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

m_Idx->x_Initialize(topseh, policy,

);

(bsx->IsFetchFailure()) {

(

*

(

.GetPointer()));

( (*it).Which() ) {

.GetBestChoice();

= (*it).AsString();

(

& annt : bsp.

()) {

(annt->IsFtable()) {

(

& feat : annt->GetData().GetFtable()) {

}

(feat->IsSetCit()) {

}

(sep.

()) {

(

& seqentry : bssp.

()) {

(

& annt : bssp.

()) {

(annt->IsFtable()) {

(

& feat : annt->GetData().GetFtable()) {

}

(feat->IsSetCit()) {

(

> 0)

;

hasLoc =

;

( (*it)->IsLoc() ) {

& loc = (*it)->GetLoc();

(loc.

())

;

(sid.Which()) {

(sid.Which()) {

& tsid = *

->GetTextseq_Id ();

& gen_id =

->GetGeneral ();

(oid.

()) {

}

(oid.

()) {

(!

.IsRsite())

;

(rsite.

()) {

resolveCount = 0;

idxl = idx.

();

resolveCount = idxl->GetGapDepth();

start = gap_it.GetPosition();

end = gap_it.GetEndPosition();

length = gap_it.GetLength();

( gap_it.IsSetData() && gap_it.GetData().IsGap() ) {

pGap = &gap_it.GetData().GetGap();

( pSeqLiteral && pSeqLiteral->IsSetSeq_data() ) {

& seq_data = pSeqLiteral->GetSeq_data();

( seq_data.

() ) {

pGap = &seq_data.

();

isUnknownLength = gap_it.IsUnknownLength();

isAssemblyGap = ( !

.empty() || ! evidence.empty() );

virus_or_phage,

(has_plasmid || wgs_suffix) {

=

;

=

;

=

;

=

;

(! virus_or_phage) {

(has_plasmid || wgs_suffix) {

(! virus_or_phage) {

=

;

=

;

=

;

(taxname.empty()) {

*common = 0;

(pon.

()) {

& lvl = te.

();

*com = 0, *acr = 0, *syn = 0, *ana = 0,

*gbacr = 0, *gbana = 0, *gbsyn = 0, *met = 0;

numcom = 0, numacr = 0, numsyn = 0, numana = 0,

numgbacr = 0, numgbana = 0, numgbsyn = 0, nummet = 0;

& omd = **omd_itr;

}

( syn != 0 ) {

}

( acr != 0 ) {

}

( ana != 0 ) {

}

( com != 0 ) {

}

( gbsyn != 0 ) {

}

( gbacr != 0 ) {

}

( gbana != 0 ) {

}

( common != 0 ) {

virus_or_phage =

;

has_plasmid =

;

wgs_suffix =

;

virus_or_phage =

;

has_plasmid =

;

list <string> *keywords =

;

num_super_kingdom = 0;

super_kingdoms_different =

;

(sd.

()) {

(! pon.

())

;

& lvl = te.

();

num_super_kingdom++;

super_kingdoms_different =

;

(num_super_kingdom > 1 && super_kingdoms_different) {

(

|| desc_it.GetSeq_entry_Handle().IsSeq() ) {

(

(

,

) != string::npos) {

& gbk = desc_it->GetGenbank();

(keywords !=

) {

& clause = *kw_itr;

&

= *k_itr;

snpOK =

;

cddOK =

;

idxl = idx.

();

(*func) (bsh, na_acc);

(na_acc.length() > 0) {

idxl = idx.

();

featDepth = idxl->GetFeatDepth();

(featDepth > 0) {

onlyGeneRNACDS =

;

onlyGeneRNACDS =

;

idxl = idx.

();

seq_id.

( *bsid );

old_loc.

().SetId( seq_id );

old_loc.

().SetFrom( 0 );

(; feat_it; ++feat_it) {

(onlyGeneRNACDS) {

gapIsSame =

;

prev_loc = feat_loc;

(loc.

()) {

idxl->SetHasOperon(

);

(prot_length > longest) {

longest = prot_length;

bestprocessed = processed;

}

(prot_length == longest) {

(processed < bestprocessed) {

longest = prot_length;

bestprocessed = processed;

idxl = idx.

();

idxl = idx.

();

idxl->HasOperon();

(to < 0 || to >= (

) vec.

()) {

&

,

vector<string>& evidence,

isUnknownLength,

m_GapEvidence(evidence),

m_IsUnknownLength(isUnknownLength),

m_IsAssemblyGap(isAssemblyGap)

bsxl = bsx.

