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NCBI C++ ToolKit: src/objtools/format/context.cpp Source File

m_pOpticalMapPoints(

),

m_IsDeltaLitOnly(

),

m_IsInNucProt(

),

m_IsJournalScan(

),

m_IsGbGenomeProject(

),

m_IsNcbiCONDiv(

),

m_IsNcbiGenomes(

),

m_IsWGSMaster(

),

m_IsTSAMaster(

),

m_IsTLSMaster(

),

m_ShowGBBSource(

),

m_HasOperon(

),

m_HasMultiIntervalGenes(

),

m_IsGenomeAssembly(

),

m_IsCrossKingdom(

),

m_UsePDBCompoundForComment(

),

m_fUnverified(fUnverified_None),

m_fUnreviewed(fUnreviewed_None),

m_ShowAnnotCommentAsCOMMENT(

),

m_ShowAnnotCommentAsCOMMENT_checked(

),

m_RefCache(

),

m_TLSeqEntryCtx(tlsec)

x_Init(seq, m_FFCtx.GetLocation());

m_PrevHandle(prev_seq),

m_NextHandle(next_seq),

m_pOpticalMapPoints(

),

m_IsDeltaLitOnly(

),

m_IsInNucProt(

),

m_IsGenbank(

),

m_IsJournalScan(

),

m_IsGbGenomeProject(

),

m_IsNcbiCONDiv(

),

m_IsNcbiGenomes(

),

m_IsWGSMaster(

),

m_IsTSAMaster(

),

m_IsTLSMaster(

),

m_ShowGBBSource(

),

m_HasOperon(

),

m_HasMultiIntervalGenes(

),

m_IsGenomeAssembly(

),

m_IsCrossKingdom(

),

m_UsePDBCompoundForComment(

),

m_fUnverified(fUnverified_None),

m_fUnreviewed(fUnreviewed_None),

m_ShowAnnotCommentAsCOMMENT(

),

m_ShowAnnotCommentAsCOMMENT_checked(

),

m_TLSeqEntryCtx(tlsec)

(

.IsGi() &&

.GetGi() ==

) {

loc.

(mapper.

(*user_loc));

}

(loc->

()) {

( ; gene_ci ; ++gene_ci ) {

(! idx)

;

(! bsx)

;

num_super_kingdom = 0;

super_kingdoms_different =

;

super_kingdom_name;

( ; desc_ci; ++desc_ci ) {

& lvl = te.

();

(super_kingdom_name.empty() && te.

()) {

super_kingdom_name = te.

();

super_kingdoms_different =

;

(num_super_kingdom > 1 && super_kingdoms_different) {

( ; biosrc_ci ; ++biosrc_ci ) {

( seq_feat && seq_feat->

() ) {

( ! pFileTrackURLField ) {

pFileTrackURLField = uo.

(

);

( pFileTrackURLField) {

( ! pFileTrackURLField->

().

().empty() ) {

vector< string > & strs = pFileTrackURLField->

().

();

( !

.empty() ) {

( pBaseModURLField) {

( ! pAuthorizedAccessField ||

( feat_loc.

() ) {

TFinStatElem sc_finstat_map[] = {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

}

( field.

().

() ==

&&

field.

().

() ==

)

( field.

().

() ==

)

replace( asn_fin_stat.begin(), asn_fin_stat.end(),

,

);

TFinStatMap::const_iterator new_fin_stat_iter = sc_FinStatMap.find(asn_fin_stat.c_str());

( new_fin_stat_iter != sc_FinStatMap.end() ) {

( ; annot_ci; ++annot_ci ) {

& one_desc = **one_desc_iter;

( ! one_desc.

() ) {

user_obj.

().

() !=

)

& policy_field = **policy_field_iter;

& policy_str = policy_field.

().

();

( policy_str ==

) {

(! idx)

;

(! bsx)

;

bTpaAssemblyPresent =

;

bTpaAssemblyPresent =

;

&

= **id_iter;

(

.Which() ) {

(

.GetPatent().IsSetSeqid()) {

(

.GetGeneral().CanGetDb() ) {

(

(

.GetGeneral().GetDb(),

) ) {

(

&& !acc.empty() ) {

(

&& !acc.empty() ) {

(

&& !acc.empty() ) {

(acc.length() == 6) {

(ch ==

|| ch ==

|| ch ==

|| ch ==

) {

desc ? &desc->

() :

;

( eh && eh.

() ) {

has_seq =

;

( it->IsSeq() && it->GetSeq() ==

) {

( it->IsSet() && it->GetSet().IsSetClass() &&

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

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

(loc.

())

;

((*it)->IsNull()) {

parent_name = parent_name.substr(4);

parent_name.length() == seg_name.length() &&

pos = parent_name.length() - 2;

(

; pos > 0; --pos) {

(parent_name[pos] !=

) {

parent_name.erase(pos + 1);

(sep.

