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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/source__item_8cpp_source.html below:

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

m_Taxname(&scm_Unknown), m_Common(&

),

m_Organelle(&

), m_Lineage(scm_Unclassified),

m_SourceLine(&

), m_Mod(&scm_EmptyList), m_Taxid(kInvalidTaxid),

m_UsingAnamorph(

)

m_Taxname(&scm_Unknown), m_Common(&

),

m_Organelle(&

), m_Lineage(scm_Unclassified),

m_SourceLine(&

), m_Mod(&scm_EmptyList), m_Taxid(kInvalidTaxid),

m_UsingAnamorph(

)

(

.IsProt()) {

(

.Config().IsFormatDDBJ() ) {

(

.IsProt()) {

(

.Config().IsFormatDDBJ() ) {

*com =

, *acr =

, *syn =

, *ana =

,

*gbacr =

, *gbana =

, *gbsyn =

, *met =

;

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

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

( (*mod)->CanGetSubtype() && (*mod)->CanGetSubname() ) {

( (*mod)->GetSubtype() ) {

com = &((*mod)->GetSubname());

acr = &((*mod)->GetSubname());

syn = &((*mod)->GetSubname());

ana = &((*mod)->GetSubname());

gbacr = &((*mod)->GetSubname());

gbana = &((*mod)->GetSubname());

gbsyn = &((*mod)->GetSubname());

met = &((*mod)->GetSubname());

}

(

->empty() && syn) {

}

(

->empty() && acr) {

}

(

->empty() && ana) {

}

(

->empty() && com) {

}

(

->empty() && gbsyn) {

}

(

->empty() && gbacr) {

}

(

->empty() && gbana) {

User-defined methods of the data storage class.

void x_SetObject(const CSerialObject &obj)

namespace ncbi::objects::

Base class for all serializable objects.

const string * m_SourceLine

EItem GetItemType() const override

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

const list< string > * m_Mod

static const string scm_Unclassified

static const list< string > scm_EmptyList

void x_GatherInfo(CBioseqContext &ctx) override

void x_SetSource(const CGB_block &gb, const CSeqdesc &desc)

static const TTaxid kInvalidTaxid

CSourceItem(CBioseqContext &ctx)

static const string scm_Unknown

const string * m_Organelle

virtual void FormatSource(const CSourceItem &keys, IFlatTextOStream &text_os)=0

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CConstRef< CSeq_feat > GetSourceFeatForProduct(const CBioseq_Handle &bsh)

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

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 bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ eNocase

Case insensitive compare.

const TSource & GetSource(void) const

Get the Source member data.

bool CanGetSource(void) const

Check if it is safe to call GetSource method.

TGenome GetGenome(void) const

Get the Genome member data.

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

bool CanGetGenome(void) const

Check if it is safe to call GetGenome method.

const TOrg & GetOrg(void) const

Get the Org member data.

const TMod & GetMod(void) const

Get the Mod member data.

const TLineage & GetLineage(void) const

Get the Lineage member data.

bool CanGetCommon(void) const

Check if it is safe to call GetCommon method.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TCommon & GetCommon(void) const

Get the Common member data.

bool CanGetTaxname(void) const

Check if it is safe to call GetTaxname method.

bool CanGetLineage(void) const

Check if it is safe to call GetLineage method.

list< CRef< COrgMod > > TMod

bool CanGetOrgname(void) const

Check if it is safe to call GetOrgname method.

const TMod & GetMod(void) const

Get the Mod member data.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_gb_acronym

used by taxonomy database

@ eSubtype_gb_synonym

used by taxonomy database

@ eSubtype_metagenome_source

@ eSubtype_gb_anamorph

used by taxonomy database

const TData & GetData(void) const

Get the Data member data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

const TSource & GetSource(void) const

Get the variant data.

const TGenbank & GetGenbank(void) const

Get the variant data.

@ e_Genbank

GenBank specific info.

@ e_Source

source of materials, includes Org-ref

void AddPeriod(string &str)

static const string s_organelle_prefix[]

static const string s_old_organelle_prefix[]

static const unsigned int s_organelle_prefix_size

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