();

idxl = idx.

();

feature::CFeatTree::eBestGene_TreeOnly);

bsxl->GetFeatIndex(best);

bsxl = bsx.

();

idxl = idx.

();

bsxl->GetFeatIndex(best);

bsxl = bsx.

();

bsxl->SetFetchFailure(fails);

bsxl = bsx.

();

(bsxl->HasSource()) {

idxl = idx.

();

bsxl->GetFeatIndex(best);

bsxl = bsx.

();

(to < 0 || to >= (

) vec.

()) {

* src =

.c_str();

(

(*src) < 128) {

= sc_ExtraTranslations.find(character);

(it != sc_ExtraTranslations.end()) {

utf8::SUnicodeTranslation* translation =

(translation->Subst !=

) {

dst += translation->Subst;

(iter != sc_StopWords.end());

= (

) dst.length();

(;

> 0;

--) {

(ch !=

&& ch !=

&& ch !=

&& ch !=

) {

(;

> 0;

--) {

ch = dst[

-1];

(ch !=

&& ch !=

&& ch !=

&& ch !=

) {

dst.erase(

-1, 1);

(dst[0] ==

&& dst[

-1] ==

) {

dst.erase(

-1, 1);

dst.erase(

-1, 1);

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

*

= ptr;

* src =

.c_str();

(*src ==

|| *src ==

) {

(!

.empty()) {

pair =

+

+ item;

( list<string>, it, terms ) {

(

= 0;

<

.length();

++) {

ch =

[

];

(ch >=

&& ch <=

) {

}

(ch >=

&& ch <=

) {

}

(ch >=

&& ch <=

) {

( list<string>, it, words ) {

nit = std::unique(

.begin(),

.end());

pit = std::unique(

.begin(),

.end());

static CRef< CScope > m_Scope

@ eExtreme_Positional

numerical value

Tracks the best score (lowest value).

bool IsSetCommon(void) const

const string & GetTaxname(void) const

const string & GetCommon(void) const

const COrgName & GetOrgname(void) const

bool IsSetOrgname(void) const

bool IsSetTaxname(void) const

CTempString GetSubstrain(void)

CBioSource::TGenome m_Genome

bool m_FeatForProdInitialized

bool m_IsUnverifiedMisassembled

bool m_BestProtFeatInitialized

vector< CRef< CFeatureIndex > > m_SfxList

TFeatIndexMap m_FeatIndexMap

CTempString m_SpecimenVoucher

CSeq_inst::TLength GetLength(void) const

CSeq_inst::TTopology m_Topology

string m_SecondSuperKingdom

CRef< CSeqVector > m_SeqVec

CTempString GetCultivar(void)

bool IsForceOnlyNearFeats(void)

CTempString GetMetaGenomeSource(void)

CTempString GetBreed(void)

const vector< CRef< CGapIndex > > & GetGapIndices(void)

CBioseqIndex(CBioseq_Handle bsh, const CBioseq &bsp, CBioseq_Handle obsh, CRef< CSeqsetIndex > prnt, CSeq_entry_Handle tseh, CRef< CScope > scope, CSeqMasterIndex &idx, CSeqEntryIndex::EPolicy policy, CSeqEntryIndex::TFlags flags)

bool m_ForceOnlyNearFeats

bool m_IsUnreviewedUnannotated

CConstRef< CBioSource > m_BioSource

CTempString GetGenus(void)

CMolInfo::TTech GetTech(void)

CRef< CFeatureIndex > GetFeatureForProduct(void)

const vector< CRef< CFeatureIndex > > & GetFeatureIndices(void)

const string & GetLineage(void)

CConstRef< CMolInfo > m_MolInfo

bool m_IsUnverifiedFeature

CTempString GetStrain(void)

bool m_IsUnverifiedContaminant

bool IsHTGSCancelled(void)

CConstRef< CMolInfo > GetMolInfo(void)

CBioseq_Handle GetBioseqHandle(void) const

bool IsUnverifiedFeature(void)

CTempString GetSpecies(void)

CRef< CFeatureIndex > GetFeatIndex(const CMappedFeat &mf)

CConstRef< CBioSource > GetBioSource(void)

string m_FirstSuperKingdom

string GetSecondSuperKingdom(void)

bool IsUsingAnamorph(void)

const string & GetAccession(void) const

CMolInfo::TCompleteness GetCompleteness(void)

