33 #ifndef C_SEQUENCE_I_STREAM_HPP
34 #define C_SEQUENCE_I_STREAM_HPP
60 typedef std::vector< CConstRef< objects::CSeq_loc > >
TMask;
99 switch( GetErrCode() ) {
100 case eOpNotSupported:
101 return "stream operation is not supported";
105 return "database parameter error";
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.