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NCBI C++ ToolKit: include/objmgr/util/indexer.hpp Source File

fHideIntronFeats = 32,

fGeneRNACDSOnly = 512,

<

Fnc>

IterateBioseqs (Fnc m);

<

Fnc>

IterateSeqsets (Fnc m);

vector<CRef<CBioseqIndex>>& GetBioseqIndices(

);

vector<CRef<CSeqsetIndex>>& GetSeqsetIndices(

);

DistributedReferences(

);

SetFeatDepth(

featDepth);

GetFeatDepth(

);

SetGapDepth(

gapDepth);

GetGapDepth(

);

IsFetchFailure(

);

IsIndexFailure (

);

<

Fnc>

IterateBioseqs (Fnc m);

<

Fnc>

IterateSeqsets (Fnc m);

vector<CRef<CBioseqIndex>>& GetBioseqIndices(

);

vector<CRef<CSeqsetIndex>>& GetSeqsetIndices(

);

SetFeatDepth(

featDepth);

GetFeatDepth(

);

SetGapDepth(

gapDepth);

GetGapDepth(

);

IsFetchFailure(

);

x_Init (

);

<

Fnc>

IterateGaps (Fnc m);

<

Fnc>

IterateDescriptors (Fnc m);

<

Fnc>

IterateFeatures (Fnc m);

<

Fnc>

IterateFeatures (

& slp, Fnc m);

vector<CRef<CGapIndex>>& GetGapIndices(

);

vector<CRef<CDescriptorIndex>>& GetDescriptorIndices(

);

vector<CRef<CFeatureIndex>>& GetFeatureIndices(

);

(

)

{

m_IsNA; }

(

)

{

m_IsAA; }

(

)

{

m_IsDelta; }

(

)

{

m_IsMap; }

(

)

{

m_IsRefSeq; }

(

)

{

m_IsNC; }

(

)

{

m_IsNM; }

(

)

{

m_IsNR; }

(

)

{

m_IsNZ; }

(

)

{

m_IsPatent; }

(

)

{

m_IsPDB; }

(

)

{

m_IsWP; }

& GetTaxname (

);

& GetDescTaxname (

);

IsHTGTech (

);

IsHTGSUnfinished (

);

IsEST_STS_GSS (

);

IsUseBiosrc (

);

& GetCommon (

);

& GetLineage (

);

IsUsingAnamorph (

);

IsMultispecies (

);

IsPlasmid (

);

IsChromosome (

);

& GetOrganelle (

);

GetFirstSuperKingdom (

);

GetSecondSuperKingdom (

);

HasClone (

);

IsHTGSCancelled (

);

IsHTGSDraft (

);

IsHTGSPooled (

);

IsTPAExp (

);

IsTPAInf (

);

IsTPAReasm (

);

IsUnordered (

);

IsForceOnlyNearFeats (

);

IsUnverified (

);

IsUnreviewed (

);

IsUnreviewedUnannotated (

);

& GetComment (

);

IsPseudogene (

);

HasOperon (

);

HasGene (

);

HasMultiIntervalGenes (

);

HasSource (

);

GetrEnzyme (

);

x_InitGaps (

);

x_InitDescs (

);

x_InitFeats (

);

x_InitFeats (

* slpp);

x_InitSource (

);

&

,

vector<string>& evidence,

isUnknownLength,

SetFetchFailure (

fails);

PopulateWordPairIndex (

);

<

Fnc>

IterateNorm (Fnc m);

<

Fnc>

IteratePair (Fnc m);

ConvertUTF8ToAscii(

&

);

TrimPunctuation (

&

);

TrimMixedContent (

&

);

IsStopWord(

&

);

vector<string>&

(

)

{

m_Norm; }

vector<string>&

(

)

{

m_Pair; }

x_AddToWordPairIndex (

item,

);

<

Fnc>

<

Fnc>

<

Fnc>

<

Fnc>

<

Fnc>

<

Fnc>

(

<<

<< e.