CWeakRef< CSeqMasterIndex > GetSeqMasterIndex(void) const

bool IsCrossKingdom(void)

const vector< CRef< CDescriptorIndex > > & GetDescriptorIndices(void)

CSeqEntryIndex::TFlags m_Flags

bool m_IsUnverifiedOrganism

CConstRef< CBioSource > m_DescBioSource

CSeq_inst::TLength m_Length

CTempString GetIsolate(void)

CTempString GetPDBCompound(void)

const string & GetTitle(void)

bool m_HasMultiIntervalGenes

bool IsUnreviewedUnannotated(void)

void GetSelector(SAnnotSelector &sel)

CTempString GetSegment(void)

CTempString GetLinkageGroup(void)

vector< CRef< CDescriptorIndex > > m_SdxList

bool HasMultiIntervalGenes(void)

CMolInfo::TBiomol m_Biomol

const string & GetTaxname(void)

bool m_SourcesInitialized

CWeakRef< CBioseqIndex > GetBioseqForProduct(void)

const string & GetOrganelle(void)

CRef< CFeatureIndex > GetBestProteinFeature(void)

CTempString GetSpecimenVoucher(void)

vector< CRef< CGapIndex > > m_GapList

CSeqEntryIndex::EPolicy m_Policy

CTempString GetClone(void)

CRef< CFeatureIndex > m_BestProteinFeature

CBioSource::TGenome GetGenome(void)

CTempString GetChromosome(void)

bool IsUnverifiedMisassembled(void)

CTempString m_TargetedLocus

CMolInfo::TBiomol GetBiomol(void)

bool IsHTGSUnfinished(void)

CTempString GetPlasmid(void)

string GetFirstSuperKingdom(void)

CTempString m_MetaGenomeSource

void x_DefaultSelector(SAnnotSelector &sel, CSeqEntryIndex::EPolicy policy, CSeqEntryIndex::TFlags flags, bool onlyNear, CScope &scope)

CTempString m_PDBCompound

bool IsUnverifiedContaminant(void)

const string & GetCommon(void)

CMolInfo::TCompleteness m_Completeness

bool IsMultispecies(void)

CRef< CFeatureIndex > m_FeatureForProduct

const string & GetComment(void)

bool IsUnverifiedOrganism(void)

CTempString GetTargetedLocus(void)

CTempString m_LinkageGroup

const string & GetDescTaxname(void)

CSeq_entry * GetParentEntry(void) const

CSeq_entry * GetParentEntry(void) const

bool IsSkippable(void) const

CSeqdesc::E_Choice m_Type

CDescriptorIndex(const CSeqdesc &sd, CBioseqIndex &bsx)

CFeatureIndex(CSeq_feat_Handle sfh, const CMappedFeat mf, CConstRef< CSeq_loc > feat_loc, CBioseqIndex &bsx)

CSeqFeatData::ESubtype m_Subtype

CSeqFeatData::ESubtype GetSubtype(void) const

CRef< CFeatureIndex > GetOverlappingSource(void)

CSeqFeatData::E_Choice GetType(void) const

CRef< CSeqVector > m_SeqVec

CRef< CFeatureIndex > GetBestParent(void)

CRef< CFeatureIndex > GetBestGene(void)

CSeqFeatData::E_Choice m_Type

const CMappedFeat GetMappedFeat(void) const

CConstRef< CSeq_loc > m_Fl

void SetFetchFailure(bool fails)

CConstRef< CSeq_loc > GetMappedLocation(void) const

CWeakRef< CBioseqIndex > GetBioseqIndex(void) const

CGapIndex(TSeqPos start, TSeqPos end, TSeqPos length, const string &type, const vector< string > &evidence, bool isUnknownLength, bool isAssemblyGap, CBioseqIndex &bsx)

const string & GetSomeNumber(void) const

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

CRef< CSeqMasterIndex > m_Idx

bool IsFetchFailure(void)

const vector< CRef< CBioseqIndex > > & GetBioseqIndices(void)

bool DistributedReferences(void)

void SetFeatDepth(int featDepth)

const vector< CRef< CSeqsetIndex > > & GetSeqsetIndices(void)

CSeqEntryIndex(CSeq_entry_Handle &topseh, EPolicy policy=eAdaptive, TFlags flags=fDefault)

bool IsIndexFailure(void)

FAddSnpFunc * GetSnpFunc(void)

void SetGapDepth(int gapDepth)

void SetSnpFunc(FAddSnpFunc *snp)

