Spec IndexEsa
An index based on an enhanced suffix array.

Extends Index
Implements StringTreeConcept
All Extended Index
All Impl'd StringTreeConcept
Defined in <seqan/index.h>
Signature template <typename TText, typename TSpec> class Index<TText, IndexEsa<TSpec> >;

Template Parameters

TText The text type.
TSpec The specialization, defaults to void.

Member Function Overview

Interface Function Overview

Interface Functions Inherited From Index

Interface Functions Inherited From StringTreeConcept

Interface Metafunction Overview

Interface Metafunctions Inherited From Index

Interface Metafunctions Inherited From StringTreeConcept

Detailed Description

The fibres (see Index and Fibre) of this index are a suffix array (see EsaSA), a lcp table (see EsaLcp), etc.

This index can be accessed as a Suffix Tree using the VSTreeIterator classes.

See Also

Member Functions Detail

Index::Index(); Index::Index(index); Index::Index(text);

Constructor

Parameters

index Other Index object to copy from.
text The text to be indexed.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Interface Functions Detail

TValue bwtAt(position, index);

Shortcut for value(indexBwt(..), ..).

Parameters

index The IndexEsa object holding the fibre.
position A position in the array on which the value should be accessed.

Returns

TValue A reference or proxy to the value.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TValue childAt(position, index);

Shortcut for value(indexChildtab(..), ..).

Parameters

position A position in the array on which the value should be accessed.
index The IndexEsa object holding the fibre.

Returns

TValue A reference or proxy to the value.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

void createChildtab(childTab, lcp[, algoTag]);

Creates a child table from a given lcp table.

Parameters

childTab A reference to the resulting child table.
lcp A given lcp table.
algoTag A tag that identifies the algorithm which is used for the creation.

The size of childTab must be at least length(text) before calling this function.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TBwt indexBwt(index);

Shortcut for getFibre(.., EsaBwt).

Parameters

index The IndexEsa object holding the fibre.

Returns

TBwt A reference to the EsaBwt fibre (Burrows-Wheeler table).

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TChildTab indexChildtab(index);

Shortcut for getFibre(.., EsaChildtab).

Parameters

index The Index object holding the fibre.

Returns

TChildTab A reference to the EsaChildtab fibre (child table).

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TIsa indexIsa(index);

Shortcut for getFibre(.., EsaIsa).

Parameters

index The Index object holding the fibre.

Returns

TIsa A reference to the inverse suffix array fibre.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TLcp indexLcp(index);

Shortcut for getFibre(.., EsaLcp).

Parameters

index The Index object holding the fibre.

Returns

TLcp A reference to the EsaLcp fibre (lcp table).

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TLcpe indexLcpe(index);

Shortcut for getFibre(.., EsaLcpe).

Parameters

index The Index object holding the fibre.

Returns

TLcpe A reference to the EsaLcpe fibre (enhanced lcp table).

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TSA indexSA(index);

Shortcut for getFibre(.., EsaSA).

Parameters

index The Index object holding the fibre.

Returns

TSA A reference to the EsaSA fibre (suffix array).

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TValue isaAt(position, index);

Shortcut for value(indexIsa(..), ..).

Parameters

index The Index object holding the fibre.
position A position in the array on which the value should be accessed.

Returns

TValue A reference or proxy to the value in the inverse suffix array.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TValue lcpAt(position, index);

Shortcut for value(indexLcp(..), ..).

Parameters

index The Index object holding the fibre.
position A position in the array on which the value should be accessed.

Returns

TValue A reference or proxy to the value.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TValue lcpeAt(position, index);

Shortcut for value(indexLcpe(..), ..).

Parameters

index The Index object holding the fibre.
position A position in the array on which the value should be accessed.

Returns

TValue A reference or proxy to the value.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TValue saAt(position, index);

Shortcut for value(indexSA(..), ..).

Parameters

index The Index object holding the fibre.
position A position in the array on which the value should be accessed.

Returns

TValue A reference or proxy to the value in the suffix array.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

TValue textAt(position, index);

Shortcut for value(indexText(..), ..).

Parameters

index The Index object holding the fibre.
position A position in the fibre on which the value should be accessed.

Returns

TValue A reference or proxy to the value in the text.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.