatureClause> > rval;

(phrases.size() < 2) {

= phrases.back();

(vector<string>, it, phrases) {

vector<CRef<CAutoDefFeatureClause> > rval;

(misc_rna.empty()) {

(

it : misc_rna) {

(misc_rna.empty()) {

(misc_rna.empty()) {

(

it : misc_rna) {

(misc_rna.empty()) {

(misc_rna.empty()) {

(!is_single_misc_feat &&

misc_rna.push_back(new_clause);

(!misc_rna.empty()) {

(

it : misc_rna) {

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

vector< CRef< CAutoDefFeatureClause > > AddMiscRNAFeatures(const CBioseq_Handle &bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

CAutoDefParsedtRNAClause * s_tRNAClauseFromNote(CBioseq_Handle bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, string comment, bool is_first, bool is_last, const CAutoDefOptions &opts)

vector< CRef< CAutoDefFeatureClause > > AddtRNAAndOther(const CBioseq_Handle &bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

const char * kMicrosatellite

void s_UseCommentBeforeSemicolon(const CSeq_feat &feat, string &label)

static string mobile_element_keywords[]

vector< CRef< CAutoDefFeatureClause > > FeatureClauseFactory(CBioseq_Handle bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts, bool is_single_misc_feat)

const char * kMinisatellite

@ eMiscRnaWordType_InternalSpacer

@ eMiscRnaWordType_RNAIntergenicSpacer

@ eMiscRnaWordType_ExternalSpacer

@ eMiscRnaWordType_IntergenicSpacer

virtual bool SameStrand(const CSeq_loc &loc) const

virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const

static vector< string > GetFeatureClausePhrases(string comment)

const string & GetProductName() const

virtual CRef< CSeq_loc > GetLocation() const

virtual bool OkToGroupUnderByType(const CAutoDefFeatureClause_Base *) const

virtual bool IsMobileElement() const

bool IsAltSpliced() const

virtual bool IsNoncodingProductFeat() const

virtual bool IsGeneCluster() const

string ListClauses(bool allow_semicolons, bool suppress_final_and, bool suppress_allele)

static ERnaMiscWord x_GetRnaMiscWordType(const string &phrase)

virtual CAutoDefFeatureClause_Base * FindBestParentClause(CAutoDefFeatureClause_Base *subclause, bool gene_cluster_opp_strand)

static CRef< CAutoDefFeatureClause > ClauseFromPhrase(const string &phrase, CBioseq_Handle bh, const CSeq_feat &cf, const CSeq_loc &mapped_loc, bool first, bool last, const CAutoDefOptions &opts)

const CAutoDefOptions & m_Opts

const string & GetGeneName() const

virtual bool IsInsertionSequence() const

static vector< string > GetMiscRNAElements(const string &product)

const string & GetAlleleName() const

virtual bool OkToGroupUnderByLocation(const CAutoDefFeatureClause_Base *, bool) const

virtual sequence::ECompare CompareLocation(const CSeq_loc &loc) const

virtual bool IsEndogenousVirusSourceFeature() const

static vector< string > GetTrnaIntergenicSpacerClausePhrases(const string &comment)

bool GetGeneIsPseudo() const

bool m_SuppressSubfeatures

static const string & x_GetRnaMiscWord(ERnaMiscWord word_type)

string x_GetGeneName(const CGene_ref &gref, bool suppress_locus_tag) const

bool x_GetFeatureTypeWord(string &typeword)

bool DoesmRNAProductNameMatch(const string &mrna_product) const

virtual bool OkToGroupUnderByType(const CAutoDefFeatureClause_Base *parent_clause) const

virtual bool IsExonWithNumber() const

virtual bool IsRecognizedFeature() const

virtual bool IsPartial() const

bool x_GetNoncodingProductFeatProduct(string &product) const

virtual bool IsPromoter() const

virtual void ReverseCDSClauseLists()

@ eEndogenousVirusRepeatRegion

void x_GetOperonSubfeatures(string &interval)

virtual CAutoDefFeatureClause_Base * FindBestParentClause(CAutoDefFeatureClause_Base *subclause, bool gene_cluster_opp_strand)

virtual bool IsMobileElement() const

virtual bool IsInsertionSequence() const

virtual bool IsGeneCluster() const

static bool IsPseudo(const CSeq_feat &f)

virtual bool ShouldRemoveExons() const

virtual void Label(bool suppress_allele)

virtual CSeqFeatData::ESubtype GetMainFeatureSubtype() const

virtual bool IsSatelliteClause() const

CConstRef< CSeq_feat > m_pMainFeat

virtual bool OkToGroupUnderByLocation(const CAutoDefFeatureClause_Base *parent_clause, bool gene_cluster_opp_strand) const

virtual bool IsBioseqPrecursorRNA() const

virtual bool x_IsPseudo()

virtual bool SameStrand(const CSeq_loc &loc) const

virtual void AddToLocation(CRef< CSeq_loc > loc, bool also_set_partials=true)

bool x_FindNoncodingFeatureKeywordProduct(string comment, string keyword, string &product_name) const

virtual sequence::ECompare CompareLocation(const CSeq_loc &loc) const

static bool IsSatellite(const CSeq_feat &feat)

virtual bool IsNoncodingProductFeat() const

virtual bool x_GetProductName(string &product_name)

