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NCBI C++ ToolKit: src/objtools/validator/validatorp.cpp Source File

sequence;

shared_ptr<SValidatorContext> pContext,

m_ErrRepository{errs},

(options, pContext->CumulativeInferenceCount, pContext->NotJustLocalOrGeneral, pContext->IsRefSeq);

(initialInferenceCount, notJustLocalOrGeneral, hasRefSeq);

.PreprocessHugeFile ||

edit::CHugeAsnReader::IsHugeSet(setClass);

(type_info == CSeqdesc::GetTypeInfo()) {

}

(type_info == CSeq_feat::GetTypeInfo()) {

}

(type_info == CBioseq::GetTypeInfo()) {

}

(type_info == CBioseq_set::GetTypeInfo()) {

}

(type_info == CSeq_annot::GetTypeInfo()) {

}

(type_info == CSeq_graph::GetTypeInfo()) {

}

(type_info == CSeq_align::GetTypeInfo()) {

}

(type_info == CSeq_entry::GetTypeInfo()) {

}

(type_info == CBioSource::GetTypeInfo()) {

}

(type_info == COrg_ref::GetTypeInfo()) {

}

(type_info == CPubdesc::GetTypeInfo()) {

}

(type_info == CSeq_submit::GetTypeInfo()) {

(sc_GenomeRaiseExceptEmblDdbjRefSeqArray.find(et) != sc_GenomeRaiseExceptEmblDdbjRefSeqArray.end()) {

(sc_GenomeRaiseExceptEmblDdbjArray.find(et) != sc_GenomeRaiseExceptEmblDdbjArray.end()) {

(sc_GenomeRaiseArray.find (et) != sc_GenomeRaiseArray.end()) {

item->SetErrIndex(et);

item->SetObj_content(content_label);

item->SetFeatureId(feature_id);

item->SetBioseq(bioseq_label);

item->SetLocation(loc_label);

item->SetSeqOffset(

);

item->SetProduct_loc(product_label);

item->SetAccession(accession);

item->SetAccnver(accession);

item->SetFeatureObjDescFromFields();

isSetClass =

.IsSetClass();

(isSetClass &&

().PreprocessHugeFile) {

(

setClass =

.GetClass();

(setClass)) {

.IsSet() &&

.GetSet().IsSetClass()) {

(

setClass =

.GetSet().GetClass();

(setClass)) {

desc{

};

desc +=

;

desc +=

;

desc +=

;

desc =

;

desc =

;

desc +=

;

desc(

);

desc +=

;

&

,

desc =

;

desc += align.ENUM_METHOD_NAME(EType)()->FindName(align.

(),

);

desc +=

;

&

,

(entry.

()) {

}

(entry.

()) {

desc =

;

&

,

desc =

;

&

,

desc =

;

&

,

desc =

;

&

,

desc =

;

&

,

& desc,

& accession,

&

,

&

,

reasons =

+

+ reasons;

has_mult =

;

desc_ci && !has_mult;

(desc_ci->GetSource().IsSetOrg()) {

& org = desc_ci->GetSource().GetOrg();

(*it)->IsSetTag() && (*it)->GetTag().IsId()) {

this_id = (*it)->GetTag().GetId();

}

(first_id == 0) {

}

(first_id != this_id) {

(has_mult || (phage_id > 0 && first_id > 0)) {

,

, *seq);

has_gi =

;

has_nucleotide_sequence =

;

bi && (!

() || !has_gi || !has_nucleotide_sequence);

((*it)->IsGi()) {

(bi->IsSetInst_Mol() && bi->IsNa()) {

has_nucleotide_sequence =

;

, *

);

vector<string> id_strings;

(!IsNCBIFILESeqId(**it)) {

(*it)->GetLabel(&

);

id_strings.push_back(

);

stable_sort (id_strings.begin(), id_strings.end());

(vector<string>::iterator id_str_it = id_strings.begin();

id_str_it != id_strings.end();

pattern = (*id_str_it).substr(0, 30);

first_id = *id_str_it;

vector<string>::iterator cmp_it = id_str_it;

(cmp_it != id_strings.end() &&

(*cmp_it, pattern)) {

+ first_id +

+

vector < int > feature_ids;

& sf = fi->GetOriginalFeature();

(feature_ids.size() > 0) {

stable_sort (feature_ids.begin(), feature_ids.end());

vector <int>::iterator it = feature_ids.begin();

(it != feature_ids.end()) {

( vector<CSeq_feat_Handle>, feat_it, handles ) {

(it != feature_ids.end() && *it ==

) {

(it != feature_ids.end()) {

has_nongps =

;

has_gps =

;

(

->IsSetClass()) {

(has_nongps && has_gps) {

,

,

prefix, remainder;

num_accessions = 0;

(

= 0;

< accessions.size();

++) {

acc_prefix, accession;

(num_accessions > 0) {

,

(seh.

()) {

}

(

exception& e ) {

(

) +

}

(seh.

()) {

}

(

exception& e ) {

(

) +

+

, *seq);

, *

);

call_once(

().ProteinHaveGeneralIDOnceFlag,

,

,

,

, *

);

,

[

, &cs, &pEntry]() {

(*cs, *pEntry, pEntry); });

, ss);

+

+

, ss);

+

+

, ss);

, ss);

(

.IsStd()) {

( (*name)->GetName().IsName() ) {

& nstd = (*name)->GetName().GetName();

+

+

, ss);

+

+

, ss);

, ss);

call_once(

().SubmitBlockOnceFlag,

(

.IsSetClass() &&

call_once(

().WgsSetInSeqSubmitOnceFlag,

,

,

(sah.

()) {

(

fi (sah); fi; ++fi) {

& sf = fi->GetOriginalFeature();

& sa = ai.GetOriginalSeq_align();

& sg = gi->GetOriginalGraph();

+ xref.

().

() +

,

+ xref.

().

() +

,

+ db +

,

isStr =

;

+ db +

+ dbv +

, obj,

);

refseq_db =

, src_db =

;

correct_caps;

xref.

