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NCBI C++ ToolKit: src/algo/gnomon/id_handler.cpp Source File

}

(sequence::CSeqIdFromHandleException& e) {

(e.GetErrCode() != sequence::CSeqIdFromHandleException::eRequestedIdNotFound)

canonical_id.

(&

);

.AsFastaString();

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gnl.

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static CRef< CScope > m_Scope

static bool IsId(const CObject_id &obj)

static CRef< CSeq_id > GnomonMRNA(Int8 id)

static void SetId(CObject_id &obj, Int8 value)

static CRef< CSeq_id > ToSeq_id(const string &str)

static string ToString(const CSeq_id &id)

static Int8 GetId(const CObject_id &obj)

static CRef< CSeq_id > GnomonProtein(Int8 id)

CConstRef< CSeq_id > ToCanonical(const CSeq_id &id) const

E_Choice GetIdType(TId8 &value) const

The NCBI C++ standard methods for dealing with std::string.

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

#define NCBI_THROW(exception_class, err_code, message)

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

CConstRef< CSeq_id > GetSeqId(void) const

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_ThrowOnError

Throw exception on errors. If not set, an empty value is returned.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

#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 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.

void SetTag(TTag &value)

Assign a value to Tag data member.

TStr & SetStr(void)

Select the variant.

void SetDb(const TDb &value)

Assign a value to Db data member.

TId & SetId(void)

Select the variant.

@ e_not_set

No variant selected.

string GetDNASequence(CConstRef< objects::CSeq_id > id, CScope &scope)

const GenericPointer< typename T::ValueType > T2 value

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