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NCBI C++ ToolKit: src/objtools/edit/feattable_edit.cpp Source File

pProduct->

(*pId);

(

.IsSetName() &&

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

productName =

.GetName().front();

(

.IsSetName() &&

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

productName =

.GetName().front();

& locusTagPrefix,

locusTagNumber,

startingFeatId,

mpMessageListener(pMessageListener),

mLocusTagPrefix(locusTagPrefix),

mLocusTagNumber(locusTagNumber),

mNextFeatId(startingFeatId)

sequenceSize,

& locusTagPrefix,

locusTagNumber,

startingFeatId,

mSequenceSize(sequenceSize),

mpMessageListener(pMessageListener),

mLocusTagPrefix(locusTagPrefix),

mLocusTagNumber(locusTagNumber),

mNextFeatId(startingFeatId)

(pOverlappingRna) {

pRna->

().SetRna().SetExt().SetName(

pRna->

().SetLocal().SetStr(rnaId);

pRnaXref->SetId(*pFeatId);

pRna->

().push_back(pRnaXref);

pRnaXref->SetId(*pGeneId);

pRna->

().push_back(pRnaXref);

infered(

);

edit::CLocationEditPolicy editPolicy(

edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd,

edit::CLocationEditPolicy::ePartialPolicy_eSetForBadEnd,

edit::CLocationEditPolicy::eMergePolicy_NoChange);

pEditedCds->

(cds);

infered = editPolicy.ApplyPolicyToFeature(*pEditedCds, *

);

geneEh.

(*pEditedGene);

(!product.empty()) {

feh.

(*pEditedFeature);

vector<string> specialQuals{

,

,

,

,

};

(it)->GetOriginalFeature()));

QUALS& quals = (*it).GetQual();

vector<string> badQuals;

(QUALS::const_iterator qual = quals.begin(); qual != quals.end();

qualKey = (*qual)->GetQual();

(std::find(specialQuals.begin(), specialQuals.end(), qualKey)

!= specialQuals.end()) {

(qualKey ==

|| qualKey ==

) {

(qualKey ==

|| qualKey ==

) {

badQuals.push_back(qualKey);

badQuals.push_back(qualKey);

(vector<string>::const_iterator badIt = badQuals.begin();

badIt != badQuals.end(); ++badIt) {

{

, list<char>({

})},

{

, list<char>({

})},

{

, list<char>({

})},

{

, list<char>({

})},

{

, list<char>({

})},

{

, list<char>({

,

})},

{

, list<char>({

,

})},

{

, list<char>({

,

})},

{

, list<char>({

,

})},

{

, list<char>({

,

})},

{

, list<char>({

,

})},

{

, list<char>({

,

,

})},

{

, list<char>({

,

,

})},

{

, list<char>({

,

,

})},

{

, list<char>({

,

,

})},

{

, list<char>({

,

,

,

})}

codonRecognized = mf.

(

);

(codonRecognized.empty()) {

(codonRecognized.size() != 3) {

pEditedFeat->

(origFeat);

(

char1 : sIUPACmap.at(codonRecognized[0])) {

(

char2 : sIUPACmap.at(codonRecognized[1])) {

(

char3 : sIUPACmap.at(codonRecognized[2])) {

.insert(codonIndex);

(

codonIndex :

) {

extTrna.SetCodon().push_back(codonIndex);

transcript_id = mrna.

(

);

transcript_id;

(noProteinIdQual) {

transcriptId = cds.

(

);

noTranscriptIdQual =

(transcriptId);

(noTranscriptIdQual && mrna) {

isGenbankTranscript =

(transcriptId);

(noProteinIdQual) {

(noTranscriptIdQual) {

(hasProteinId && hasTranscriptId) {

(!isGenbankProtein && (transcriptId == proteinId)) {

proteinId =

+ proteinId;

(hasProteinId && !isGenbankProtein) {

transcriptId =

+ proteinId;

hasTranscriptId =

;

(hasTranscriptId && !isGenbankTranscript) {

proteinId =

+ transcriptId;

hasProteinId =

;

(!hasTranscriptId && mrna) {

& cds_transcript_id,

& cds_protein_id,

use_local_ids =

;

transcript_id = mrna.

