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NCBI C++ ToolKit: include/objtools/format/context.hpp Source File

UsingSeqEntryIndex(

)

;

(

)

{

m_IsProt; }

(

)

{

!m_IsProt; }

(

)

{

m_HasParts; }

(

)

{

m_IsPart; }

GetTotalNumParts(

)

;

IsSeqIdInSameTopLevelSeqEntry(

& seq_id );

(

)

{

m_IsWGS; }

(

)

{

m_IsTSA; }

(

)

{

m_IsTLS; }

DoContigStyle(

)

;

(

)

{

m_IsInSGS; }

(

)

{

m_IsInGPS; }

(

)

{

m_IsGED; }

(

)

{

m_IsEMBL; }

(

)

{

m_IsDDBJ; }

(

)

{

m_IsPDB; }

(

)

{

m_IsSP; }

(

)

{

m_IsTPA; }

(

)

{

m_IsPatent; }

(

)

{

m_IsRefSeq; }

IsRSCompleteGenomic (

)

;

IsRSIncompleteGenomic(

)

;

IsRSMRna (

)

;

IsRSNonCodingRna (

)

;

IsRSProtein (

)

;

IsRSContig (

)

;

IsRSIntermedWGS (

)

;

IsRSPredictedMRna (

)

;

IsRSPredictedNCRna (

)

;

IsRSPredictedProtein (

)

;

IsRSWGSNuc (

)

;

IsRSWGSProt (

)

;

IsRSUniqueProt (

)

;

IsEncode (

)

;

&GetFinishingStatus(

)

;

IsGenomeAssembly(

)

;

UsePDBCompoundForComment(

)

;

SetPDBCompoundForComment(

);

fUnverified_None = 0,

fUnverified_Organism = 1 << 0,

fUnverified_SequenceOrAnnotation = 1 << 1,

fUnverified_Misassembled = 1 << 2,

fUnverified_Contaminant = 1 << 3

fUnreviewed_None = 0,

fUnreviewed_Unannotated = 1 << 0

ShowAnnotCommentAsCOMMENT()

;

(

)

{

m_IsHup; }

* GetMasterLocation(

)

;

GetSGS(

)

;

IsGenbankFormat(

)

;

HasOperon(

)

;

HasMultiIntervalGenes(

)

;

ThrowIfCanceled(

)

;

& GetTaxname(

)

;

m_pOpticalMapPoints; }

x_SetId(

);

x_HasParts(

)

;

x_IsDeltaLitOnly(

)

;

x_IsPart(

)

;

x_IsInSGS(

)

;

x_IsInGPS(

)

;

x_IsInNucProt(

)

;

x_SetLocation(

* user_loc =

);

x_SetMapper(

& loc);

x_SetHasMultiIntervalGenes(

)

;

x_SetDataFromUserObjects(

);

x_CheckForShowComments()

;

x_SetTaxname(

)

;

x_SetOpticalMapPoints(

);

* x_GetMolInfo(

)

;

x_HasOperon(

)

;

x_SetBaseName(

);

x_SetNumParts(

);

feature::CFeatTree*

(

)

{

m_FeatTree; }

(

)

{

m_SmallGenomeSet; }

(

sgs) { m_SmallGenomeSet = sgs; }

(

().IsFormatGenbank() ||

().IsFormatGBSeq() ||

().IsFormatDDBJ());

User-defined methods of the data storage class.

const TReferences & GetReferences(void) const

bool IsDeltaLitOnly(void) const

CBioseq_Handle m_NextHandle

bool IsRSPredictedNCRna(void) const

CRef< CSeq_loc_Mapper > m_Mapper

const string & GetTSAMasterName(void) const

bool IsNcbiCONDiv(void) const

CBioseq_Handle & GetHandle(void)

CSeq_inst::TMol GetMol(void) const

CConstRef< CSeq_loc > m_Location

bool IsGenomeAssembly(void) const

CMasterContext & GetMaster(void)

CTopLevelSeqEntryContext & GetTLSeqEntryCtx(void)