CRef< CBioseqIndex > GetBioseqIndex(void)

@ eSubtype_bad

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

bool m_DistributedReferences

CSeqEntryIndex::TFlags m_Flags

const vector< CRef< CSeqsetIndex > > & GetSeqsetIndices(void)

CConstRef< CSeq_descr > m_TopDescr

const vector< CRef< CBioseqIndex > > & GetBioseqIndices(void)

bool DistributedReferences(void) const

void x_Initialize(CSeq_entry_Handle &topseh, CSeqEntryIndex::EPolicy policy, CSeqEntryIndex::TFlags flags)

CSeqEntryIndex::EPolicy m_Policy

TAccnIndexMap m_AccnIndexMap

void x_InitSeqs(const CSeq_entry &sep, CRef< CSeqsetIndex > prnt, int level=0)

CConstRef< CSubmit_block > m_SbtBlk

FAddSnpFunc * GetSnpFunc(void)

bool IsFetchFailure(void)

void SetGapDepth(int gapDepth)

CRef< CObjectManager > m_Objmgr

TBestIdIndexMap m_BestIdIndexMap

void SetFeatDepth(int featDepth)

vector< CRef< CBioseqIndex > > m_BsxList

void SetSnpFunc(FAddSnpFunc *snp)

CConstRef< CSeq_entry > m_Tsep

CRef< CBioseqIndex > GetBioseqIndex(void)

vector< CRef< CSeqsetIndex > > m_SsxList

bool IsIndexFailure(void) const

CRef< feature::CFeatTree > m_FeatTree

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

namespace ncbi::objects::

CBioseq_set::TClass m_Class

CBioseq_set::TClass GetClass(void) const

CSeqsetIndex(CBioseq_set_Handle ssh, const CBioseq_set &bssp, CRef< CSeqsetIndex > prnt)

TBase::const_iterator const_iterator

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

TBase::const_iterator const_iterator

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

bool IsUnverifiedMisassembled() const

bool IsUnverifiedOrganism() const

bool IsUnverifiedContaminant() const

bool IsUnverifiedFeature() const

bool IsUnreviewedUnannotated() const

static string TrimMixedContent(const string &str)

static bool IsStopWord(const string &str)

void PopulateWordPairIndex(string str)

string x_AddToWordPairIndex(string item, string prev)

static string TrimPunctuation(const string &str)

static string ConvertUTF8ToAscii(const string &str)

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

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

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

#define FOR_EACH_USERFIELD_ON_USEROBJECT(Itr, Var)

FOR_EACH_USERFIELD_ON_USEROBJECT EDIT_EACH_USERFIELD_ON_USEROBJECT.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

void Set(TValue new_value) THROWS_NONE

Set atomic counter value.

void SetDiagFilter(EDiagFilter what, const char *filter_str)

Set diagnostic filter.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

@ eDiagFilter_All

for all non-FATAL

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

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

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

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

string AsString(void) const

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

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestParentForFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype parent_subtype, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

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

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

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

vector< string > gap_linkage_evidences

A vector representing the linkage-evidences of the gap.

string gap_type

String representing the gap type.

static void GetGapModText(const CSeq_gap &seq_gap, SGapModText &out_gap_mod_text)

Given a CSeq_gap object, this outputs the Gap information.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CSeq_loc_Mapper_Base & TruncateNonmappingRanges(void)

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CBioseq_set_Handle GetBioseq_setHandle(const CBioseq_set &seqset, EMissing action=eMissing_Default)

void SetFuzzOption(TFuzzOption newOption)

@ fFuzzOption_RemoveLimTlOrTr

vector< CSeq_id_Handle > TId

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

TClass GetClass(void) const

const TInst_Ext & GetInst_Ext(void) const

bool IsSetInst_Ext(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

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

bool IsSetInst_Length(void) const

TInst_Topology GetInst_Topology(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

TInst_Length GetInst_Length(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.

bool IsSetInst_Topology(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TId & GetId(void) const

bool IsSetData(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

SAnnotSelector & ExcludeFeatSubtype(TFeatSubtype subtype)

Exclude feature subtype from the search.

CSeq_id_Handle GetProductId(void) const

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & ExcludeFeatType(TFeatType type)

Exclude feature type from the search.

SAnnotSelector & SetMaxSearchSegmentsAction(EMaxSearchSegmentsAction action)

const CSeq_loc & GetLocation(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

SAnnotSelector & SetFeatComparator(IFeatComparator *comparator)

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetMaxSearchTime(TMaxSearchTime max_time)

Set maximum time (in seconds) to search before giving up.