());

<

Fnc>

<

Fnc>

<

Fnc>

<

Fnc>

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.

CBioSource::TGenome m_Genome

bool m_FeatForProdInitialized

bool m_IsUnverifiedMisassembled

bool m_BestProtFeatInitialized

int GetPatentSequence(void) const

bool IsFetchFailure(void) const

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

void SetFetchFailure(bool fails)

bool m_ForceOnlyNearFeats

bool m_IsUnreviewedUnannotated

CConstRef< CBioSource > m_BioSource

map< CMappedFeat, CRef< CFeatureIndex > > TFeatIndexMap

CConstRef< CMolInfo > m_MolInfo

bool m_IsUnverifiedFeature

bool IsTSAMaster(void) const

CRef< CScope > GetScope(void) const

bool m_IsUnverifiedContaminant

bool IsThirdParty(void) const

bool IsPatent(void) const

CBioseq_Handle GetBioseqHandle(void) const

CRef< CSeqVector > GetSeqVector(void) const

CRef< CSeqsetIndex > GetParent(void) const

string m_FirstSuperKingdom

size_t IterateGaps(Fnc m)

bool IsWGSMaster(void) const

bool IsTLSMaster(void) const

const string & GetAccession(void) const

int GetPDBChain(void) const

CWeakRef< CSeqMasterIndex > GetSeqMasterIndex(void) const

string GetPatentCountry(void) const

CWeakRef< CSeqMasterIndex > m_Idx

CSeqEntryIndex::TFlags m_Flags

string GetPDBChainID(void) const

bool m_IsUnverifiedOrganism

CConstRef< CBioSource > m_DescBioSource

const CBioseq & GetBioseq(void) const

CSeq_inst::TLength m_Length

CTempString m_UnverifiedPrefix

bool m_HasMultiIntervalGenes

string GetPatentNumber(void) const

vector< CRef< CDescriptorIndex > > m_SdxList

CMolInfo::TBiomol m_Biomol

size_t IterateDescriptors(Fnc m)

size_t IterateFeatures(Fnc m)

