Class Specialization
SwiftLocal
The specialization for the general swift filter that finds epsilon matches between haystack and needle.
Finder<THaystack, Swift<SwiftLocal> >
Pattern<TIndex, Swift<SwiftLocal> >
Include Headers
seqan/index.h
Parameters
THaystack
A haystack type.
TIndex
A q-gram index of needle(s).
Types: IndexQGram
Specialization of
Metafunctions
ContainerType of the container given an iterator. (Finder)
DifferenceType of an object that stores the difference between two iterators. (Finder)
HaystackReturns the haystack type of a Finder type. (Finder)
HostType of the object a given object depends on. (Pattern)
IteratorType of iterator objects that are used to traverse the container. (Finder)
NeedleReturns the needle type of a Pattern type. (Pattern)
ScoringSchemeReturns the scoring scheme of an approximate searching algorithm. (Pattern)
ValueType of the items in the container or behind an iterator. (Finder)
Member Functions
FinderConstructor (Finder)
Functions
beginThe begin of a container. (Finder)
beginPositionBegin position of object in host. (Finder)
clearResets an object. (Finder)
endThe end of a container. (Finder)
endPositionEnd position of object in host. (Finder)
findSearch for a Pattern in a Finder object. (Pattern)
findBeginSearch the begin of an approximate match. (Pattern)
getMaxDeviationOfOrderReturns the maximal out-of-order distance of adjacent hits. (Swift)
getWindowFindHitsReturns the string of hits from the finder. (Swift)
haystackReturns the haystack of a Finder object. (Finder)
hostThe object a given object depends on. (Pattern)
infixReturns the segment of the last found match in haystack. (Swift)
lengthThe number of items/characters. (Finder)
needleReturns the needle of a Pattern object (not implemented for some online-algorithms). (Pattern)
positionPosition of an iterator. (Pattern)
positionRangeReturns a pair of the begin and end position in the haystack or needle for the last hit found. (Swift)
positionRangeNoClipReturns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. (Swift)
scoringSchemeThe scoring scheme used for finding or aligning. (Pattern)
setHaystackSets the haystack of a Finder object. (Finder)
setNeedleSets the needle of a Pattern object and optionally induces preprocessing. (Pattern)
setPositionSets the position of a finder. (Finder)
setScoringSchemeSets the scoring scheme used for finding or aligning. (Pattern)
windowFindBeginInitializes 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)
windowFindEndFlushes the pattern. Used together with windowFindBegin and windowFindNext. (Swift)
windowFindNextSearches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin and windowFindEnd. (Swift)
SeqAn - Sequence Analysis Library - www.seqan.de
 

Page built @2013/07/11 09:12:39