SAnnotSelector & SetFailUnresolved(void)

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

SAnnotSelector & SetMaxSearchSegments(TMaxSearchSegments max_segments)

Set maximum number of empty segments to search before giving up.

SAnnotSelector & ExcludeNamedAnnotAccession(const string &acc)

CSeq_id_Handle GetLocationId(void) const

@ eMaxSearchSegmentsSilent

bool CanGetRange(TSeqPos start, TSeqPos stop) const

Check if the sequence data is available for the interval [start, stop).

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

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

void SetCoding(TCoding coding)

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

TRefType Lock(void) const

Lock the object and return reference to it.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-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 list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static 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 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.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

void clear(void)

Clears the string.

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 string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

const char *const kEmptyCStr

Empty "C" string (points to a '\0').

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

bool IsSetKeywords(void) const

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

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

bool IsSetKeywords(void) const

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

const TCountry & GetCountry(void) const

Get the Country member data.

TGenome GetGenome(void) const

Get the Genome member data.

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

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.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

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

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsSetTag(void) const

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

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

const TStr & GetStr(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

TId GetId(void) const

Get the variant data.

const TLineage & GetLineage(void) const

Get the Lineage member data.

TFixed_level GetFixed_level(void) const

Get the Fixed_level member data.

const TSubname & GetSubname(void) const

Get the Subname member data.

bool IsSetFixed_level(void) const

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

bool IsPartial(void) const

Check if variant Partial is selected.

const TName & GetName(void) const

Get the Name member data.

const TLevel & GetLevel(void) const

Get the Level member data.

bool IsSetName(void) const

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

const TBinomial & GetBinomial(void) const

Get the variant data.

bool CanGetLineage(void) const

Check if it is safe to call GetLineage method.

const Tdata & Get(void) const

Get the member data.

const TName & GetName(void) const

Get the Name member data.

bool IsSetGenus(void) const

required Check if a value has been assigned to Genus data member.

const TSpecies & GetSpecies(void) const

Get the Species member data.

list< CRef< CTaxElement > > Tdata

bool IsSetSubname(void) const

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

bool IsSetLevel(void) const

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

const TGenus & GetGenus(void) const

Get the Genus member data.

const TPartial & GetPartial(void) const

Get the variant data.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetSpecies(void) const

species required if subspecies used Check if a value has been assigned to Species data member.

bool IsSetName(void) const

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

bool IsBinomial(void) const

Check if variant Binomial is selected.

EProcessed

processing status

TProcessed GetProcessed(void) const

Get the Processed member data.

bool IsSetProcessed(void) const

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

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

E_Choice

Choice variants.

const TData & GetData(void) const

Get the Data member data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

@ e_Region

named region (globin locus)

@ e_Pub

publication applies to this seq

@ e_Comment

just a comment

TChain GetChain(void) const

Get the Chain member data.

bool IsSetChain_id(void) const

chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to ...

bool IsSetChain(void) const

Deprecated: 'chain' can't support multiple character PDB chain identifiers (introduced in 2015).

bool IsSetAccession(void) const

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

bool IsSetCit(void) const

patent citation Check if a value has been assigned to Cit data member.

E_Choice Which(void) const

Which variant is currently selected.

TSeqid GetSeqid(void) const

Get the Seqid member data.

E_Choice

Choice variants.

const TChain_id & GetChain_id(void) const

Get the Chain_id member data.

bool IsNull(void) const

Check if variant Null is selected.

bool IsSetSeqid(void) const

number of sequence in patent Check if a value has been assigned to Seqid data member.

const TCit & GetCit(void) const

Get the Cit member data.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ 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_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Tpg

Third Party Annot/Seq Genbank.

@ e_Equiv

equivalent sets of locations

const TSeq & GetSeq(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetAnnot(void) const

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

bool IsSetDescr(void) const

Check if a value has been assigned to Descr 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.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TSeq & SetSeq(void)

Select the variant.

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

bool IsMap(void) const

Check if variant Map is selected.

const TUser & GetUser(void) const

Get the variant data.

ERepr

representation class

const TGap & GetGap(void) const

Get the variant data.

bool IsSetAnnot(void) const

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

const Tdata & Get(void) const

Get the member data.

const TTitle & GetTitle(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TMap & GetMap(void) const

Get the variant data.

const TAnnot & GetAnnot(void) const

Get the Annot member data.