(refseq_db, src_db, correct_caps);

message =

+ db +

+ dbv +

+ correct_caps;

message +=

;

message +=

;

+ db +

+ dbv +

,

+ db +

+ dbv +

,

+ db +

+ dbv +

,

+ db +

+ dbv +

,

+ db +

+ dbv +

,

(isStr && db ==

) {

+ db +

+ dbv +

,

&& (*xref)->IsSetDb()) {

+ last_db +

,

last_db = (*xref)->GetDb();

.int_cur = (*it);

.id_prv =

.id_cur;

.strand_prv =

.strand_cur;

.int_prv =

.int_cur;

id_cur = &int_cur->

();

*

=

;

*

=

;

*

=

;

*

=

;

has_fuzz_from =

;

has_fuzz_to =

;

has_fuzz_from =

;

has_fuzz_to =

;

(! has_fuzz_from && ! has_fuzz_to) {

(has_fuzz_from && has_fuzz_to && fuzz_from == fuzz_to) {

, obj);

, obj);

, obj);

(; lit; ++lit) {

(loc_choice) {

num_mix = 0;

(; lit; ++lit) {

.unmarked_strand =

;

.mixed_strand =

;

.has_other =

;

.has_not_other =

;

.id_cur =

;

.id_prv =

;

.int_cur =

;

.int_prv =

;

.prefix = prefix;

(

.id_cur &&

.id_prv &&

(

.strand_prv !=

.strand_cur) {

.unmarked_strand =

;

.mixed_strand =

;

.has_other =

;

.has_not_other =

;

(loc.Which()) {

.int_cur = &loc.GetInt();

.has_other =

;

((!

.chk) && lowerSev) {

fr = loc.GetInt().GetFrom();

to = loc.GetInt().GetTo();

(fr < length && to >= length) {

.strand_cur = loc.GetPnt().IsSetStrand() ?

.has_other =

;

.id_cur = &loc.GetPnt().GetId();

.int_prv =

;

.strand_cur = loc.GetPacked_pnt().IsSetStrand() ?

.has_other =

;

.id_cur = &loc.GetPacked_pnt().GetId();

.int_prv =

;

(

: loc.GetMix().Get()) {

.id_cur =

;

.int_prv =

;

.prefix +

+ lbl +

, obj);

.strand_prv =

.strand_cur;

.id_prv =

.id_cur;

}

(

exception& e ) {

+

+

+ e.what(), obj);

.id_cur =

;

.int_prv =

;

(

CSeq_loc& loc,

report_abutting,

& prefix,

(

.has_other &&

.has_not_other) {

prefix +

+

+

, obj);

}

(

.has_other &&

(prefix,

)) {

, obj);

, obj);

loc.GetLabel(&

);

prefix +

+

+

,

trans_splice =

;

circular_rna =

;

exception =

;

sfp =

*

(&obj);

.mixed_strand =

;

.unmarked_strand =

;

trans_splice =

;

circular_rna =

;

prefix +

+

loc_lbl +

, obj);

(trans_splice && !

(prefix,

)) {

CSeq_loc_CI li(loc);

ordered =

;

circular =

;

loc.GetLabel(&

);

+

+

+ ex.

(), obj);

(

.mixed_strand ||

.unmarked_strand || !ordered) {

(loc_lbl.empty()) {

(

.mixed_strand) {

prefix +

+ loc_lbl +

, obj);

prefix +

+ loc_lbl +

, obj);

}

(

.unmarked_strand) {

prefix +

+ loc_lbl +

, obj);

(!ordered && !circular_rna) {

prefix +

+

loc_lbl +

, obj);

prefix +

+

loc_lbl +

, obj);

(loc_lbl.empty()) {

loc.GetLabel(&loc_lbl);

prefix +

+

loc_lbl +

, obj);

(loc_lbl.empty()) {

loc.GetLabel(&loc_lbl);

prefix +

+

loc_lbl +

, obj);

, *(seq.

()));

((*it)->IsMolinfo() && (*it)->GetMolinfo().IsSetTech()

is_other =

;

has_gi =

;

((*it)->IsOther()) {

}

((*it)->IsGi()) {

(!is_other || has_gi) {

((*it)->IsMolinfo() && (*it)->GetMolinfo().IsSetTech()

is_other =

;

has_gi =

;

((*it)->IsOther()) {

}

((*it)->IsGi()) {

(!is_other || has_gi) {

, se);

(

= 0;

< num_no_source; ++

) {

,

( parent->

() ) {

(

.IsSetClass() &&

.GetClass() == clss ) {

pos = comment.find(

, 0);

( pos != string::npos ) {

(

((

) comment[pos]) ) {

(comment[pos] ==

) {

(

((

) comment[pos]) ) {

( comment[pos] ==

&& okay ) {

pos = comment.find(

, pos);

( sid && sid->

() ) {

(

().IsSeq() ) {

vector<TEntrezId>& pmids, vector<TEntrezId>& muids, vector<int>& serials,

vector<string>& published_labels, vector<string>& unpublished_labels)

((*it)->IsPub()) {

vector<TEntrezId> pmids;

vector<TEntrezId> muids;

vector<int> serials;

vector<string> published_labels;

vector<string> unpublished_labels;

(

->IsSetCit() &&

->GetCit().IsPub()) {

found =

;

((*cit_it)->IsPmid()) {

vector<TEntrezId>::iterator it = pmids.begin();

(it != pmids.end() && !found) {

(*it == (*cit_it)->GetPmid()) {

+

,

->GetOriginalFeature());

}

((*cit_it)->IsMuid()) {

vector<TEntrezId>::iterator it = muids.begin();

(it != muids.end() && !found) {

(*it == (*cit_it)->GetMuid()) {

+

,

->GetOriginalFeature());

}

((*cit_it)->IsEquiv()) {

vector<string>::iterator unpub_it = unpublished_labels.begin();

(unpub_it != unpublished_labels.end() && !found) {

it_len =(*unpub_it).length();

vector<string>::iterator pub_it = published_labels.begin();

(pub_it != published_labels.end() && !found) {

it_len =(*pub_it).length();

,

->GetOriginalFeature());

,

->GetOriginalFeature());

&

= *it;

& ch = *c_it;

chu = ch;

(ch > 127 || (ch < 32 && ch !=

&& ch !=

&& ch !=

)) {

CScriptTagTextFsm :

<int>

CScriptTagTextFsm() {

* script_tags[] = {

,

,

,

,

,

,

};

AddWord(script_tags[idx],

);

DoesStrHaveFsmHits(

&

) {

= GetInitialState();

( IsMatchFound(

) ) {

(s_ScriptTagFsm->DoesStrHaveFsmHits(*it)) {

, obj);

CSeq_loc_CI curr(loc);

CSeq_loc_CI

= curr;

( CSeq_loc_CI it(loc); it && !rval; ++it ) {

(it.GetSeq_id().IsGi()) {

}

(!se.

()) {

(pub && !pub->IsSub()) {

(

->IsSetClass ()) {

& sid = **sid_itr;

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

}

(acc ==

) {

(desc_ci->GetSource().IsSetGenome()

( desc_ci->GetUser().IsSetType() ) {

( ! oi.