CScope & GetScope(void) const

bool IsWGSMaster(void) const

bool IsUnverified(void) const

bool IsRSPredictedProtein(void) const

const string & GetTLSMasterAccn(void) const

const string & GetFinishingStatus(void) const

bool CanGetMaster(void) const

bool IsEncode(void) const

bool IsJournalScan(void) const

bool m_ShowAnnotCommentAsCOMMENT

bool IsRSIncompleteGenomic(void) const

SAnnotSelector & SetAnnotSelector(void)

bool UsingSeqEntryIndex(void) const

TUnreviewed m_fUnreviewed

TUnverified GetUnverifiedType(void) const

bool IsTLSMaster(void) const

bool IsRSWGSProt(void) const

const CMolInfo * GetMolinfo(void) const

int GetPatentSeqId(void) const

bool m_UsePDBCompoundForComment

bool IsGbGenomeProject(void) const

const CFlatFileConfig & Config(void) const

vector< TRef > TReferences

CBioseq_Handle & GetPrevHandle(void)

unique_ptr< CPacked_seqpnt > m_pOpticalMapPointsDestroyer

unsigned int m_RefseqInfo

TUnreviewed GetUnreviewedType(void) const

CMolInfo::TBiomol GetBiomol(void) const

bool IsBioseqInSameTopLevelSeqEntry(const CBioseq_Handle &seq)

const CSubmit_block * GetSubmitBlock(void) const

CSeq_inst::TRepr GetRepr(void) const

CRef< CSeq_id > m_PrimaryId

CSeq_loc_Mapper * GetMapper(void)

bool IsRSMRna(void) const

bool IsNcbiGenomes(void) const

bool IsTSAMaster(void) const

bool IsRSIntermedWGS(void) const

CSeq_id * GetPrimaryId(void)

const CPacked_seqpnt * m_pOpticalMapPoints

const string & GetWGSMasterAccn(void) const

const CSeq_entry_Handle & GetTopLevelEntry(void) const

CRef< CReferenceItem > TRef

bool IsRefSeq(void) const

void ThrowIfCanceled(void) const

Checks if CFlatFileConfig has an ICanceled, and throws if it indicates cancellation.

bool IsRSContig(void) const

bool m_HasMultiIntervalGenes

CConstRef< CUser_object > m_Encode

bool ShowGBBSource(void) const

const CBioseq::TId & GetBioseqIds(void) const

CConstRef< CMolInfo > m_Molinfo

TReferences & SetReferences(void)

void SetRefCache(vector< string > *rc)

bool CanGetTLSeqEntryCtx(void) const

bool IsRSNonCodingRna(void) const

CBioseq_Handle x_GetMasterForPart(void) const

const CUser_object & GetEncode(void) const

bool IsRSUniqueProt(void) const

const CPacked_seqpnt * GetOpticalMapPoints(void) const

Empty or NULL if no points or if this bioseq isn't an optical map.

const CSeq_loc & GetLocation(void) const

vector< string > * m_RefCache

bool IsRSProtein(void) const

bool IsRSWGSNuc(void) const

SIZE_TYPE GetTotalNumParts(void) const

bool m_ShowAnnotCommentAsCOMMENT_checked

bool IsGenbank(void) const

SIZE_TYPE GetPartNumber(void) const

const CSeq_loc * GetMasterLocation(void) const

const vector< string > & GetBasemodURLs(void) const

Empty if no Basemod URLs.

bool IsInNucProt(void) const

CMolInfo::TTech GetTech(void) const

const CRef< CSeqEntryIndex > GetSeqEntryIndex(void) const

bool IsSegmented(void) const

void SetMaster(CMasterContext &mctx)

vector< string > * GetRefCache(void) const

const CBioseq_Handle & GetHandle(void) const

CBioseq_Handle & GetNextHandle(void)

