Class
FMIndexConfigA configuration object that determines the data types of certain fibres of the FMIndex.
A configuration object that determines the data types of certain fibres of the FMIndex.
Defined in | <seqan/index.h> |
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Signature |
template <[typename TSpec[, typename TLengthSum[, unsigned LEVELS[, unsigned WORDS_PER_BLOCK]]]]>
struct FMIndexConfig;
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Template Parameters
TSpec |
The specializating type, defaults to void. |
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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
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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 Variable Overview
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unsigned FMIndexConfig::SAMPLING
The sampling rate determines how many suffix array entries are represented with one entry in the CompressedSA.
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.