() )

;

((*field)->IsSetLabel() && (*field)->GetLabel().IsStr()) {

(

((*field)->GetLabel().GetStr(),

)) {

(

((*field)->GetData().GetStr(),

)) {

(feat_ci->IsSetProduct() &&

(feat_ci->GetProduct())) {

(feat_ci->IsSetData() && feat_ci->GetData().IsGene()

&& feat_ci->GetData().GetGene().IsSetLocus_tag()

&& !

(feat_ci->GetData().GetGene().GetLocus_tag())) {

(

CSeq_loc& loc,

( CSeq_loc_CI lit(loc); lit; ++lit ) {

& id1 = lit.GetSeq_id();

CSeq_loc_CI lit2 = lit;

( ++lit2; lit2; ++lit2 ) {

& id2 = lit2.GetSeq_id();

, obj);

, obj);

, obj);

& sq = *(

.bsh.GetCompleteBioseq());

(!

.percent_n.empty()) {

(!

.empty()) {

(

.collection_date) {

(

.order_assignment) {

(

.low_trace) {

(

.frame_shift) {

(!

.structured_voucher) {

&

,

&

,

&

,

&

,

&

,

&

,

&

,

&

,

&

,

&

,

(!parent || !parent.

()) {

}

(seh.

()) {

appropriate_parent = gps;

appropriate_parent = gp;

appropriate_parent = np;

appropriate_parent = seh;

appropriate_parent;

*find_iter->second;

*pub, pInfo->m_pmids, pInfo->m_muids,

pInfo->m_serials, pInfo->m_published_labels,

pInfo->m_unpublished_labels);

find_iter->second;

( ; feat_ci; ++feat_ci ) {

any_type_key = inner_feat_key;

any_subtype_key = inner_feat_key;

[any_subtype_key].push_back(*feat_ci);

any_type_or_subtype_key = inner_feat_key;

[any_type_or_subtype_key].push_back(*feat_ci);

vector<SFeatKey> &featKeys)

( featKeys.empty() ) {

(vector<SFeatKey>, feat_it, featKeys) {

( feat_it->bioseq_h != bioseq_h ) {

runtime_error(

);

(vector<SFeatKey>, key_it, featKeys ) {

set_of_feats, set_of_feats.

()));

( set_of_feats.

(*feat_it) != set_of_feats.

() ) {

answer->push_back(*feat_it);

(search_bsh || tse_arg);

( ; gene_ci; ++gene_ci ) {

& locus_tag = (

find_iter->second;

( ; bioseq_ci; ++bioseq_ci ) {

( ; feat_ci; ++feat_ci ) {

find_iter->second;

kEmptyFeatToBioseqCache.

();

( ; bioseq_ci; ++bioseq_ci ) {

find_iter->second;

s_EmptyResult.

();

( CSeq_loc_CI citer (loc); citer; ++citer) {

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eErr_SEQ_FEAT_WrongQualOnImpFeat