(

);

transcript_id = cds_transcript_id;

use_local_ids =

;

protein_id = mrna.

(

);

protein_id = cds_protein_id;

((protein_id == transcript_id) && !

(protein_id,

)) {

protein_id =

+ protein_id;

use_local_ids =

;

(transcript_id != cds_transcript_id) {

(protein_id != cds_protein_id) {

transcriptId = mrna.

(

);

(noTranscriptIdQual) {

isGenbankTranscript =

(transcriptId);

(noTranscriptIdQual) {

((transcriptId == proteinId) &&

!isGenbankTranscript) {

proteinId =

+ proteinId;

transcriptId =

+ proteinId;

(!isGenbankTranscript && !

(transcriptId)) {

proteinId =

+ transcriptId;

& transcript_id,

locus_tag_prefix;

(update_protein_id || update_transcript_id) {

(update_protein_id) {

protein_id =

+ locus_tag_prefix +

+ protein_id;

(update_transcript_id) {

transcript_id =

+ locus_tag_prefix +

+ transcript_id;

(update_protein_id) {

protein_id =

+ seq_label +

+ protein_id;

(update_transcript_id) {

transcript_id =

+ seq_label +

+ transcript_id;

geneEH.

(*pEditedGene);

(sequenceSize == 0) {

pGene->

().SetLocal().SetStr(geneId);

pGeneXref->SetId(*pFeatId);

pGene->

().push_back(pGeneXref);

(!orig_tid.empty()) {

(!orig_pid.empty()) {

(!

.

()) {

mRnaTid = parent.

(

);

(tid == mRnaTid) {

tid =

(

) + tid;

orig_tid = mf.

(

);

(!orig_tid.empty()) {

(!

.

()) {

orig_tid = mf.

(

);

(!orig_tid.empty()) {

& rawId)

(string::npos != rawId.find(

)) {

);

(locusTagPrefix.empty()) {

+

(mf) +

);

(!rawId.empty()) {

(

) + locusTagPrefix +

+ rawId;

(

.

()) {

(

.

()) {

(!

.

()) {

(

) + locusTagPrefix +

+ id;

(

.

()) {

(!

.

()) {

(

) + locusTagPrefix +

+ id;

+

(mf) +

);

feh.

(

, transcriptId);

transcriptId =

.GetNamedQual(

);

feh.

(

, transcriptId);

proteinId =

.GetNamedQual(

);

transcriptId = mf.

(

);

(transcriptId.empty()) {

(proteinId.empty()) {

transcriptId = mf.

(

);

(transcriptId.empty()) {

(; itGenes; ++itGenes) {

vector<CSeq_id_Handle> annotIds;

(; itGenes; ++itGenes) {

vector<CSeq_id_Handle>::const_iterator compIt;

(compIt = annotIds.begin();

compIt != annotIds.end();

(*compIt == idh) {

(compIt == annotIds.end()) {

annotIds.push_back(idh);

(vector<CSeq_id_Handle>::const_iterator idIt = annotIds.begin();

idIt != annotIds.end();

(; itGenes; ++itGenes) {

(; itOther; ++itOther) {

(itOther)->GetOriginalFeature()));

(

parent =

.GetParent(*it); parent) {

subtype = parent.GetOriginalFeature().GetData().GetSubtype();

& qualKey,

& qualVal)

& qualKey)

& qualKey,

& qualVal)

(!existing.empty()) {

& proteinIdStr)

pEditedFeat->

(origFeat);

pEditedFeat->

().SetWhole(*pProteinId);

WIDTH = 6;

(suffix.size() < WIDTH) {

suffix =

.substr(0, WIDTH - suffix.size()) + suffix;

nextTag(

);

nextTag + suffix;

WIDTH = 6;

(suffix.size() < WIDTH) {

suffix =

.substr(0, WIDTH - suffix.size()) + suffix;

dbPrefix(

);

(locusTag.empty() &&

prefix, suffix;

dbPrefix(

);

(locusTag.empty() &&

prefix, suffix;

transcriptId;

& baseId = *baseLoc.

