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

(id->

()) {

(vector<CSeq_id_Handle>, it, unique_ids) {

unique_ids.push_back(idh);

bHtml =

.Config().DoHTML();

(idh.

()) {

vector<CSeq_id_Handle> unique_ids;

(vector<CSeq_id_Handle>, it, unique_ids) {

(cds_seq_id && cds_seq_id->

()) {

replace( it->begin(), it->end(),

,

);

containsHostLine =

;

containsHostLine =

;

.push_back(

);

*

=

;

((*it)->Which()) {

xrefs.push_back(

+ (*it)->GetSeqIdString(

));

( !xrefs.empty() ) {

( ! containsHostLine ) {

.push_back(

);

.push_back(

);

s(

);

s(

);

s(

);

xrefs.push_back(acc);

( !xrefs.empty() ) {

= (

.IsStr() ?

.GetStr()

db = (*it)->GetDb();

(

.Config().DoHTML()) {

+

+

+

+

);

xrefs.push_back(

+

);

(

.substr(0, db.length() + 1) == (db +

) ) {

xrefs.push_back(

);

xrefs.push_back(db +

+

);

(

+

(xrefs,

));

*it += (&*it == &

.back() ?

:

);

s(

);

( !rep.

().empty() ) {

s(

);

*it += (&*it == &

.back() ?

:

);

s(

), sep;

s +=

+ pdb.

().

();

s += sep +

;

s, sep, comma, ht;

is_uniprot =

;

: s =

; is_uniprot =

;

;

s +=

+ tsid->

();

s += comma + sep +

+ ht;

& a_source = *source_iter;

( ! answer.empty() ) {

kMmdbIdPrefix =

;

answer +=

+ url + url_suffix +

;

answer += url_suffix;

& a_source,

& out_url_suffix )

{

m_must_be_all_digits;

} potentialPrefixes[] = {

{

,

,

}

numPotentialPrefixes =

(potentialPrefixes)/

(potentialPrefixes[0]);

(

idx = 0; idx < numPotentialPrefixes; ++idx ) {

& prefix = potentialPrefixes[idx].m_prefix;

& url = potentialPrefixes[idx].m_url;

must_be_all_digits = potentialPrefixes[idx].m_must_be_all_digits;

( a_source.length() <= prefix.length() ) {

string::size_type first_non_space_pos = prefix.length();

( ; first_non_space_pos < a_source.length(); ++first_non_space_pos ) {

( !

(a_source[first_non_space_pos]) ) {

( first_non_space_pos >= a_source.length() ) {

( must_be_all_digits ) {

non_digit_found =

;

string::size_type test_pos = first_non_space_pos;

( ; test_pos < a_source.length(); ++test_pos ) {

( !

(a_source[test_pos]) ) {

non_digit_found =

;

( non_digit_found ) {

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.

User-defined methods of the data storage class.

const CFlatFileConfig & Config(void) const

void x_AddSPBlock(CBioseqContext &ctx)

string x_FormatPDBSource(const CPDB_block &pdb)

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

void x_AddPDBBlock(CBioseqContext &ctx)

bool x_ExtractLinkableSource(const string &a_source, string &out_prefix, string &out_url, string &out_url_suffix)

void x_AddPIRBlock(CBioseqContext &ctx)

void x_GatherInfo(CBioseqContext &ctx) override

string x_FormatDBSourceID(const CSeq_id_Handle &idh)

EItem GetItemType() const override

void x_AddPRFBlock(CBioseqContext &ctx)

CTime AsCTime(CTime::ETimeZone tz=CTime::eLocal) const

const IHTMLFormatter & GetHTMLFormatter() const

CBioseqContext * GetContext(void)

void x_SetObject(const CSerialObject &obj)

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

virtual void FormatDBSource(const CDBSourceItem &dbs, IFlatTextOStream &text_os)=0

virtual void FormatNucId(string &str, const CSeq_id &seq_id, TIntId gi, const string &acc_id) const =0

virtual void FormatUniProtId(string &str, const string &prot_id) const =0

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

static bool s_HasLocalBioseq(const CSeq_loc &loc, const CSeq_entry_Handle &tse)

static void s_FormatDate(const CDate &date, string &str)

static void s_AddToUniqueIdList(const CSeq_id_Handle &idh, vector< CSeq_id_Handle > &unique_ids)

static const CSeq_id_Handle s_FindBestChoiceForDbsource(const CSeq_id_Handle &idh, CScope &scope)

static int s_ScoreForDBSource(const CSeq_id_Handle &idh)

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TPrim & Get(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CSeq_id::E_Choice Which(void) const

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

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,...

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

const CSeq_feat * GetPROTForProduct(const CBioseq &product, CScope *scope)

Get the mature peptide feature of a protein.

@ eGetId_Best

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

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

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

Get bioseq handle for sequence withing one TSE.

vector< CSeq_id_Handle > TId

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TId & GetId(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 IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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

Check if a string starts with a specified prefix value.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ eNocase

Case insensitive compare.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsStr(void) const

Check if variant Str is selected.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

TChain GetChain(void) const

Get the Chain member data.

bool IsSetChain_id(void) const

chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to ...

bool IsSetChain(void) const

Deprecated: 'chain' can't support multiple character PDB chain identifiers (introduced in 2015).

const TName & GetName(void) const

Get the Name member data.

bool CanGetName(void) const

Check if it is safe to call GetName method.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSwissprot(void) const

Check if variant Swissprot is selected.

TGi GetGi(void) const

Get the variant data.

TVersion GetVersion(void) const

Get the Version member data.

bool CanGetVersion(void) const

Check if it is safe to call GetVersion method.

const TMol & GetMol(void) const

Get the Mol member data.