@ eErr_SEQ_DESCR_ObsoleteSourceQual

@ eErr_SEQ_DESCR_ObsoleteSourceLocation

@ eErr_SEQ_INST_FarFetchFailure

@ eErr_SEQ_FEAT_WholeLocation

@ eErr_GENERIC_MissingPubRequirement

@ eErr_SEQ_FEAT_EcNumberProblem

@ eErr_SEQ_FEAT_DuplicateAnticodonInterval

@ eErr_SEQ_INST_CompleteGenomeHasGaps

@ eErr_SEQ_FEAT_CDShasTooManyXs

@ eErr_SEQ_FEAT_TranslExceptPhase

@ eErr_SEQ_FEAT_MinusStrandProtein

@ eErr_SEQ_INST_CompleteTitleProblem

@ eErr_SEQ_DESCR_UnwantedCompleteFlag

@ eErr_SEQ_FEAT_GeneXrefWithoutLocus

@ eErr_SEQ_FEAT_BadLocation

@ eErr_SEQ_FEAT_GenesInconsistent

@ eErr_SEQ_INST_HighNContentStretch

@ eErr_SEQ_PKG_NoBioseqFound

@ eErr_SEQ_FEAT_PseudoRnaHasProduct

@ eErr_SEQ_DESCR_InconsistentBioSources

@ eErr_GENERIC_PastReleaseDate

@ eErr_SEQ_DESCR_BioSourceDbTagConflict

@ eErr_SEQ_FEAT_UnknownImpFeatQual

@ eErr_SEQ_FEAT_DuplicateExonInterval

@ eErr_GENERIC_UnnecessaryPubEquiv

@ eErr_SEQ_DESCR_BioSourceOnProtein

@ eErr_SEQ_DESCR_LatLonRange

@ eErr_SEQ_FEAT_UnnecessaryTranslExcept

@ eErr_SEQ_GRAPH_GraphBioseqId

@ eErr_SEQ_FEAT_MixedStrand

@ eErr_SEQ_FEAT_BadRRNAcomponentOrder

@ eErr_SEQ_DESCR_DuplicatePCRPrimerSequence

@ eErr_SEQ_FEAT_BadGeneOntologyFormat

@ eErr_SEQ_DESCR_LatLonCountry

@ eErr_SEQ_PKG_NucProtSetHasTitle

@ eErr_SEQ_FEAT_IllegalDbXref

@ eErr_GENERIC_SgmlPresentInText

@ eErr_SEQ_FEAT_BadAnticodonAA

@ eErr_SEQ_FEAT_MissingCDSproduct

@ eErr_SEQ_FEAT_FeatureBeginsOrEndsInGap

@ eErr_SEQ_FEAT_TranslExceptAndRnaEditing

@ eErr_GENERIC_BarcodeTooManyNs

@ eErr_SEQ_PKG_BioseqSetClassNotSet

@ eErr_SEQ_DESCR_NoOrgFound

@ eErr_SEQ_FEAT_MissingProteinName

@ eErr_SEQ_DESCR_BadPCRPrimerSequence

@ eErr_SEQ_FEAT_GeneXrefWithoutGene

@ eErr_SEQ_DESCR_TransgenicProblem

@ eErr_SEQ_PKG_MissingSetTitle

@ eErr_SEQ_FEAT_InvalidQualifierValue

@ eErr_SEQ_FEAT_GeneOntologyTermMissingGOID

@ eErr_SEQ_FEAT_ProtRefHasNoData

@ eErr_SEQ_GRAPH_GraphSeqLocLen

@ eErr_SEQ_DESCR_InvalidForType

@ eErr_SEQ_DESCR_LatLonValue

@ eErr_SEQ_FEAT_FeatureCitationProblem

@ eErr_SEQ_DESCR_IdenticalInstitutionCode

@ eErr_SEQ_PKG_ImproperlyNestedSets

@ eErr_SEQ_INST_UnknownLengthGapNot100

@ eErr_SEQ_FEAT_WrongQualOnFeature

@ eErr_SEQ_FEAT_MultipleProtRefs

@ eErr_SEQ_FEAT_MultipleEquivPublications

@ eErr_SEQ_PKG_SeqSubmitWithWgsSet

@ eErr_SEQ_PKG_InconsistentMoltypeSet

@ eErr_SEQ_INST_ConflictingBiomolTech

@ eErr_SEQ_FEAT_MissingQualOnImpFeat

@ eErr_SEQ_PKG_INSDRefSeqPackaging

@ eErr_SEQ_FEAT_LocusCollidesWithLocusTag

@ eErr_SEQ_PKG_GPSnonGPSPackaging

@ eErr_SEQ_DESCR_BadCollectionDate

@ eErr_SEQ_FEAT_MultipleEquivBioSources

@ eErr_SEQ_FEAT_CDSwithNoMRNAOverlap

@ eErr_SEQ_DESCR_BadInstitutionCode

@ eErr_SEQ_FEAT_PeptideFeatOutOfFrame

@ eErr_SEQ_FEAT_ProteinNameHasPMID

@ eErr_SEQ_FEAT_RepeatRegionNeedsNote

@ eErr_SEQ_DESCR_BadAltitude

@ eErr_SEQ_FEAT_GeneXrefStrandProblem

@ eErr_SEQ_FEAT_MissingTrnaAA

@ eErr_GENERIC_NonAsciiAsn

@ eErr_SEQ_FEAT_CDSwithMultipleMRNAs

@ eErr_SEQ_FEAT_CollidingFeatureIDs

@ eErr_SEQ_DESCR_IncorrectlyFormattedVoucherID

@ eErr_SEQ_FEAT_OrfCdsHasProduct

@ eErr_SEQ_FEAT_ImproperBondLocation

@ eErr_SEQ_PKG_GraphPackagingProblem

@ eErr_SEQ_INST_OverlappingDeltaRange

@ eErr_SEQ_FEAT_BadTranssplicedInterval

@ eErr_SEQ_INST_SeqLocLength

@ eErr_SEQ_DESCR_MultipleTaxonIDs

@ eErr_SEQ_DESCR_BadKeyword

@ eErr_SEQ_FEAT_UnknownImpFeatKey

@ eErr_SEQ_DESCR_Inconsistent

@ eErr_SEQ_PKG_ArchaicFeatureLocation

@ eErr_GENERIC_BarcodeTestFails

@ eErr_SEQ_FEAT_NestedSeqLocMix

@ eErr_SEQ_FEAT_ShortIntron

@ eErr_SEQ_FEAT_UnknownFeatureQual

@ eErr_SEQ_DESCR_MultipleChromosomes

@ eErr_SEQ_FEAT_InconsistentGeneOntologyTermAndId

@ eErr_SEQ_PKG_MisplacedMolInfo

@ eErr_GENERIC_EmbeddedScript

@ eErr_GENERIC_BarcodeTestPasses

@ eErr_SEQ_GRAPH_GraphAbove

@ eErr_SEQ_FEAT_FeatureInsideGap

@ eErr_SEQ_FEAT_DifferntIdTypesInSeqLoc

@ eErr_SEQ_FEAT_BadFullLengthFeature

@ eErr_SEQ_FEAT_BadCharInAuthorName

@ eErr_SEQ_FEAT_FarLocation

@ eErr_SEQ_INST_BadHTGSeq

@ eErr_SEQ_FEAT_InvalidFuzz

@ eErr_SEQ_FEAT_InvalidInferenceValue

@ eErr_SEQ_FEAT_GeneXrefNeeded

@ eErr_SEQ_INST_UnexpectedIdentifierChange

@ eErr_SEQ_FEAT_InconsistentRRNAstrands

@ eErr_SEQ_PKG_ArchaicFeatureProduct

@ eErr_SEQ_DESCR_MultipleSourceQualifiers

@ eErr_SEQ_FEAT_BadRRNAcomponentOverlap

@ eErr_SEQ_FEAT_BadTrailingCharacter

@ eErr_SEQ_DESCR_WrongVoucherType

@ eErr_SEQ_INST_ProteinsHaveGeneralID

@ eErr_SEQ_GRAPH_GraphOutOfOrder

@ eErr_SEQ_FEAT_BadInternalCharacter

@ eErr_SEQ_DESCR_NoSourceDescriptor

@ eErr_SEQ_DESCR_BadCollectionCode

@ eErr_SEQ_FEAT_BadProteinName

@ eErr_SEQ_FEAT_FeatureProductInconsistency

@ eErr_GENERIC_PublicationInconsistency

@ eErr_GENERIC_BadSubmissionAuthorName

@ eErr_GENERIC_CollidingSerialNumbers

@ eErr_SEQ_PKG_ComponentMissingTitle

@ eErr_SEQ_DESCR_DBLinkMissingUserObject

@ eErr_SEQ_PKG_InternalGenBankSet

@ eErr_SEQ_DESCR_BioSourceMissing

@ eErr_SEQ_FEAT_BadAnticodonCodon

@ eErr_SEQ_FEAT_BadTrailingHyphen

@ eErr_SEQ_FEAT_OldLocusTagMismtach

@ eErr_SEQ_DESCR_MolInfoConflictsWithBioSource

@ eErr_SEQ_FEAT_UTRdoesNotAbutCDS

@ eErr_SEQ_FEAT_PseudoRnaViaGeneHasProduct

@ eErr_SEQ_FEAT_ConflictFlagSet

@ eErr_SEQ_FEAT_StrandOther

@ eErr_SEQ_PKG_FeaturePackagingProblem

@ eErr_SEQ_DESCR_MultipleNames

@ eErr_SEQ_INST_BadSeqIdFormat

@ eErr_SEQ_PKG_GenomicProductPackagingProblem

@ eErr_INTERNAL_Exception

@ eErr_SEQ_FEAT_BadEcNumberFormat

@ eErr_SEQ_FEAT_CDSproductPackagingProblem

@ eErr_SEQ_FEAT_RedundantFields

@ eErr_SEQ_INST_InternalNsInSeqRaw

@ eErr_SEQ_DESCR_BadOrgMod

@ eErr_SEQ_INST_TerminalNs

@ eErr_SEQ_DESCR_BadOrganelleLocation

@ eErr_SEQ_FEAT_NoNameForProtein

@ eErr_SEQ_FEAT_RptUnitRangeProblem

@ eErr_SEQ_FEAT_SeqLocOrder

@ eErr_SEQ_DESCR_TaxonomyIsSpeciesProblem

@ eErr_SEQ_FEAT_CDSmRNAXrefLocationProblem