();

(sequenceSize == 0 || baseStart <= baseStop) {

pEnvelope->

(baseId);

pEnvelope->

().SetFrom(baseStart);

pEnvelope->

().SetTo(baseStop);

pTop->

().Assign(baseId);

pTop->

(sequenceSize-1);

pBottom->

().Assign(baseId);

pBottom->

(baseStop);

pBottom->

().Assign(baseId);

pBottom->

(baseStop);

pTop->

().Assign(baseId);

pTop->

(sequenceSize-1);

& message)

message = subName +

;

message = subName +

;

codonRecognized)

message =

+

codonRecognized +

;

message = subName +

;

(

);

(

);

stringstream strstr;

&

= mf.

();

(

.Which()) {

;

.GetLocal().AsString(strstr);

strstr.str();

(geneRef.IsSetLocus_tag()) {

prefix, suffix;

locusTagFromQualifier = geneFeature.

(

);

(!locusTagFromQualifier.empty()) {

prefix, suffix;

(feature.

())

append_nonduplicated_item = [](list<string>& current_list,

list<string>& other_list)

unordered_set<string> current_set;

(

& item : current_list) {

current_set.insert(item);

(

& item : other_list) {

(current_set.find(item) == current_set.end()) {

current_list.push_back(item);

append_nonduplicated_item(current_ref.

(),

append_nonduplicated_item(current_ref.

(),

other_ref.

());

append_nonduplicated_item(current_ref.

(),

(

& pDBtag : other_ref.

()) {

current_ref.

().push_back(pDBtag);

& product_name = cds.

(

);

prot_ref.

().push_back(product_name);

(pMrna.

()) {

(

& prot_name : prot_ref.

()) {

feature.

().SetLocal().SetId(

++);

(feat.NotEmpty() && feat->IsSetData() && feat->GetData().IsCdregion())

was_extended =

;

(replacement.

())

(protein.

())

protein_entry->

(*protein);

(protein->

().empty())

* protein_ids = 0;

qual_to_remove =

;

protein_ids = &cd_feature.

(qual_to_remove);

(protein_ids->empty())

qual_to_remove =

;

protein_ids = &cd_feature.

(qual_to_remove);

(protein_ids->empty())

(protein_ids->empty())

protein_ids = &cd_feature.

(

);

(!protein_ids->empty())

MergeSeqIds(*protein, new_ids);

(protein->

().empty())

(base_name.empty() && !bioseq.GetId().empty())

newid = GetNewProteinId(*m_scope, base_name);

protein->

().push_back(newid);

& prot_feat = CreateOrSetFTable(*protein);

prot_ref.

().push_back(

);

cd_feature.

().SetName().push_back(

);

prot_feat.

().SetInt().SetId().Assign(*GetAccessionId(protein->

()));

cd_feature.

().SetWhole().Assign(*GetAccessionId(protein->

()));

cd_feature.

().clear();

& ext = mrna_feature.

().SetRna().SetExt();

(ext.IsName() && ext.SetName().empty()))

ext.SetName() = prot_ref.

().front();

protein_entry;

(objectId.

()) {

objectId.

();

(

pThisFeat: thisFeatures) {

(!pThisFeat->IsSetId() || !pThisFeat->GetId().IsLocal()) {

& this_oid = pThisFeat->GetId().GetLocal();

(

pOtherFeat: otherFeatures) {

(!pOtherFeat->IsSetId() || !pOtherFeat->GetId().IsLocal()) {

thisFeatures.push_back(pOtherFeat);

& other_oid = pOtherFeat->GetId().GetLocal();

thisFeatures.push_back(pOtherFeat);

thisFeatures.push_back(pOtherFeat);

(lhs.