()) {

(

& sid : bsp.

()) {

}

(sep.

()) {

(

& seqentry : bssp.

()) {

(useIndexedFasterSets) {

( ; bioseq_iter; ++bioseq_iter ) {

( ! seqId.

() ) {

( seqId->

() ) {

( entry_handle.

() ) {

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.

bool IsReverse(ENa_strand s)

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const string & GetTaxname(void) const

const COrgName & GetOrgname(void) const

bool IsSetOrgname(void) const

bool IsSetTaxname(void) const

bool IsDeltaLitOnly(void) const

CRef< CSeq_loc_Mapper > m_Mapper

void x_SetLocation(const CSeq_loc *user_loc=nullptr)

CConstRef< CSeq_loc > m_Location

bool x_IsInGPS(void) const

CScope & GetScope(void) const

bool HasMultiIntervalGenes(void) const

bool IsCrossKingdom(void) const

@ fUnreviewed_Unannotated

void x_SetOpticalMapPoints(void)

void SetPDBCompoundForComment(bool value)

bool x_HasOperon(void) const

CSeq_inst::TRepr x_GetRepr(void) const

bool m_ShowAnnotCommentAsCOMMENT

SAnnotSelector & SetAnnotSelector(void)

bool UsingSeqEntryIndex(void) const

TUnreviewed m_fUnreviewed

CBioseqContext(const CBioseq_Handle &seq, CFlatFileContext &ffctx, CMasterContext *mctx=nullptr, CTopLevelSeqEntryContext *tlsec=nullptr)

bool m_UsePDBCompoundForComment

const CFlatFileConfig & Config(void) const

unique_ptr< CPacked_seqpnt > m_pOpticalMapPointsDestroyer

unsigned int m_RefseqInfo

void x_SetDataFromUserObjects(void)

bool x_IsPart(void) const

CSeq_inst::TRepr GetRepr(void) const

CRef< CSeq_id > m_PrimaryId

bool x_HasParts(void) const

void x_SetAuthorizedAccess(const CUser_object &uo)

void x_SetEncode(const CUser_object &uo)

const CPacked_seqpnt * m_pOpticalMapPoints

const CSeq_entry_Handle & GetTopLevelEntry(void) const

bool HasOperon(void) const

bool IsRefSeq(void) const

bool m_HasMultiIntervalGenes

CConstRef< CUser_object > m_Encode

CConstRef< CMolInfo > m_Molinfo

void x_Init(const CBioseq_Handle &seq, const CSeq_loc *user_loc)

bool ShowAnnotCommentAsCOMMENT() const

void x_CheckForShowComments() const

const CMolInfo * x_GetMolInfo(void) const

CSeq_id_Handle GetPreferredSynonym(const CSeq_id &id) const

bool DoContigStyle(void) const

bool x_IsDeltaLitOnly(void) const

void x_SetFiletrackURL(const CUser_object &uo)

void x_SetHasMultiIntervalGenes(void) const

bool m_ShowAnnotCommentAsCOMMENT_checked

void x_SetMapper(const CSeq_loc &loc)

const string & GetTaxname(void) const

Empty string if unavailable.

CMolInfo::TTech GetTech(void) const

const CRef< CSeqEntryIndex > GetSeqEntryIndex(void) const

bool IsSegmented(void) const

bool UsePDBCompoundForComment(void) const

CFlatFileContext & m_FFCtx

bool x_IsInNucProt(void) const

TUnverified m_fUnverified

SIZE_TYPE x_GetPartNumber(void)

string m_AuthorizedAccess

bool HasParts(void) const

void x_SetTaxname(void) const

bool x_IsInSGS(void) const

vector< string > m_BasemodURLs

@ fUnverified_Contaminant

@ fUnverified_SequenceOrAnnotation

@ fUnverified_Misassembled

CRef< CMasterContext > m_Master

const string & GetAccession(void) const

bool IsCrossKingdom(void)

bool HasMultiIntervalGenes(void)

const string & GetTaxname(void)

void SetRefSeqConventions(void)

bool IsStyleNormal(void) const

bool IsStyleContig(void) const

CFlatFileConfig & SetConfig(void)

const CSeq_loc * GetLocation(void) const

CMasterContext(const CBioseq_Handle &master)

SIZE_TYPE GetPartNumber(const CBioseq_Handle &part)

CRef< CBioseqIndex > GetBioseqIndex(void)

namespace ncbi::objects::

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

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

bool m_CanSourcePubsBeFused

void x_InitSeqs(const CSeq_entry &sep)

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

@ eObjectType_StructuredComment

bool IsUnverifiedMisassembled() const

bool IsUnverifiedOrganism() const

bool IsUnverifiedContaminant() const

bool IsUnverifiedFeature() const

bool IsUnreviewedUnannotated() const

EObjectType GetObjectType() const

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

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

CRange< Position > Map(const CRange< Position > &target, const CRange< Position > &range)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

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

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

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

EAccessionInfo

For IdentifyAccession (below)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

@ eContent

Untagged human-readable accession or the like.