TTech GetTech(void) const

Get the Tech member data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_feat > > Tdata

bool IsDelta(void) const

Check if variant Delta is selected.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

const TDelta & GetDelta(void) const

Get the variant data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

list< CRef< CDelta_seq > > Tdata

bool IsGap(void) const

Check if variant Gap is selected.

const TDescr & GetDescr(void) const

Get the Descr member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

const TComment & GetComment(void) const

Get the variant data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_map

ordered map of any kind

@ eRepr_virtual

no seq data

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Embl

EMBL specific information.

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Genbank

GenBank specific info.

@ e_Comment

a more extensive comment

@ e_Molinfo

info on the molecule and techniques

@ e_Title

a title for this sequence

@ e_Pdb

PDB specific information.

@ e_Source

source of materials, includes Org-ref

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsEntrys(void) const

Check if variant Entrys is selected.

bool CanGetSub(void) const

Check if it is safe to call GetSub method.

bool CanGetData(void) const

Check if it is safe to call GetData method.

unsigned int

A callback function used to compare two keys in a database.

const SUnicodeTranslation * UnicodeToAscii(TUnicode character, const TUnicodeTable *table=NULL, const SUnicodeTranslation *default_translation=NULL)

Convert Unicode character into ASCII string.

size_t UTF8ToUnicode(const char *utf, TUnicode *unicode)

Convert UTF8 into Unicode character.

@ eSkip

Unicode to be skipped in translation. Usually it is combined mark.

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

CStaticArraySet< const char *, PCase_CStr > TStopWords

static const char *const mixedTags[]

NCBI_DEFINE_ERR_SUBCODE_X(11)

static bool s_BlankOrNotSpecialTaxname(string taxname)

CStaticPairArrayMap< utf8::TUnicode, char > TExtraTranslations

static int SkipMixedContent(const char *ptr)

static const TExtraTranslationPair kExtraTranslations[]

static CSeq_id_Handle s_IdxFindBestIdChoice(const CBioseq_Handle::TId &ids)

static const char * x_OrganelleName(TBIOSOURCE_GENOME genome, bool has_plasmid, bool virus_or_phage, bool wgs_suffix)

static string s_IdxGetBestIdString(CBioseq_Handle bsh)

DEFINE_STATIC_ARRAY_MAP(TExtraTranslations, sc_ExtraTranslations, kExtraTranslations)

SStaticPair< utf8::TUnicode, char > TExtraTranslationPair

static int s_IdxSeqIdHandle(const CSeq_id_Handle &idh)

static const char *const idxStopWords[]

void(* FAddSnpFunc)(CBioseq_Handle bsh, string &na_acc)

constexpr auto sort(_Init &&init)

#define NCBI_SEQTOPOLOGY(Type)

#define FOR_EACH_COMPOUND_ON_PDBBLOCK(Itr, Var)

FOR_EACH_COMPOUND_ON_PDBBLOCK EDIT_EACH_COMPOUND_ON_PDBBLOCK.

#define NCBI_GENOME(Type)

@NAME Convenience macros for NCBI objects

#define SWITCH_ON_SUBSOURCE_CHOICE(Var)

SWITCH_ON_SUBSOURCE_CHOICE.

#define NCBI_ORGMOD(Type)

COrgMod definitions.

#define FOR_EACH_ORGMOD_ON_BIOSOURCE(Itr, Var)

FOR_EACH_ORGMOD_ON_BIOSOURCE EDIT_EACH_ORGMOD_ON_BIOSOURCE.

#define SWITCH_ON_ORGMOD_CHOICE(Var)

SWITCH_ON_ORGMOD_CHOICE.

#define FOR_EACH_SUBSOURCE_ON_BIOSOURCE(Itr, Var)

FOR_EACH_SUBSOURCE_ON_BIOSOURCE EDIT_EACH_SUBSOURCE_ON_BIOSOURCE.

#define NCBI_SUBSOURCE(Type)

CSubSource definitions.

CBioSource::TGenome TBIOSOURCE_GENOME

CSeq_id::EAccessionInfo TACCN_CHOICE

#define NCBI_SEQID(Type)

@NAME Convenience macros for NCBI objects

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define FOR_EACH_STRING_IN_LIST(Itr, Var)

FOR_EACH_STRING_IN_LIST EDIT_EACH_STRING_IN_LIST.

#define GET_FIELD(Var, Fld)

GET_FIELD base macro.

This indicates the text of the modifiers of a gap.

Selector used in CSeqMap methods returning iterators.

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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