()) {

oldFeatIdAsStr;

(oldFeatId.

()) {

oldFeatIdAsStr = oldFeatId.

();

newFeatIdAsStr = oldFeatIdAsStr +

;

pNewFeatId->

(oldFeatIdAsStr +

);

pNewFeatId->

() +=

;

pBaseFeat->SetId().SetLocal(*pNewFeatId);

(

it = featMap.

(); it != featMap.

(); ++it) {

pFeat = it->second;

(

& pXref: pFeat->SetXref()) {

(!pXref->IsSetId() || !pXref->GetId().IsLocal()) {

pXref->SetId().SetLocal(*pNewFeatId);

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

string GetIdHashOrValue(const string &base, int offset)

CSeqdesc & Set(bool skip_lookup=false)

static bool ExtendToStopIfShortAndNotPartial(CSeq_feat &f, CBioseq_Handle bsh, bool check_for_stop=true)

Extends a coding region up to 50 nt.

static bool ExtendStopPosition(CSeq_feat &f, const CSeq_feat *cdregion, size_t extension=0)

static bool LocationMayBeExtendedToMatch(const CSeq_loc &orig, const CSeq_loc &improved)

Checks whether it is possible to extend the original location up to improved one.

void InstantiateProducts()

void xFeatureSetQualifier(CMappedFeat, const std::string &, const std::string &)

unsigned int mSequenceSize

CConstRef< CSeq_feat > xGetLinkedFeature(const CSeq_feat &cd_feature, bool gene)

void GenerateMissingGeneForMrna()

void GenerateMissingGeneForCds()

void xFeatureAddTranscriptIdMrna(CMappedFeat)

IObjtoolsListener * mpMessageListener

set< CMappedFeat > mProcessedMrnas

bool xAdjustExistingParentGene(CMappedFeat)

void xGenerateMissingMrnaForCds(const CMappedFeat &cds)

void xGenerateLocusIdsRegenerate()

void xFeatureRemoveQualifier(CMappedFeat, const std::string &)

CRef< CSeq_loc > xGetGeneLocation(const CSeq_loc &, TSeqPos)

unsigned int mLocusTagNumber

void xPutError(const string &message)

void ProcessCodonRecognized()

void xFeatureAddTranscriptIdCds(CMappedFeat)

void xGenerateMissingGeneForChoice(CSeqFeatData::E_Choice, const CGff3LocationMerger *=nullptr)

static std::string xGetIdStr(CMappedFeat)

CSeq_annot_EditHandle mEditHandle

void xPutErrorMissingLocustag(CMappedFeat)

void GenerateProteinAndTranscriptIds()

CRef< CSeq_feat > xMakeGeneForFeature(const CMappedFeat &, TSeqPos)

void GenerateMissingParentFeaturesForProkaryote(const objects::CGff3LocationMerger *=nullptr)

bool AnnotHasAllLocusTags() const

void xFeatureAddProteinIdCds(CMappedFeat)

void xAddTranscriptAndProteinIdsToUnmatchedMrna(CMappedFeat &mrna)

std::string xGetCurrentLocusTagPrefix(CMappedFeat)

void GenerateMissingParentFeaturesForEukaryote(const objects::CGff3LocationMerger *=nullptr)

void xConvertToGeneralIds(const CMappedFeat &mf, string &transcript_id, string &protein_id)

void xFeatureAddTranscriptIdDefault(CMappedFeat)

