Class FMIndexConfig
A configuration object that determines the data types of certain fibres of the FMIndex.

Defined in <seqan/index.h>
Signature template <[typename TSpec[, typename TLengthSum[, unsigned LEVELS[, unsigned WORDS_PER_BLOCK]]]]> struct FMIndexConfig;

Template Parameters

TSpec The specializating type, defaults to void.
TLengthSum The underlying type to store precomputed rank values, defaults to size_t. The type must hold a value equal to the length of the bit vector.
LEVELS The number of levels of the rank dictionary, defaults to 1.
WORDS_PER_BLOCK Number of popcount operations per rank query, defaults to 0. If set to 0, the number equals the size of the underlying alphabet type.

Member Typedef Overview

Member Variable Overview

Member Typedef Detail

typedef WaveletTree<TSpec, TConfig> Bwt;

The Bwt determines the type of the occurrence table. In the default FMIndexConfig object the type of Bwt is a wavelet tree (WaveletTree).

typedef Levels<TSpec, TConfig> Sentinels;

The Sentinels determines the type of the sentinels in the FMIndex. In the default FMIndexConfig object the type of Sentinels is a one level RankDictionary.

Member Variables Detail

unsigned FMIndexConfig::SAMPLING

The sampling rate determines how many suffix array entries are represented with one entry in the CompressedSA.