@ eErr_SEQ_PKG_SingleItemSet

@ eErr_SEQ_DESCR_BioSourceNeedsChromosome

@ eErr_SEQ_FEAT_VectorContamination

@ eErr_SEQ_FEAT_AbuttingIntervals

@ eErr_SEQ_FEAT_LocusTagProblem

@ eErr_SEQ_DESCR_BioSourceInconsistency

@ eErr_SEQ_FEAT_OnlyGeneXrefs

@ eErr_SEQ_FEAT_TranslExcept

@ eErr_SEQ_INST_InternalGapsInSeqRaw

@ eErr_SEQ_FEAT_GeneRefHasNoData

@ eErr_SEQ_INST_DuplicateSegmentReferences

@ eErr_SEQ_FEAT_TooManyInferenceAccessions

@ eErr_SEQ_FEAT_TerminalXDiscrepancy

@ eErr_SEQ_FEAT_MiscFeatureNeedsNote

@ eErr_SEQ_DESCR_CollidingPublications

@ eErr_SEQ_FEAT_GenomeSetMixedStrand

@ eErr_SEQ_FEAT_BadCharInAuthorLastName

@ eErr_SEQ_FEAT_HypotheticalProteinMismatch

@ eErr_SEQ_INST_TpaAssemblyProblem

@ eErr_SEQ_FEAT_MissingGeneXref

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

CSeq_entry * GetParentEntry(void) const

static void GetPubdescLabels(const CPubdesc &pd, vector< TEntrezId > &pmids, vector< TEntrezId > &muids, vector< int > &serials, vector< string > &published_labels, vector< string > &unpublished_labels)

For Publication Citations Get labels for a pubdesc.

bool GetDBFlags(bool &is_refseq, bool &is_src, string &correct_caps) const

bool IsSkippable(void) const

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

void GetLabel(string *label) const

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

static CNcbiApplication * Instance(void)

Singleton method.

const string & GetDivision(void) const

bool IsSetDivision(void) const

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

T & Get(void)

Create the variable if not created yet, return the reference.

ESubtype GetSubtype(void) const

static bool RequireLocationIntervalsInBiologicalOrder(ESubtype subtype)

static bool AllowAdjacentIntervals(ESubtype subtype)

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

void GetLabel(string *label, ELabelType type) const

CSeq_entry * GetParentEntry(void) const

namespace ncbi::objects::

Base class for all serializable objects.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TSeq_feat_Handles GetFeaturesWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

CScope & GetScope(void) const

Returns scope.

Template class for iteration on objects of class C (non-medifiable version)

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

Thrown on an attempt to write unassigned data member.

static string GetFeatureBioseqLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static string GetDescriptorContent(const CSeqdesc &ds)

static string GetFeatureLocationLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static string GetFeatureProductLocLabel(const CSeq_feat &ft, CRef< CScope > scope, bool suppress_context)

static string GetDescriptorLabel(const CSeqdesc &ds, const CSeq_entry &ctx, CRef< CScope > scope, bool suppress_context)

static string GetFeatureContentLabel(const CSeq_feat &feat, CRef< CScope > scope)

static string GetFeatureIdLabel(const CSeq_feat &ft)

static string GetBioseqSetLabel(const CBioseq_set &st, CRef< CScope > scope, bool suppress_context)

void ValidateSeqAlign(const CSeq_align &align, int order=-1)

void ValidateSeqAnnot(const CSeq_annot_Handle &annot)

virtual ~CValidError_base()

static CSeq_entry_Handle GetAppropriateXrefParent(CSeq_entry_Handle seh)

void PostErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)

CValidError_base(CValidError_imp &imp)

void ValidateBioseq(const CBioseq &seq)

bool GetTSAConflictingBiomolTechErrors(const CBioseq &seq)

bool GetTSANStretchErrors(const CBioseq &seq)

void ValidateBioseqSet(const CBioseq_set &seqset)

void ValidateSeqDesc(const CSeqdesc &desc, const CSeq_entry &ctx)

Validate descriptors as stand alone objects (no context)

void SetScope(CScope &scope)

void SetTSE(CSeq_entry_Handle seh)

bool GetTSACDSOnMinusStrandErrors(const CSeq_feat &feat, const CBioseq &seq)

static bool GetPrefixAndAccessionFromInferenceAccession(string inf_accession, string &prefix, string &accession)

void ValidateSeqFeat(const CSeq_feat &feat)

static vector< string > GetAccessionsFromInferenceString(string inference, string &prefix, string &remainder, bool &same_species)

void ValidateSeqGraph(const CSeq_graph &graph)

void x_ReportInvalidFuzz(const CPacked_seqint &packed_int, const CSerialObject &obj)

CRef< CObjectManager > m_ObjMgr

void SetScope(const CSeq_entry &se)

void FindCollidingSerialNumbers(const CSerialObject &obj)

const CSeq_entry_Handle & GetTSEH()

static bool BadMultipleSequenceLocation(const CSeq_loc &loc, CScope &scope)

void PostErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)

static bool IsTSAIntermediate(const CBioseq &seq)

void x_CheckPackedInt(const CPacked_seqint &packed_int, SLocCheck &lc, const CSerialObject &obj)

bool m_NewStrainValidation

static bool IsInOrganelleSmallGenomeSet(const CSeq_id &id, CScope &scope)

const CBioSourceKind & BioSourceKind() const

bool m_ValidateAlignments

bool HasGiOrAccnVer() const

void SetTSE(const CSeq_entry_Handle &seh)

bool m_FarFetchCDSproducts

const SValidatorContext & GetContext() const

CValidator::TProgressCallback m_PrgCallback

bool m_GenerateGoldenFile

IValidError * m_ErrRepository

size_t m_NumMisplacedGraphs

bool m_NotJustLocalOrGeneral

CConstRef< CSeq_feat > GetmRNAGivenProduct(const CBioseq &seq)

bool IsValidateAlignments() const

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id)

size_t m_NumTopSetSiblings

void ValidateCitations(const CSeq_entry_Handle &seh)

bool DoesAnyFeatLocHaveGI() const

void FindNonAsciiText(const CSerialObject &obj)

void AddBioseqWithNoBiosource(const CBioseq &seq)

void ValidateSeqLocIds(const CSeq_loc &loc, const CSerialObject &obj)

bool GenerateGoldenFile() const

bool IsStandaloneAnnot() const

void x_DoBarcodeTests(CSeq_entry_Handle seh)

