Spec PexPattern
Provides a fast approximate string matching filter that splits the needle into several pieces that are searched with a multiple exact string matching algorithm and later verified.

Extends Pattern
All Extended Pattern
All Subcl's HierarchicalPexPattern, NonHierarchicalPexPattern
Defined in <seqan/find.h>
Signature template <typename TNeedle, typename TVerification, typename TMultiFinder> class Pattern<TNeedle, Pex<TVerification, TMultiFinder> >;

Template Parameters

TNeedle The needle type. Type: SequenceConcept
TVerification Determines if the hierarchical verification proposed by Navarro and Beaza-Yates is used or not.
TMultiFinder Specifies the algorithm for the multiple exact string matching algorithm. Type: AhoCorasick.

Interface Function Overview

Interface Functions Inherited From Pattern

Interface Metafunction Overview

Interface Metafunctions Inherited From Pattern

Detailed Description

There are two defaults available: PexHierarchical and PexNonHiearchical (e.g. Pattern<CharString>, PexHierarchical> that both use the Aho-Corasick algorithm for the multiple exact string matching.

Interface Functions Detail

TScoreValue getScore(pattern);

Score of the last found match in approximate searching.

Parameters

pattern A pex pattern that can be used for approximate searching.

Returns

TScoreValue The score of the last match found using pattern. If no match was found then the value is undefined.

TScoreValue scoreLimit(pattern);

The minimal score a match must reach in approximate searching.

Parameters

pattern The pattern to query.

Returns

TScoreValue The score limit value.

void setScoreLimit(pattern, limit);

Set the minimal score a match must reach in approximate serach.

Parameters

pattern The pattern to set the limit for.
limit The limit score value to set.

Returns

TScoreValue The score limit value.