virtual bool IsControlRegion() const

virtual bool AddmRNA(CAutoDefFeatureClause_Base *mRNAClause)

void x_TypewordFromSequence()

virtual bool AddGene(CAutoDefFeatureClause_Base *gene_clause, bool suppress_allele)

virtual CRef< CSeq_loc > GetLocation() const

virtual bool IsLTR() const

CMolInfo::TBiomol m_Biomol

bool x_GetExonDescription(string &description)

bool x_GetGenericInterval(string &interval, bool suppress_allele)

virtual bool IsEndogenousVirusSourceFeature() const

CRef< CSeq_loc > m_ClauseLocation

bool x_ShowTypewordFirst(string typeword)

bool x_GetDescription(string &description)

virtual EClauseType GetClauseType() const

bool GetSuppressLocusTag()

virtual bool x_IsPseudo()

CAutoDefGeneClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

virtual bool x_GetProductName(string &product_name)

~CAutoDefGeneClusterClause()

virtual void Label(bool suppress_allele)

CAutoDefGeneClusterClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

~CAutoDefIntergenicSpacerClause()

void InitWithString(string comment, bool suppress_allele)

virtual void Label(bool suppress_allele)

CAutoDefIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

virtual void Label(bool suppress_allele)

~CAutoDefMobileElementClause()

CAutoDefMobileElementClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

virtual bool x_GetProductName(string &product_name)

CAutoDefNcRNAClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

TMiscFeatRule GetMiscFeatRule() const

bool IsFeatureSuppressed(CSeqFeatData::ESubtype subtype) const

void SetTypewordFirst(bool typeword_first)

CAutoDefParsedClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, bool is_first, bool is_last, const CAutoDefOptions &opts)

void SetTypeword(string typeword)

void SetMiscRNAWord(const string &phrase)

CAutoDefParsedIntergenicSpacerClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const string &description, bool is_first, bool is_last, const CAutoDefOptions &opts)

~CAutoDefParsedIntergenicSpacerClause()

CAutoDefParsedRegionClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string product, const CAutoDefOptions &opts)

virtual void Label(bool suppress_allele)

~CAutoDefParsedRegionClause()

~CAutoDefParsedtRNAClause()

CAutoDefParsedtRNAClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, string gene_name, string product_name, bool is_first, bool is_last, const CAutoDefOptions &opts)

static bool ParseString(string comment, string &gene_name, string &product_name)

CAutoDefSatelliteClause(CBioseq_Handle bh, const CSeq_feat &main_feat, const CSeq_loc &mapped_loc, const CAutoDefOptions &opts)

~CAutoDefSatelliteClause()

virtual void Label(bool suppress_allele)

bool IsSuppressed(void) const

string GetRnaProductName(void) const

ESubtype GetSubtype(void) const

@ eSubtype_mobile_element

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

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

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

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

static int BestRank(const CRef< CSeq_id > &id)

string GetLabel(const CSeq_id &id)

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.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

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

@ fFGL_Content

Include its content if there is any.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

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

Returns the sequence::ECompare containment relationship between CSeq_locs.

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

Add two seq-locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ eContained

First CSeq_loc contained by second.

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

const CSeqFeatData & GetData(void) const

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

void Reset(void)

Reset reference 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.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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 void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

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 string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ eNocase

Case insensitive compare.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

bool CanGetSubtype(void) const

Check if it is safe to call GetSubtype method.

list< CRef< CSubSource > > TSubtype

@ eSubtype_endogenous_virus_name

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetPseudo(void) const

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

bool CanGetLocus(void) const

Check if it is safe to call GetLocus method.

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 IsSetDesc(void) const

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

bool CanGetAllele(void) const

Check if it is safe to call GetAllele method.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

bool CanGetPseudo(void) const

Check if it is safe to call GetPseudo method.

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 TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

bool IsSetProduct(void) const

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

bool IsSetExt(void) const

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

bool IsGen(void) const

Check if variant Gen is selected.

const TGen & GetGen(void) const

Get the variant data.

const TName & GetName(void) const

Get the variant data.

bool IsSetClass(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsName(void) const

Check if variant Name is selected.

const TClass & GetClass(void) const

Get the Class member data.

bool IsSetComment(void) const

Check if a value has been assigned to Comment 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.

E_Choice Which(void) const

Which variant is currently selected.

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.

const TData & GetData(void) const

Get the Data member data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member 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.

const TGene & GetGene(void) const

Get the variant data.

TPartial GetPartial(void) const

Get the Partial member data.

const TProt & GetProt(void) const

Get the variant data.

vector< CRef< CGb_qual > > TQual

const TRna & GetRna(void) const

Get the variant data.

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.

bool CanGetPseudo(void) const

Check if it is safe to call GetPseudo method.

bool CanGetComment(void) const

Check if it is safe to call GetComment method.

ENa_strand

strand of nucleic acid

bool IsSetBiomol(void) const

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

const TId & GetId(void) const

Get the Id member data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eBiomol_pre_RNA

precursor RNA of any sort really

@ eBiomol_cRNA

viral RNA genome copy intermediate

@ eBiomol_other_genetic

other genetic material

@ e_Molinfo

info on the molecule and techniques

use n only the LMDB cache</td > n</tr > n< tr > n< td ></td > n< td > use the LMDB cache if at all possible

Miscellaneous common-use basic types and functionality.

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