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NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbobj.cpp Source File

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<

TSource>

seq_i = unsigned(src.Get()) & 0xFF;

retval += seq_i + 12345;

unsigned int TSeqPos

Type for sequence locations and lengths.

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

Defines exception class and several constants for SeqDB.

USING_SCOPE(objects)

Include definitions from the objects namespace.

unsigned SeqDB_ComputeSequenceHash(TSource &src)

Compute a sequence hash from a (generic) source of ncbi8na values.

unsigned SeqDB_SequenceHash(const char *sequence, int length)

Compute the hash of a sequence in ncbi8na format.

Forward iteration (only) for an array of sequence data.

const char * end

Pointer to the end of the sequence data array.

bool More()

Check whether there is more data to fetch.

const char * begin

Pointer to the first unprocessed byte of sequence data.

unsigned char Get()

Get a nucleotide base value and move iteration forward.

SSeqDB_ArraySource(const char *ptr, int len)

Construct sequence data source from existing array.

Forward iteration (only) for sequence data of a Bioseq object.

bool More()

Check whether there is more data to fetch.

SSeqDB_SVCISource(const CBioseq &bs)

Constructor.

TSeqPos index

Index of the next base of sequence data to return.

CSeqVector seqvector

Pointer to the first unprocessed byte of sequence data.

TSeqPos size

Total number of bases of sequence data to iterate over.

unsigned char Get()

Get a nucleotide base value and move iteration forward.

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