Class Specialization
Swift
Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential ε-matches. An ε-match is a matching region of minimal length and an error rate of at most ε.

Finder | Pattern

Swift

SwiftLocal | SwiftSemiGlobal

Finder<TIndex, Swift<TSpec> >
Pattern<TIndex, Swift<TSpec> >
Include Headers
seqan/index.h
Parameters

TIndex | A q-gram index of needle(s). Types: IndexQGram
TSpec | Specifies the type of Swift filter. Types: SwiftLocal, SwiftSemiGlobal

Specialization of
Pattern, Finder
Specializations

SwiftLocal | The specialization for the general swift filter that finds epsilon matches between haystack and needle.
SwiftSemiGlobal | The specialization for the semi-global swift filter that finds regions of the haystack where a needle matches with an error rate less than ε.

Metafunctions

Container | Type of the container given an iterator. (Finder)
Difference | Type of an object that stores the difference between two iterators. (Finder)
Haystack | Returns the haystack type of a Finder type. (Finder)
Host | Type of the object a given object depends on. (Pattern)
Host | Type of the object a given object depends on. (Pattern)
Iterator | Type of iterator objects that are used to traverse the container. (Finder)
Needle | Returns the needle type of a Pattern type. (Pattern)
ScoringScheme | Returns the scoring scheme of an approximate searching algorithm. (Pattern)
Value | Type of the items in the container. (Finder)

Member Functions

Finder | Constructor (Finder)

Functions

begin | The begin of a container. (Finder)
beginPosition | Begin position of object in host. (Finder)
clear | Resets an object. (Finder)
end | The end of a container. (Finder)
endPosition | End position of object in host. (Finder)
find | Search for a Pattern in a Finder object. (Pattern)
find | Search for a Pattern in a Finder object. (Pattern)
findBegin | Search the begin of an approximate match. (Pattern)
findBegin | Search the begin of an approximate match. (Pattern)
haystack | Returns the haystack of a Finder object. (Finder)
host | The object a given object depends on. (Pattern)
infix | Creates infix object.
infix | Creates infix object.
length | The number of items/characters. (Finder)
needle | Returns the needle of a Pattern object (not implemented for some online-algorithms). (Pattern)
position | Position of an iterator. (Pattern)
position | Position of an iterator. (Pattern)
positionRange | Returns a pair of the begin and end position in the haystack or needle for the last hit found.
positionRange | Returns a pair of the begin and end position in the haystack or needle for the last hit found.
positionRangeNoClip | Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
positionRangeNoClip | Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
scoringScheme | The scoring scheme used for finding or aligning. (Pattern)
setHaystack | Sets the haystack of a Finder object. (Finder)
setNeedle | Sets the needle of a Pattern object and optionally induces preprocessing. (Pattern)
setScoringScheme | Sets the scoring scheme used for finding or aligning. (Pattern)

Example Programs
Index Finder, Index Finder StringSet
SeqAn - Sequence Analysis Library - www.seqan.de

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