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NCBI C++ ToolKit: include/algo/blast/dbindex/sequence_istream.hpp Source File

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std::vector< CConstRef< objects::CSeq_loc > >

;

( GetErrCode() ) {

eOpNotSupported:

;

;

Defines to provide correct exporting from BLAST DLL in Windows.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Class representing error conditions in the sequence stream.

virtual const char * GetErrCodeString() const override

Get the exception description string.

NCBI_EXCEPTION_DEFAULT(CSequenceIStream_Exception, CException)

EErrCode

Numerical error codes.

Class used to abstract reading nucleotide sequences from various sources.

Uint4 TStreamPos

Type used to represent positions within a sequence stream.

virtual CRef< TSeqData > next()=0

Extract the next sequence from the stream.

virtual void putback()=0

Roll back to the start of the previousely read sequence.

TSeqData::TMask TMask

Public alias for type containing masking info.

CSeqData TSeqData

Public alias for sequence info data type.

virtual ~CSequenceIStream()

Object destructor.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

uint32_t Uint4

4-byte (32-bit) unsigned 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.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Type containing the sequence itself along with the masking information.

CRef< objects::CSeq_entry > seq_entry_

Sequence data.

CSeqData()

Object constructor.

TMask mask_locs_

Masked portion of the sequence.

std::vector< CConstRef< objects::CSeq_loc > > TMask

Type representing masked portions of a sequence.

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