CSeq_annot_Handle mHandle

void xGenerateLocusIdsUseExisting()

void xFeatureAddQualifier(CMappedFeat, const std::string &, const std::string &)

string xNextTranscriptId(const CMappedFeat &)

void xPutErrorBadCodonRecognized(const string codonRecognized)

bool m_use_hypothetic_protein

void xGenerateMissingGeneForFeats(const SAnnotSelector &sel, const CGff3LocationMerger *=nullptr)

void xPutErrorMissingProteinId(CMappedFeat)

string xNextProteinId(const CMappedFeat &)

void xGenerateMissingGeneForFeat(const CMappedFeat &feat)

void xPutErrorMissingTranscriptId(CMappedFeat)

void xGenerateMissingGeneForSubtype(CSeqFeatData::ESubtype, const CGff3LocationMerger *=nullptr)

void GenerateMissingParentFeatures(bool forEukaryote, const objects::CGff3LocationMerger *=nullptr)

void xFeatureAddProteinIdDefault(CMappedFeat)

void xFeatureSetProduct(CMappedFeat, const string &)

map< string, int > mMapProtIdCounts

bool xCreateMissingParentGene(CMappedFeat, TSeqPos)

void MergeFeatures(const CSeq_annot::TData::TFtable &other)

std::string xGenerateTranscriptOrProteinId(CMappedFeat, const std::string &)

void GenerateMissingMrnaForCds()

void xAddTranscriptAndProteinIdsToCdsAndParentMrna(CMappedFeat &cds)

void EliminateBadQualifiers()

void xGenerate_mRNA_Product(CSeq_feat &cd_feature)

void InstantiateProductsNames()

void xAddTranscriptAndProteinIdsToMrna(const string &cds_transcript_id, const string &cds_protein_id, CMappedFeat &mrna)

void xPutErrorDifferingTranscriptIds(const CMappedFeat &mrna)

CFeatTableEdit(CSeq_annot &, const string &="", unsigned int=1, unsigned int=1, IObjtoolsListener *=nullptr)

void xFeatureAddProteinIdMrna(CMappedFeat)

void xPutErrorDifferingProteinIds(const CMappedFeat &mrna)

void xRenameFeatureId(const CObject_id &, FeatMap &)

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

TSeqPos GetSequenceSize(const string &) const

bool IsLegalQualifier(EQualifier qual) const

Test wheather a certain qualifier is legal for the feature.

EQualifier

List of available qualifiers for feature keys.

ESubtype GetSubtype(void) const

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...

CSeq_feat_EditHandle –.

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 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.

bool AddSeqFeatXref(const CSeqFeatXref::TId &id)

void SetProtXref(CProt_ref &value)

static bool GetOrgName(string &name, const objects::CSeq_entry &entry)

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

CRef< CSeq_loc > sProductFromString(const string str)

static string s_GetTranscriptIdFromMrna(const CMappedFeat &mrna)

static void s_SetProtRef(const CSeq_feat &cds, CConstRef< CSeq_feat > pMrna, CProt_ref &prot_ref)

static bool s_IsGenbankId(const string &id)

static bool AssignLocalIdIfEmpty(CSeq_feat &feature, unsigned &id)

static void s_AppendProtRefInfo(CProt_ref &current_ref, const CProt_ref &other_ref)

static bool s_ShouldConvertToGeneral(const string &id)

string sGetCdsProductName(const CSeq_feat &cds, CScope &scope)

bool idAlpha(const CSeq_id_Handle &idh1, const CSeq_id_Handle idh2)

bool OjectIdsAreEqual(const CObject_id &lhs, const CObject_id &rhs)

string sGetFeatMapKey(const CObject_id &objectId)

static bool s_IsGeneralId(const string &id)

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

const TResidue codons[4][4]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eDiag_Error

Error message.

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

Set object to copy of another one.

static SIZE_TYPE ParseIDs(CBioseq::TId &ids, const CTempString &s, TParseFlags flags=fParse_Default)

Parse a string representing one or more Seq-ids, appending the results to IDS.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

string AsString(void) const

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_ValidLocal

Treat otherwise unidentified strings as raw accessions, provided that they pass rudimentary validatio...

