Class Specialization
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.

Finder | Pattern

Swift

SwiftSemiGlobal

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

THaystack | A haystack type. Types: Index, String, StringSet
TIndex | A q-gram index of needle(s). Types: IndexQGram

Specialization of
Swift
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)
Iterator | Type of iterator objects that are used to traverse the container. (Finder)
Needle | Returns the needle type of a Pattern type. (Pattern)
Position | Type of an object that represents a position in a container. (Finder)
Reference | Reference type. (Finder)
ScoringScheme | Returns the scoring scheme of an approximate searching algorithm. (Pattern)
Value | Type of the items in the container or behind an iterator. (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)
findBegin | Search the begin of an approximate match. (Pattern)
getMaxDeviationOfOrder | Returns the maximal out-of-order distance of adjacent hits. (Swift)
getWindowFindHits | Returns the string of hits from the finder. (Swift)
haystack | Returns the haystack of a Finder object. (Finder)
host | The object a given object depends on. (Pattern)
infix | Returns the segment of the last found match in haystack. (Swift)
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)
positionRange | Returns a pair of the begin and end position in the haystack or needle for the last hit found. (Swift)
positionRangeNoClip | Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. (Swift)
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)
setPosition | Sets the position of a finder. (Finder)
setScoringScheme | Sets the scoring scheme used for finding or aligning. (Pattern)
windowFindBegin | Initializes the pattern. Sets the finder on the begin position. Gets the first non-repeat range and sets it in the finder. Used together with windowFindBegin and windowFindEnd. (Swift)
windowFindEnd | Flushes the pattern. Used together with windowFindBegin and windowFindNext. (Swift)
windowFindNext | Searches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin and windowFindEnd. (Swift)

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

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