Spec
FMIndexAn index based on the Burrows-Wheeler transform.
An index based on the Burrows-Wheeler transform.
Extends | Index |
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Implements | StringTrieConcept |
All Extended | Index |
All Impl'd | StringTrieConcept |
Defined in | <seqan/index.h> |
Signature |
template <typename TText[, typename TSpec[, typename TConfig]]>
class Index<TText, FMIndex<TSpec, TConfig> >;
|
Template Parameters
TText |
The text type. Types: String, StringSet |
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TSpec |
FM index specialisation, defaults to void. |
TConfig |
A config object which determines the data types of the different fibres, defaults to FMIndexConfig<TSpec>. |
Interface Function Overview
-
TIterator begin(index, tag);
Returns an iterator pointing to the root node of the virtual prefix trie of the reversed text of the index. -
TFibre indexLF(index);
A shortcut for getFibre(index, FibreLF()). -
TSAValue toSuffixPosition(index, pos, offset);
This function computes the position of a specified position in the compressed suffix array (additionally containing entries for the sentinels). The returned position corresponds to the suffix array of the original text without sentinels.
Interface Functions Inherited From Index
Interface Metafunction Overview
Interface Metafunctions Inherited From Index
Detailed Description
Structure
The FM index consists of various Fibre of which the most important ones are the compressed suffix array and the LF table, which provides all necessary information for the LF mapping.
Interface Functions Detail
TIterator begin(index, tag);
Returns an iterator pointing to the root node of the virtual prefix trie of the reversed text of the index.
Parameters
index
|
The index to be traversed. |
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tag
|
The specialisation of the iterator to be returned by the function. Types: VSTree Iterator |
Returns
TIterator |
Returns an iterator pointing to the root node of the virtual prefix trie of the reversed text of the the index. Types: The result of Iterator<Index<TText, TIndexSpec>, TSpec>::Type |
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Data Races
Thread safety unknown!
TFibre indexLF(index);
A shortcut for getFibre(index, FibreLF()).
Parameters
index
|
The FM index. |
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Returns
TFibre |
A reference to the FibreLF. |
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Data Races
Thread safety unknown!
TSAValue toSuffixPosition(index, pos, offset);
This function computes the position of a specified position in the compressed suffix array (additionally
containing entries for the sentinels). The returned position corresponds to the suffix array of the original
text without sentinels.
Parameters
index
|
The FM index. |
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pos
|
The position in the suffix array of the FM index (with sentinels). Types: UnsignedIntegerConcept |
offset
|
The number of sequences in the original text. Types: UnsignedIntegerConcept |
Returns
TSAValue |
The function function computes the position of a specified position in the compressed suffix array (additionally containing entries for the sentinels). The returned position corresponds to the suffix array of the original text without sentinels. The return type is SAValue<Index<TText, FMIndex<TSpec, TConfig> > >::Type |
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Data Races
Thread safety unknown!