CConstRef< CSeq_annot > m_SeqAnnot

TSuppressed & SetSuppressed()

bool DoesAnyProductLocHaveGI() const

bool GetTSAConflictingBiomolTechErrors(const CSeq_entry_Handle &se)

bool x_IsSuppressed(CValidErrItem::TErrIndex errType) const

void x_AddValidErrItem(EDiagSev sev, EErrType type, const string &msg, const string &desc, const CSerialObject &obj, const string &accession, const int version)

unique_ptr< CValidatorEntryInfo > m_pEntryInfo

void x_Init(Uint4 options, size_t initialInferenceCount, bool notJustLocalOrGeneral, bool hasRefSeq)

void PostObjErr(EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

TSuppressed m_SuppressedErrors

void Setup(const CSeq_entry_Handle &seh)

bool Validate(const CSeq_entry &se, const CCit_sub *cs=nullptr, CScope *scope=nullptr)

void InitializeSourceQualTags()

static bool IsWGSIntermediate(const CBioseq &seq)

CValidator::CProgressInfo m_PrgInfo

void ValidateDbxref(const CDbtag &xref, const CSerialObject &obj, bool biosource=false, const CSeq_entry *ctx=nullptr)

bool IsSerialNumberInComment(const string &comment)

void ValidateTaxonomy(const CSeq_entry &se)

bool IsFarSequence(const CSeq_id &id)

const CTSE_Handle & GetTSE_Handle()

size_t m_NumMisplacedFeatures

void FindEmbeddedScript(const CSerialObject &obj)

bool IsHugeFileMode() const

void ValidateCitSub(const CCit_sub &cs, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

void SetOptions(Uint4 options)

bool m_ValidateInferenceAccessions

bool m_LocusTagGeneralMatch

void ValidateSubmitBlock(const CSubmit_block &block, const CSeq_submit &ss)

void Reset(size_t initialInferenceCount, bool notJustLocalOrGeneral, bool hasRefSeq)

bool IsNoCitSubPubs() const

vector< CConstRef< CBioseq > > m_BioseqWithNoSource

void ValidateAffil(const CAffil::TStd &std, const CSerialObject &obj, const CSeq_entry *ctx)

CConstRef< CSeq_feat > GetCDSGivenProduct(const CBioseq &seq)

CBioseq_Handle GetLocalBioseqHandle(const CSeq_id &id)

size_t m_NumTpaWithHistory

const CSeq_entry * GetAncestor(const CBioseq &seq, CBioseq_set::EClass clss)

bool x_IsFarFetchFailure(const CSeq_loc &loc)

size_t m_NumTpaWithoutHistory

void PostBadDateError(EDiagSev sv, const string &msg, int flags, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

void AddProtWithoutFullRef(const CBioseq_Handle &seq)

void ValidateBioSource(const CBioSource &bsrc, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

const CValidatorEntryInfo & GetEntryInfo() const

bool RaiseGenomeSeverity(EErrType et)

bool RequireLocalProduct(const CSeq_id *sid) const

bool m_ReportSpliceAsError

bool IsFarFetchCDSproducts() const

bool DoesAnyProteinHaveGeneralID() const

virtual ~CValidError_imp()

size_t m_NumSmallGenomeSetMisplaced

void ReportMissingPubs(const CSeq_entry &se, const CCit_sub *cs)

bool IsNoBioSource() const

bool IsMixedStrands(const CSeq_loc &loc)

bool m_FarFetchMRNAproducts

bool IsLocalGeneralOnly() const

CBioSourceKind m_biosource_kind

CConstRef< CSeq_entry > m_TSE

void x_InitLocCheck(SLocCheck &lc, const string &prefix)

SValidatorContext & SetContext()

bool IsIndexerVersion() const

CGeneCache & GetGeneCache()

void SetErrorRepository(IValidError *errors)

bool IsSmallGenomeSet() const

void SetProgressCallback(CValidator::TProgressCallback callback, void *user_data)

bool GetTSACDSOnMinusStrandErrors(const CSeq_entry_Handle &se)

size_t m_CumulativeInferenceCount

void ValidateMultipleTaxIds(const CSeq_entry_Handle &seh)

bool IsHugeSet(const CBioseq_set &bioseqSet) const

CValidError_imp(CObjectManager &objmgr, shared_ptr< SValidatorContext > pContext, IValidError *errors, Uint4 options=0)

void ValidateSeqLoc(const CSeq_loc &loc, const CBioseq_Handle &seq, bool report_abutting, const string &prefix, const CSerialObject &obj, bool lowerSev=false)

bool GetTSANStretchErrors(const CSeq_entry_Handle &se)

shared_ptr< SValidatorContext > m_pContext

bool x_CheckSeqInt(CConstRef< CSeq_id > &id_cur, const CSeq_interval *int_cur, ENa_strand &strand_cur)

bool DoesAnyGeneHaveLocusTag() const

void x_CheckLoc(const CSeq_loc &loc, const CSerialObject &obj, SLocCheck &lc, bool lowerSev=false)

const CSeq_entry & GetTSE() const

bool IsFarFetchMRNAproducts() const

CValidatorEntryInfo & x_SetEntryInfo()

void x_CheckForStrandChange(SLocCheck &lc)

void ReportMissingBiosource(const CSeq_entry &se)

void ValidatePubdesc(const CPubdesc &pub, const CSerialObject &obj, const CSeq_entry *ctx=nullptr)

void SetNoBioSource(bool val=true)

void SetPatent(bool val=true)

void SetGpipe(bool val=true)

void SetGenomic(bool val=true)

void SetProductLocHasGI(bool val=true)

bool DoesAnyGeneHaveLocusTag() const

void SetPDB(bool val=true)

bool DoesAnyProteinHaveGeneralID() const

void SetProteinHasGeneralID(bool val=true)

void SetGeneious(bool val=true)

void SetNoCitSubPubs(bool val=true)

void SetGeneHasLocusTag(bool val=true)

bool IsNoCitSubPubs() const

bool HasGiOrAccnVer() const

void SetGI(bool val=true)

void SetEmbl(bool val=true)

bool IsLocalGeneralOnly() const

bool DoesAnyFeatLocHaveGI() const

bool DoesAnyProductLocHaveGI() const

void SetSeqSubmit(bool val=true)

void SetRefSeq(bool val=true)

void SetTPE(bool val=true)

void SetFeatLocHasGI(bool val=true)

void SetGPS(bool val=true)

void SetGenbank(bool val=true)

void SetINSDInSep(bool val=true)

void SetLocalGeneralOnly(bool val=true)

void SetNoPubs(bool val=true)

void SetDdbj(bool val=true)

void SetSmallGenomeSet(bool val=true)

bool IsSmallGenomeSet() const

void SetGED(bool val=true)

void SetGiOrAccnVer(bool val=true)

bool IsNoBioSource() const

Cache various information for one validation run.

