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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/feature__item_8hpp_source.html below:

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

: m_Key(

), m_Loc(&loc), m_Feat(feat) { }

vector<CRef<CFormatQual> >

;

&

(

)

{

m_Key; }

m_Feat < f2.

;

suppressAccession =

);

EMapped mapped = eMapped_not_mapped,

suppressAccession =

,

GetKey(

)

;

(

)

{

m_Mapped != eMapped_not_mapped; }

x_AddQualDbXref(

x_AddQualCitation();

x_AddQualProtDesc(

* );

x_AddQualProtActivity(

* );

x_AddRptUnitQual(

& rpt_unit);

x_AddRptTypeQual(

& rpt_type,

check_qual_syntax);

x_AddRegulatoryClassQual(

& regulatory_class,

check_qual_syntax);

x_AddRecombinationClassQual(

& recombination_class,

check_qual_syntax);

x_SeqIdWriteForTable(

& seq,

suppress_local,

giOK);

x_AddFTableProtQuals(

& prot_ref);

x_AddFTableBiosrcQuals(

& src);

kProteinId =

;

kTranscriptId =

;

}

(

(name,

)) {

kTranscriptId;

m_Quals.AddQual(slot,

);

m_Quals.RemoveQuals(slot);

m_Quals.HasQual(slot);

&

(m_Quals).LowerBound(slot);

x_DropIllegalQuals(

)

;

x_HasMethodtRNAscanSE(

)

;

( ! gene_ref || ! gene_ref->

() ) {

(

)

{

m_WasDesc; }

m_Feat.GetData().GetBiosrc();

(

)

{

; }

(

)

{

m_IsFocus; }

m_Quals.AddQual(slot,

);

CRef< feature::CFeatTree > m_Feat_Tree

bool operator<(const CFeatureItemBase &f2) const

virtual void x_AddQuals(CBioseqContext &ctx)=0

virtual string GetKey(void) const

const CMappedFeat & GetFeat(void) const

const CSeq_loc & GetLoc(void) const

bool IsSuppressAccession(void) const

virtual void x_FormatQuals(CFlatFeature &ff) const =0

CConstRef< CSeq_loc > m_Loc

void Format(IFormatter &formatter, IFlatTextOStream &text_os) const

void x_AddQual(EFeatureQualifier slot, const IFlatQVal *value)

bool IsMappedFromProt(void) const

void x_AddQualDb(const CGene_ref *)

void x_AddQualsExt(const CUser_field &field, const CSeq_feat::TExt &ext)

vector< CRef< CFormatQual > > TQualVec

void x_AddFTableQual(const string &name, const string &val=kEmptyStr, CFormatQual::ETrim trim=CFormatQual::eTrim_Normal)

CConstRef< CGene_ref > m_GeneRef

bool IsMappedFromGenomic(void) const

void x_RemoveQuals(EFeatureQualifier slot) const

TQuals::const_iterator TQCI

IFlatQVal::TFlags TQualFlags

void x_AddQualsGb(CBioseqContext &)

CQualContainer< EFeatureQualifier > TQuals

void x_AddQuals(CBioseqContext &ctx) override

void x_AddQualsIdx(CBioseqContext &ctx)

const string & x_GetFtableNameAlias(const string &name)

void x_AddQuals(const CProt_ref &prot)

CSeqFeatData::ESubtype m_Type

void x_ImportQuals(CBioseqContext &ctx)

bool IsMappedFromCDNA(void) const

void x_AddQualsRecombinationClass(CBioseqContext &ctx, CSeqFeatData::ESubtype subtype)

TQCI x_GetQual(EFeatureQualifier slot) const

bool IsMapped(void) const

bool x_HasQual(EFeatureQualifier slot) const

const CFlatSeqLoc & GetLoc(void) const

const TQuals & GetQuals(void) const

vector< CRef< CFormatQual > > TQuals

const CMappedFeat & GetFeat(void) const

CFlatFeature(const string &key, const CFlatSeqLoc &loc, const CMappedFeat &feat)

const string & GetKey(void) const

CConstRef< CFlatSeqLoc > m_Loc

void x_SetObject(const CSerialObject &obj)

virtual void Format(IFormatter &formatter, IFlatTextOStream &text_os) const =0

virtual void x_GatherInfo(CBioseqContext &)

TQualMMap::iterator iterator

TQualMMap::const_iterator const_iterator

EQualifier

List of available qualifiers for feature keys.

namespace ncbi::objects::

Base class for all serializable objects.

const CBioSource & GetSource(void) const

TQuals::const_iterator TQCI

void x_AddQual(ESourceQualifier slot, const IFlatQVal *value) const

bool IsSynthetic(void) const

CQualContainer< ESourceQualifier > TQuals

void SetObject(const CSerialObject &obj)

IFlatQVal::TFlags TQualFlags

string GetKey(void) const override

void x_FormatNoteQual(ESourceQualifier slot, const char *name, CFlatFeature::TQuals &qvec, TQualFlags flags=0) const

CRef< feature::CFeatTree > m_Feat_Tree

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

virtual EItem GetItemType(void) const =0

virtual void FormatFeature(const CFeatureItemBase &feat, IFlatTextOStream &text_os)=0

virtual void FormatFeatHeader(const CFeatHeaderItem &fh, IFlatTextOStream &text_os)=0

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

const CPub_set & GetCit(void) const

const CUser_object & GetExt(void) const

bool IsSetQual(void) const

bool IsSetExt(void) const

bool IsSetCit(void) const

#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 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.

#define NCBI_FORMAT_EXPORT

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

const TDb & GetDb(void) const

Get the Db member data.

vector< CRef< CDbtag > > TDbxref

EPsec_str

protein secondary structure

E_Choice

Choice variants.

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

const GenericPointer< typename T::ValueType > T2 value

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

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