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

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.

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

Retrieve the Bioseq Handle from a location.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

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

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

CSeq_loc_Mapper_Base & SetMergeAbutting(void)

Merge only abutting intervals, keep overlapping.

CSeq_loc_Mapper_Base & SetGapRemove(void)

@ eSeqMap_Up

map from segments to the top level bioseq

vector< CSeq_id_Handle > TId

TClass GetClass(void) const

const TInst_Ext & GetInst_Ext(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool CanGetClass(void) const

bool IsSetInst_Ext(void) const

TInst_Mol GetInst_Mol(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.

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const CSeq_annot::TDesc & Seq_annot_GetDesc(void) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of 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.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetExactComplexityLevel(CBioseq_set::EClass cls) const

Return level with exact complexity, or empty handle if not found.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const TId & GetId(void) const

bool Seq_annot_IsSetDesc(void) const

CConstRef< CSeq_entry > GetSeq_entryCore(void) const

Get const reference to the seq-entry.

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

CSeqMap_CI BeginResolved(CScope *scope) const

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#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

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 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 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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsSetData(void) const

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

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 TStrs & GetStrs(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

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 TData & GetData(void) const

Get the Data member 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.

vector< CRef< CUser_field > > TData

TFixed_level GetFixed_level(void) const

Get the Fixed_level 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 Tdata & Get(void) const

Get the member data.

const TName & GetName(void) const

Get the Name member data.

list< CRef< CTaxElement > > Tdata

bool IsSetLevel(void) const

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

const TPartial & GetPartial(void) const

Get the variant data.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSetName(void) const

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

bool IsSetData(void) const

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

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

bool IsSetLocation(void) const

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

bool IsGenbank(void) const

Check if variant Genbank is selected.

bool IsSetAccession(void) const

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

bool IsTpg(void) const

Check if variant Tpg is selected.

const TName & GetName(void) const

Get the Name member data.

bool IsSetPoint(void) const

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

const TPnt & GetPnt(void) const

Get the variant data.

bool IsTpd(void) const

Check if variant Tpd is selected.

TPoint GetPoint(void) const

Get the Point member data.

bool CanGetName(void) const

Check if it is safe to call GetName method.

bool IsEmbl(void) const

Check if variant Embl is selected.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

E_Choice

Choice variants.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsNull(void) const

Check if variant Null is selected.

bool IsTpe(void) const

Check if variant Tpe is selected.

const TAccession & GetAccession(void) const

Get the Accession member data.

bool IsDdbj(void) const

Check if variant Ddbj is selected.

@ 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.

@ e_Equiv

equivalent sets of locations

const TSeq & GetSeq(void) const

Get the variant data.

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 CanGetClass(void) const

Check if it is safe to call GetClass method.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

@ eClass_parts

parts for 2 or 3

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

@ eClass_segset

segmented sequence + parts

@ eClass_small_genome_set

viral segments or mitochondrial minicircles

const TSeg & GetSeg(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

ERepr

representation class

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

const TMap & GetMap(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

const TUser & GetUser(void) const

Get the variant data.

list< CRef< CSeq_id > > TId

bool IsSeg(void) const

Check if variant Seg is selected.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

const TDelta & GetDelta(void) const

Get the variant data.

bool IsUser(void) const

Check if variant User is selected.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_loc > > Tdata

const TMolinfo & GetMolinfo(void) const

Get the variant data.

list< CRef< CAnnotdesc > > Tdata

@ eRepr_const

constructed sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_map

ordered map of any kind

@ eRepr_raw

continuous sequence

@ eRepr_virtual

no seq data

@ eTech_targeted

targeted locus sets/studies

@ eTech_tsa

transcriptome shotgun assembly

@ e_User

user defined object

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

const GenericPointer< typename T::ValueType > T2 value

static void s_GetNameForBioseq(const CBioseq_Handle &seq, string &name)

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define FOR_EACH_SEQFEAT_ON_MAPEXT(Itr, Var)

SEQANNOT_IS_SEQFEAT.

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define FOR_EACH_STRING_IN_VECTOR(Itr, Var)

FOR_EACH_STRING_IN_VECTOR EDIT_EACH_STRING_IN_VECTOR.

#define ASSIGN_IF_SET_ELSE_RESET(DestVar, DestFld, SrcVar, SrcFld)

ASSIGN_IF_SET_ELSE_RESET.

#define CLONE_IF_SET_ELSE_RESET(DestVar, DestFld, SrcVar, SrcFld)

CLONE_IF_SET base macro (Useful to copy and object from a variable of one type to a variable of anoth...

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

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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