const TFeatValue & GetFeatFromCache(const SFeatKey &featKey)

TFeatStrKeyToFeatsCache m_featStrKeyToFeatsCache

AutoPtr< TFeatValue > GetFeatFromCacheMulti(const vector< SFeatKey > &featKeys)

const CPubdescInfo & GetPubdescToInfo(CConstRef< CPubdesc > pub)

TIdToBioseqCache m_IdToBioseqCache

static const CSeqFeatData::ESubtype kAnyFeatSubtype

TPubdescCache m_pubdescCache

CBioseq_Handle GetBioseqHandleFromLocation(CScope *scope, const CSeq_loc &loc, const CTSE_Handle &tse)

static const TFeatValue kEmptyFeatValue

static const CTSE_Handle kEmptyTSEHandle

static const CSeqFeatData::E_Choice kAnyFeatType

std::vector< CMappedFeat > TFeatValue

const TFeatToBioseqValue & GetBioseqsOfFeatCache(const TFeatToBioseqKey &feat_to_bioseq_key, const CTSE_Handle &tse)

const TFeatValue & GetFeatStrKeyToFeats(const SFeatStrKey &feat_str_key, const CTSE_Handle &tse)

TFeatToBioseqCache m_featToBioseqCache

static const CBioseq_Handle kAnyBioseq

const TIdToBioseqValue & GetIdToBioseq(const TIdToBioseqKey &key, const CTSE_Handle &tse)

static const CBioseq_Handle kEmptyBioseqHandle

@ eVal_refseq_conventions

@ eVal_generate_golden_file

@ eVal_collect_locus_tags

@ eVal_report_splice_as_error

@ eVal_locus_tag_general_match

@ eVal_far_fetch_cds_products

@ eVal_new_strain_validation

@ eVal_latlon_check_state

@ eVal_far_fetch_mrna_products

@ eVal_latlon_ignore_water

@ eVal_compare_vdjc_to_cds

static TDbxrefValidFlags IsValidDbxref(const CDbtag &xref, bool is_biosource, bool is_refseq_or_gps)

bool(* TProgressCallback)(CProgressInfo *)

static bool DoesSeqLocContainDuplicateIntervals(const CSeq_loc &loc, CScope &scope)

static bool DoesSeqLocContainAdjacentIntervals(const CSeq_loc &loc, CScope &scope)

static bool IsSeqLocCorrectlyOrdered(const CSeq_loc &loc, CScope &scope)

@ fLabel_Unique

Append a unique tag [V1].

virtual void AddValidErrItem(EDiagSev sev, unsigned int ec, const string &msg, const string &desc, const CSerialObject &obj, const string &acc, const int ver, const string &location=kEmptyStr, const int seq_offset=0)=0

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

static const char si[8][64]

static void chk(int check, const char *fmt,...)

static const struct name_t names[]

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

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

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

static const char location[]

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

#define ITERATE_0_IDX(idx, up_to)

idx loops from 0 (inclusive) to up_to (exclusive)

unsigned int TSeqPos

Type for sequence locations and lengths.

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

@ eDiag_Critical

Critical error message.

void Warning(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

bool BadSeqLocSortOrder(const CBioseq_Handle &bsh, const CSeq_loc &loc)

Returns true if the order of Seq_locs is bad, otherwise, false.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

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.

ESeqLocCheck SeqLocCheck(const CSeq_loc &loc, CScope *scope)

Checks that a CSeq_loc is all on one strand on one CBioseq.

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 GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

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...

CSeq_entry_Handle GetSeq_entryHandle(CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)

Get Seq-entry handle by its blob-id, with possible loading.

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.

vector< CSeq_id_Handle > TId

CSeq_annot::C_Data::E_Choice Which(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

E_Choice Which(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

const CTSE_Handle & GetTSE_Handle(void) const

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

TInst_Topology GetInst_Topology(void) const

bool IsSetInst(void) const

bool IsSetInst_Repr(void) const

bool IsSetClass(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeqFeatData::E_Choice GetFeatType(void) const

bool IsSetInst_Topology(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const TId & GetId(void) const

const TInst & GetInst(void) const

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetByProduct(bool byProduct=true)

Set flag indicating if the features should be searched by their product rather than location.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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 string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

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 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 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 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 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[]

const TAffil & GetAffil(void) const

Get the Affil member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

bool IsSetAffil(void) const

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

bool IsSetAuthors(void) const

not necessarily authors of the paper Check if a value has been assigned to Authors data member.

const TName & GetName(void) const

Get the Name member data.

list< CRef< CAuthor > > TStd

const TStd & GetStd(void) const

Get the variant data.

const TNames & GetNames(void) const

Get the Names member data.

bool IsStd(void) const

Check if variant Std is selected.

TGenome GetGenome(void) const

Get the Genome member data.

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSetGenome(void) const

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

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.

bool IsSetDb(void) const

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

bool IsLim(void) const

Check if variant Lim is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

bool IsSetTag(void) const

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

bool IsName(void) const

Check if variant Name is selected.

const TDb & GetDb(void) const

Get the Db member data.

TLim GetLim(void) const

Get the variant data.

bool IsSetLast(void) const

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

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TType & GetType(void) const

Get the Type member data.

const TFirst & GetFirst(void) const

Get the First member data.

const TLast & GetLast(void) const

Get the Last member data.

const TName & GetName(void) const

Get the variant data.

bool IsSetFirst(void) const

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

vector< CRef< CUser_field > > TData

TId GetId(void) const

Get the variant data.

@ eLim_circle

artificial break at origin of circle

@ eLim_tl

space to left of position

@ eLim_tr

space to right of position

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

vector< CRef< CDbtag > > TDb

const TDb & GetDb(void) const

Get the Db member data.

list< CRef< CPub > > TPub

E_Choice Which(void) const

Which variant is currently selected.

