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NCBI C++ ToolKit: src/misc/hgvs/seq_id_resolver.cpp Source File

acc_idh ? acc_idh : orig_idh;

& dbtag = **it;

query_str =

+ s +

;

->Query(query_str,

, gis, 0, 5);

(gis.size() != 1) {

&& std::all_of(s.begin(), s.end(), [](

c) { return std::isdigit(c); });

(idh && !idh.

()) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CSeq_id_Resolver__CCDS(CScope &scope)

virtual CSeq_id_Handle x_Create(const string &s)

virtual ~CSeq_id_Resolver__CCDS()

objects::CEntrez2Client * m_entrez

CSeq_id_Resolver__ChrNamesFromGC(const CGC_Assembly &assembly, CScope &scope)

unique_ptr< TLocCache > m_loccache

virtual bool CanCreate(const string &s)

virtual CConstRef< CSeq_loc > x_MapLoc(const CSeq_loc &loc) const

CRef< CSeq_loc_Mapper > m_SLMapper

virtual CSeq_id_Handle x_Create(const string &s)

virtual CSeq_id_Handle x_Create(const string &s)

CSeq_id_Resolver__LRG(CScope &scope)

A helper class to convert a string to a seq-id.

virtual CSeq_id_Handle x_Create(const string &s)

virtual bool CanCreate(const string &s)

virtual ~CSeq_id_Resolver()

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ fGet_NoInsert

Do not insert created values.

@ eGet_Found

The key was found in the cache.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqIdOrNull(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

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,...

@ eGetId_Best

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

@ eGetId_ForceAcc

return only an accession based seq-id

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsSetDbxref(void) const

bool IsSetProduct(void) const

const CSeq_feat::TDbxref & GetDbxref(void) const

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

const CSeq_loc & GetProduct(void) const

bool IsNull(void) const THROWS_NONE

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

void Reset(void)

Reset reference object.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

CTempString GetSub(CTempString str, size_t idx=0) const

Get pattern/subpattern from previous GetMatch().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

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

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 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.

static bool is_numeric(const char *)

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

vector< CRef< CDbtag > > TDbxref

TLocal & SetLocal(void)

Select the variant.

bool IsNull(void) const

Check if variant Null is selected.

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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