CTempString m_UnreviewedPrefix

bool m_SourcesInitialized

CSeq_inst::TTopology GetTopology(void) const

int GetGeneralId(void) const

string GetGeneralStr(void) const

bool IsVirtual(void) const

vector< CRef< CGapIndex > > m_GapList

CSeqEntryIndex::EPolicy m_Policy

CBioseqIndex(const CBioseqIndex &)=delete

CRef< CFeatureIndex > m_BestProteinFeature

CTempString m_TargetedLocus

CTempString m_MetaGenomeSource

bool IsDeltaLitOnly(void) const

CTempString m_PDBCompound

CBioseq_Handle GetOrigBioseqHandle(void) const

bool IsRefSeq(void) const

CMolInfo::TCompleteness m_Completeness

CRef< CSeqsetIndex > m_Prnt

CRef< CFeatureIndex > m_FeatureForProduct

CTempString m_LinkageGroup

CSeqdesc::E_Choice m_Type

CSeqdesc::E_Choice GetType(void) const

CDescriptorIndex(const CDescriptorIndex &)=delete

CWeakRef< CBioseqIndex > GetBioseqIndex(void) const

const CSeqdesc & GetSeqDesc(void) const

CWeakRef< CBioseqIndex > m_Bsx

CSeqFeatData::ESubtype m_Subtype

CSeqFeatData::ESubtype GetSubtype(void) const

CSeqFeatData::E_Choice GetType(void) const

CFeatureIndex(const CFeatureIndex &)=delete

TSeqPos GetStart(void) const

CRef< CSeqVector > GetSeqVector(void) const

CRef< CSeqVector > m_SeqVec

CSeq_feat_Handle GetSeqFeatHandle(void) const

CSeqFeatData::E_Choice m_Type

const CMappedFeat GetMappedFeat(void) const

CConstRef< CSeq_loc > m_Fl

CConstRef< CSeq_loc > GetMappedLocation(void) const

CWeakRef< CBioseqIndex > GetBioseqIndex(void) const

TSeqPos GetEnd(void) const

CWeakRef< CBioseqIndex > m_Bsx

const vector< string > & GetGapEvidence(void) const

const string GetGapType(void) const

CWeakRef< CBioseqIndex > GetBioseqIndex(void) const

bool IsAssemblyGap(void) const

TSeqPos GetLength(void) const

CGapIndex(const CGapIndex &)=delete

TSeqPos GetStart(void) const

vector< string > m_GapEvidence

bool IsUnknownLength(void) const

TSeqPos GetEnd(void) const

CWeakRef< CBioseqIndex > m_Bsx

CRef< CSeqMasterIndex > GetMasterIndex(void) const

CRef< CSeqMasterIndex > m_Idx

size_t IterateBioseqs(Fnc m)

size_t IterateSeqsets(Fnc m)

CSeqEntryIndex(const CSeqEntryIndex &)=delete

bool m_DistributedReferences

CSeqEntryIndex::TFlags m_Flags

bool IsSmallGenomeSet(void) const

CConstRef< CSeq_descr > m_TopDescr

CRef< CObjectManager > GetObjectManager(void) const

CSeqMasterIndex(const CSeqMasterIndex &)=delete

void SetIndexFailure(bool fails)

CConstRef< CSeq_entry > GetTopSEP(void) const

bool DistributedReferences(void) const

CSeqEntryIndex::EPolicy m_Policy

TAccnIndexMap m_AccnIndexMap

CConstRef< CSeq_descr > GetTopDescr(void) const

CConstRef< CSubmit_block > m_SbtBlk

CConstRef< CSubmit_block > GetSbtBlk(void) const

CRef< CObjectManager > m_Objmgr

map< string, CRef< CBioseqIndex > > TAccnIndexMap

bool HasOperon(void) const

TBestIdIndexMap m_BestIdIndexMap

size_t IterateBioseqs(Fnc m)

size_t IterateSeqsets(Fnc m)

map< string, CRef< CBioseqIndex > > TBestIdIndexMap

CSeq_entry_Handle GetTopSEH(void) const

vector< CRef< CBioseqIndex > > m_BsxList

CConstRef< CSeq_entry > m_Tsep

CRef< CScope > GetScope(void) const

CRef< feature::CFeatTree > GetFeatTree(void) const

void SetHasOperon(bool hasOp)

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.

const CBioseq_set & m_Bssp

CRef< CSeqsetIndex > m_Prnt

CBioseq_set_Handle GetSeqsetHandle(void) const

const CBioseq_set & GetSeqset(void) const

CBioseq_set::TClass m_Class

CBioseq_set::TClass GetClass(void) const

CSeqsetIndex(const CSeqsetIndex &)=delete

CRef< CSeqsetIndex > GetParent(void) const

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

const vector< string > & GetPair(void) const

const vector< string > & GetNorm(void) const

CWordPairIndexer(const CWordPairIndexer &)=delete

bool IsCrossKingdom(const COrg_ref &org, string &first_kingdom, string &second_kingdom)

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

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

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

unsigned int TSeqPos

Type for sequence locations and lengths.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

const CMolInfo * GetMolInfo(const CBioseq &bioseq)

Retrieve the MolInfo object for a given bioseq handle.

CObject & operator=(const CObject &src) THROWS_NONE

Assignment operator.

#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.

#define NCBI_XOBJUTIL_EXPORT

E_Choice

Choice variants.

E_Choice

Choice variants.

ETopology

topology of molecule

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

bool IsUnverifiedMisassembled(const CBioseq &seq)

bool IsUnverifiedOrganism(const CBioseq &seq)

bool IsUnverifiedContaminant(const CBioseq &seq)

bool IsUnverifiedFeature(const CBioseq &seq)

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