TDim GetDim(void) const

Get the Dim member data.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

bool IsSetSegs(void) const

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

bool IsSetType(void) const

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

TType GetType(void) const

Get the Type member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetData(void) const

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

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

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 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.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool CanGetExcept_text(void) const

Check if it is safe to call GetExcept_text method.

bool IsSetId(void) const

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

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

const TGene & GetGene(void) const

Get the variant data.

TExcept GetExcept(void) const

Get the Except member data.

bool IsSetLocation(void) const

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

@ e_not_set

No variant selected.

@ e_Pub

publication applies to this seq

const TFuzz_from & GetFuzz_from(void) const

Get the Fuzz_from member data.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

bool IsSetAccession(void) const

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

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetPoint(void) const

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

TPoint GetPoint(void) const

Get the Point member data.

bool IsOther(void) const

Check if variant Other is selected.

const TFuzz_to & GetFuzz_to(void) const

Get the Fuzz_to member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetFuzz(void) const

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

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

TVersion GetVersion(void) const

Get the Version member data.

E_Choice

Choice variants.

const TOther & GetOther(void) const

Get the variant data.

bool IsSetTo(void) const

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

bool IsSetStrand(void) const

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

bool IsSetFuzz_to(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

TTo GetTo(void) const

Get the To member data.

bool IsSetFrom(void) const

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

bool IsSetVersion(void) const

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

bool IsSetFuzz_from(void) const

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

E_Choice

Choice variants.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

const TTitle & GetTitle(void) const

Get the Title member data.

const TLoc & GetLoc(void) const

Get the Loc member data.

bool IsSetTitle(void) const

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

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSetClass(void) const

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

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetSeq_set(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

TSeq & SetSeq(void)

Select the variant.

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_wgs_set

whole genome shotgun project

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_genbank

converted genbank

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

@ e_not_set

No variant selected.

TTopology GetTopology(void) const

Get the Topology member data.

ETopology

topology of molecule

bool IsSetTopology(void) const

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

@ eRepr_seg

segmented sequence

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_wgs

whole genome shotgun sequencing

@ e_User

user defined object

@ e_Source

source of materials, includes Org-ref

@ eMol_not_set

> cdna = rna

@ eMol_na

just a nucleic acid

bool IsSetTool(void) const

tool used to make submission Check if a value has been assigned to Tool data member.

const TTool & GetTool(void) const

Get the Tool member data.

const TContact & GetContact(void) const

Get the Contact member data.

const TReldate & GetReldate(void) const

Get the Reldate member data.

const TCit & GetCit(void) const

Get the Cit member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetReldate(void) const

release by date Check if a value has been assigned to Reldate data member.

const TData & GetData(void) const

Get the Data member data.

bool IsSetHup(void) const

hold until publish Check if a value has been assigned to Hup data member.

THup GetHup(void) const

Get the Hup member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsSetSub(void) const

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

const TContact & GetContact(void) const

Get the Contact member data.

bool IsSetCit(void) const

citation for this submission Check if a value has been assigned to Cit data member.

bool IsSetContact(void) const

who to contact Check if a value has been assigned to Contact data member.

bool IsSetContact(void) const

WARNING: this will replace the above Check if a value has been assigned to Contact data member.

Lightweight interface for getting lines of data with minimal memory copying.

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

const string version

version string

const struct ncbi::grid::netcache::search::fields::KEY key

Static variables safety - create on demand, destroy on application termination.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

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

#define FOR_EACH_DESCRIPTOR_ON_BIOSEQ

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define FOR_EACH_GBQUAL_ON_FEATURE

#define FOR_EACH_SEQENTRY_ON_SEQSET(Itr, Var)

FOR_EACH_SEQENTRY_ON_SEQSET EDIT_EACH_SEQENTRY_ON_SEQSET.

#define FOR_EACH_SEQDESC_ON_SEQENTRY(Itr, Var)

FOR_EACH_SEQDESC_ON_SEQENTRY EDIT_EACH_SEQDESC_ON_SEQENTRY.

#define FOR_EACH_CHAR_IN_STRING(Itr, Var)

FOR_EACH_CHAR_IN_STRING EDIT_EACH_CHAR_IN_STRING.

#define BEGIN_COMMA_END(container)

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

bool operator==(const SFeatKey &rhs) const

CSeqFeatData::E_Choice feat_type

bool operator<(const SFeatKey &rhs) const

CSeqFeatData::ESubtype feat_subtype

EFeatKeyStr m_eFeatKeyStr

bool operator<(const SFeatStrKey &rhs) const

bool operator==(const SFeatStrKey &rhs) const

PQuickStringLess implements an ordering of strings, that is more efficient than usual lexicographical...

#define FOR_EACH_SEQENTRY_ON_SEQSUBMIT(Itr, Var)

FOR_EACH_SEQENTRY_ON_SEQSUBMIT EDIT_EACH_SEQENTRY_ON_SEQSUBMIT.

bool BarcodeTestFails(const SBarcode &b)

vector< SBarcode > TBarcodeResults

TBarcodeResults GetBarcodeValues(CSeq_entry_Handle seh)

const int InferenceAccessionCutoff

const string kMissingPrimers

static bool s_IsPhage(const COrg_ref &org)

#define ADD_BARCODE_ERR(TestName)

const string kBadCollectionDate

const string kMissingCountry

bool s_HasTopSetSiblings(CSeq_entry_Handle seh)

static const char * kSpaceLeftFirst

static const char * kSpaceLeftCircle

size_t s_CountTopSetSiblings(const CSeq_entry &se)

bool s_IsGoodTopSetClass(CBioseq_set::EClass set_class)

static bool s_SeqLocHasGI(const CSeq_loc &loc)

static const EErrType sc_ValidGenomeRaiseExceptEmblDdbj[]

DEFINE_STATIC_ARRAY_MAP(CStaticArraySet< EErrType >, sc_GenomeRaiseArray, sc_ValidGenomeRaise)

unsigned int s_CountMix(const CSeq_loc &loc)

static void s_CollectPubDescriptorLabels(const CSeq_entry &se, vector< TEntrezId > &pmids, vector< TEntrezId > &muids, vector< int > &serials, vector< string > &published_labels, vector< string > &unpublished_labels)

static const char * kSpaceRightCircle

const string kMissingVoucher

const string kMissingOrderAssignment

static const EErrType sc_ValidGenomeRaise[]

static const char * kSpaceRightLast

const string kStructuredVoucher

static const EErrType sc_ValidGenomeRaiseExceptEmblDdbjRefSeq[]

static CS_CONTEXT * context

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