@ eContent

Untagged human-readable accession or the like.

void SetPacked_int(TPacked_int &v)

ENa_strand GetStrand(void) const

Get the location's strand.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

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.

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

bool CopyFeaturePartials(CSeq_feat &dst, const CSeq_feat &src)

CopyFeaturePartials A function to copy the start and end partialness from one feature to another.

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetBestGeneForFeat(const CMappedFeat &feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

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

bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

CMappedFeat GetBestCdsForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

@ eOverlap_CheckIntRev

1st is a subset of 2nd with matching boundaries

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)

Retrieve the Bioseq Handle from a location.

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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)

CBioseq_EditHandle GetEditHandle(const CBioseq_Handle &seq)

Get editable Biosec handle by regular one.

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

CBioseq_Handle GetObjectHandle(const CBioseq &bioseq, EMissing action=eMissing_Default)

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

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

Add a qualifier to this feature.

virtual CSeq_id_Handle GetLocationId(void) const

const CFeat_id & GetId(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeqFeatData & GetData(void) const

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

bool IsSetProduct(void) const

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name on this feature.

CSeqFeatData::ESubtype GetFeatSubtype(void) const

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & ExcludeFeatSubtype(TFeatSubtype subtype)

Exclude feature subtype from the search.

bool IsSetPartial(void) const

const CSeq_loc & GetLocation(void) const

bool GetPartial(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

CSeq_id_Handle GetLocationId(void) const

@ eSortOrder_Normal

default - increasing start, decreasing length

@ eSortOrder_None

do not sort annotations for faster retrieval

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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 int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

Convert int to 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 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 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.

bool IsSetLocus_tag(void) const

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

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

bool IsStr(void) const

Check if variant Str is selected.

E_Choice Which(void) const

Which variant is currently selected.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

TId GetId(void) const

Get the variant data.

TActivity & SetActivity(void)

Assign a value to Activity data member.

bool IsSetDesc(void) const

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

const TDb & GetDb(void) const

Get the Db member data.

const TActivity & GetActivity(void) const

Get the Activity member data.

TEc & SetEc(void)

Assign a value to Ec data member.

const TName & GetName(void) const

Get the Name member data.

bool IsSetDb(void) const

ids in other dbases Check if a value has been assigned to Db data member.

bool IsSetEc(void) const

E.C.

void SetDesc(const TDesc &value)

Assign a value to Desc data member.

TProcessed GetProcessed(void) const

Get the Processed member data.

void SetProcessed(TProcessed value)

Assign a value to Processed data member.

bool IsSetName(void) const

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

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetActivity(void) const

activities Check if a value has been assigned to Activity data member.

const TEc & GetEc(void) const

Get the Ec member data.

TDb & SetDb(void)

Assign a value to Db data member.

TName & SetName(void)

Assign a value to Name data member.

bool IsSetExt(void) const

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

const TName & GetName(void) const

Get the variant data.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsName(void) const

Check if variant Name is selected.

@ e_not_set

No variant selected.

TXref & SetXref(void)

Assign a value to Xref data member.

void ResetPartial(void)

Reset Partial data member.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetXref(void) const

cite other relevant features Check if a value has been assigned to Xref data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetData(void) const

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

void SetId(TId &value)

Assign a value to Id data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetId(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TGene & GetGene(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

void ResetProduct(void)

Reset Product data member.

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 IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ e_Local

for local software use

void SetTo(TTo value)

Assign a value to To data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

const TSeq & GetSeq(void) const

Get the variant data.

TSeq & SetSeq(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

const TId & GetId(void) const

Get the Id member data.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

const TData & GetData(void) const

Get the Data member data.

void SetTech(TTech value)

Assign a value to Tech data member.

TMolinfo & SetMolinfo(void)

Select the variant.

@ eTech_concept_trans

conceptual translation

@ e_Molinfo

info on the molecule and techniques

constexpr auto sort(_Init &&init)

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

IMessage/IMessageListener interfaces and basic implementations.

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