Class Specialization
Pigeonhole
Provides a fast filter alogrithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text, every partition into k+1 parts contains one part that matches without error.

Finder | Pattern

Pigeonhole

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

THaystack | The type of the sequence that should be searched.
TIndex | A q-gram index of needle(s) that should be searched for. Types: IndexQGram
TSpec | Specifies the type of Swift filter.

Remarks
The Pattern must be a q-gram index over multiple patterns. The tolerated error rate must be given when find or windowFindBegin is called. In these functions the length of the index Shape is set automatically thus it must be modifiable at runtime, e.g. OneGappedShape.
Specialization of
Pattern, Finder
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.
getWindowFindHits | Returns the string of hits from the finder.
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.
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.
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)
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.
windowFindEnd | Flushes the pattern. Used together with windowFindBegin and windowFindNext.
windowFindNext | Searches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin and windowFindEnd.

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

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