CFlatFileContext & m_FFCtx

const string & GetTSAMasterAccn(void) const

const string & GetTLSMasterName(void) const

TUnverified m_fUnverified

string m_AuthorizedAccess

feature::CFeatTree m_FeatTree

bool HasParts(void) const

bool IsRSCompleteGenomic(void) const

vector< string > m_BasemodURLs

const SAnnotSelector * GetAnnotSelector(void) const

bool IsGenbankFormat(void) const

CRef< CTopLevelSeqEntryContext > m_TLSeqEntryCtx

bool IsRSPredictedMRna(void) const

bool IsSeqIdInSameTopLevelSeqEntry(const CSeq_id &seq_id)

CRef< CMasterContext > m_Master

const string & GetWGSMasterName(void) const

feature::CFeatTree & GetFeatTree(void)

CBioseq_Handle m_PrevHandle

const string & GetAuthorizedAccess(void) const

bool IsPatent(void) const

const string & GetFiletrackURL(void) const

Empty if no Filetrack URL.

const string & GetAccession(void) const

void ThrowIfCanceled(void) const

This throws a CFlatException if flatfile generation cancellation has been requested via ICanceled.

CFlatFileConfig & SetConfig(void)

unique_ptr< SAnnotSelector > m_Selector

void SetLocation(const CSeq_loc *loc)

CSeq_entry_Handle m_Entry

const CSubmit_block * GetSubmitBlock(void) const

const SAnnotSelector * GetAnnotSelector(void) const

SAnnotSelector & SetAnnotSelector(void)

const CRef< CSeqEntryIndex > GetSeqEntryIndex(void) const

CFlatFileContext(const CFlatFileConfig &cfg)

void SetSubmit(const CSubmit_block &sub)

CRef< CSeqEntryIndex > m_Idx

CConstRef< CSeq_loc > m_Loc

CRef< feature::CFeatTree > m_FeatTree

void SetSeqEntryIndex(CRef< CSeqEntryIndex > idx)

feature::CFeatTree * GetFeatTree(void)

void ResetSeqEntryIndex(void)

bool UsingSeqEntryIndex(void) const

CRef< CBioseqContext > TSection

CConstRef< CSubmit_block > m_Submit

void SetConfig(const CFlatFileConfig &cfg)

const CSeq_entry_Handle & GetEntry(void) const

vector< CRef< CBioseqContext > > TSections

const feature::CFeatTree * GetFeatTree(void) const

void SetSGS(const bool sgs)

const CFlatFileConfig & GetConfig(void) const

void SetEntry(const CSeq_entry_Handle &entry)

const CSeq_loc * GetLocation(void) const

void SetFeatTree(feature::CFeatTree *tree)

void AddSection(TSection &section)

const string & GetBaseName(void) const

const CBioseq_Handle & GetHandle(void) const

SIZE_TYPE GetNumParts(void) const

CTopLevelSeqEntryContext(const CSeq_entry_Handle &entry_handle, bool useIndexedFasterSets=false)

bool GetHasSmallGenomeSet(void) const

bool GetCanSourcePubsBeFused(void) const

bool m_CanSourcePubsBeFused

void x_InitSeqs(const CSeq_entry &sep)

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

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

EUnverifiedType GetUnverifiedType(const string &value)

@ eAcc_refseq_unique_prot

@ eAcc_refseq_mrna_predicted

@ eAcc_refseq_prot_predicted

@ eAcc_refseq_ncrna_predicted

@ eAcc_refseq_wgs_intermed

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

Get bioseq handle for sequence withing one TSE.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

void Reset(void)

Reset handle and make it not to point to any seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

int64_t Int8

8-byte (64-bit) signed 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.

NCBI_NS_STD::string::size_type SIZE_TYPE

#define NCBI_FORMAT_EXPORT

ERepr

representation class

const TId & GetId(void) const

Get the Id member data.

TTech GetTech(void) const

Get the Tech member data.

list< CRef< CSeq_id > > TId

TBiomol GetBiomol(void) const

Get the Biomol member data.

EMol

molecule class in living organism

@ eRepr_seg

segmented sequence

@ eRepr_delta

sequence made by changes (delta) to others

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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