E_Choice

Choice variants.

bool CanGetRel(void) const

Check if it is safe to call GetRel method.

bool CanGetAccession(void) const

Check if it is safe to call GetAccession method.

const TChain_id & GetChain_id(void) const

Get the Chain_id member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

const TRel & GetRel(void) const

Get the Rel member data.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ 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.

const TPdb & GetPdb(void) const

Get the variant data.

const TSp & GetSp(void) const

Get the variant data.

const TPrf & GetPrf(void) const

Get the variant data.

const TPir & GetPir(void) const

Get the variant data.

@ e_Pir

PIR specific info.

@ e_Prf

PRF specific information.

@ e_Sp

SWISSPROT specific info.

@ e_Pdb

PDB specific information.

const TDate & GetDate(void) const

Get the Date member data.

const TSource & GetSource(void) const

Get the Source member data.

const TExp_method & GetExp_method(void) const

Get the Exp_method member data.

bool IsSetSource(void) const

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

bool CanGetExp_method(void) const

Check if it is safe to call GetExp_method method.

const TReplace & GetReplace(void) const

Get the Replace member data.

const TClass & GetClass(void) const

Get the Class member data.

bool CanGetReplace(void) const

Check if it is safe to call GetReplace method.

const TDeposition & GetDeposition(void) const

Get the Deposition member data.

const TIds & GetIds(void) const

Get the Ids member data.

bool CanGetSeqref(void) const

Check if it is safe to call GetSeqref method.

const TCross_reference & GetCross_reference(void) const

Get the Cross_reference member data.

THad_punct GetHad_punct(void) const

Get the Had_punct member data.

const TIncludes & GetIncludes(void) const

Get the Includes member data.

const TSummary & GetSummary(void) const

Get the Summary member data.

const TPlacement & GetPlacement(void) const

Get the Placement member data.

bool CanGetSummary(void) const

Check if it is safe to call GetSummary method.

bool CanGetHad_punct(void) const

Check if it is safe to call GetHad_punct method.

bool CanGetCross_reference(void) const

Check if it is safe to call GetCross_reference method.

bool CanGetSource(void) const

Check if it is safe to call GetSource method.

const THost & GetHost(void) const

Get the Host member data.

bool CanGetDate(void) const

Check if it is safe to call GetDate method.

bool CanGetPlacement(void) const

Check if it is safe to call GetPlacement method.

bool CanGetSuperfamily(void) const

Check if it is safe to call GetSuperfamily method.

const TSource & GetSource(void) const

Get the Source member data.

bool CanGetHost(void) const

Check if it is safe to call GetHost method.

list< CRef< CSeq_id > > TSeqref

const TSeqref & GetSeqref(void) const

Get the Seqref member data.

const TSuperfamily & GetSuperfamily(void) const

Get the Superfamily member data.

bool CanGetIncludes(void) const

Check if it is safe to call GetIncludes method.

const TDate & GetDate(void) const

Get the Date member data.

const TGenetic & GetGenetic(void) const

Get the Genetic member data.

bool CanGetGenetic(void) const

Check if it is safe to call GetGenetic method.

const TTaxon & GetTaxon(void) const

Get the Taxon member data.

const TPart & GetPart(void) const

Get the Part member data.

const TExtra_src & GetExtra_src(void) const

Get the Extra_src member data.

bool CanGetState(void) const

Check if it is safe to call GetState method.

const THost & GetHost(void) const

Get the Host member data.

const TStrain & GetStrain(void) const

Get the Strain member data.

bool CanGetHost(void) const

Check if it is safe to call GetHost method.

const TState & GetState(void) const

Get the State member data.

bool CanGetStrain(void) const

Check if it is safe to call GetStrain method.

bool CanGetExtra_src(void) const

Check if it is safe to call GetExtra_src method.

bool CanGetTaxon(void) const

Check if it is safe to call GetTaxon method.

bool CanGetPart(void) const

Check if it is safe to call GetPart method.

TImeth GetImeth(void) const

Get the Imeth member data.

const TExtra_acc & GetExtra_acc(void) const

Get the Extra_acc member data.

TClass GetClass(void) const

Get the Class member data.

bool CanGetCreated(void) const

Check if it is safe to call GetCreated method.

bool CanGetDbref(void) const

Check if it is safe to call GetDbref method.

bool CanGetPlasnm(void) const

Check if it is safe to call GetPlasnm method.

const TCreated & GetCreated(void) const

Get the Created member data.

bool CanGetAnnotupd(void) const

Check if it is safe to call GetAnnotupd method.

bool CanGetExtra_acc(void) const

Check if it is safe to call GetExtra_acc method.

bool CanGetSeqref(void) const

Check if it is safe to call GetSeqref method.

list< CRef< CSeq_id > > TSeqref

const TDbref & GetDbref(void) const

Get the Dbref member data.

const TPlasnm & GetPlasnm(void) const

Get the Plasnm member data.

const TAnnotupd & GetAnnotupd(void) const

Get the Annotupd member data.

list< CRef< CDbtag > > TDbref

const TSequpd & GetSequpd(void) const

Get the Sequpd member data.

const TSeqref & GetSeqref(void) const

Get the Seqref member data.

bool CanGetSequpd(void) const

Check if it is safe to call GetSequpd method.

@ eClass_standard

conforms to all SWISSPROT checks

@ eClass_prelim

only seq and biblio checked

const CharType(& source)[N]

Useful/utility classes and methods.

void DateToString(const CDate &date, string &str, EDateToString format_choice=eDateToString_regular)

bool ConvertQuotesNotInHTMLTags(string &str)

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