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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/accession__item_8cpp_source.html below:

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

83 if

ctx

.GetPrimaryId()) {

92 if

ctx

.GetLocation().IsWhole()) {

100 if

((

id

.IsGeneral() ||

id

.IsLocal()) &&

101

(

ctx

.Config().IsModeEntrez() ||

ctx

.Config().IsModeGBench())) {

110 size_t

nz_len = (

m_Accession

.substr(0,3) ==

"NZ_"

? 3 : 0);

111 if

(acclen >= 12+nz_len) {

112 size_t

pos =

m_Accession

.find_first_of(

"0123456789"

);

113 if

(pos == 4+nz_len || pos == 6+nz_len) {

114 size_t

stem_len = pos + 2;

115 size_t

tail_len = acclen - stem_len;

129 if

(

ctx

.GetLocation().IsWhole() ) {

131 const

list<string>* xtra =

nullptr

;

150 const int

kAccessionValidationCutoff = 20;

151 ITERATE

(list<string>, it, *xtra) {

152 if

( xtra->size() >= kAccessionValidationCutoff ) {

162 if

(okay && !

id

.IsOther() && !

id

.IsGpipe()) {

164 if

((*it)->IsGpipe()) {

User-defined methods of the data storage class.

TExtra_accessions m_ExtraAccessions

EItem GetItemType() const override

CConstRef< CSeq_loc > m_Region

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

void x_GatherInfo(CBioseqContext &ctx) override

void x_SetObject(const CSerialObject &obj)

virtual void FormatAccession(const CAccessionItem &acc, 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.

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.

const TExtra_acc & GetExtra_acc(void) const

Get the Extra_acc member data.

const TExtra_accessions & GetExtra_accessions(void) const

Get the Extra_accessions member data.

list< CRef< CSeq_id > > TId

const TGenbank & GetGenbank(void) const

Get the variant data.

const TEmbl & GetEmbl(void) const

Get the variant data.

@ eTech_wgs

whole genome shotgun sequencing

@ e_Embl

EMBL specific information.

@ e_Genbank

GenBank specific info.

constexpr auto sort(_Init &&init)

bool IsValidAccession(const string &accn, EAccValFlag flag=eValidateAcc)

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